Figure 3.

Results for the ligands with an R1 methoxy group. The black mark indicates the reference ligand, and the red marks indicate ligands containing an R1 methoxy group. The upper row shows (a) the Glide docking score and (b) the MM-GBSA binding free energy for the more favorable pose compared to the experimental binding free energy. The lower row shows the FEP calculated free energy for the more favorable pose which was predicted using (c) Glide docking and (d) MM-GBSA. Equation 8 was used to calculate (e) the corrected free energy. The solid black line represents a perfect fit to the experimental free energies. The dashed lines represent a 1 kcal/mol deviation from experiment, and the dotted lines represent a 2 kcal/mol deviation. The predicted dG values were computed by adding the predicted relative binding free energy between the reference and each ligand to the experimental absolute binding free energy for the reference.