Table 3.
Summary of the binding free energy of protein–ligand complexes (in kcal/mol).
| Protein-ligand complexes | ELE1 | VDW2 | GAS3 | PBSOL4 | PBTOT5 | GBSOL4 | GBTOT5 | -TS6 | △GPB7 | △GGB7 |
|---|---|---|---|---|---|---|---|---|---|---|
| RdRp_14 | −3.37 ± 2.49 | −25.62 ± 2.11 | −28.99 ± 3.55 | 11.07 ± 3.93 | −17.92 ± 2.75 | 9.80 ± 2.43 | −19.19 ± 1.79 | 14.17 ± 1.94 | −3.75 | −5.02 |
| RdRp_3 | −48.71 ± 11.17 | −25.82 ± 3.77 | −74.53 ± 12.36 | 65.94 ± 11.97 | −8.59 ± 4.81 | 65.13 ± 10.48 | −9.40 ± 3.27 | 20.39 ± 3.48 | 11.80 | 10.99 |
| RdRp_21 | −8.40 ± 1.99 | −30.20 ± 2.94 | −38.60 ± 3.95 | 17.56 ± 3.17 | −21.04 ± 3.02 | 13.32 ± 1.77 | −25.28 ± 2.99 | 13.33 ± 1.93 | −7.71 | −11.95 |
1Electrostatic energy as calculated by the MM force field; 2Van der Waals contribution from MM; 3Total gas-phase energy; 4Non-polar and polar contributions to solvation based on PB/GB model; 5Final estimated binding free energy calculated from GAS and PBSOL/GBSOL; 6Entropy; 7Binding free energy with entropy