Table 2.
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculation and the individual energy components of the RdRp in complex with ligands.
| Complex Name | MM/GBSA (kcal/mol) |
||||
|---|---|---|---|---|---|
| ΔEvdW | ΔEelec | ΔGgas | SASA | ΔG Total | |
| RdRp–suramin | –29.61 ± 3.55 | 40.38 ± 26.33 | 10.77 ± 24.02 | –4.94 ± 0.42 | –9.94 ± 5.34 |
| RdRp–ZINC285540154 | –53.84 ± 2.89 | – | –53.84 ± 2.89 | –7.60 ± 0.30 | –37.74 ± 2.90 |
| RdRp–ZINC28467879 | –42.84 ± 4.22 | – | –42.84 ± 4.22 | –5.58 ± 0.40 | –26.36 ± 3.76 |
| RdRp–ZINC611516532 | –25.02 ± 2.58 | –193.2 ± 12.92 | –218.25 ± 12.35 | –3.55 ± 0.31 | –22.03 ± 4.03 |
| RdRp–ZINC1398350200 | –28.22 ± 2.93 | –244.77 ± 16.70 | –273.00 ± 16.88 | –4.95 ± 0.27 | –20.82 ± 2.90 |
| RdRp–ZINC739681614 | –25.15 ± 3.88 | –14.65 ± 13.02 | –39.80 ± 13.15 | –3.43 ± 0.78 | –16.04 ± 4.72 |
| RdRp–ZINC1602963057 | –27.82 ± 2.44 | –53.40 ± 9.58 | –81.22 ± 8.83 | –4.035 ± 0.21 | –12.87 ± 2.74 |
| RdRp–ZINC1166211307 | –13.82 ± 7.47 | –143.16 ± 11.29 | –156.99 ± 13.39 | –1.76 ± 0.95 | –7.83 ± 5.54 |
| RdRp–ZINC98208626 | –43.32 ± 4.11 | –145.05 ± 16.99 | –188.37 ± 16.64 | –6.55 ± 0.21 | –6.50 ± 7.6 |
ΔEvdw, van der Waals free energy: ΔEelec, electrostatic free energy: ΔGgas, gas-phase free energy: SASA: solvent accessible surface area free energy: ΔG Total, total binding free energy.