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openforcefield / protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations
MIT License
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SHP2 ligands have some suspect conformations #80

Open Yoshanuikabundi opened 2 years ago

Yoshanuikabundi commented 2 years ago

I'm going over ligands to choose something to demonstrate BespokeFit's symmetry cleverness, and I noticed that data/shp2/02_ligands/ligands.sdf has some suspect structures, such as lig_E23, (state 14 in PyMOL):

Screenshot from 2022-10-13 16-48-28

That six-membered heterocycle is not a trick of perspective. The same ring distortion is present in states 14, 15, 19, 20 and 24.

Yoshanuikabundi commented 2 years ago

lig_p38a_2z (state 3) in data/p38/02_ligands/ligands.sdf doesn't look right either: Screenshot from 2022-10-13 16-58-46

There are a bunch of ligands with similar issues in most of the systems, actually. Not sure what the procedure is for using them so maybe it's not a big deal but I thought I'd point it out.

IAlibay commented 2 years ago

@bobym this is the same problem as the cdk2 issue it seems?