Table 1 The decomposition of the binding free energy (kcal/mol).
From: Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy
Charge | Trajectory |
|
|
|
|
|
|
| Exp* |
|---|---|---|---|---|---|---|---|---|---|
AMBER | AMBER | −15.01 ± 5.9 | −53.59 ± 5.5 | 47.00 ± 7.2 | −5.19 ± 0.2 | −26.80 ± 7.9 | 23.10 ± 4.4 | −3.70 | −13.70 |
PPC | PPC | −27.76 ± 5.8 | −52.42 ± 4.4 | 47.90 ± 7.2 | −4.95 ± 0.3 | −37.23 ± 7.4 | 24.19 ± 5.8 | −13.04 | |
AMBER | PPC | −18.75 ± 4.4 | −52.42 ± 4.4 | 46.85 ± 6.2 | −4.95 ± 0.3 | −29.26 ± 6.4 | 25.60 ± 5.0 | −3.66 | |
PPC | AMBER | −15.53 ± 9.0 | −53.59 ± 5.5 | 52.15 ± 8.4 | −5.19 ± 0.2 | −22.15 ± 10 | 21.75 ± 4.9 | −0.40 | |
AMBER | X-ray | −22.18 | −62.18 | 65.00 | −5.26 | −24.62 | −22.42 | −2.20 | |
PPC | X-ray | −31.81 | −62.18 | 59.95 | −5.26 | −39.30 | −25.26 | −14.04 |
