Skip to main content
. 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 10.

Figure 10

Ligand 1NFX:RDR (left) and ligand 1NFU:RRR (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=−0.59kcal/mol. The optimized 3- and 5-parameter functionals predicted ΔΔG3p=+1.94 and ΔΔG5p=+1.53 respectively. The poor agreement of the theory with experiment here is due to the poor interaction energy of the S1 pocket sulfur atom of 1NFX:RDR with Ser195 compared with hydration 5, which is not displaced when ligand 1NFU:RRR docks with the receptor.