Strain Problems got you in a Twist? Try StrainRelief: A Quantum-Accurate Tool for Ligand Strain Calculations
Paper • 2503.13352 • Published
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ligand_id stringlengths 12 15 ⌀ | raw_mol unknown | xtb_local_min_mol unknown | xtb_local_min_energy float64 -1,858,015.73 -244,584.43 ⌀ | crest_global_min_mol unknown | crest_global_min_energy float64 -1,858,014.42 -244,584.7 ⌀ | SMILES stringlengths 37 352 ⌀ |
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End of preview. Expand in Data Studio
YAML Metadata Warning:empty or missing yaml metadata in repo card
Check out the documentation for more information.
LigBoundConf 2.0
LigBoundConf 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] [code].
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
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