diff --git a/README.md b/README.md index 7e6c849e..004d7d51 100644 --- a/README.md +++ b/README.md @@ -297,6 +297,7 @@ These are currently used to find a minimum energy conformation of a molecule. | `OpenFF Lipid Optimization Training Supplement v1.0` | [2024-10-08-OpenFF-Lipid-Optimization-Training-Supplement-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-10-08-OpenFF-Lipid-Optimization-Training-Supplement-v1.0) | Additional optimization training data for Sage from representative LIPID MAPS fragments | I, Br, O, H, P, C, N, Cl, F, S | | | `OpenFF NAGL2 Training Optimization Dataset Part 1 v4.0` | [2024-11-19-OpenFF-NAGL2-Training-Optimization-Dataset-Part-1-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-11-19-OpenFF-NAGL2-Training-Optimization-Dataset-Part-1-v4.0) | Optimization dataset for NAGL2 training, part 1 | Cl, O, C, P, I, Br, B, S, N, F, H, Si | | | `OpenFF NAGL2 Training Optimization Dataset Part 2 v4.0` | [2024-11-19-OpenFF-NAGL2-Training-Optimization-Dataset-Part-2-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-11-19-OpenFF-NAGL2-Training-Optimization-Dataset-Part-2-v4.0) | Optimization dataset for NAGL2 training, part 2 | Si, B, O, I, S, Cl, N, H, C, P, F, Br | | +| `OpenFF Organometallics Exploratory Optimization Dataset` | [2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset) | Optimization training data for organometallic molecules | F, P, O, C, Zn, N, Ni, Pt, S, Pd, Mg, Br, Rh, Fe, H, Cl, B, Li | | | `OpenFF NAGL2 Training Optimization Dataset v4.0` | [2024-12-09-OpenFF-NAGL2-Training-Optimization-Dataset-v4.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-12-09-OpenFF-NAGL2-Training-Optimization-Dataset-v4.0) | Optimization dataset for NAGL2 training, combined and filtered | Si, B, O, I, S, Cl, N, H, C, P, F, Br | | diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/README.md b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/README.md new file mode 100644 index 00000000..5d1e5949 --- /dev/null +++ b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/README.md @@ -0,0 +1,65 @@ +# OpenFF Organometallics Exploratory Optimization Dataset + +## Description + +An optimization dataset created to test the OpenFF and QCArchive infrastructure +for calculations involving organometallic molecules. The molecules in this +dataset were extracted from the `OpenEye SMILES` entries in the [Chemical +Component Dictionary](https://www.wwpdb.org/data/ccd) mmCIF file. These were +filtered to remove molecules with radical electrons and to include only +molecules with the desired metal atoms: Pd, Fe, Zn, Mg, Cu, Li, Rh, Ir, Pt, Ni, +Cr, and Ag. These were further filtered to retain only molecules with at least +10 atoms, an absolute charge of less than 4, and those not present in any of our +existing training data. From this candidate set, the molecules were sorted based +on their number of atoms, and the smallest 100 were selected. Of these, 56 were +further removed by errors in the dataset preparation process, leaving 44 +molecules. + +## General Information + +* Date: 2024-12-03 +* Class: OpenFF Optimization Dataset +* Purpose: Provide training data for metal-containing molecules +* Name: OpenFF Organometallics Exploratory Optimization Dataset +* Number of unique molecules: 44 +* Number of filtered molecules: 55 +* Number of conformers: 239 +* Number of conformers per molecule (min, mean, max): 1, 5.43, 10 +* Mean molecular weight: 424.38 +* Max molecular weight: 741.40 +* Charges: [0.0, 1.0, 2.0, 3.0] +* Dataset submitter: Brent Westbrook +* Dataset generator: Brent Westbrook + +## QCSubmit Generation Pipeline + +* `main.py`: This script shows how the dataset was prepared from `components.cif`, retrieved +from the CCD, and `inchis.dat`, which contains the InCHI keys of our existing +training data. + + +## QCSubmit Manifest + +* `main.py`: Script describing dataset generation and submission +* `input-environment.yaml`: Environment file used to create the Python environment for the script +* `full-environment.yaml`: Fully-resolved environment used to execute the script +* `opt.toml`: Experimental [qcaide](https://github.com/ntBre/qcaide) input file for defining +variables used throughout the QCA submission process +* `dataset.json.bz2`: Compressed dataset ready for submission +* `dataset.pdf`: Visualization of dataset molecules +* `output.smi`: SMILES strings for dataset molecules + +## Metadata +* Elements: {F, P, O, C, Zn, N, Ni, Pt, S, Pd, Mg, Br, Rh, Fe, H, Cl, B, Li} +* Spec: BP86/def2-TZVP + * basis: def2-TZVP + * implicit_solvent: None + * keywords: {} + * maxiter: 200 + * method: BP86 + * program: psi4 + * SCF properties: + * dipole + * quadrupole + * wiberg_lowdin_indices + * mayer_indices diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/dataset.json.bz2 b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/dataset.json.bz2 new file mode 100644 index 00000000..f0c3ae00 --- /dev/null +++ b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/dataset.json.bz2 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e2c640a77dc60585caa354fb271ce54d88d8f414868db3ad9f7aa527f023cc07 +size 179881 diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/dataset.pdf b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/dataset.pdf new file mode 100644 index 00000000..5603d5d1 Binary files /dev/null and b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/dataset.pdf differ diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/full-environment.yaml b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/full-environment.yaml new file mode 100644 index 00000000..af9b20d1 --- /dev/null +++ b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/full-environment.yaml @@ -0,0 +1,306 @@ +name: qcarchive-user-submit +channels: + - 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pydantic-core=2.16.1=py311h46250e7_0 + - pyedr=0.8.0=pyhd8ed1ab_0 + - pygments=2.17.2=pyhd8ed1ab_0 + - pyjwt=2.8.0=pyhd8ed1ab_0 + - pyparsing=3.1.1=pyhd8ed1ab_0 + - pysocks=1.7.1=pyha2e5f31_6 + - pytables=3.9.2=py311h10c7f7f_1 + - pytest=8.0.0=pyhd8ed1ab_0 + - python=3.11.7=hab00c5b_1_cpython + - python-constraint=1.4.0=py_0 + - python-dateutil=2.8.2=pyhd8ed1ab_0 + - python-fastjsonschema=2.19.1=pyhd8ed1ab_0 + - python-json-logger=2.0.7=pyhd8ed1ab_0 + - python-tzdata=2023.4=pyhd8ed1ab_0 + - python_abi=3.11=4_cp311 + - pytz=2023.4=pyhd8ed1ab_0 + - pyyaml=6.0.1=py311h459d7ec_1 + - pyzmq=25.1.2=py311h34ded2d_0 + - qcelemental=0.27.1=pyhd8ed1ab_0 + - qcportal=0.55=pyhd8ed1ab_0 + - rdkit=2023.09.4=py311h4c2f14b_0 + - readline=8.2=h8228510_1 + - referencing=0.33.0=pyhd8ed1ab_0 + - regex=2023.12.25=py311h459d7ec_0 + - reportlab=4.0.9=py311h459d7ec_0 + - requests=2.31.0=pyhd8ed1ab_0 + - rfc3339-validator=0.1.4=pyhd8ed1ab_0 + - rfc3986-validator=0.1.1=pyh9f0ad1d_0 + - rlpycairo=0.2.0=pyhd8ed1ab_0 + - rpds-py=0.17.1=py311h46250e7_0 + - scipy=1.12.0=py311h64a7726_2 + - send2trash=1.8.2=pyh41d4057_0 + - setuptools=69.0.3=pyhd8ed1ab_0 + - six=1.16.0=pyh6c4a22f_0 + - smirnoff99frosst=1.1.0=pyh44b312d_0 + - snappy=1.1.10=h9fff704_0 + - sniffio=1.3.0=pyhd8ed1ab_0 + - soupsieve=2.5=pyhd8ed1ab_1 + - sqlalchemy=2.0.25=py311h459d7ec_0 + - sqlite=3.46.0=h6d4b2fc_0 + - stack_data=0.6.2=pyhd8ed1ab_0 + - tabulate=0.9.0=pyhd8ed1ab_1 + - terminado=0.18.0=pyh0d859eb_0 + - tinycss2=1.2.1=pyhd8ed1ab_0 + - tk=8.6.13=noxft_h4845f30_101 + - tomli=2.0.1=pyhd8ed1ab_0 + - tornado=6.3.3=py311h459d7ec_1 + - tqdm=4.66.1=pyhd8ed1ab_0 + - traitlets=5.14.1=pyhd8ed1ab_0 + - types-python-dateutil=2.8.19.20240106=pyhd8ed1ab_0 + - typing-extensions=4.9.0=hd8ed1ab_0 + - typing_extensions=4.9.0=pyha770c72_0 + - typing_utils=0.1.0=pyhd8ed1ab_0 + - tzdata=2023d=h0c530f3_0 + - unidecode=1.3.8=pyhd8ed1ab_0 + - uri-template=1.3.0=pyhd8ed1ab_0 + - urllib3=2.2.0=pyhd8ed1ab_0 + - wcwidth=0.2.13=pyhd8ed1ab_0 + - webcolors=1.13=pyhd8ed1ab_0 + - webencodings=0.5.1=pyhd8ed1ab_2 + - websocket-client=1.7.0=pyhd8ed1ab_0 + - wheel=0.42.0=pyhd8ed1ab_0 + - widgetsnbextension=4.0.9=pyhd8ed1ab_0 + - xmltodict=0.13.0=pyhd8ed1ab_0 + - xorg-kbproto=1.0.7=h7f98852_1002 + - xorg-libice=1.1.1=hd590300_0 + - xorg-libsm=1.2.4=h7391055_0 + - xorg-libx11=1.8.7=h8ee46fc_0 + - xorg-libxau=1.0.11=hd590300_0 + - xorg-libxdmcp=1.1.3=h7f98852_0 + - xorg-libxext=1.3.4=h0b41bf4_2 + - xorg-libxrender=0.9.11=hd590300_0 + - xorg-libxt=1.3.0=hd590300_1 + - xorg-renderproto=0.11.1=h7f98852_1002 + - xorg-xextproto=7.3.0=h0b41bf4_1003 + - xorg-xproto=7.0.31=h7f98852_1007 + - xz=5.2.6=h166bdaf_0 + - yaml=0.2.5=h7f98852_2 + - zeromq=4.3.5=h59595ed_0 + - zipp=3.17.0=pyhd8ed1ab_0 + - zlib=1.2.13=hd590300_5 + - zlib-ng=2.0.7=h0b41bf4_0 + - zstandard=0.22.0=py311haa97af0_0 + - zstd=1.5.5=hfc55251_0 + - pip: + - amberutils==21.0 + - edgembar==0.2 + - mmpbsa-py==16.0 + - packmol-memgen==2023.2.24 + - pdb4amber==22.0 + - pymsmt==22.0 + - pytraj==2.0.6 + - sander==22.0 +prefix: /home/brent/mambaforge/envs/qcarchive-user-submit diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/generate.txt b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/generate.txt new file mode 100644 index 00000000..46009959 --- /dev/null +++ b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/generate.txt @@ -0,0 +1,1682 @@ +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C4C(=O)C(C5=C6C(=C(C7=CC8=[N]9C(=CC(=C1C)N2[Mg]9(N76)[N]3=C54)C(=C8C)C(=O)C)C)CCC(=O)OCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)C(=O)OC)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1c2c(cc3c1C4=[N]([Ru]356([S]7CC[S]5CC[S]6CC7)N=C=S)C=CC=C4)C(=O)NC2=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[NH2][Pt+]2([NH2]1)I[Pt+]3(I2)[NH2]CC[NH2]3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C(=O)c3ccc4c(c3C2=O)nc5c6c7c8c(c5n4)C=CC=[N]8[Ru+2]91([N]7=CC=C6)([N]2=CC=Cc3c2c2c(cc3)C=CC=[N]92)[N]2=CC=Cc3c2c2c(cc3)C=CC=[N]12. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Ag]45. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CN(C(=O)NC1=O)C2CC(C(O2)CN=[N]=N)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=CC=Cc1c9c2c(cc1)C=CC=[N]72)[N]1=CC=Cc2c1c1c(cc2)C=CC=[N]81. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=N[N]2=C(C1c3c(cc(cc3OC)Br)OC)N=C(N=C2N(CCCC(F)(F)F)CCCC(F)(F)F)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[N]12C3CSC1C4CSC5=[N]4[Fe]2(Oc6c5cccc6)OC3=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe][S]3[Fe]1[S]([Fe]2)[Fe]3S45[Fe]6[S]7[Fe]4[S]8[Fe]7[S]6[Fe]58. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1C(C2=CC3=C(C(=C4N3[Fe+2]56[N]2=C1C(=C7N5C(=CC8=[N]6C(=C4)C(=C8C)CCC(=O)O)C(=C7C=C)C)c9ccccc9)CCC(=O)O)C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N](C(=C1)N)CCO. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)C12=CC=C([Os]1([N]3=C(C=CC=C3)C(=S)Nc4ccc(cc4)F)Cl)(C=C2)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1CCC2C(C1)[NH2][Pt+2][NH2]2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCN1c2c(cccn2)N(C(=O)c3c1ncc(c3)CCOC4=CC=[N](c5c4cccc5)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[As](C)(C)CCO. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 2 radical electrons on molecule CC([C]O)C(C(=O)(=O)O)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)C3=CC=CC=[N]3[Ru+2]245([N]6=c7c(=CC=C6)c8c(c9c7[N]4=CC=C9)nc1c2c3c4c(c1n8)C=CC=[N]4[Ru+2]14([N]3=CC=C2)([N]2=C(C=CC=C2)C2=[N]1C=CC=C2)[N]1=C(C=CC=C1)C1=[N]4C=CC=C1)[N]1=C(C=CC=C1)C1=[N]5C=CC=C1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=C(C(=C4N3[Zn]56[N]2=C1C=C7N5C8=C(C(=C(C8=C7C)O)C(=O)OC)C9=[N]6C(=C4)C(=C9CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C)C(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cccc2c1nc3c4c5c6=[N](C=CC=c6c3n2)[Ru+2]78([N]5=CC=C4)([N]9=CC=Nc1c9c2c(cc1)N=CC=[N]72)[N]1=CC=Nc2c1c1c(cc2)N=CC=[N]81. