Table 2.

The relative catalytic efficiency (log Ω) calculated for DNA polymerase with and without the water flooding postprocessing and 4.0 kcal/mol Ų hydrogen bond constraint between the backbone nitrogen of the Y416 and 3OH′ in the substrate.

		Without H bond const		With H bond const
	exp	Original	Water Flooding	Original	Water Flooding
WT	−4.80	−7.29	−5.78	−8.48	−7.03
Y416A	−1.28	−1.78	−2.00	−1.24	−1.52
Y416F	−4.19	−6.25	−4.57	−9.32	−6.37

^aThe calculations are based on the alchemical thermodynamic cycle described in Figure 4. The last column includes the effect of using our water flooding approach.