Table 2.
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.