Why are there ugly contacts in the Glide results?

There can be occasional ugly contacts in Glide results because:

1) Glide docks ligand with the non-polar vdW radii scaled by a factor of 0.8 (by default), while the contacts are calculated with respect to the full atomic radii; and

2) in trying to fit ligands into a rigid-receptor active site, there can be trade-offs between some poor vdW interactions and other favorable interactions (e.g., H-bonds or improved overall vdW interactions).

Keywords: ugly contacts, Glide results

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