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. Author manuscript; available in PMC: 2009 Oct 14.
Published in final edited form as: J Am Chem Soc. 2008 Feb 12;130(9):2817–2831. doi: 10.1021/ja0771033

Figure 9.

Figure 9

Ligand 1V3X:D76 (left) and ligand Haginoya:57 (right) in the factor Xa active site. The hydration sites that receive an energetic score in equation 1 are depicted in gray wireframe, the hydration sites that receive an entropic score are depicted in green wireframe, and the hydration sites that receive both energetic and entropic scores are depicted in purple wireframe. Several hydration sites discussed in the text are labeled in yellow. The experimentally measured affinity difference between these two compounds is ΔΔGexp=−0.05kcal/mol. The optimized 3- and 5-parameter functionals predicted ΔΔG3p=0.0 and ΔΔG5p=0.0 respectively. The addition of the amide group to ligand D76 contribute negligibly to the binding affinity of the complex, which the method predicted from the the location of the amide group away from any structured or energetically depleted hydration sites.