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule N(=O)[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CNC(=[S][Pt+2]1[NH2]CC[NH2]1)N(C)CCNc2c3ccccc3[nH+]c4c2cccc4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S][Fe]1[S]2[Fe][S]3[Fe]2[S]1[Fe]3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)CCCC(=O)NC2=C(C=C[N](=C2)O)C(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1O)-c3c4c(c5=CC(=C[N]6=c5c3N2[Ru]678([S]9CC[S]7CC[S]8CC9)[N]CS)F)C(=O)NC4=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc(c2c(c1)nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=CC=Nc1c9c2c(cc1)N=CC=[N]72)[N]1=CC=Nc2c1c1c(cc2)N=CC=[N]81)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[In]36N7C(=C2)C(=C(C7=CC8=[N]6C(=C5)C(=C8C)CCC(=O)O)C=C)C)CCC(=O)O)C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1NC[S]2[Fe]3([S]1[Fe]2(C3=O)(C#N)C#[O+])(C#N)C#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36(N7C(=CC8=[N]6C(=C5)C(=C8C=C)C)C(=C(C7=C2)CCC(=O)O)C)c9ccc(cc9)Cl)C=C)C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[CH]12[CH]3([Ir+2]1456([CH]2(C4(=C53C)C)C)([NH2]CC[NH]6S(=O)(=O)c7ccc(cc7)NC(=O)CCCCC8C9C(CS8)NC(=O)N9)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCSC1=[S][Pt](OC(=C1)c2cccc(c2)O)(S(C)(C)O)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1OC[S]2[Fe]3([S]1[Fe]2(C3=O)(C#N)C#[O+])(C#N)C#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[S]2[Fe]3(C(=O)[Fe]2([S]3C1)(C#N)C#[O+])(C#N)C#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1SC[S]2[Fe]3([S]1[Fe]2(C3=O)(C#N)C#[O+])(C#N)C#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=CC8=[N]6C(=C5)C(=C8C)C(C)OO)C(=C(C7=C2)CCC(=O)O)C)C)C=C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc(ccc1NC(=O)CCCCC2C3C(CS2)NC(=O)N3)S(=O)(=O)[N-]4CC[NH2][Ir+3]4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[N]1=C(N(C=C1)c2ccccn2)[Pt]3(c4cc(cc(c4C5=[N]3C=CC=C5)F)F)C6=[N](C=CN6C)c7ccccn7. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1nc(c2c(n1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)[N]5=CC=CC(=C5)C(=O)N)F)O)O)O)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C4C5=[N]3[Mg]67N2C(=C1C)C=C8[N]6=C(C=C9N7C(=C5C(C4=O)(C(=O)OC)O)C(=C9C)CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C(=C8CC)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36(N7C(=CC8=[N]6C(=C5)C(=C8C=C)C)C(=C(C7=C2)CCC(=O)O)C)c9ccccc9)C=C)C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cccc(c1)[Fe]234N5C6=CC7=[N]2C(=CC8=C(C(=C(N38)C=C9[N]4=C(C=C5C(=C6C)CCC(=O)O)C(=C9C)CCC(=O)O)C=C)C)C(=C7C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Co]36N7C(=C2)C(=C(C7=CC8=[N]6C(=C5)C(=C8CC)CC)CC)CC)CC)CC)CC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O1[Fe](O[Fe]2S[Fe]3[S]2[Fe]1S3)[S]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CNC1C[S]2CC[S]3[Ru]24([N]5=CC(=Cc6c5c7c(c8c6C(=O)NC8=O)-c9cc(ccc9N47)OC)F)([S](C1)CC3)[N]CS. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [CH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Mn]36N7C(=CC8=[N]6C(=C5)C(=C8C)CCC(=O)O)C(=C(C7=C2)CCC(=O)O)C)C)CCC(=O)O)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC2=C(C3=[N]4C(=C(C5=CC=C6N5[Zn]47N2C1=C(C8=[N]7C(=C6C(F)(F)F)C=C8)C(F)(F)F)C(F)(F)F)C=C3)C(F)(F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cnccc1C2=C3C=CC4=C(C5=[N]6C(=C(C7=CC=C8N7[Fe]6(N34)[N]9=C2C=CC9=C8c1ccncc1)c1ccncc1)C=C5)c1ccncc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN(C)C1=N[N]2=CC3=CC=c4ccccc4=[N]3[In]2(S1)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=NC5=[N]6C(=C(C7=CC=C8N7[Fe]6(N34)[N]9=C2C=CC9=N8)c1ccccc1)C=C5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C(C4=[N]3[Fe]56N2C(=C1C)C=C7[N]5=C(C=C8N6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)CC)C(F)(F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(NC(SC1)C(C(=O)O)NC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12)C(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O1[Fe]S[Fe]2S[Fe]3[S]2[Fe]1S3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCC12C3([Ir]1456(C3(C4(C52C)C)C)(N(CC7=[N]6C=CC(=C7)c8ccc(cc8)S(=O)(=O)N)S(=O)(=O)c9ccccc9)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC=CC2=[N]1[Cu]3[N](=C2)NC(=[S]3)N(C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C2C(C(S1)CCCCC(=O)NCCCOC34C5=[N]6C(=CC=C5)C7=[N]([Co]68([N]9=CC=CC=C9C1=CC=CC3=[N]81)([N]1=CC=CC=C41)[O])C=CC=C7)NC(=O)N2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=CC5=[N]6C(=C(C7=CC=C8N7[Zn]6(N43)[N]9=C2C=CC9=C8)c1ccc(cc1)C(=O)O)C=C5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe][S]2[Fe]13S[Fe][S]3[Fe]2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1NC[Se]2[Fe]3([Se]1[Fe]2(C3=O)(C#N)C#[O+])(C#N)C#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[C-]12C3(=C4([Ir+3]1356(C2(=C54C)C)([N-](CC7=[N]6C=CC(=C7)c8ccc(cc8)S(=O)(=O)N)S(=O)(=O)c9ccccc9)[Cl-])C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [B]1B234B5B6[Co]17891%10%11(B2C72C866B55B33B65B432)B2B345B9C11(B33B446B522B%105B242C%1151B623)CNS(=O)(=O)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc(nc(n1)N)Nc2cc(cc(c2)NC(=O)c3cccc(c3)Nc4ccnc5c4cccc5)C[N+](C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule B1(N2C(=CC(=C2C(=C3[N]1=C(C=C3C)C)CCCCCCCCCCC(=O)OCC(CO)O)C)C)(F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN(C)c1ccc2c(c1)OC3=CC(=[N](C)C)C=CC3=C2c4cc(ccc4C(=O)NS(=O)(=O)N(C)C)C(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1CCCN(C1)CC2=C[N]3=C(C(=C2)C(F)(F)F)NN(C3=O)c4cccc(c4)C5(CCNC(=O)C5)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC=C1C(C2=CC3=C(C(=C4N3[Mg]56[N]2=C1C=C7N5C8=C(C(C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)C(C9CCC(=O)OCC=C(C)CCCC(C)CCC=C(C)CCCC(C)C)C)C)C(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1C(C2=[N]3C1=CC4=C(C(=C5N4[Mg]36[N]7=C(C=C8N6C9=C2C(C(=O)C9=C8C)C(=O)OC)C(C(C7=C5)C)C=C)C(=O)C)C)CCC(=O)OCC=C(C)CCCC(C)CCC=C(C)CCCC(C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C(CCC[NH2][Pt]([NH3])([NH3])[NH3])CCN. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCC[NH2][Pt]([NH3])([NH3])[NH2]CCCCCC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 3 radical electrons on molecule [As]. +atomic number must be positive, given 0. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1ncc(c(n1)N)C[N]2=C(SC(=C2C)CCOP(=O)(O)OP(=O)(O)O)C(C)(O)OO. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2c(cc1C)N(C=N2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89[N]5=C4C(=C1[NH]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2c(cc1C)N3C=[N]2[Co]456([N]7=C8C(=C9[N]4=C(C=C1[N]5=C(C(=C2N6C(C7C(C8(CCC(=O)NCC(OP(=O)(OC4C(OC3C4O)CO)O)C)C)CC(=O)N)(C(C2CCC(=O)N)(C)CC(=O)N)C)C)C(C1CCC(=O)N)(C)CC(=O)N)C(C9CCC(=O)N)(C)C)C)CC1C(C(C(O1)N1C=Nc2c1ncnc2N)O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Ni]45. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1C(=N)N)NC3=[N]2[Zn+2][N]4=C(C3)Nc5c4ccc(c5)C(=N)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1C(C2=CC3=C(C(=C4[N-]3[Mg+2]56[N]2=C1C=C7[N-]5C8=C(C(C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)C(C9CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C)C(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O1[Fe][S]2[Fe]3[S]4[Fe]2[S]5[Fe]4[S]3[Ni]51. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C(CO)C(C[O])O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S([Fe]12[S]3[Fe]4[S]1[Fe]5[S]4[Fe]3[S]25)[Fe]67[S]8[Fe]9[S]6[Fe]1[S]9[Fe]8[S]71. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1C(N)N)NC3=[N]2[Zn+2][N]4=C(C3=O)Nc5c4ccc(c5)C(N)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C(CC[NH2][Pt]([NH3])([NH3])Cl)C[NH2][Pt]([NH3])([NH3])Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC=[N]2C(=C1)C3=CC(=CC=[N]3[Fe]2(C#N)(C#N)(C#N)C#N)CNC(=O)CCCCC4C5C(CS4)NC(=O)N5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Cr]36N7C(=CC8=[N]6C(=C5)C(=C8C=C)C)C(=C(C7=C2)CCC(=O)O)C)C=C)C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=C5C=CC6=[N]5[Co]7(N43)[N]8=C(C=CC8=C2c9ccccc9)C1=CC=C(N71)C(=C6c1ccccc1)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cl([Cu])[Cu]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N](C=C1)[Pt+2]([NH3])([NH3])Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C2C(C(C3[N-]2[Co+2]45[N]6=C1C(C(C6=CC7=[N]4C(=C(C8=[N]5C3(C(C8CCC(=O)N)(C)CC(=O)N)C)C)C(C7CCC(=O)N)(C)CC(=O)N)(C)C)CCC(=O)N)CC(=O)N)(C)CCC(=O)NCC(C)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=CC8=[N]6C(=C5)C(=C8C)C=O)C(=C(C7=C2)CCC(=O)O)C)C)C=C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe]2[S]3[Fe]4S[Fe]5[S]6[Fe]1[S]7[Mo]6[S]5[Fe]7S[Fe]8[S]2[Fe]3[S]48. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule N12345[Fe]67S[Fe]18[S]9[Fe]21S[Fe]32[S]6[Fe]3[S]7[Fe]4([S]23)S[Fe]52[S]8[Mo]9[S]12. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 2 radical electrons on molecule [CH2]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=C(C(=C4N3[Mg]56[N]2=C1C=C7N5C8=C(C(C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)C(C9CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C)C=C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]3[S]4[Fe]1S567([Fe]2[S]3[Fe]45)[Fe]8[S]9[Fe]6[S]1[Fe]9[S]8[Fe]71. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Fe]47N2C1=CC8=[N]7C(=C6)C(=C8C)CCC(=O)O)CCC(=O)O)C)C9C3(SC=C9)C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]3[S]4[Fe]1S5([Fe]2[S]3[Fe]45)S67[Fe]8[S]9[Fe]6[S]1[Fe]9[S]8[Fe]71. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2c(cc1C)N(C=N2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89(N5C4=C(C1=[N]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)C#N)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2c(cc1C)N(C=N2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5=[N-]6C4=C(C7=[N]8[Co+2]69([N]1=C(C=C8C(C7CCC(=O)N)(C)C)C(C(C1=C(C1=[N]9C5(C(C1CCC(=O)N)(C)CC(=O)N)C)C)(C)CC(=O)N)CCC(=O)N)C)C)CC(=O)N)C)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Co]47N2C1=CC8=[N]7C(=C6)C(=C8C)CCC(=O)O)CCC(=O)O)C)C(=C3C)C=C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH3][Co+3]([NH3])([NH3])[NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH3][Pt]([NH3])(Cl)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 2 radical electrons on molecule C(C(C(=O)O)N)S[Pb+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2([N]4=C1C=CC=C4)([O])[O])CCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1OCCN3CCCCC3)O[Cu]45[N](=C2)c6cc(c(cc6[N]4=Cc7ccc(cc7O5)OCCN8CCCCC8)F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)CC2C(=O)O[Cu]3[N]2=Cc4ccccc4O3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)CC1C(=O)O[Cu]2[N]1=Cc3ccccc3O2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe][S]2[Fe]1S[Fe]2S[Fe][Ni]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=C(C(=C4N3[Rh]56[N]2=C1C=C7N5C(=CC8=[N]6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C)CC)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[Co]56O[W]78(O1)(O2P91O2[W]%10%11(O5)(O[W]5%12(O6)(O9[W]6(O7)(O5)(O[W]57(O8)(O1[W]1(O3)(O5)(O[W]2(O4)(O%10)(O[W]234(O[W]58(O%11)(O2P29O%10[W]%11(O%12)(O5)(O[W]%105(O6)(O[W]6%10(O7)(O2[W](O1)(O3)(O6)(O[W]12(O4)(O93[W](O8)(O%11)(O1)(O[W]3(O5)(O%10)(O2)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +period in smiles: `O.O` +period in smiles: `O.O.O` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C(C(C(=O)O)N)S[As]O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)C12=C3[Ru]1456(C2=C4C5(=C63)C)([P]78CN9CN(C7)CN(C9)C8)(Cl)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C12345[Fe]6[S]7[Fe]18[N][Fe]29[S]1[Fe]3[S]2[Fe]1[S]9[Fe]42S[Fe]51[S]6[V]7[S]81. