Table 7.
MM/GBSA | QM-MM/GBSA | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
Radii Sets | GB | R26nsa,b | R26nsc | R26nsd | R26nse | Radii Sets | GB | R26nsa,b | R26nsc | R26nsd | R26nse |
bondi | GBHCT | 0.41 | 0.24 | 0.37 | 0.14 | bondi | GBHCT | 0.54 | 0.52 | 0.54 | 0.48 |
mbondi | GBHCT | 0.44 | 0.3 | 0.42 | 0.22 | mbondi | GBHCT | 0.57 | 0.59 | 0.59 | 0.58 |
mbondi2 | GBHCT | 0.41 | 0.24 | 0.37 | 0.14 | mbondi2 | GBHCT | 0.54 | 0.54 | 0.54 | 0.50 |
bondi | GBOBC | 0.38 | 0.12 | 0.31 | 0.04 | bondi | GBOBC | 0.56 | 0.51 | 0.56 | 0.41 |
mbondi | GBOBC | 0.36 | 0.12 | 0.30 | 0.04 | mbondi | GBOBC | 0.56 | 0.54 | 0.57 | 0.49 |
mbondi2 | GBOBC | 0.36 | 0.12 | 0.29 | 0.03 | mbondi2 | GBOBC | 0.55 | 0.52 | 0.55 | 0.43 |
bondi | GBOBC2 | 0.36 | 0.13 | 0.27 | 0.04 | bondi | GBOBC2 | 0.51 | 0.45 | 0.49 | 0.36 |
mbondi | GBOBC2 | 0.24 | 0.05 | 0.16 | 0.00 | mbondi | GBOBC2 | 0.46 | 0.42 | 0.43 | 0.35 |
mbondi2 | GBOBC2 | 0.32 | 0.1 | 0.23 | 0.02 | mbondi2 | GBOBC2 | 0.49 | 0.45 | 0.46 | 0.35 |
bondi | GBNeck | 0.16 | 0.00 | 0.07 | 0.02 | bondi | GBNeck | 0.42 | 0.28 | 0.35 | 0.14 |
mbondi2 | GBNeck | 0.15 | 0.00 | 0.06 | 0.02 | mbondi2 | GBNeck | 0.4 | 0.28 | 0.34 | 0.15 |
bondi | GBNeck2 | 0.5 | 0.07 | 0.42 | 0.06 | bondi | GBNeck2 | 0.86 | 0.47 | 0.75 | 0.42 |
mbondi2 | GBNeck2 | 0.51 | 0.07 | 0.43 | 0.07 | mbondi2 | GBNeck2 | 0.88 | 0.52 | 0.76 | 0.46 |
R2n: “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.
2,400 frames calculated enthalpy & no calculated entropy
2,400 frames calculated enthalpy & 48 frames calculated entropy
48 frames calculated enthalpy & no calculated entropy
48 frames calculated enthalpy & 48 frames calculated entropy