TABLE 1.

Comparison of the H-bond geometries near W402 in the BR crystal structures (PDB ID codes 1C3W at 1.55 Å resolution and 2NTU at 1.53 Å resolution) in the QM/MM geometry by Hayashi and Ohmine (8) and in this study (models 1 and 2, Fig. 4)

Distances are in Å, and angles are in degrees. ND, not determined. An underlined number indicates a significant deviation from the distance in the crystal structure. See supplemental S1 for the atomic coordinates of the QM/MM geometries.

Donor…acceptor	1C3W	1C3W; QM/MM Hayashi and Ohminea (model 1)	1C3W; QM/MM (model 1)	1C3W; QM/MM (model 2)	2NTU	2NTU; QM/MM (model 1)	2NTU; QM/MM (model 2)
	Å	Å	Å	Å	Å	Å	Å
W402…Asp-85	2.63	2.58	2.61	2.57	2.52	2.63	2.59
W402…Asp-212	2.85	4.07	2.92	2.99	3.01	2.90	2.95
W401…Asp-85	2.59	2.63	2.51	2.64	2.69	2.59	2.68
(OH without acceptor)b		(W401)	(W401)	(W406)		(W401)	(W406)
W406…W401	2.75	2.77	2.76	3.06	2.69	2.78	3.07
W406…Asp-212	2.75	2.78	2.64	2.64	2.81	2.73	2.65
Lys-216…W402	2.87	2.63	2.78	2.76	2.94	2.80	2.77
Arg82…W406	2.49	2.72	2.74	2.87	2.87	2.73	2.86
Root mean square deviation	ND	ND	0.19	0.18	ND	0.17	0.18
Angle (NLys-216…OW402…OAsp-85) (degrees)	106	ND	108	108	111	111	111

^a See Ref. 8.

^b A water molecule in which one of the two O-H bonds does not possess the H-bond acceptor molecule; W401 in model 1 and W402 in model 2 (Fig. 4).