agz7 dataset

Complete enumerations of amons with up to 7 heavy atoms for GDB17 and ZINC

For how-to on amons generation, go to https://github.com/binghuang2018/aqml

Features

• A wide coverage of organic chemistry, including H, B, C, N, O, F, Si, S, P, Cl, Br, I, Sn
• AGZ7 could be easily extended by inclusion of more accurate properties and/or all conformers, thanks to the small molecular size of AMON (no more than 7 non-hydrogen atoms)
• AGZ7 can be used as a dictionary for the look-up of the most pertinent amons for a query, or the whole as a single training set for QML models (in particular deep neural network) for quantum chemistry problems involving organic molecules
  • quantum properties prediction
  • geometry optimization
  • molecular dynamics
  • ...

Notes on files/folders

• Files containing SMILES string (canonicalized by OEChem)
  • gdb17-zinc-comm.can: SMILES strings of amons that are shared by gdb17 & zinc
  • gdb17.can: SMILES strings of amons that are unique to gdb17
  • zinc.can: SMILES strings of amons that are unique to ZINC
• Folders containing 3d geometries of amons
  • gdb17/ covers the complete set of gdb17 amons (i.e., gdb17-zinc-comm.can+gdb17.can) that survived geometry relaxation.
  • zinc/ covers only a subset of SMILES strings in zinc.can, that is, amons that are unique to gdb17 and survived geometry relaxation.
• Compressed tar files
  • Files in say, zinc/ni5.tar.gz indicates the subset of all ZINC amons containing only 5 heavy atoms
  • Geometry and prperties of each AMON are stored as key:value pair in a json file (see zinc/README.md for content details), except for AMONs that didn't survive geometry optimization (i.e., dissociated), for which only xyz file is provided in subfolder diss/.
  • SMILES string (canonicalized by OEChem) & bond order matrix are both available in json file for all but AMONs that underwent graph changes, including dissociated AMONs and undissociated ones (in subfolder newg/ or compressed file newg.tar.gz).
  • The name of a json file is of format [[ID]].json, with ID being a unique identity assigned to the associated molecular graph

Notes on geometries

• Each amon is accompanied with only one conformer
• Each conformer corresponds to the coarse "global minima", determined through MMFF94 in RDKit
• Reported final geometry (see sdf files) were calculated at the level of theory DF-B3LYP by Molpro
  • default geometry convergence thresholds were used
  • basis: cc-pVTZ-PP for Sn/I, cc-pVTZ for all others
  • df basis: def2-QZVPP/jkfit for Sn/I, cc-pVQZ/jkfit for all others

Reference

@misc{agz7,
    title={Dictionary of 140k GDB and ZINC derived AMONs},
    author={Bing Huang and O. Anatole von Lilienfeld},
    year={2020},
    eprint={2008.05260},
    archivePrefix={arXiv},
    primaryClass={physics.chem-ph}
}