. Author manuscript; available in PMC: 2008 Sep 25.

Published in final edited form as: J Am Chem Soc. 2006 Jun 28;128(25):8310–8319. doi: 10.1021/ja061216p

Table 3.

Hydrogen bonding interactions between 1 and 2, and dGMII over the 10-ns trajectories, computed using the carnal module in AMBER 7.0. The first value is the average distance between the specified atoms in Å, the values in parentheses indicate the percent occupancies.

Donor atom	Acceptor atom	1	2	2^a
R228NH2	S	3.8 (5)	3.9 (0.1)	3.8 (32)
Y727OH	O-2	3.0 (40)	3.1 (74)	3.2 (51)
O-2	D472OD1	3.2 (100)	3.0 (100)	3.0 (98)
O-2	D472OD2	2.6 (100)	2.9 (100)	2.9 (100)
O-3	D472OD1	3.9 (0.6)	3.8 (29)	3.9 (14)
O-3	D472OD2	2.5 (100)	2.5 (100)	2.5 (100)
O-4	Y269OH	3.7 (54)	3.8 (0.2)	3.8 (1.5)
O-4	D341OD1	2.5 (100)	3.6 (90)	3.6 (93)
O-4	D341OD2	3.8 (7)	2.6 (100)	2.6 (100)
N	D204OD1	3.6 (33)	3.6 (97)	3.6 (83)
N	D204OD2	3.2 (49)	3.4 (97)	3.4 (81)
N	Y269OH	2.9 (52)	2.9 (91)	3.0 (96)
N	D341OD1	3.0 (43)	3.1 (100)	3.4 (99)
N	D341OD2	3.5 (43)	3.4 (99)	3.3 (99)