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Relationship of the final QMOD standard pocket model to the GyrB binding site. Compound 20 in its optimal predicted QMOD pose (atom color) had rmsd of 0.5 Å from the experimentally determined bound state (yellow). Alignment of the QMOD pocketmol and optimal ligand poses to the protein structure was done with a single alignment transformation that produced a close alignment of the benzimidazole inhibitor core. Configurational deviations are reflected primarily in the pendant moieties.
