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Article ID: 694 - Last Modified: May 16, 2011

In the XP Visualizer, there are ligands for which the H-bond pair term is zero but their H-bond table cell is still enabled and yellow dotted lines are shown on the structure in the Workspace. Why is this? Is it due to a difference between Glide and Maestro definitions?

Charged-neutral H-bonds do not receive a GlideScore reward; only neutral-neutral and charged-charged H-bond interactions are rewarded. This different treatment of different types of H-bonds arose from our observation that a charged-neutral term does not help enrichment in our parameter-optimization studies on a large set of screens.

The H-bond criteria in Glide actually are more permissive than in Maestro. Glide gives partial rewards for H-bonds with lengths and angles deviating significantly from "ideal" (1.65 Å H-A distance, 180° D-H..A angle). The correlated, hydrophobically-enclosed H-bonds (which can be viewed with the XP Visualizer) have slightly different rules again.

Keywords: H-bonds, neutral , charged, H-bond criteria, Glide

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