The strain energy � defined as the difference between the energy of the isolated ligand and the protein bound ligand structure � serves as an important quality indicator of the protein-ligand structures. However, the crystal structures deposited to PDB often exhibit unreasonable ligand strain energies due to problematic ligand geometry as a consequence of using conventional refinement methods. Recently we replaced the stereochemistry restraints used in conventional refinement with semi-empirical quantum mechanics  (SE-QM) gradients generated in real-time over the course of the refinement to achieve improved protein-ligand structure.We conducted a systematic characterization of the strain energy for population of pharmaceutically relevant protein-ligand structures downloaded from PDB. Those structures with resolutions ranging from 1.5 to 3� and with the highest deposited ligand-structure strain energy were re-refined and scored using our PHENIX/DivCon methodology. Observed improvements in ligand strain will be reported along with the results pertaining to changes in predicted SE-QM interaction energies

Systematic study of the ligand strain energy derived from the quantum mechanics crystallographic refinement using the linear scaling program DivCon integrated into the PHENIX package

244th National Meeting (2012)

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