What does the internal energy include in the Glide docking results? Is it just the energy difference of the final pose and its minimized conformation?

The internal energy ('Einternal', 'Eint', 'Intern', or 'glide einternal') is computed with a truncated version of the OPLS_2005 force field that includes only torsions and 1,4 vdW interactions (OPLS_2001 in releases earlier than Suite 2011) Longer-range interactions are ignored in order not to penalize close intra-ligand contacts that form when fitting the ligand into the rigid-receptor active site.

Einternal is not included in the GlideScore, so differences in this term won't be reflected in the GlideScores. However, Einternal is a component of Emodel, so it plays an important role in pose selection (i.e., choosing which poses of a given ligand are the best, and therefore retained for final scoring).

There also is an optional strain rescoring (on the Output tab) that penalizes ligand poses that have significant energy differences between
1) the ligand minimized with constraints (i.e., bound form), and
2) the ligand minimized without constraints (i.e., free form).

Keywords: Glide, Einternal, pose selection

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