| # LigBoundConf 2.0 | |
| [LigBoundConf](https://pubs.acs.org/doi/full/10.1021/acs.jcim.0c01197) is a set of high-quality drug-like bound ligand structures in the Protein Data Bank (PDB). The original set contains three sets | |
| of structures: "raw” structures taken directly from the PDB, "bound” structures, obtained by performing a local minimization of the ligand | |
| in the presence of the protein pocket with an empirical force field, and “global minimum” structures, obtained by finding the lowest energy | |
| conformation of the ligand with an empirical force field and implicit water solvation model. | |
| LigBoundConf 2.0 is a neutral subset of LigBoundConf in which we have recalculated the "bound" and "global minimum" structures in vaccuo | |
| without an implicit solvent. To obtain the "bound” structures we sought to relieve any artificial high-energy artifacts from the deposited PDB | |
| structures. We did this by running a local minimization with the semi-empirical quantum chemistry method GFN2-xTB using the “crude” | |
| convergence criteria. This ensured that artifacts were removed without significantly altering the bound pose of the ligand. We then performed | |
| single point energy (SPE) density fucntional theory (DFT) calculations at the ωB97M-D3(BJ)/def2-TZVPPD level of theory. | |
| To obtain the "global minimum” structures, we used the CREST enumeration method with 50 conformers, which uses the same GFN2-xTB energy | |
| function to search for low energy gas phase structures. We took the lowest energy structure as the ``global minimum” conformation and | |
| performed a SPE DFT calculation at the same ωB97M-D3(BJ)/def2-TZVPPD level of theory. | |
| The LigBoundConf 2.0 neutral dataset ended up with 3132 ligands. | |
| This dataset is used to validate the StrainRelief method presented here [[pre-print]](https://arxiv.org/abs/2503.13352) [[code]](https://github.com/prescient-design/StrainRelief). | |
| ## Datasets | |
| - SMILES.csv (mapping from ligand ids to SMILE strings) | |
| - ligboundconf_2_raw.sdf | |
| - ligboundconf_2_crest_local_min.sdf | |
| - ligboundconf_2_xtb_global_min.sdf | |
| - ligboundconf_2_molecules_and_energies.parquet (all structures for the sdfs above as RDKit.Mol binary objects with their corresponding DFT energies) | |
| - strain_releif_output_mace_from_ligboundconf_xtb.parquet (the output from the StrainRelief tool when run on the xtb structures) | |
| --- | |
| license: apache-2.0 | |
| --- | |