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=CC8=[N]6C(=C5)C(=C8C)C(=C)O)C(=C(C7=C2)CCC(=O)O)C)C)C(=O)C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=C(C(=C4N3[Fe]56N2C1=CC7=[N]5C(=CC8=[N]6C(=C4)C(C8=O)(C)CC(=O)O)C(C7=O)(C)CC(=O)O)C)CCC(=O)O)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1ccc(cc1NS(=O)(=O)C)C2=NN3C(=NN=C3C(=C2)NC(=O)CCNC(=O)C(CN)NC(=O)CCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCC(=O)NC(CN)C(=O)NCC(=O)[N]C4=[C]C(=NN5C4=NN=C5[C])c6[c][c]c(c([c]6)[N]S(=O)(=O)[C])[C]([C])[C])C. +period in smiles: `[CH3].[CH3]` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)C3=[N]([Os+2]24([N]5=CC=CC=C5C6=CC=CC=[N]46)N7C=CN=C7)C=CC=C3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)C3=[N]([Ru+2]24([N]5=CC=CC=C5C6=CC=CC=[N]46)N7C=CN=C7)C=CC=C3. +atomic number must be positive, given 0. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC=c2ccc3=CC=C([N]4=c3c2=[N]1[Pt]45(CC5)[N]6=CN(C(=C6)C7=CN(N=N7)C8C(C(C(C(O8)O)O)O)O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2=[N]3c4c(=c2cc1O)c5c(c6=CC=CN(c64)[Ru]3(C#O)C7C=CC=C7)C(=O)NC5=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1O)-c3c4c(c5c6c3N2[Ru]7891([N]6=CC=C5)([CH]2=[CH]7C8[CH]9=[CH]12)C#O)C(=O)NC4=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC=c2ccc3=CC=C([N]4=c3c2=[N]1[Pt]45([C][C]5)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(CO)(CO)NC(=O)C12[CH]3=[CH]4[Ru]3156([CH]4=[CH]52)([N]7=CC(=Cc8c7c9c(c1c8C(=O)N(C1=O)C)-c1cc(ccc1N69)O)F)C#O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)(C)c1ccc(cn1)C(=O)NC2=C[N]3=C(N2)C=CC(=C3)C4=CNN=C4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN1C=CN2[C]1[Pt]3(c4cc(cc(c4C5=[N]3C=CC=C5)F)F)[N]6=C2C=CC=C6. +period in smiles: `Cc1ccc(cc1)C(C)C.c1ccc(cc1)NC2=[S][Os]([N]3=C2C=CC=C3)Cl` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2=NC=C[N]3=c2c4=[N]([Ru]356([N]7=c8c(=NC=C7)ccc9=NC=C[N]5=c98)[N]2=CC=Cc3c2c2c(c5c3nc3cc(c(cc3n5)C#N)C#N)C=CC=[N]62)C=CN=c41. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe]2[S]3[Fe][S]4[Fe]1[S]2[Fe]34. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[CH2]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(c2cc3c(cc2C(N1[O])(C)C)OC4=CN(C(=O)N=C4N3)C5CC(C(O5)COP(=O)(O)O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Ni+2]47N2C1=CC8=[N]7C(=C6)C(C8CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O)C(=C3CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Co+2]47N2C1=CC8=[N]7C(=C6)C(C8CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O)C(=C3CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe]2S[Fe]3[S]2[Fe]1S3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12CC(=O)NC13CC4C(C(C5=[N]4[Ni+]67[N]3=C(C2CCC(=O)O)C=C8N6C(=C9C(=O)CCC1C9=[N]7C(C5)C1CC(=O)O)C(C8CC(=O)O)CCC(=O)O)(C)CC(=O)N)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe][S]3[Fe]1[S]([Fe]2)[Fe]3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C4C(=O)C(C5=C6C(=C(C7=CC8=[N]9C(=CC(=C1C)N2[Mg]9(N76)[N]3=C54)C(=C8C=O)C=C)C)CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C(=O)OC)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C([OH][Fe]234[OH]C(CC56[OH]2[Fe]7([OH]3C1(CC([OH]7)[O])C([OH]4)[O])([OH]C(C5)[O])[OH]C6[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC2=CC3=C(C=C4N3[Fe]56[N]2=C1C=C7N5C(=CC8=[N]6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)N2CC3=[N]([Ru]24(N5C=C(C=c6c5c7c(=c8cc(ccc8=[N]47)O)c9c6C(=O)NC9=O)F)(C#O)Cl)C=CC=C3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O1[Fe]O2[Fe]134O[Fe]356[S]4[Fe]52S6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe]234[Fe]156[S]2[Fe]35(S4)S6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]3456[Fe]1789[Fe]2312[Fe]47([S]58)([S]61)[S]92. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S(SS[Fe]12[S]3[Fe]4[S]1[Fe]5[S]4[Fe]3[S]25)SS[Fe]67[S]8[Fe]9[S]6[Fe]1[S]9[Fe]8[S]71. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O1[Fe][Fe][S]2[Fe]13[Fe]2S3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][Fe]1O[Fe]23S[Fe]245[S]3[Fe]4(O1)S5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[S]2[Fe]3([S]1[Fe]2(C3=O)(C#N)C#[O+])(C#N)C#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][Mo]12(O[Mo]3(O[Mo]456(O3[Mo]7(O1)(O2[Mo]8(O7[Mo]91(O4)(O8[Mo]2(O9[Mo](O15)(O2)(O6)([O])[O])([O])([O])[O])[O])([O])([O])[O])([O])[O])[O])([O])([O])[O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=[N]3C1=CC4=C(C5=C6N4[Mg]37N8C(=CC9=[N]7C(=C6C(C5=O)C(=O)OC)C(C9C)CCC(=O)OCC=C(C)CC=CC(C)CCCC(C)CCCC(C)C)C(=C(C8=C2)C=C)C)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=C(C(=C4N3[Mg]56[N]2=C1C=C7N5C8=C(C(C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)C(C9CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C)C=O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Ga]S[Ga]1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C4C(=O)C(C5=C6C(=C(C7=CC8=[N]9C(=CC(=C1C)N2[Mg]9(N76)[N]3=C54)C(=C8C)CC)C)CCC(=O)OCC=C(C)CCC=C(C)CCC=C(C)C)C(=O)OC)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C4C(=O)C(C5=C6C(=C(C7=CC8=[N]9C(=CC(=C1C)N2[Mg]9(N76)[N]3=C54)C(=C8C)CC)C)CCC(=O)OCC=C(C)CCC=C(C)CCC=C(C)C)C(=O)OC)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=C(NC=N1)CC(CO[As](O)(O)O)N. +atomic number must be positive, given 0. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1C(C2=CC3=C(C(=C4N3[Mg]56[N]2=C1C=C7N5C8=C(C(C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)C(C9CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C)C(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [OH]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[Cu]56O[W]78(O1)(O2P91O2[W]%10%11(O5)(O[W]5%12(O6)(O9[W]6(O7)(O5)(O[W]57(O8)(O1[W]1(O3)(O5)(O[W]2(O4)(O%10)(O[W]234(O[W]58(O%11)(O2P29O%10[W]%11(O%12)(O5)(O[W]%105(O6)(O[W]6%10(O7)(O2[W](O1)(O3)(O6)(O[W]12(O4)(O93[W](O8)(O%11)(O1)(O[W]3(O5)(O%10)(O2)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[Ni]56O[W]78(O1)(O2P91O2[W]%10%11(O5)(O[W]5%12(O6)(O9[W]6(O7)(O5)(O[W]57(O8)(O1[W]1(O3)(O5)(O[W]2(O4)(O%10)(O[W]234(O[W]58(O%11)(O2P29O%10[W]%11(O%12)(O5)(O[W]%105(O6)(O[W]6%10(O7)(O2[W](O1)(O3)(O6)(O[W]12(O4)(O93[W](O8)(O%11)(O1)(O[W]3(O5)(O%10)(O2)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O=[V](O[V]([O])([O])O[V]([O])([O])O[V]([O])O[V]([O])([O])[O])O([V]([O])[O])[V]([O])([O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1C(C(C(N1)C2=CN(N=N2)CC=CC34[C]5[Fe]3678912([C]5[C]6[C]74)[C]3[C]8[C]9[C]1[C]23)O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c3c4c1C=CC=[N]4[Pt]5([N]3=CC=C2)[N]6=c7c(=CC=C6)ccc8c7[N]5=CC=C8. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N]4C(=CC5=[N]6[Fe]47N2C1=CC8=C(C(=C(N78)C=C6C(=C5C)C(CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)O)C)C=C)C(=C3CCC(=O)O)C=O)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)-c3c4c(c5c6c3[NH]2[Ru]7891([N]6=CC=C5)([CH]2=[CH]7[CH]8=C9=[CH]12)C#O)C(=O)NC4=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=C2)C(=C(C7=CC8=[N]6C(=C5)C(=C8C(=O)O)C)C(=O)O)C)C)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=C2)C(=C(C7=CC8=[N]6C(=C5)C(=C8C)C(CCC=C(C)CCC=C(C)CCC=C(C)C)O)C=O)CCC(=O)O)C)C=C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=C2)C(=C(C7=CC8=[N]6C(=C5)C(=C8CCC(=O)O)C)CCC(=O)O)C)C=C)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=C2)C(=C(C7=CC8=[N]6C(=C5)C(=C8C)CCC(=O)O)C=C)C)CCC(=O)O)C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=CC8=[N]6C(=C5)C(=C8C=C)C=C)C(=C(C7=C2)CCC(=O)O)C)C=C)C=C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(C(=O)C4=[N]3[Fe]56N2C(=C1C)C=C7[N]5=C(C=C8N6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)(C)CC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Ir]36(N7C(=C2)C(=C(C7=CC8=[N]6C(=C5)C(=C8C)CCC(=O)O)C=C)C)C=O)CCC(=O)O)C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=C(C(=C4N3[Fe]56[N]2=C1C=C7N5C8=C(CC(=O)C8=C7C)C9=[N]6C(=C4)C(C9CCC(=O)OC)C)C)C=C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Ni]47N2C1=CC8=[N]7C(=C6)C(=C8C)CCC(=O)O)CCC(=O)O)C)C(=C3C)C=C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=CC8=[N]6C(=C5)C(=C8C=C)C)C(=C(C7=C2)CCC(=O)O)C)C(=C)OO)C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2c(cc1C)N3C=[N]2[Co]456(N7C8C(C(C7=C(C9=[N]4C(=CC1=[N]5C(=C(C2=[N]6C8(C(C2CCC(=O)N)(C)CC(=O)N)C)C)C(C1C=CC(=O)N)(C)CC(=O)N)C(C9CCC(=O)N)(C)C)C)(CCC(=O)NCC(OP(=O)(OC1C(OC3C1O)CO)O)C)C)CC(=O)N)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C(C(C(C(=O)O)O[Ca])C(=O)O)C(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C12345[Fe]6[S]7[Fe]18S[Fe]29[S]1[Fe]3[S]2[Fe]4([S]9[Mo]12)S[Fe]51[S]6[Fe]7[S]81. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C12345[Fe]67S[Fe]18[S]9[Fe]21S[Fe]32[S]6[Fe]3[S]7[Fe]4([S]23)[Se][Fe]52[S]8[Mo]9[S]12. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C12345[Fe]67[S]8[Fe]19[S]1[Fe]8[S]6[Fe]21[Se][Fe]31[S]2[Fe]4([Se]7)[S]3[Fe]5([S]1[Mo]32)[Se]9. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C12345[Fe]67S[Fe]18[S]9[Fe]21S[Fe]32[S]6[Fe]3[S]7[Fe]4([S]23)S[Fe]52[S]8[Mo]9[S]12. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C12345[Fe]6[S]7[Fe]1[S]8[Fe]7[S]6[Fe]28S[Fe]39[S]1[Fe]4[S]2[Fe]5[S]9[Mo]21. +period in smiles: `[H].C(CCCCN=[N+]=[N-])CCCNC1C(C(C(C(C1O)O)O)O)C(=O)O` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]123(O[W]456(O[W]789(O[W]%10%11(O7)(O[W]7%12%13(O[W]%14%15(O7)(O[W](O4)(O5)(O[W]45(O%14)(O[W]7(O6)(O8)(O4[W](O%10)(O%12)(O7)(O5)[O])[O])[O])(O[W]4(O1)(O2)(O[W]12(O%15)(O4[W]45(O[W]6(O3)(O9)(O[W](O%11)(O6)(O4)(O[W](O%13)(O5)(O1)(O2)[O])[O])[O])([O])([O])[O])([O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN1C(=C(CN1)C(=O)NC2=CC=[N]3CC(NC3=N2)c4ccccc4)C(=O)N5CCC5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=C[N](=CN1)[Cu+]([N]2=CNC=C2)([N]3=CNC=C3)([N]4=CNC=C4)([OH2])[OH2]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH3][Ir+3]([NH3])([NH3])([NH3])([NH3])[NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1c(cc2c(c1F)C3=[N]([Ir+3]245(c6cc(cc(c6C7=CC=CC=[N]47)F)F)[N]8=C(C=CC=C8)C9=[N]5C=C(C=C9)CN1C(=O)CCC1=O)C=CC=C3)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C2CC3C(=C(C4=[N]3[Fe]56N2C(=C1C=C)C=C7[N]5=C(C=C8N6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C(C(C(C(=O)O)O[Mg])C(=O)O)C(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]123(O[W]45(O16[W]7(O2)(O[W]891(O7[W]626(O3)O4[W]34(O282[W](O3)(O9)(O[W]2(O4)(O1)(O6)[O])([O])[O])(O5)[O])[O])([O])[O])([O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1(O[W]2(O1[W]345(O2[W]678(O391[W]2(O4)(O6[W]34(O2[W]9269O73[W]3(O4)(O2[W]2(O3)(O63[W]1(O5)(O8)(O[W]3(O2)(O9)([O])[O])[O])([O])[O])([O])[O])([O])[O])([O])[O])[O])[O])([O])([O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]12(O[W]34(O15[W]67(O3[W](O4)(O6[W]89(O713[W]54(O8)(O2[W]1(O[W]3(O9)(O4)([O])[O])([O])[O])[O])([O])[O])([O])([O])[O])[O])([O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]12(O3[W]45(O[W]36(O[W]78(O1[W]9(O7)(O[W]13(O2[W](O1)(O4)(O[W]12(O5)(O[W]4(O6)(O8)(O1[W](O3)(O9)(O2)(O4)[O])[O])[O])([O])[O])([O])[O])([O])[O])([O])[O])([O])[O])([O])[O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]12(O[W]3(O1[W](O2)(O3)([O])[O])([O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12C3([Ir]1456(C2(C4(C53C)C)C)([N]7=C(C=C(C=C7)O)C(=O)N6CCc8ccc(cc8)S(=O)(=O)N)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12C3([Ir]1456(C2(C4(C53C)C)C)([N]7=C(C=CC=C7)C(=O)N6CCc8ccc(cc8)S(=O)(=O)N)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C[N](C)(C)C)OC(=O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2(C3(C(=C(C4=[N]3[Co+]56[N]2=C1C=C7N5C(=CC8=[N]6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C)C)C)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2(C3(C(=C(C4=[N]3[Co+]56[N]2=C1C=C7N5C(=CC8=[N]6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C)C)C)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c3c(ccc4c3c1C(=O)NC4=O)C(=O)N(C2=O)CC5=CC=[N](C=C5)[Pt]67[NH2]CC[NH]6CC[NH2]7. