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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 6.

Figure 6

Ligand Young:38 (left) and ligand 2J4I:GSJ (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=−6.26kcal/mol. The optimized 3- and 5-parameter functionals predicted ΔΔG3p=−4.87 and ΔΔG5p=−4.83 respectively. The isopropyl group of ligand 2J4I:GSJ displaces three energetically depleted hydration sites, two of which are predicted to also be entropically structured, which resulted in a large predicted contribution to the binding affinity of the complex.