MM/generalized Born surface area (GBSA) binding free energy calculations

For all of the calculations below, a total of 50 snapshots from 13–15 ns were evenly extracted from the single MD trajectory at a time interval of 40 ps. The absolute binding free energy (ΔG_binding) was then predicted by applying the MM/GBSA approaches according to the following equation (Massova and Kollman, 2000):

where G_complex, G_protein, and G_ligand represent the free energies of the complex, protein, and ligand, respectively. ΔE_MM is the gas-phase interaction energy calculated using the sander program in AMBER 11, including the internal, electrostatic, and VDW energies, and the internal energy was cancelled based on the single MD trajectory. The solvation free energy ΔE_solv consists of both the polar and nonpolar parts, which were denoted as ΔG_GB and ΔG_SA, respectively.