Table 3.
Radii Sets | GB | R20.25nsa | R20.5ns | R20.75ns | R21ns | R22ns | R23ns | R24ns | R25ns | R26ns |
---|---|---|---|---|---|---|---|---|---|---|
bondi | GBHCT | 0.78 | 0.81 | 0.78 | 0.73 | 0.64 | 0.58 | 0.53 | 0.52 | 0.54 |
mbondi | GBHCT | 0.76 | 0.79 | 0.75 | 0.69 | 0.59 | 0.56 | 0.54 | 0.55 | 0.57 |
mbondi2 | GBHCT | 0.78 | 0.81 | 0.78 | 0.73 | 0.64 | 0.58 | 0.54 | 0.52 | 0.54 |
bondi | GBOBC | 0.76 | 0.79 | 0.76 | 0.72 | 0.64 | 0.6 | 0.56 | 0.54 | 0.56 |
mbondi | GBOBC | 0.72 | 0.75 | 0.71 | 0.67 | 0.57 | 0.55 | 0.53 | 0.54 | 0.56 |
mbondi2 | GBOBC | 0.76 | 0.79 | 0.76 | 0.71 | 0.63 | 0.59 | 0.55 | 0.53 | 0.55 |
bondi | GBOBC2 | 0.75 | 0.79 | 0.75 | 0.71 | 0.62 | 0.56 | 0.51 | 0.49 | 0.51 |
mbondi | GBOBC2 | 0.72 | 0.75 | 0.71 | 0.64 | 0.51 | 0.47 | 0.44 | 0.44 | 0.46 |
mbondi2 | GBOBC2 | 0.75 | 0.78 | 0.75 | 0.69 | 0.59 | 0.54 | 0.49 | 0.47 | 0.49 |
bondi | GBNeck | 0.73 | 0.73 | 0.69 | 0.64 | 0.52 | 0.46 | 0.4 | 0.39 | 0.42 |
mbondi2 | GBNeck | 0.72 | 0.72 | 0.68 | 0.63 | 0.51 | 0.44 | 0.38 | 0.37 | 0.4 |
bondi | GBNeck2 | 0.62 | 0.66 | 0.62 | 0.65 | 0.69 | 0.76 | 0.79 | 0.82 | 0.86 |
mbondi2 | GBNeck2 | 0.64 | 0.67 | 0.64 | 0.67 | 0.7 | 0.78 | 0.81 | 0.83 | 0.88 |
R2n: “R2” stands for coefficient of determination in the QM-MM/GBSA calculation. Here 100, 400, 1200, 2400 MD simulation frames were evenly extracted from one 0.25, 1, 3, 6 ns MD simulation trajectories, respectively.