Table 5.
Energy rank, interaction energy, RMSD relative to the native structure and cluster population for the four lowest energy geometries of the six studied complexes after systematic docking without charge. The rank of the closest cluster in the simulation with charges is also reported.
| complex | energy rank | interaction energy [RT] | RMSD [Å]/native | cluster population | simulation with charge rank (RMSD/pop) |
|---|---|---|---|---|---|
| 1K79 | 1 | −27.0 | 1.2 | 6 | 1 (0.1/27) |
| 2‡ | −25.8 | 29.1 | 5 | 2 (0.1/9) | |
| 3‡ | −25.3 | 28.7 | 1 | 3 (0.1/9) | |
| 4 | −24.3 | 13.1 | 2 | - | |
| 1PAR | 1 | −54.2 | 0.7 | 4 | 1 (0.0/20) |
| 2† | −53.2 | 43.2 | 3 | 2 (0.1/14) | |
| 3 | −32.4 | 43.4 | 1 | 10 (0.1/1) | |
| 4 | −29.5 | 26.0 | 1 | 13 (0.1/5) | |
| 2BOP* | 1 | −37.6 | 0.2 | 1 | 1 (0.1/17) |
| 2† | −37.6 | 32.5 | 2 | 2 (0.1/14) | |
| 3 | −26.4 | 35.0 | 6 | - | |
| 4 | −26.4 | 24.1 | 11 | - | |
| 1A74* | 1† | −56.9 | 37.5 | 3 | 3 (0.1/23) |
| 2 | −30.7 | 45.8 | 2 | - | |
| 3 | −30.4 | 26.6 | 2 | - | |
| 4 | −30.4 | 28.7 | 2 | 67 (0.2/1) | |
| 1YTB | 1 | −46.8 | 3.8 | 3 | 1 (0.1/3) |
| 2 | −40.5 | 3.7 | 7 | 3 (0.2/12) | |
| 3 | −37.0 | 28.4 | 8 | 4 (0.1/10) | |
| 4 | −32.0 | 32.1 | 4 | 6 (0.1/3) | |
| 1A66 | 1 | −24.7 | 1.2 | 3 | 1 (0.1/21) |
| 2 | −24.0 | 37.2 | 3 | 47 (0.2/3) | |
| 3 | −23.0 | 44.3 | 3 | - | |
| 4 | −21.8 | 41.0 | 1 | - | |
The RMSD with respect to the uncharged corresponding cluster and the population are also indicated in parentheses. A dash indicates that no cluster was found with a RMSD less than 0.5 Å.