Since we restrained the dihedral, to calculate binding free energies, we must account for the energetic costs of the dihedral restraints in the thermodynamic cycle. We did this by first turning the restraints on with the ligand interacting in the binding site, then decoupling the ligand while simultaneously switching the restraints to the orientation in the apo structure. Finally the restraints were then turned off again. The cost for restraining the side chain was very low (0.1 kcal/mol for restraining and -0.1 kcal/mol for unrestraining) since Val111 was restrained to its preferred orientation in both the holo and apo structure.