OpenFF Organometallics Exploratory Optimization Dataset

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 | |
 
 

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

submissions/2024-12-03-OpenFF-Organometallics-Exploratory-Optimization-Dataset/full-environment.yaml

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+name: qcarchive-user-submit
+channels:
+  - openeye
+  - conda-forge
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+  - 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