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. Author manuscript; available in PMC: 2010 Aug 1.
Published in final edited form as: J Comput Chem. 2009 Aug;30(11):1701–1711. doi: 10.1002/jcc.21268

Figure 5.

Figure 5

Figure 5

Evolution of the hydrogen bond distances between the ligand and the surroundings: (a) water hydrogen bonding to amidinium N2 from simulations of ligand C and D. A similar water molecule is present in the crystal structure of trypsin-benzamidine; (b) ligand B hydrogen bonding to the Asp 189 residue in the binding pocket.