Table 2.
Adaptation energy for the peptide and hairpin RNA including eight explicit interface water molecules
| Energy | N-peptide |
boxB RNA |
||||
|---|---|---|---|---|---|---|
| Bound | Free | Adaptation energy∗ | Bound | Free | Adaptation energy∗ | |
| BOND† | 460.1 (± 2) | 456.0 (± 2) | 4.1 (± 1) | 757.8 (± 2) | 763.2 (± 1) | −5.9 (± 1) |
| VDW‡ | −49.5 (± 1) | −24.1 (± 1) | −25.4 (± 1) | −118.2 (± 1) | −123.8 (± 2) | 5.7 (± 0.4) |
| ELE§ | −22.3 (± 5) | −418.2 (± 3) | 395.9 (± 4) | −535.4 (± 6) | −664.2 (± 5) | 128.8 (± 5) |
| SURNP¶ | 17.5 (± 0.1) | 18.1 (± 0.01) | −0.6 (± 0.1) | 23.1 (± 0.01) | 22.3 (± 0.03) | 0.1 (± 0.01) |
| PB‖ | −1557.2 (± 6) | −1171.5 (± 3) | −385.7 (± 5) | −3407.4 (± 9) | −3289.8 (± 6) | −117.6 (± 8) |
| GB∗∗ | −1559.5 (± 6) | −1174.0 (± 3) | −385.4 (± 5) | −3322.9 (± 4) | −3202.7 (± 2) | −120.1 (± 3) |
| ΔG††PB | −1151.3 (± 3) | −1139.6 (± 1) | −11.7 (± 2) | −3280.4 (± 1) | −3291.6 (± 2) | 11.2 (± 2) |
| ΔG††GB | −1153.6 (± 3) | −1142.2 (± 1) | −11.4 (± 1) | −3195.9 (± 1) | −3204.6 (± 2) | 8.7 (± 2) |
MM/PBSA free energies are averages over the last 10 ns of the trajectories (2500 frames).
∗
Adaptation energy (kcal/mol) is calculated by subtracting the energy of the free state from that of the bound state.
†
Bond, angle, dihedral energy.
‡
van der Waals energy.
§
Electrostatic energy.
¶
Contribution of the nonpolar surface area to the solvation free energy.
‖
Electrostatic solvation free energy with the PB model.
∗∗
Electrostatic solvation free energy with the GB model.
††
Total energy, sum of all the above energy terms.