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O[Mo]O[Mo]1(O[Mo](O[Mo](O[Mo](O1)([O])([O])([O])O[Mo]([O])([O])([O])[O])([O])([O])([O])[O])([O])([O])([O])O[Mo]([O])([O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][Mo]([O])([O])O[Mo]12(O[Mo]34(O1[Mo]567(O2[Mo]89(O5[Mo]1(O8)(O[Mo]2(O1[Mo]1(O63[Mo](O12)(O4)(O7)([O])[O])(O9)[O])([O])([O])[O])([O])[O])([O])[O])[O])([O])[O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=C(C5=[N]6C(=C(C7=CC=C8N7[Cr]6(N34)[N]9=C2C=CC9=C8c1ccccc1)c1ccccc1)C=C5)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=C(C5=[N]6C(=C(C7=CC=C8N7[Mn]6(N34)[N]9=C2C=CC9=C8c1ccccc1)c1ccccc1)C=C5)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=C(C5=[N]6C(=C(C7=CC=C8N7[Co]6(N34)[N]9=C2C=CC9=C8c1ccccc1)c1ccccc1)C=C5)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O[Mo]O([Mo]O)[Mo](=O)([O])O([Mo]O)[Mo]([O])([O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][Mo]12(O[Mo]34(O1[Mo]56(O2[Mo]78(O59[Mo]1(O7)(O[Mo]2(O1[Mo]91(O8)(O2[Mo](O13)(O6)(O4)([O])[O])[O])([O])[O])([O])[O])([O])[O])[O])([O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O[Mo]O[Mo]1(O[Mo](O1[Mo]O)([O])([O])[O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1ccc2ccc3c4c2[n+]1[Pt]5(N4C(=CC3)C)([C]=[C]5)(C)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C(=CC3=[N]2[Ru]4567([C]8[C]4[C]5[C]6[C]78)(OC3=O)[O])N9CCN(CC9)C(=O)CCCCC1C2C(CS1)NC(=O)N2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[Ce]56789(O[W]%10%11(O1)(O2P12O%12%13[W]%14%15(O5)(O[W]5%16(O6)(O11[W]6(O%10)(O5)(O[W]5%10(O%11)(O22[W]%11(O3)(O5)(O[W]%12(O4)(O%14)(O[W]%133(O%15)(O[W]1(O%16)(O6)(O[W]2(O%11)(O%10)(O3)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])O[W]123(O[W]45(O7)(O1P16O7%10[W]%11%12(O8)(O[W]8%13(O9)(O11[W]9(O4)(O8)(O[W]48(O5)(O65[W]6(O2)(O4)(O[W]7(O3)(O%11)(O[W]%102(O%12)(O[W]1(O%13)(O9)(O[W]5(O6)(O8)(O2)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C1C(=O)O[Cu]2[N]1=Cc3ccccc3O2)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN1C(=C(CN1)C(=O)NCC2=NCCO2)C(=O)NC3=NC4=[N](CC(=N4)c5ccccc5)C=C3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)-c3c4c(c5=CC(=C[N]6=c5c3N2[Ru]67891(C2C7C8C9C12)C#[O+])F)C(=O)NC4=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][V]1(O2[V]34(O[V]56(O[V]78(O1[V]91(O7[V]7%10(O8[V]8%11(O7[V]7%12(O8[V]8(O%115)(O6[V]5(O3)(O8[V]3(O7)(O5[V]56(O3[V](O3[V](O%12)(O%10)(O7[V]3(O5)(O3[V]7(O9)(O5[V]2(O1)(O4[V]53(O6)[O])[O])[O])[O])[O])([O])O[V]([O])([O])([O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])O[V]([O])([O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2=[N](C3=C4(C(=C(C5[N]4=c2c(c1C)C(C5)(C)C)C(=O)O)c6ccccc6)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)O)O)O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12C3([Ir]1456(C2(C4(C53C)C)C)([N]7=CC=C(C=C7C(=O)N6CC(=O)Nc8ccc(cc8)S(=O)(=O)N)O)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12C3([Ir]1456(C2(C4(C53C)C)C)[N]7=CC=C(C=C7C(=O)[N]6(CCCc8ccc(cc8)S(=O)(=O)N)Cl)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(NC(S1)C(C(=O)O)NC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12)C(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(NC(S1)CNC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12)C(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(NC(S1)C(C(=O)O)NC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12)C(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12=C3([Rh+3]145([C-]2(C4(=C53C)C)CCNC(=O)CCCCC6C7C(CS6)NC(=O)N7)([Cl-])([Cl-])[Cl-])C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC[P](C)(CC)[Rh]([P](C)(CC)CC)([P](CC)(CC)CNCC(=O)NCCN1C(=O)CCC1=O)[P](CC)(CC)CNCC(=O)NCCN2C(=O)CCC2=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC[N](C)(C)C)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]23CC[N]4([Lu]256([N]7=C(C3)C=CC=C7C(=O5)O)[N]8=C(C=CC=C8C4)C(=O)O6)CCN1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC[N](C)(C)C)OC(=O)CCCCCCCC=CCCCCCCCC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [C](=O)[Re]12(O3[Re]4(O1[Re]5(O2[Re]3(O45)([C]=O)([C]=O)[C]=O)([C]=O)([C]=O)[C]=O)([C]=O)([C]=O)[C]=O)([C]=O)[C]=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O=[W]1234O[W]567(=O)O18[P]91O%10%11[W]%12%13(=O)(O2)O[W]%102(=O)(O5)O[W]%115(=O)(O%12)O[W]%10%11%12(=O)O99[W](=O)(O%10)(O3)(O%13)O[W]93(=O)(O%11)O[W]8(=O)(O4)(O6)O[W]46(=O)(O3)O11[W](=O)(O4)(O7)(O2)O[W]1(=O)(O6)(O5)O%12. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1N(=O)=O)nc3c4=CC=C[N]5=c4c6=[N]([Ru]578([N]9=CC=Cc1c9c4c(cc1)C=CC=[N]74)[N]1=CC=Cc4c1c1c(cc4)C=CC=[N]81)C=CC=c6c3n2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(c(c1)[N+](=O)[OH-])nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=c1c(=CC=C9)ccc2=CC=C[N]7=c21)[N]1=c2c(=CC=C1)ccc1=CC=C[N]8=c12. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1c(cc2c(c1F)C3=CC=CC=[N]3[Ir+3]245(c6cc(cc(c6C7=CC=CC=[N]47)F)F)[N]8=C(C=CC=C8)C9=[N]5C=C(C=C9)CN1C(=O)CCC1=O)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][Mg](F)(F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=[CH]2C=C3([Ru+]24([CH]1=C3)([NH2]C5CN(CC5[NH2]4)C(=O)CCCCC6C7C(CS6)NC(=O)N7)Cl)C(C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc(ccc1C(=O)NC2=CNN=C2C3=Nc4ccc(cc4N3)C[NH]5CCOCC5)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)NC(=O)NC2=CNN=C2C3=Nc4cc(ccc4N3)C[NH]5CCOCC5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1CCC2C(C1)[N]34CC5=[N]([Fe]367([N]2(CC8=CC=CC=[N]68)CC(=O)O7)OC(=O)C4)C=CC=C5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[N]12CC3=CC=CC=[N]3[Fe+2]145[N]6=CC=CC=C6C[N]4(CC(=O)O5)C7C2CCCC7. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[N]12CC[N]34[Fe+2]1([N]5=C(C2)C=CC=C5)([N]6=CC=CC=C6C3)OC(=O)C4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(SC2=C1C(=NC(C3=NN=C(N32)C)CC(=O)NC45C6=C7[Fe]6489123(C7=C85)C4=C9[C]1C2=C34)c1ccc(cc1)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1NC[S]2[Fe]3([S-]1[Fe]2(C3=O)(C#N)(C#[O+])[S])(C#N)C#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)C3=[N]([Os+2]24([N]5=C(C=CC=C5)C6=CC=CC=[N]46)N7C=CN=C7)C=CC=C3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe][S]2[Fe]1S[Fe]2[S]3[Fe]4S[Fe]5[S]4[Fe]3S5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1CCC(CC1)[NH2][Pt+2][NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)C3=CC=CC=[N]3[Ru+2]24([N]5=C(C=CC=C5)C6=[N]4C=CC=C6)N7C=CN=C7. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12CC(=O)NC13CC4C(C(C5=[N]4[Ni+]67[N]3=C(C2CCC(=O)O)C=C8N6C(=C9C1=[N]7C(C5)C(C1CC(C9=O)SC)CC(=O)O)C(C8CC(=O)O)CCC(=O)O)(C)CC(=O)N)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCCCCCCC(=O)NC12CO34[Al]5678O9[Mo]33(O[Mo]44(O5[Mo]5(O4)(O6(C1)[Mo]1(O5)(O7[Mo]4(O1)(O8(C2)[Mo]9(O4)(O3)([O])[O])([O])[O])([O])[O])([O])[O])([O])[O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1nc(c2c(n1)N(C=N2)C3C(C(C(O3)COP(=O)(O[Mg])OP(=O)(NP(=O)(O)O)O)O)O)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC2=CC3=[N]4C(=CC5=C(C(=C6N5[Mg]47N2C1=CC8=[N]7C(=C6)C(=C8C)CCC(=O)O)CCC(=O)O)C)C=C3C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCOC(=O)C12C3[Ru]1456(C3C4C52)([N]7=CC=Cc8c7c9c(c1c8C(=O)NC1=O)-c1cc(ccc1N69)O)[CH]#O. +period in smiles: `O.O` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=[N]4C(=CC5=[N]6[Fe]47[N]2=C1C=C8[N]7=C(C=C6C(=C5CCC(=O)O)C)C(=C8C)CC)C(=C3C)CCC(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1NC[S]2[Fe+]3([S]1[Fe+]2(C3=O)([C-]#N)([C-]#[O+])[C-]#[O+])([C-]#N)[C-]#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C(C4=[N]3[Mo]56(=O)N2C(=C1C)C=C7[N]5=C(C=C8N6C(=C4)C(=C8C)CCC(=O)O)C(=C7CC)C)CCC(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[NH]2CC[NH]3[Cu]24[NH](C1)CC[NH]4CCC3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc(ccc1C[N]23CCC[NH]4[Cu]25[NH](CCC[NH]5CC3)CC4)C[N]67CCC[NH]8[Cu]69[NH](CCC[NH]9CC7)CC8. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc(ccc1C[N]23CCCN4[Ni]25N(CCCN5CC3)CC4)C[N]67CCCN8[Ni]69N(CCCN9CC7)CC8. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=C(C(=C4[N]3([Cu]56[N]2=C1C=C7N5C(=CC8=[N]6C(=C4)C(=C8CCC(=O)O)C)C(=C7C)CCC(=O)O)C)C)CC)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=C(C5=[N]6C(=C(C7=CC=C8N7[Fe]6(N34)[N]9=C2C=CC9=C8c1ccccc1)c1ccccc1)C=C5)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C=C(C(N1[O])(C)C)CSS(=O)(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule COc1cc(cc(c1O)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)NC(=O)CCC6C[NH2][Pt]([NH2]6)(Cl)Cl)OCO4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule COc1cc(cc(c1O)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)NC(=O)CCC6C[NH2][Pt]([NH2]6)(Cl)Cl)OCO4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule COc1cc(cc(c1O)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)NC(=O)CCC6C[NH2][Pt]([NH2]6)Cl)OCO4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule COc1cc(cc(c1O)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)NC(=O)CCC6C[NH2][Pt]([NH2]6)Cl)OCO4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH3][Co+3]([NH3])([NH3])([NH3])([NH3])[NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe][S]2[Fe]3[S]4[Fe]2[S]5[Fe]4[S]3[Ni]51. