Table 1.
List of MD simulations and contribution of individual, first three, and first 25 PC modes to the total motion
| Simulation setup | Abbrev. | Box size | Final structure | Contribution (%) |
||||
|---|---|---|---|---|---|---|---|---|
| 1st | 2nd | 3rd | First 3 | First 25 | ||||
| Closed-liganded | CL | Normal | Closed | 21.3 | 12.6 | 7.3 | 41.1 | 79.0 |
| CL big | Big | Closed | 19.9 | 16.3 | 7.0 | 43.1 | 79.8 | |
| Closed-unliganded | CU | Normal | Closed | 17.1 | 14.5 | 8.3 | 39.9 | 78.8 |
| Open-liganded | OL | Normal | Open | 29.9 | 13.5 | 7.3 | 50.7 | 82.1 |
| OL big | Big | Open | 46.7 | 10.2 | 6.3 | 63.2 | 86.5 | |
| OL/N∗ | Normal | Closed | 87.3 | 2.0 | 1.6 | 90.9 | 96.7 | |
| OL/N2∗ | Normal | Closed | 85.0 | 3.0 | 2.0 | 90.0 | 96.6 | |
| Open-unliganded | OU | Normal | Open | 42.6 | 12.2 | 6.0 | 60.7 | 86.0 |
∗
For these two cases, restraint MD simulations were done before production. The percentages are computed from PCA analysis over the entire trajectory. See Analysis of Closing Trajectories in main text for details.