Extended Data Table 1 -. Ligand energies by different refinement schemes.

Comparative table of ligand energies when ligands are refined using phenix.eLBOW generated restraints and the PHENIX force field versus when ligands are decoupled from the receptor environment and refined with PHENIX-OPLS3e/VSGB2.1. Energies were evaluated by Prime with OPLS3e/VSGB2.1.

Compound	Energy CIF refinement (kcal/mol)	Energy OPLS3e/VSGB2.1 (kcal/mol)	Delta (kcal/mol)
VM2	65.80	−93.28	−159.08
21	146.35	−91.09	−237.44
40e	702.53	−127.58	−829.11
40o	128.09	−136.21	−264.30
40q	200.53	−115.57	−316.10
41q, confA	199.19	−118.32	−317.51
41q, conf B	284.39	−120.96	−405.35
46	84.43	−82.77	−167.20
47	107.20	−68.53	−175.73