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 2 radical electrons on molecule [NH]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH2]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [N]=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [N]=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH3][Ru+3]([NH3])([NH3])([NH3])([NH3])[NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [C-](#N)[Fe+2]([C-]#N)([C-]#N)([C-]#N)([C-]#N)[N]#[OH+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Fe]47N2C1=CC8=[N]7C(=C6)C(=C8C=C[N+](=O)[O-])C)C)CCC(=O)O)C(=C3C)CCC(=O)O)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1OCCN3CCCCC3)O[Ni]45[N](=C2)c6cc(c(cc6[N]4=Cc7ccc(cc7O5)OCCN8CCCCC8)F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCOP(=O)(CCCc1cc2c3c(c1)C[N]([Pt]3([N](C2)(C)C)Cl)(C)C)Oc4ccc(cc4)[N+](=O)[O-]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)C12[C]3[Os]1456([C]3C4([C]5[C]62)C)(C7=[N](c8ccccc8N7C)C)(Cl)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C=CC3=[N]2[Ir]45(c6c3cccc6)(c7ccccc7C8=[N]4c9ccccc9C=C8)[N]1=C(C=CC=C1)C1=[N]5C=C(C=C1)CNC(=O)CCSCc1cccnc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C3=[N]([Ir]245(c6ccccc6C7=[N]4C=CC=C7)[N]8=CC=CC=C8C9=CC=C(C=[N]59)CNC(=O)CCSCc1cccnc1)C=CC=C3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C(C2=CC3=C(C(=C4N3[Zn]56[N]2=C1C=C7N5C8=C(C(C(=O)C8=C7C)C(=O)OC)C9=[N]6C(=C4)C(C9CCC(=O)OC)C)C)C=C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[CH2]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1O[Co]23(O4[Co]5(O1)(O2[Co]67(O3[Co]4(O56)(OC(O7)CCNC(=O)CCCCC8C9C(CS8)NC(=O)N9)([N]1=CC=CC=C1)[O])([N]1=CC=CC=C1)[O])([N]1=CC=CC=C1)[O])[N]1=CC=CC=C1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C2C(C(S1)CCCCC(=O)NCCC3O[Co]45(O6[Co]7(O4[Co]8(O3)(O7[Co]6(O58)([N]9=CC=CC=C9)[O])([N]1=CC=CC=C1)[O])([N]1=CC=CC=C1)[O])[O])NC(=O)N2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1O[Co]23(O4[Co]5(O1)(O2[Co]67(O3[Co]4(O56)(OC(O7)CCNC(=O)CCCCC8C9C(CS8)NC(=O)N9)([N]1=CC=CC=C1)[O])([N]1=CC=CC=C1)[O])[O])[N]1=CC=CC=C1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C2C(C(S1)CCCCC(=O)NCCC3O[Co]45(O6[Co]7(O4[Co]8(O3)(O7[Co]6(O58)([N]9=CC=CC=C9)([O])[O])([N]1=CC=CC=C1)[O])[N]1=CC=CC=C1)([N]1=CC=CC=C1)[O])NC(=O)N2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [CH2][O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc(c(c(c1)Cl)CS(=O)(=O)c2ccc3c(c2)NC(=O)C(=Cc4ccc(c(c4)[N](=O)O)O)S3)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)-c3c4c(c5c6c3N2[Ru]7([N]6=CC(=C5)N)(NCC8=[N]7C=CC=C8)(C#O)Cl)C(=O)NC4=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12C3([Ir]145(C2(C4(C53C)C)C)(C6=[N](c7ccccc7N6C)C)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [B]1B2B13B4B56B2B578B649[Co]7124567(B9[C+]31(C82)CCS(=O)(=O)N)B1B2B38B229B1B212B93B41(B52)[C+]68(C7)CCS(=O)(=O)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCC(=O)NCCOCCOCCOCCNC(=O)C[N]1=C(Sc2c1cccc2)CC3=CC=[N](c4c3cccc4)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C(=NN1C2CCN(CC2)CC(=O)N(C)C)C)NC3=NC=C(C(=C4C=N[N]5=C4C=CC=C5)N3)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CN(C=N1)C2C(C(C(O2)CO[V]([O])([O])O[V]([O])([O])[O])O[V]([O])([O])O[V]([O])([O])O[V]([O])([O])[O])O[V]([O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2=[N](C3=C(C(=O)NC(=O)N3)[N](=c2cc1C)C=CC=NCC(=O)O)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=Nc6c5ncnc6N)O)O)O)O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2=c3ccccc3=[N](C=c2c1)[Pt](N)(N)[N]4=CN(C5=C4C(=O)NC(=N5)N)C6CC(C(O6)COP(=O)(O)O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)-c3ccccc3I2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C(C(C(C(C1O)O)O)CN[N]#N)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC2=CC3=[N]4C(=CC5=CC=C6N5[Fe]47N2C1=CC8=[N]7C(=C6)C=C8)C=C3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCCCCCCCCCOP(=O)(O)OCC[N](C)(C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)[P](c2ccccc2)(c3ccccc3)[Pt+2]4(c5ccccc5C6=CC=CC=[N]64)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC2=[N](C=C1)[Pt]34[N]5=C(C=CC=C5)NC6=CC=CC(=[N]63)C7=[N]4C(=CC=C7)N2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH3][Pt+2]([NH3])[NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c3c(ccc4c3c1C(=O)NC4=O)C(=O)N(C2=O)CC5=CC=[N](C=C5)[Pt]([NH3])[NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=NC2=C(N1C3C4C(C(O3)COP(=O)(O)O)O[V](=O)(O4)[O])N=C(NC2=O)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C(N(C1(C)C)[O])(C)C)CSS(=O)(=O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(=C(C(N1[O])(C)C)c2ccccc2)CSS(=O)(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC12C3([Rh]145(C2(C4(C53C)C)C)(C6=[N](c7ccccc7N6C)C)Cl)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)nc3c4=CC=C[N]5=c4c6=[N]([Ru]578([N]9=C(C=CC=C9)C1=[N]7C=CC=C1)[N]1=CC=CC=C1C1=CC=CC=[N]81)C=CC=c6c3n2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[Ni]56O[W]78(O1)(O2[Si]91O2%10[W]%11%12(O5)(O[W]5%13(O6)(O96[W]9(O7)(O5)(O[W]57(O8)(O11[W]8(O3)(O5)(O[W]2(O4)(O%11)(O[W]%102(O%12)(O[W]6(O%13)(O9)(O[W]1(O8)(O7)(O2)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[Co]56O[W]78(O1)(O2[Si]91O2%10[W]%11%12(O5)(O[W]5%13(O6)(O96[W]9(O7)(O5)(O[W]57(O8)(O11[W]8(O3)(O5)(O[W]2(O4)(O%11)(O[W]%102(O%12)(O[W]6(O%13)(O9)(O[W]1(O8)(O7)(O2)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(=C(C(N1[O])(C)C)Br)CSS(=O)(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C2C(C(S1)CCCCC(=O)NC34C[O+2]56[Mn]7891[O+2]%10(C3)[Mo]3%11([O+2]77[Mo]5(O3)(O[Mo]63([O+2]85CC(C7)(C[O+2]96[Mo]%10(O%11)(O[Mo]66([O+2]1(C4)[Mo]5(O3)(O6)([O])[O])([O])[O])([O])[O])NC(=O)CCC=CC1C3C(CS1)NC(=O)N3)([O])[O])([O])[O])([O])[O])NC(=O)N2. +period in smiles: `Cc1ccccc1.C1N2CN3CN1C[P](C2)(C3)[Ru](Cl)Cl` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccnc(c1)C2=[N](C=CC=C2)[Ru]([N]3=CNC=C3)[N]4=C(C=CC=C4)c5ccccn5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(CC(C(N1[O])(C)C)N2C(=O)CCC2=O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1Cl)nc3c4=CC=C[N]5=c4c6c(c3n2)C=CC=[N]6[Ru+2]578([N]9=CC=Nc1c9c2c(cc1)N=CC=[N]72)[N]1=CC=Nc2c1c1c(cc2)N=CC=[N]81. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=C[N](=CN1)[Re+](C#O)(C#O)(C#O)[OH2]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C(C1C(=O)O[Re+]([NH2]1)(C#O)(C#O)C#O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2=CC=C[N]3=c2c4=[N]([Re]3(C#O)(C#O)C#O)C=CC=c41. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=c2ccc3c4c2=[N](C=C1)[Re]([N]4=CC=C3C)(C#O)(C#O)C#O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc(cc(c1)NC(=N)C2=CC=CS2)C(COc3cccc(c3)[N]C(=N)C4=CC=CS4)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [NH3][Rh+3]([NH3])([NH3])([NH3])([NH3])[NH3]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCCCCCCC(=O)N1C2=[N](C=CC=C2)[Rh][N]3=CC=CC=C31. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2COC3=[N]2[Rh]4c5c3cccc5C6=[N]4C(CO6)c7ccccc7. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c3c4c1N=CC=[N]4[Ru+2]56([N]3=CC=N2)([N]7=c8c(=CC=C7)c9c(c1=CC=C[N]5=c18)nc1cc(c(cc1n9)F)F)[N]1=CC=Nc2c1c1c(cc2)N=CC=[N]61. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)nc3c4=CC=C[N]5=c4c6=[N]([Ru+2]578([N]9=c1c(=NC=C9)ccc4=NC=C[N]7=c41)[N]1=c4c(=NC=C1)ccc1=NC=C[N]8=c14)C=CC=c6c3n2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1ccc2c(c1)nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=CC=Nc1c9c2c(cc1)N=CC=[N]72)[N]1=CC=Nc2c1c1c(cc2)N=CC=[N]81. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=CC=Cc1c9c2c(cc1)C=CC=[N]72)[N]1=CC=Cc2c1c1c(cc2)C=CC=[N]81. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)nc3c4=CC=C[N]5=c4c6=[N]([Ru]578([N]9=C(C=CC=C9)C1=CC=CC=[N]71)[N]1=CC=CC=C1C1=CC=CC=[N]81)C=CC=c6c3n2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1c2c(cc3c1C4=[N]([Ru]356([S]7CC[S]5CC[S]6CC7)C#[O+])C=CC=C4)C(=O)NC2=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]1([Fe]2[S]3[Fe]1[S]4[Fe]3[S]2[Ni]4)[Fe]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c(cc1c3ccc4c(c3)nc5c6=CC=C[N]7=c6c8=[N]([Ru]791([N]3=CC=Cc6c3c3c(cc6)C=CC=[N]93)[N]3=CC=Cc6c3c3c(cc6)C=CC=[N]13)C=CC=c8c5n4)nc1c3=CC=C[N]4=c3c3=[N]([Ru]445([N]6=CC=Cc7c6c6c(cc7)C=CC=[N]46)[N]4=CC=Cc6c4c4c(cc6)C=CC=[N]54)C=CC=c3c1n2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [C](=O)[Re+]([C]=O)([C]=O)([O])([O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2=CC=C[N]3=c2c4=[N]([Ru+2]356[N]7=C(C=CC=C7)C8=CC=CC(=[N]58)C9=CC=CC=[N]69)C=CC=c41. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1c2c3c4c(c1NC(=O)CI)C=CC=[N]4[Ru+2]56([N]3=CC=C2)([N]7=C(C=CC=C7)C8=[N]5C=CC=C8)[N]9=C(C=CC=C9)C1=CC=CC=[N]61. +period in smiles: `Cc1ccc(cc1)CCC(=O)O.C1N2CN3CN1C[P](C2)(C3)[Ru](Cl)Cl` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N][Ru]23456([N]1)(C7=C2C38=C4(C5=C67)CC9=C(C8)CC=CC9)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc2c3c4c1C=CC=[N]4[Ru]5678(C3=CNC2=O)(C9=C5[C]6C7=C89)C#O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)C3=CC=CC=[N]3[Ru+2]245([N]6=c7c(=CC=C6)c8c(c9=CC=C[N]4=c97)nc1c2c3c4c(c1n8)C=CC=[N]4[Ru+2]14([N]3=CC=C2)([N]2=C(C=CC=C2)C2=[N]1C=CC=C2)[N]1=C(C=CC=C1)C1=[N]4C=CC=C1)[N]1=CC=CC=C1C1=CC=CC=[N]51. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C=C3C(=C(C4=[N]3[Ru]56N2C(=C1C)C=C7[N]5=C(C=C8N6C(=C4)C(=C8C)CCC(=O)O)C(=C7CC)C)CCC(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1nc2cc3c(cc2c(n1)N)C4=CC=CC=[N]4[Ru]3([C-]#[O+])C5(C=CC=C5)C(=O)Oc6c(cccc6OC)OC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(=C(C(N1[O])(C)C)CS)CS)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2([N]4=C1C=CC=C4)N=[N+]=[NH-])CCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2([N]4=C1C=CC=C4)(N=[N+]=[NH-])[O])CCCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2([N]4=C1C=CC=C4)[O])CCCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][Fe]1[S]([Fe]2[S]1[Fe]S2)[Fe]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Cc1cc2c(cc1C)N(C=N2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Rh]89[N]5=C4C(=C1N8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe][S]2[Fe]1[S]([Fe]2)[Fe]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O[SH](=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [Fe]12[Se]3[Fe]4[Se]1[Fe]5[Se]2[Fe]3[Se]45. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2([N]4=C1C=CC=C4)([O])OO)CCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2[N]4=C1C=CC=C4)CCCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2([N]4=C1C=CC=C4)[O])CCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2([N]4=C1C=CC=C4)OO)CCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=CC=CC=[N]3[Cu]2[N]4=CC=CC=C41)CCCCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C2C(C(S1)CCCCC(=O)NC(CS(=O)(=O)O)C(=O)NCC3=C4C=CC5=CC6=CC=C7N6[Fe]8(=[N]9C3=CC=C9C=C1N8C(=C7CNC(=O)C(CS(=O)(=O)O)NC(=O)CCCCC3C6C(CS3)NC(=O)N6)C=C1)N54)NC(=O)N2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[W]567(O18[Si]91O%10%11[W]%12%13(O2)(O[W]%102(O5)(O[W]%115(O%12)(O[W]%10%11%12(O99[W](O%10)(O3)(O%13)(O[W]93(O%11)(O[W]8(O4)(O6)(O[W]46(O3)(O11[W](O4)(O7)(O2)(O[W]1(O6)(O5)(O%12)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1C[N]2=CC3=[N]([Ni]24[N]1=CC5=CC=CC=[N]45)C=CC=C3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[N]2(CCC3=[N]([Cu]2[N]4=C1C=CC=C4)C=CC=C3)CCNC(=O)CCCCC5C6C(CS5)NC(=O)N6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(C2=[N]3C1=CC4=[N]5[Fe]36N7C(=C2)C(=C(C7=CC8=C(C(=C(N68)C=C5C(C4CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)(C)[P](CCNC(=O)CCCCC1C2C(CS1)NC(=O)N2)(C(C)(C)C)[Pd]3(CC=C3c4ccccc4)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C(=O)CN2C=[N](C3=C2C(=O)NC(=N3)N)C4C(C(C(O4)COP(=O)(O)O)O)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)[Sn](c2ccccc2)c3ccccc3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule Br[Ta]123456Br[Ta]17891%10[Ta]22%11(Br7)[Ta]337%12%13([Ta]484([Ta]923(Br%11)(Br1)(Br4)(Br7)Br%12)(Br5)(Br%10)Br%13)Br6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCC[Sn](CCCC)CCCC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C=C1CSC(N=C1C(=O)O)C(C(=O)O)NC(=O)CCC(=O)C23[C]4[Ru]2567891([C]4[C]5[C]63)[C]2[C]7[C]8[C]9[C]12. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O-]=[W]123(O[W]45(=O)(O1[Te]6789O2[W]1(=O)(O3)(O6[W]2(=O)(O1)(O7[W]1(=O)(O2)(O8[W](=O)(O94)(O5)(O1)[O-])[O-])[O-])[O-])[O-])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C=[N]3c4ccc(cc4O[Cr+]3O2)CCC(=O)O. +period in smiles: `[CH3].[CH3].[CH3]` +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)C3=CC=CC4=[N]3[Pt+]2([N]5=C4C=CC=C5)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule COc1cc(cc(c1OC)OC)C(=O)OCCCN2CCCN(CC2)CCCOC(=O)c3cc(c(c(c3)OCc4ccc(cc4)[N](=O)O)OC)OC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN1C=CN([C]1[Ru](Cl)Cl)Cc2c3ccccc3cc4c2cccc4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN(C)C1=N[N]2=C(C3=CC=CC=[N]3[Pd]2S1)c4ccccc4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)(C)OC(=O)NC(CC1=C[N](=C(N1C)[Rh])C)C(=O)OC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCCCCCCNC(=O)[N+]1CCC(CC1)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1C(C(=O)NC(C(=O)N2CCCC2C(=O)N(C(C(=O)N3CCC(CC3C(=O)NC(C(=O)O1)c4ccccc4)O)Cc5ccccc5)C)CCN=[N]=N)NC(=O)c6c(cccn6)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=C2C(=C(C3=[N]2[Fe]45N6C(=CC7=[N]4C(=CC8=C(C(=C1N58)CCC(=O)O)CC(=O)O)C(=C7CCC(=O)O)CC(=O)O)C(=C(C6=C3)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe]2S[Fe]3[S]2[Fe]1[S]345[Fe]6[S]7[Fe]4[S]8[Fe]7[S]6[Fe]58. