Table 2:

The average number of hydrogen bonds (with standard deviations in parentheses) between atoms in different regions, where cc = core M2/core M2, co = core M2/M5 selection, oo = M5 selection/M5 selection.

Ensemble a	QM/MM Model	cc	co	oo
RX	M2+D3	0.43 (0.57)	4.50 (1.36)	3.28 (1.32)
	M3+D3	0.60 (0.64)	3.98 (1.41)	2.98 (1.32)
	M4+D3	0.72 (0.65)	3.92 (1.32)	2.79 (1.26)
	M5+D3	0.52 (0.63)	4.25 (1.42)	3.38 (1.24)
TS	M2+D3	0.64 (0.66)	3.56 (1.33)	3.16 (1.39)
	M3+D3	0.51 (0.62)	4.03 (1.45)	3.56 (1.28)
	M4+D3	0.55 (0.63)	3.71 (1.41)	2.64 (1.24)
	M5+D3	0.47 (0.60)	4.40 (1.44)	3.21 (1.25)
PD	M2+D3	0.55 (0.56)	4.16 (1.33)	3.23 (1.24)
	M3+D3	0.43 (0.55)	4.32 (1.45)	3.51 (1.27)
	M4+D3	0.46 (0.57)	3.80 (1.43)	2.57 (1.17)
	M5+D3	0.52 (0.60)	4.25 (1.40)	3.22 (1.25)

^a).A window size of 0.2 Å was used for the reactant (RX) and product (PD) while a window size of 0.1 Å was used for the transition state (TS).