TABLE III.

Statistics of protein-ligand and water-ligand hydrogen-bonds observed in the simulation of the [Hyd]^TS model. The criteria for the existence of hydrogen bonds are 1) a maximum H ⋯ A(acceptor) distance of 2.4 Å 2) a minimum $\widehat{\mathit{\text{DHA}}}$ of 120° and 3) a hydrogen bond lifetime τ ≥ 5.0 ps. The occupancy, Occ, is defined as the total lifetime of each hydrogen bond by the production time. The events are the number of times each hydrogen bond is formed.

All distances are in Å. HSP stands for a doubly protonated His.

Atom pair	Distance		Hydrogen Bond
	MD†	MD‡	Occupancy	Lifetime-Average(ps)	# Events
GLN 11 Hε21 - CYT O1P	2.053(0.388)	2.963(0.284)	0.86	62.54	71
LYS 41 Hζ1 - CYT O1P	2.957(0.776)	3.029(0.385)	0.21	62.65	17
LYS 41 Hζ2 - CYT O1P	2.988(0.627)		0.14	46.56	16
LYS 41 Hζ3 - CYT O1P	2.814(0.668)		0.22	59.48	19
WATER - CYT O1P			1.47	39.38	193
HSP 12 Hε2 - CYT O2P	1.729(0.119)	2.723(0.099)	1.00	573.33	9
HSP 119 Hδ1 - CYT O2P	3.102(0.308)	3.863(0.288)	0.00	10.00	1
PHE 120 HN - CYT O2P	2.157(0.259)	3.120(0.231)	0.85	50.17	88
WATER 397 - CYT O2P		2.695(0.131)	0.99	341.33	15
HSP 12 Hε2 - CYT O2′	2.488(0.197)	3.162(0.171)	0.13	11.67	57
LYS 41 Hζ1 - CYT O2′	3.173(0.683)	3.205(0.383)	0.12	55.47	11
LYS 41 Hζ2 - CYT O2′	3.274(0.821)		0.15	83.88	9
LYS 41 Hζ3 - CYT O2′	3.135(0.839)		0.19	64.65	15
WATER 6130 - CYT O2′		13.333(13.670)	0.55	188.34	15
HSP 119 Hδ1 - CYT O3′	2.165(0.230)	2.961(0.149)	0.79	31.77	128
WATER - CYT O3′			0.40	14.48	144
HSP 119 Hδ1 - CYT O3T	2.060(0.296)	2.991(0.252)	0.88	76.77	59
WATER - CYT O3T			0.19	12.47	79

^†Arithmetic average hydrogen bond distance for 5 ns of the production simulation, with standard deviation in parentheses.

^‡Arithmetic average distance between the corresponding heavy atoms in the production trajectory, with standard deviation in parentheses.