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)(C)c1cccc2=C[N]3=[Co]4([N](=Cc5cccc(c5O4)C(C)(C)C)c6c3cc(cc6)C(=O)NCCNC(=O)CCCCC7C8C(CS7)NC(=O)N8)O=c21. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O[Sb](O)(O)O. +atomic number must be positive, given 0. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCSC1=NC(=[N](C(=N1)S)Cc2cccnc2)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1CC2(C(C3CC4=[N]5C(CC67C(CC(=O)N6)(C(C8=[N]7[Ni]59[N]3=C2C(=C2N9C(=C8)C(C2CCC(=O)O)CC(=O)O)C1=O)CCC(=O)O)C)C(C4(C)CC(=O)N)CCC(=O)O)CC(=O)O)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1(C(=NC(N1[O])(C)C)SS(=O)(=O)C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1CCC(CC1)CNCC2=CN3C=C(N=C3C=C2)CNC(=O)C4=CC(=O)[N]5=CC=CC=C5N4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC2=[N](C=C1)[Pt+2]3([N]4=C(C=CC=C4)C5=[N]3N=C6N5C=CC=C6)[N]7=C2N8C=CC=CC8=N7. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CN1C=[N](C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=Nc6c5ncnc6N)OC)O)O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O-]=[V]([O])(O[V](=O)=O)O[V](=O)=O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=C2)C(=C(C7=CC8=[N]6C(=[O+]5)C(=C8C=C)C)C)CCC(=O)O)C=C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CN(C=N1)[Re+]([C-]#[O+])([C-]#[O+])([C-]#[O+])N2C=CN=C2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1NC[S]2[Fe+]3([S]1[Fe+]2(C3=O)([C-]#N)([C-]#N)[C-]#[O+])([C-]#N)[C-]#[O+]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule COc1ccc(cc1OC)C(CC2=C(C=[N](C=C2Cl)O)Cl)OC(=O)C3=CC=C(S3)CNC(c4ccccc4)C(=O)OC5CN6CCC5CC6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C(=O)C(N2C=[N](C=N2)F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Fe]47N2C1=CC8=[N]7C(=C6)C(=C8C=C)C)C)CCC(=O)O)C(=C3C)CCC(=O)O)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2=C3N=C4c5ccccc5C6=[N]4[Ga]78N3C(=c2c1)N=C9[N]7=C(c1c9cccc1)N=C1N8C(=N6)c2c1cccc2. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O1[Fe]O[Fe]2S[Fe]3[S]2[Fe]1O3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCC1=C2C(=[O-][V+5]3(=O)(O2)O[V+5]45(=O)([O-]C6=C([N+](C=CC6=O4[V+5]7(=O)(O3)(O5)[O-]=C8C=CN(C(=C8O7)CC)C)C)CC)[O])C=CN1C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]S34[Fe]1[S]([Fe]23)[Fe]4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1c(cc(cc1C(=O)NC(COCC2=CN(N=N2)C3C(C(C(C(O3)CO)O)O)O)(COCC4=CN(N=N4)C5C(C(C(C(O5)CO)O)O)O)COC6=[C]N(N=N6)[C]7[C]([C]([C]([C](O7)[C][O])[O])[O])[O])C(=O)NC(COCC8=CN(N=N8)C9C(C(C(C(O9)CO)O)O)O)(COCC1=CN(N=N1)[C]1[C]([C]([C]([C](O1)[C][O])[O])[O])[O])OCC1=CN(N=N1)C1C(C(C(C(O1)CO)O)O)O)CO. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36N7C(=CC8=[N]6C(=C5)C(=C8C(F)(F)F)C)C(=C(C7=C2)CCC(=O)O)C)C)C(F)(F)F)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Ni]45. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 3 radical electrons on molecule [C][C][C][C][C][C][C][C][CH][CH][CH][CH][CH][C][C][C][C]C(=O)OCC(CO[PH](=O)(O)OCC(C(=O)O)[NH3])O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC2=C(c3cc(ccc3O2)OC)C(=[N]1O)c4ccc(cc4)OC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule [O][W]1234O[W]567(O[W]89%10(O5[P]5%11O%12[W]%13%14(O6)(O[W]6%15(O1)(O[W]1%16%17(O6[P]6%18O2[W]2(O8)(O3)(O[W]38%19(O6[W](O3)(O1)(O[W]136(O5[W](O8)(O1)(O9)(O[W]15(O%10)(O%118[W](O7)(O%13)(O1)(O[W]8(O3)(O5)(O[W]%12(O%16)(O%14)(O6)[O])[O])[O])[O])[O])[O])(O[W]13(O%17)(O%185[W](O4)(O%15)(O1)(O[W]5(O2)(O%19)(O3)[O])[O])[O])[O])[O])[O])[O])[O])[O])[O])[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N+](C(=CC4=C(C(=C5N4[Fe]6N2C1=CC7=[N]6C(=C5)C(=C7C)C=C)C)C=C)C(=C3CCC(=O)O)C)CC(=O)Cc8ccccc8)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Fe]36(N7C(=CC8=[N]6C(=C5)C(=C8C=C)C)C(=C(C7=C2)CCC(=O)O)C)Cc9ccccc9)C=C)C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=CC5=[N]6C(=C(C7=CC=C8N7[Fe]6(N43)[N]9=C2C=CC9=C8)c1ccccc1)C=C5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C#CC1=C2C=CC3=C(C4=[N]5C(=C(C6=CC=C7N6[Fe]5(N23)[N]8=C1C=CC8=C7c9ccccc9)C#C)C=C4)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C2=C3C=CC4=C(C5=[N]6C(=C(C7=CC=C8N7[Fe]6(N34)[N]9=C2C=CC9=C8)c1ccccc1)C=C5)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C#CC1=C2C=CC3=C(C4=[N]5C(=CC6=CC=C7N6[Fe]5(N23)[N]8=C1C=CC8=C7c9ccccc9)C=C4)c1ccccc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)(C)OC(=O)NC(Cc1ccncc1)C(=O)NCC2=C[N]3=C(C=C2)C4=CC=CC=[N]4[Ir+]356(c7ccccc7C8=[N]5c9ccccc9C=C8)c1ccccc1C1=CC=c2ccccc2=[N]61. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1nc(c2c(n1)N(C=N2)C3C(C(C(O3)COP(=O)([N]4=C(N(C=C4)P(=O)(O)OCC5C(C(C(O5)N6C=NC7=C6N=C(NC7=O)N)O)O)N)O)O)O)N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)(C)OC(=O)NC(Cc1ccncc1)C(=O)NCC2=C[N]3=C(C=C2)C4=CC=CC=[N]4[Ir+]356(c7ccccc7C8=[N]5c9ccccc9C=C8)c1ccccc1C1=CC=c2ccccc2=[N]61. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C=CC3=[N]2[Ir+]45(c6c3cccc6)(c7ccccc7C8=CC=c9ccccc9=[N]48)[N]1=C(C=CC=C1)C1=[N]5C=C(C=C1)CNC(=O)CCc1ccncc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(C)(C)OC(=O)NC(Cc1ccncc1)C(=O)N=CC2=C[N]3=C(C=C2)C4=[N]([Ir+]356(c7cc(cc(c7C8=[N]5C=CC=C8)F)F)c9cc(cc(c9C1=CC=CC=[N]61)F)F)C=CC=C4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cnccc1CCC(=O)NCC2=CC=C3C4=CC=CC=[N]4[Ir+]56([N]3=C2)(c7cc(cc(c7C8=[N]5C=CC=C8)F)F)c9cc(cc(c9C1=CC=CC=[N]61)F)F. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)C(=O)NC(Cc2ccncc2)C(=O)NCC3=C[N]4=C(C=C3)C5=[N]([Ir+]467(c8ccccc8C9=[N]6c1ccccc1C=C9)c1ccccc1C1=CC=c2ccccc2=[N]71)C=CC=C5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C=CC3=[N]2[Ir+]45(C6=C3Sc7c6cccc7)(C8=C(C9=CC=c1ccccc1=[N]49)Sc1c8cccc1)[N]1=C(C=CC=C1)C1=[N]5C=C(C=C1)CNC(=O)CCc1ccncc1. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCCCCCC(=O)OC(COC(=O)CCCCCCC)COP(=O)(O)OCC[N](C)(C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2=[N]3C(=CC=c2c1)C4=C([Ir+]356(C7=C(C8=CC=c9ccccc9=[N]58)Sc1c7cccc1)[N]1=CC=CC=C1C1=CC=C(C=[N]61)CNC(=O)CCc1cccnc1)c1ccccc1S4. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCN(CC)c1ccc(cc1[N](=O)O)C2=NNC(=O)CC2C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC=CC2=[N]1[Ru]34([N]5=C(C=CC=C5)C6=[N]3C(=CC=C6)C7=CC=CC=[N]47)([N]8=C2C=CC=C8C)[N]9=CC=CC(=C9)CCCNC(=O)C(Cc1ccccc1)SCC(Cc1ccccc1)NC(=O)OC(C)(C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC=CC2=[N]1[Ru]34([N]5=CC=CC=C5C6=[N]3C(=CC=C6)C7=CC=CC=[N]47)([N]8=C2C=CC=C8C)[N]9=CC(=CC=C9)CNC(=O)CCSCC(Cc1ccccc1)NC(=O)OC(C)(C)C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule S1[Fe]2[S]([Fe]3[S]2[Fe]1[S]3[Ni])[Fe]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O=[W]1234O[Co]567O18[Si]91O%10%11[W]%12%13(=O)(O5)O[W]5%14(=O)(O6)O96[W]9%15(=O)(O5)O[W]%105(=O)(O%12)O[W]%11(=O)(O2)(O%13)O[W]2%10(=O)(O5)O11[W]5(=O)(O3)(O2)O[W]1(=O)(O9)(O%10)O[W]6(=O)(O%14)(O%15)O[W]8(O7)(O4)(O5)[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC(=O)[C](C=C1[N+](=O)[O-])O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CSC2=[N]1C(=O)CC(=N2)CO. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC(=NN2C1=NC(=C2)C)C3=CC(=O)[N]4=C(N3)C=CC(=C4)N5CCNC6(C5)CC6. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC(=CCOP(=O)(O)O)CCN=[N]=N. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1C[OH][Y]234[N]1(CC[OH]2)C(C[OH]3)(C[OH]4)CO. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(SC=N1)c2ccc(cc2)C(C)NC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)CCCCCCC(=O)N4CCN(CC4)CC5(CCC(=C(C5)CN6CCN(CC6)c7ccc(cc7)C(=O)NS(=O)(=O)c8ccc(c(c8)S(=O)(=O)C(F)(F)F)NC(CCN9CCOCC9)CSc1ccccc1)c1ccc(cc1)Cl)C)[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[N]1(CCN(CC1)C(=O)N(CC2=CC=C(O2)C(=O)NCCc3ccc(cc3)F)c4ccc(cc4)F)CCCc5ccccc5. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)CCC[N]2(CCN(CC2)C(=O)N(CC3=CC=C(O3)C(=O)NCCc4ccc(cc4)F)c5ccc(cc5)F)Cc6ccc(c(c6)Cl)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc(cc1)CCC[N]2(CCN(CC2)C(=O)NCC3=CC=C(O3)C(=O)NCCc4ccc(cc4)F)Cc5ccc(c(c5)Cl)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCCC[N](CCCCC)(CCCCC)CCCCC. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CCCC[N](CCCC)(CCCC)Cc1ccc(cc1)C(c2ccccc2)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1CC(=O)N(C1=O)CCCCCN2C3=[N](C=CC=C3)[Ru]([N]4=CC=CC=C42)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C1=CC=[N]2C(=C1)N(C3=[N]([Ru]2Cl)C=CC=C3)CCCCCN. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=CC3=[N]4C(=CC5=C(C(=C6N5[Zn]47N2C1=CC8=[N]7C(=C6O)C(=C8C=C)C)C)CCC(=O)O)C(=C3C)CCC(=O)O)C=C. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1ccc2c(c1)C(=[N]3[Pt]2[S]=C(N3)N)c4cc(ccc4N)Cl. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule C[S]1[Fe]2S[Fe]3[S]2[Fe]1S3. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=CC2=CC3=[N]4C(=CC5=C(C(=C6N5[Zn]47N2C1=CC8=[N]7C(=C6)C(=C8)C)C)CCC(=O)O)C(=C3C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule CC1=C(C2=[N]3C1=CC4=C(C(=C5N4[Zn]36N7C(=CC8=[N]6C(=C5)C(=C8C)C=C)C(=C(C7=C2)CCC(=O)O)C)C)C=C)CCC(=O)O. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule O=[W]1234O[Zr]56O[W]78(=O)(O1)O[W]91%10(=O)O[W]%11%12(=O)(O2)O[W]2%13%14(=O)O%11P%11%15O9[W]9%16(=O)(O1)O[W]1%17(=O)(O7)O8P78O3[W]3(=O)(O4)(O2)O[W]24(=O)(O5)O7[W](O6)(O2)(O1)(O[W]12(=O)(O%17)O8[W](=O)(O4)(O3)(O1)O[W]13(=O)(O%13)O%11[W](=O)(O1)(O9)(O2)O[W]12(=O)(O%16)O%154[W](=O)(O%12)(O%10)(O1)O[W]4(=O)(O%14)(O3)O2)[O]. +The OpenFF Toolkit does not currently support parsing molecules with radicals. Found 1 radical electrons on molecule c1cc(ccc1NC(=O)C[N]2=C(SC=C2)N)F. +found 44566/44606 smiles +Converting 448/44566 molecules failed +100 + Deduplication : 0%| | 0/100 [00:00 0.0 +---------- +Stacktrace: + 0# Invar::Invariant::toString[abi:cxx11]() const in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libRDKitRDGeneral.so.1 + 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libRDKitRDGeneral.so.1 + 2# RDKit::DGeomHelpers::_setTwoInSameRing14Bounds(RDKit::ROMol const&, RDKit::Bond const*, RDKit::Bond const*, RDKit::Bond const*, RDKit::DGeomHelpers::ComputedData&, boost::shared_ptr, double*) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 3# RDKit::DGeomHelpers::set14Bounds(RDKit::ROMol const&, boost::shared_ptr, RDKit::DGeomHelpers::ComputedData&, double*, bool, bool) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 4# RDKit::DGeomHelpers::setTopolBounds(RDKit::ROMol const&, boost::shared_ptr, std::vector, std::allocator > >&, std::vector >, std::allocator > > >&, bool, bool, bool, bool) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 5# RDKit::DGeomHelpers::EmbeddingOps::setupInitialBoundsMatrix(RDKit::ROMol*, boost::shared_ptr, std::map, std::allocator > > const*, RDKit::DGeomHelpers::EmbedParameters const&, ForceFields::CrystalFF::CrystalFFDetails&) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 6# RDKit::DGeomHelpers::EmbedMultipleConfs(RDKit::ROMol&, std::vector >&, unsigned int, RDKit::DGeomHelpers::EmbedParameters&) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 7# RDKit::EmbedMultipleConfs(RDKit::ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool, bool, bool, unsigned