Table 2.
Binding free-energy differences for all simulated mutations (kcal/mol)
| FF/Mutation | 1→2 | 2→3 | 3→4 | 4→1 | 1→5 |
|---|---|---|---|---|---|
| Trypsin | |||||
| QMPFF3 | 2.1 (4) | 1.7 (5) | −2.2 (4) | −2.0 (5) | 3.7 (7) |
| MMFF | 1.1 (4) | −0.5 (2) | −1.4 (3) | 0.7 (3) | 0.6 (6) |
| exp.* | 1.3 | 1.2 | −1.4 | −1.1 | 2.4 |
| Thrombin | |||||
| QMPFF3 | 4.9 (4) | 0.5 (5) | −3.3 (5) | −2.5 (5) | 2.0 (7) |
| MMFF | 6.9 (4) | −1.7 (3) | −6.0 (4) | 0.5 (3) | −7.5 (11) |
| exp.* | 2.8, 3.1† | 0.2, 0.4† | −1.4, −1.8† | −1.6, −1.7† | 1.6 |
| uPA | |||||
| QMPFF3 | 0.8 (3) | 2.0 (5) | −0.4 (3) | −2.1 (4) | 3.4 (7) |
| MMFF | 2.5 (3) | 0.6 (3) | −3.0 (3) | −0.5 (3) | 1.1 (6) |
| exp.* | −1.0, 0.1† | 2.5, 3.2† | −0.4, −0.9† | −1.1, −2.4† | 2.2 |