Table 4.

Binding free energy calculation for the protein-inhibitor complex based on WaterSwap calculations; Top1 = Ggp with bounded top 1 inhibitor, Top2 = Ggp with bounded top 1 inhibitor, Top1-combine = complex of Ggp and human receptor in complex with the top 1 inhibitor, Top2-combine = complex of Ggp and human receptor in complex with the top 2 inhibitor.

Algorithm	Waterswap Energy (kcal/mol)
	Top1-Combine	Top1	Top2-Combine	Top2
Bennetts	−27.69	−25.89	−35.53	−30.80
FEP	−24.75	−20.15	−33.23	−26.60
TI	−26.01	−23.05	−33.13	−30.20
Quadrature	−22.4	−21.4	−31.24	−23.6