int, bool) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdDistGeom.so + 8# 0x00007537748C1CC5 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdDistGeom.so + 9# boost::python::objects::function::call(_object*, _object*) const in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +10# 0x0000753762BE2449 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +11# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +12# 0x0000753774250E04 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdSLNParse.so +13# 0x00007537744E0264 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdDepictor.so +14# 0x0000753774799154 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdChemReactions.so +15# 0x00007537747991A4 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdChemReactions.so +16# 0x000075377491C414 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdMolChemicalFeatures.so +17# 0x00007537429C7644 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdmolfiles.so +18# 0x00007537429C7694 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdmolfiles.so +19# 0x0000753765D95D44 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdCIPLabeler.so +20# 0x00007537431758D4 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +21# 0x000075374310A7FD in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +22# 0x000075374310A37D in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +23# 0x0000753743109EFD in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +24# 0x0000753743109A7D in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +25# 0x00007537431095FD in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +26# 0x0000753744175F74 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +27# 0x0000753744175FC4 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +28# 0x0000753744176014 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +29# 0x0000753744176064 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +30# boost::python::handle_exception_impl(boost::function0) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +31# 0x0000753762BDF9B3 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +32# _PyObject_MakeTpCall in python +33# _PyEval_EvalFrameDefault in python +34# 0x0000655487CB96C2 in python +35# 0x0000655487CB8F46 in python +36# PyObject_Call in python +37# _PyEval_EvalFrameDefault in python +38# 0x0000655487CB8E48 in python +39# _PyEval_EvalFrameDefault in python +40# _PyFunction_Vectorcall in python +41# _PyEval_EvalFrameDefault in python +42# _PyFunction_Vectorcall in python +43# 0x0000655487CA1B49 in python +44# _PyObject_MakeTpCall in python +45# _PyEval_EvalFrameDefault in python +46# _PyFunction_Vectorcall in python +47# 0x0000655487CA1BED in python +48# _PyObject_MakeTpCall in python +49# _PyEval_EvalFrameDefault in python +50# 0x0000655487D2CC5D in python +51# PyEval_EvalCode in python +52# 0x0000655487D4A31A in python +53# 0x0000655487D45F93 in python +54# 0x0000655487D5B540 in python +55# _PyRun_SimpleFileObject in python +56# _PyRun_AnyFileObject in python +57# Py_RunMain in python +58# Py_BytesMain in python +59# 0x00007537F7D9FE08 in /usr/lib/libc.so.6 +60# __libc_start_main in /usr/lib/libc.so.6 +61# 0x0000655487D1C4CA in python +---------- +**** + +Warning: OEMMFFParams::PrepMol() : unable to type atom 30 Mg on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +Warning: OEMMFFParams::PrepMol() : unable to type atom 30 Mg on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +[11:28:17] UFFTYPER: Unrecognized charge state for atom: 30 +[11:28:18] UFFTYPER: Unrecognized hybridization for atom: 15 +[11:28:18] UFFTYPER: Unrecognized atom type: Fe+2 (15) +Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 12 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 34 Mg on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +[11:28:19] UFFTYPER: Warning: hybridization set to SP3 for atom 34 +Warning: OEMMFFParams::PrepMol() : unable to type atom 35 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +Warning: OEMMFFParams::PrepMol() : unable to type atom 35 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +[11:28:21] UFFTYPER: Unrecognized hybridization for atom: 16 +[11:28:21] UFFTYPER: Unrecognized atom type: Fe+2 (16) +Warning: OEMMFFParams::PrepMol() : unable to type atom 34 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +Warning: OEMMFFParams::PrepMol() : unable to type atom 34 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters + StandardConformerGenerator : 34%|███▊ | 34/99 [00:28<01:04, 1.01it/s]Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 30 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 12 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 12 Fe on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 12 Zn on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +[11:28:26] UFFTYPER: Unrecognized charge state for atom: 12 +[11:28:26] UFFTYPER: Unrecognized atom type: Zn2+2 (12) +[11:28:26] + +**** +Invariant Violation + +Violation occurred on line 757 in file /home/conda/feedstock_root/build_artifacts/rdkit-meta_1722844818947/work/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp +Failed Expression: ba23 > 0.0 +---------- +Stacktrace: + 0# Invar::Invariant::toString[abi:cxx11]() const in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libRDKitRDGeneral.so.1 + 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libRDKitRDGeneral.so.1 + 2# RDKit::DGeomHelpers::_setTwoInSameRing14Bounds(RDKit::ROMol const&, RDKit::Bond const*, RDKit::Bond const*, RDKit::Bond const*, RDKit::DGeomHelpers::ComputedData&, boost::shared_ptr, double*) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 3# RDKit::DGeomHelpers::set14Bounds(RDKit::ROMol const&, boost::shared_ptr, RDKit::DGeomHelpers::ComputedData&, double*, bool, bool) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 4# RDKit::DGeomHelpers::setTopolBounds(RDKit::ROMol const&, boost::shared_ptr, std::vector, std::allocator > >&, std::vector >, std::allocator > > >&, bool, bool, bool, bool) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 5# RDKit::DGeomHelpers::EmbeddingOps::setupInitialBoundsMatrix(RDKit::ROMol*, boost::shared_ptr, std::map, std::allocator > > const*, RDKit::DGeomHelpers::EmbedParameters const&, ForceFields::CrystalFF::CrystalFFDetails&) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 6# RDKit::DGeomHelpers::EmbedMultipleConfs(RDKit::ROMol&, std::vector >&, unsigned int, RDKit::DGeomHelpers::EmbedParameters&) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/../../../../libRDKitDistGeomHelpers.so.1 + 7# RDKit::EmbedMultipleConfs(RDKit::ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool, bool, bool, unsigned int, bool) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdDistGeom.so + 8# 0x00007537748C1CC5 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdDistGeom.so + 9# boost::python::objects::function::call(_object*, _object*) const in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +10# 0x0000753762BE2449 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +11# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +12# 0x0000753774250E04 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdSLNParse.so +13# 0x00007537744E0264 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdDepictor.so +14# 0x0000753774799154 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdChemReactions.so +15# 0x00007537747991A4 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdChemReactions.so +16# 0x000075377491C414 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdMolChemicalFeatures.so +17# 0x00007537429C7644 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdmolfiles.so +18# 0x00007537429C7694 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdmolfiles.so +19# 0x0000753765D95D44 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdCIPLabeler.so +20# 0x00007537431758D4 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +21# 0x000075374310A7FD in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +22# 0x000075374310A37D in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +23# 0x0000753743109EFD in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +24# 0x0000753743109A7D in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +25# 0x00007537431095FD in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/Chem/rdchem.so +26# 0x0000753744175F74 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +27# 0x0000753744175FC4 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +28# 0x0000753744176014 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +29# 0x0000753744176064 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/rdBase.so +30# boost::python::handle_exception_impl(boost::function0) in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +31# 0x0000753762BDF9B3 in /home/brent/mambaforge/envs/qcarchive-user-submit/lib/python3.11/site-packages/rdkit/../../../libboost_python311.so.1.84.0 +32# _PyObject_MakeTpCall in python +33# _PyEval_EvalFrameDefault in python +34# 0x0000655487CB96C2 in python +35# 0x0000655487CB8F46 in python +36# PyObject_Call in python +37# _PyEval_EvalFrameDefault in python +38# 0x0000655487CB8E48 in python +39# _PyEval_EvalFrameDefault in python +40# _PyFunction_Vectorcall in python +41# _PyEval_EvalFrameDefault in python +42# _PyFunction_Vectorcall in python +43# 0x0000655487CA1B49 in python +44# _PyObject_MakeTpCall in python +45# _PyEval_EvalFrameDefault in python +46# _PyFunction_Vectorcall in python +47# 0x0000655487CA1BED in python +48# _PyObject_MakeTpCall in python +49# _PyEval_EvalFrameDefault in python +50# 0x0000655487D2CC5D in python +51# PyEval_EvalCode in python +52# 0x0000655487D4A31A in python +53# 0x0000655487D45F93 in python +54# 0x0000655487D5B540 in python +55# _PyRun_SimpleFileObject in python +56# _PyRun_AnyFileObject in python +57# Py_RunMain in python +58# Py_BytesMain in python +59# 0x00007537F7D9FE08 in /usr/lib/libc.so.6 +60# __libc_start_main in /usr/lib/libc.so.6 +61# 0x0000655487D1C4CA in python +---------- +**** + +Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 32 Mg on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +[11:28:26] UFFTYPER: Unrecognized charge state for atom: 32 +Warning: : Failed due to unspecified stereochemistry +Warning: OEMMFFParams::PrepMol() : unable to type atom 29 W on residue UNL-1 +Warning: OEMMFFParams::PrepMol() : unable to type atom 41 Mg on residue UNL-1 +Warning: : Force field setup failed due to missing parameters +[11:28:26] UFFTYPER: Unrecognized atom type: W_5 (29) +[11:28:26] UFFTYPER: Warning: hybridization set to SP3 for atom 41 +[11:28:39] UFFTYPER: Unrecognized hybridization for atom: 35 +[11:28:39] UFFTYPER: Unrecognized atom type: Fe+2 (35) +[11:28:55] UFFTYPER: Unrecognized hybridization for atom: 49 +[11:28:55] UFFTYPER: Unrecognized atom type: Fe+2 (49) + StandardConformerGenerator : 40%|████▍ | 40/99 [01:12<02:30, 2.56s/it] StandardConformerGenerator : 60%|██████▌ | 59/99 [02:27<02:11, 3.28s/it] StandardConformerGenerator : 77%|████████▍ | 76/99 [05:37<02:28, 6.47s/it] StandardConformerGenerator : 93%|██████████▏| 92/99 [05:37<00:29, 4.20s/it] StandardConformerGenerator : 100%|███████████| 99/99 [05:37<00:00, 3.41s/it] + Preparation : 0%| | 0/75 [00:00=0.49 + - openff-qcsubmit + - openff-toolkit + - openeye-toolkits + - click + - pip: + - git+https://github.com/ntBre/qcaide + - git+https://github.com/ntBre/curato diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/main.py b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/main.py new file mode 100644 index 00000000..0a54b45f --- /dev/null +++ b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/main.py @@ -0,0 +1,220 @@ +import re +import sys +from collections import namedtuple +from pathlib import Path + +import numpy as np +import qcportal # noqa avoid zstd disaster +from openff.qcsubmit import workflow_components +from openff.qcsubmit.common_structures import QCSpec +from openff.qcsubmit.factories import OptimizationDatasetFactory +from openff.toolkit import Molecule +from qcaide import Submission + + +def load_ccd(filename: str) -> list[str]: + "Load OpenEye SMILES from the CCD CIF" + + blocks = 0 + in_block = False + smiles = list() + with open(filename) as inp: + for line in inp: + if re.match(r"^data_", line): + blocks += 1 + in_block = True + sp = line.split() + # previously taking first smiles arbitrarily, now looking for + # OpenEye smiles because the cactvs ones are weird + if ( + in_block + and len(sp) > 5 + and "SMILES" == sp[1] + and "OpenEye" in sp[2] + ): + in_block = False + # SMILES in the sixth position, some are wrapped in quotes + smiles.append(sp[5].removeprefix('"').removesuffix('"')) + + print(f"found {len(smiles)}/{blocks} smiles") + return smiles + + +def try_from_smiles(s: str) -> Molecule | None: + "Try to build a Molecule from SMILES, return None on failure" + if "." in s: + print(f"period in smiles: `{s}`", file=sys.stderr) + return None + try: + mol = Molecule.from_smiles(s, allow_undefined_stereo=True) + except Exception as e: + print(e, file=sys.stderr) + return None + + return mol + + +def elements(mol: Molecule) -> set[int]: + return {atom.atomic_number for atom in mol.atoms} + + +Mol = namedtuple("M", ["smiles", "natoms", "charge", "inchi", "elements"]) + +with open("inchis.dat") as inp: + inchis = {line.strip() for line in inp} + +# retrieved and unzipped from +# https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz +smiles = load_ccd("components.cif") + +mols = list() +failed = 0 +for s in smiles: + if (mol := try_from_smiles(s)) is None: + failed += 1 + continue + mols.append( + Mol( + charge=mol.total_charge, + natoms=mol.n_atoms, + smiles=mol.to_smiles(), + inchi=mol.to_inchikey(), + elements=elements(mol), + ) + ) + + +print(f"Converting {failed}/{len(smiles)} molecules failed") + +weird_smiles = [ + "B1234B567B189B212B33%10B454B656B787B911C232B4%105C7612", +] + +# from the strategy document +target_metals = { + # at minimum: Pd, Fe, Zn, Mg, Cu, Li + 46, + 26, + 30, + 12, + 29, + 3, + # also desirable: Rh, Ir, Pt, Ni, Cr, Ag + 45, + 77, + 78, + 28, + 24, + 47, +} + +# Also include organic elements and halides: C, H, P, S, O, N, F, Cl, Br, but +# skipping explicit search for these for now to focus on the metals. most if +# not all of these are already covered by our existing datasets + +dsmols = list() +for m in sorted( + filter( + lambda m: m.natoms > 10 + and abs(m.charge.magnitude) < 4.0 + and "." not in m.smiles + and m.smiles not in weird_smiles + and m.inchi not in inchis + and len(m.elements & target_metals) > 0, + mols, + ), + key=lambda m: m.natoms, +)[:100]: + dsmols.append(Molecule.from_smiles(m.smiles, allow_undefined_stereo=True)) + +print(len(dsmols)) + +# Generate dataset +config = Submission.from_toml("opt.toml") +# we want to store more properties and info from the wavefunction, but that +# will come later in a separate singlepoint dataset +dataset_factory = OptimizationDatasetFactory( + qc_specifications={ + "BP86/def2-TZVP": QCSpec( + method="BP86", + basis="def2-TZVP", + spec_name="BP86/def2-TZVP", + ) + } +) +dataset_factory.add_workflow_components( + workflow_components.StandardConformerGenerator( + max_conformers=10, rms_cutoff=0.5 + ) +) +dataset = dataset_factory.create_dataset( + dataset_name=config.name, + tagline=config.name, + description=config.description, + molecules=dsmols, + processors=6, +) +print(dataset.n_molecules, dataset.n_records) +dataset.metadata.submitter = config.submitter +dataset.metadata.long_description_url = ( + "https://github.com/openforcefield/qca-dataset-submission/tree/master/" + "submissions/" + str(Path.cwd().name) +) + +# verify that no new molecules appear in the output; can't use symmetric +# difference like I usually do because some molecules (~32) do get filtered +# out, I think from conformer generation failure +old_smiles = {m.to_smiles(isomeric=False) for m in dsmols} +new_smiles = {m.to_smiles(isomeric=False) for m in dataset.molecules} +assert not (new_smiles - old_smiles) + + +# summarize dataset for readme +confs = np.array([len(mol.conformers) for mol in dataset.molecules]) + +print("* Number of unique molecules:", dataset.n_molecules) +print("* Number of filtered molecules:", dataset.n_filtered) +print("* Number of conformers:", sum(confs)) +print( + "* Number of conformers per molecule (min, mean, max): " + f"{confs.min()}, {confs.mean():.2f}, {confs.max()}" +) + +masses = [ + [ + sum([atom.mass.m for atom in molecule.atoms]) + for molecule in dataset.molecules + ] +] +print(f"* Mean molecular weight: {np.mean(np.array(masses)):.2f}") +print(f"* Max molecular weight: {np.max(np.array(masses)):.2f}") +print("* Charges:", sorted(set(m.total_charge.m for m in dataset.molecules))) + +print("## Metadata") +print(f"* Elements: {{{', '.join(dataset.metadata.dict()['elements'])}}}") + + +def print_field(od, field): + print(f"\t* {field}: {od[field]}") + + +fields = [ + "basis", + "implicit_solvent", + "keywords", + "maxiter", + "method", + "program", +] +for spec, obj in dataset.qc_specifications.items(): + od = obj.dict() + print("* Spec:", spec) + for field in fields: + print_field(od, field) + print("\t* SCF properties:") + for field in od["scf_properties"]: + print(f"\t\t* {field}") + +dataset.export_dataset("dataset.json.bz2") +dataset.molecules_to_file("output.smi", "smi") +dataset.visualize("dataset.pdf", columns=8) diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/opt.toml b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/opt.toml new file mode 100644 index 00000000..1c1cc80b --- /dev/null +++ b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/opt.toml @@ -0,0 +1,62 @@ +name = "OpenFF Organometallics Exploratory Optimization Dataset" +description = """ + +An optimization dataset created to test the OpenFF and QCArchive infrastructure +for calculations involving organometallic molecules. The molecules in this +dataset were extracted from the `OpenEye SMILES` entries in the [Chemical +Component Dictionary](https://www.wwpdb.org/data/ccd) mmCIF file. These were +filtered to remove molecules with radical electrons and to include only +molecules with the desired metal atoms: Pd, Fe, Zn, Mg, Cu, Li, Rh, Ir, Pt, Ni, +Cr, and Ag. These were further filtered to retain only molecules with at least +10 atoms, an absolute charge of less than 4, and those not present in any of our +existing training data. From this candidate set, the molecules were sorted based +on their number of atoms, and the smallest 100 were selected. Of these, 56 were +further removed by errors in the dataset preparation process, leaving 44 +molecules. + +""" +short_description = "Optimization training data for organometallic molecules" +class = "optimization" +purpose = "Provide training data for metal-containing molecules" +submitter = "Brent Westbrook" + +[[pipeline]] +filename = "main.py" +description = """ +This script shows how the dataset was prepared from `components.cif`, retrieved +from the CCD, and `inchis.dat`, which contains the InCHI keys of our existing +training data. +""" + +# input files +[[manifest]] +filename = "main.py" +description = "Script describing dataset generation and submission" + +[[manifest]] +filename = "input-environment.yaml" +description = "Environment file used to create the Python environment for the script" + +[[manifest]] +filename = "full-environment.yaml" +description = "Fully-resolved environment used to execute the script" + +[[manifest]] +filename = "opt.toml" +description = """ +Experimental [qcaide](https://github.com/ntBre/qcaide) input file for defining +variables used throughout the QCA submission process +""" + +# output files +[[manifest]] +filename = "dataset.json.bz2" +description = "Compressed dataset ready for submission" + +[[manifest]] +filename = "dataset.pdf" +description = "Visualization of dataset molecules" + +[[manifest]] +filename = "output.smi" +description = "SMILES strings for dataset molecules" \ No newline at end of file diff --git a/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/output.smi b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/output.smi new file mode 100644 index 00000000..a93bbedb --- /dev/null +++ b/submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/output.smi @@ -0,0 +1,44 @@ +[Li]OB(O)OB(O)O +CN(C)[Zn]O +c1cc[n+]2c(c1)S[Zn]O2 +[OH2][Ni+2]([OH2])([OH2])([OH2])[OH2] +CN[Pt](N(C)C)(Cl)Cl +C1=CC2(C(=N)C(=C1)C(=O)[O-])OO[Fe+2]O2 +O[Fe]1(O[Fe](O[Fe](O1)(O)(O)O)(O)(O)O)O +CC1O[Rh+]([Rh+](O1)(O)(O)O)(O)(O)O +S1[Fe]234S5[Fe]2678[Fe]592S3[Fe]493(S26)S[Fe]3234[Fe]1156[Fe]722(S8)S1[Fe]5(S63)S24 +C1CCC2C(C1)N[Pt](N2)(Cl)Cl +CC1=O[Rh]([Rh](O1)(O)O)(N2C=CN=C2)(O)O +C1CC2CCC1[NH2+][Pt]([NH2+]2)(Cl)Cl +C1CC2(C1)C(=O)O[Pt](OC2=O)([NH3+])[NH3+] +CC1O[Rh+]2(OC(O[Rh+]2(O1)(O)O)C)(O)O +C1OCS2[Fe]3(S1[Fe]2(C3=O)(C=O)(C#N)[OH2])(C=O)C#N +CC12C3([Rh]145(C2(C4(C53C)C)C)(Cl)Cl)C +CC1O[Rh]23(OC(O[Rh]2(O1)(OC(O3)C)O)C)O +CC1O[Rh+]23(OC(O[Rh+]2(O1)(OC(O3)C(F)(F)F)O)C)O +c1cc2ccc3ccc[n+]4c3c2[n+](c1)[Pt]45NCCN5 +CN(C)C(=O)C12C3[Fe]1456789(C3C4C52)C1C6C7C8(C91)C(=O)O +C1CN2CCN3[Ni]24N(C1)CCN4CCC3 +C[N+]12C3CSC1C4CSC5=[N+]4[Fe]2(Oc6c5cccc6)OC3=O +c1ccc2c(c1)-c3ccccc3N2CCN[Pt](N)(N)Cl +C1C(=O)O[Fe]234(OC(=O)CC1(C(=O)O2)O)OC(=O)CC(CC(=O)O3)(C(=O)O4)O +c1ccc2c(c1)C=[N+]3c4ccccc4[N+]5=Cc6ccccc6O[Fe]35O2 +c1ccc2c(c1)N(C3=[N+]2[Pd]([n+]4c3cccc4)(Cl)Cl)CCCS(=O)(=O)O +c1ccc2c(c1)N(C3=[N+]2[Pt]([n+]4c3cccc4)(Cl)Cl)CCCS(=O)(=O)O +c1nc(c2c(n1)N(C=N2)C3C(C(C(O3)COP4(=O)O[Mg]OP(=O)(O4)N)O)O)N +c1ccc2c(c1)C=[N+]3c4ccc(cc4[N+]5=Cc6ccccc6O[Fe]35O2)C(=O)O +C1CC2C3[Rh]245678(C1C4CC3)C9C5C6C7(C89)CCN1C(=O)CCC1=O +c1ccc2c(c1)C=[N+]3c4ccc(cc4[N+]5=Cc6ccccc6O[Fe]35O2)CCC(=O)O +CC1C(C(C(N1)CCNCC2=CC(C=C2)[Fe]C3C=CC=C3)O)O +C1C2C(C(S1)CCCCC(C34C5[Fe]3678913(C5C6C74)C4C8C9C1C34)O)NC(=O)N2 +CC1C(C(C(N1)CCNCCCC2=CC(C=C2)[Fe]C3C=CC=C3)O)O +CC1CNCCN2CC(N[Rh+2]23(N1)N=c4c5ccccc5c6ccccc6c4=N3)C +c1ccc2c(c1)c3nc-4[n+]5c(nc6c7ccccc7c8nc-9[n+]1c(nc2N3[Fe]51N68)-c1c9cccc1)-c1c4cccc1 +CC1=CC=c2ccc3=CC=C(N4c3c2N1[Pt+2]45(C=C5)(C)C6=[N+](C=C(N6C)C7=CN=NN7)C)C +CCOP(=O)(CCCc1cc2c3c(c1)C[S+]([Pd]3([S+](C2)C)Br)C)Oc4ccc(cc4)[N+](=O)[O-] +c1ccnc(c1)C[N+]2(Cc3cccc[n+]3[Fe]2)CCNC(=O)CCCCC4C5C(CS4)NC(=O)N5 +Cc1c2cc3nc(c4c5c(c(c6cc7nc(cc(c1C=C)N2[Mg]N65)C(=C7C=C)C)C)C(=O)C4C(=O)OC)C(=C3C)C=CC(=O)O +CCC1=C(c2cc3c(c(c4cc5nc(c6c7c(c(c(cc1n2)N7[Mg]N43)C)C(=O)C6C(=O)OC)C(=C5C)C=CC(=O)O)C)C=C)C +Cc1c2cc3[n+]4c(c(c5c(c(c6cc7[n+]8c(cc(c1C=C)N2[Fe]84N65)C(=C7CCC(=O)[O-])C)CCC(=O)[O-])C)N(=O)=O)C(=C3C=C)C +CC1=C(C2=CC3=C(C(=C4N3[Fe]56N2C1=CC7=C(C(=C(N75)C=C8N6C(=C4)C(C89CCC(=O)O9)(C)O)CCC(=O)O)C)C=C)C)C=C +CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=CC7=C(C(=C(N75)C=C8N6C(=C4)C(=C8CCC(=O)O)C)CCC(=O)O)C)C)C