. Author manuscript; available in PMC: 2008 Dec 11.

Published in final edited form as: J Chem Theory Comput. 2006;2(4):1057–1069. doi: 10.1021/ct0600060

Table 3. Key hydrogen bond lengths in the structures of the 32i and 228i states refined by Protocol II and Protocol III and in the 1FKN structure.

Hydrogen Bond		Protocol II		Protocol III		1FKN Structure
Acceptor	Donor	32i	228i	32i	228i	1FKN Structure
O^outer(Asp32)	Oγ(Ser35)	2.66	2.65	2.63	2.61	2.64
O^outer(Asp32)	O(Inhibitor)	3.12	3.17	3.00	3.06	3.26
O^γ (Ser35)	O(Wat2)	2.70	2.69	2.74	2.75	2.67
O^inner(Asp32)	N(Gly34)	3.39	3.35	3.02	2.82	3.56
O^inner(Asp32)	O(Inhibitor)	2.65	2.66	2.77	2.89	2.51
O^outer(Asp228)	O^γ (Thr230)	2.60	2.63	2.61	2.67	2.53
O^outer(Asp228)	O(Inhibitor)	2.64	2.58	2.84	2.97	2.54
O^γ (Thr230)	O(Wat101)	2.76	2.73	2.76	2.77	2.80
O^inner(Asp228)	N(Gly230)	2.81	2.87	2.84	2.99	2.66
O^inner(Asp228)	O(Inhibitor)	3.15	3.10	3.20	3.05	3.10
O^inner(Asp228)	O^inner(Asp32)	2.75	2.75	2.49	2.58	2.89