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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 7.

Figure 7

Ligand 1MQ5:XLC (left) and ligand 1MQ6:XLD (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=−2.94kcal/mol. The optimized 3- and 5-parameter functionals predicted ΔΔG3p=−2.85 and ΔΔG5p=−2.54 respectively. Unlike the S4 group of ligand 1MQ5:XLC, the S4 pocket group of ligand 1MQ6:XLD displaced the energetically depleted and entropically structured hydration site 13 and partially displaced entropically structured hydration sites 20, which resulted in a large solvent related contribution to the binding affinity quantitatively predicted by our theory.