Table 6.

Summary of the Impact of Entropy on Predicted Binding Free Energies of MD Trajectories of Different Lengths and Radii Sets in MM/PBSA Calculations.

1	2	3	4	5
Radii Sets	R26nsa,b	R26nsc	R26nsd	R26nse
bondi	0.36	0.06	0.21	0
mbondi	0.45	0.12	0.29	0
mbondi2	0.37	0.06	0.22	0
PARSE	0.48	0.15	0.27	0.01

^aR²_n: “R²” stands for coefficient of determination in the MM/PBSA calculation. Here 2,400 MD simulation frames were evenly extracted from 6 ns MD simulation trajectories.

^b2,400 frames calculated enthalpy & no calculated entropy

^c2,400 frames calculated enthalpy & 48 frames calculated entropy

^d48 frames calculated enthalpy & no calculated entropy

^e48 frames calculated enthalpy & 48 frames calculated entropy