Table 3.
Energetic components of the binding free energy for 3CLpro of SARS-CoV-2 complexed with human metabolites, estimated using the MM/GBSA (kcal/mol) method
| Systems | ΔEvdW | ΔEelec | ΔGpol | ΔGnp | ΔEMMa | ΔGsolvb | ΔHc | − TΔS | ΔGbindd |
|---|---|---|---|---|---|---|---|---|---|
| Complex1 | − 52.91 (0.10) | − 57.22 (0.35) | 70.40 (0.30) | − 6.79 (0.01) | − 110.13 (0.39) | 63.61 (0.29) | − 46.51 (0.11) | 28.43 (0.86) | − 18.08 (0.87) |
| Complex2 | − 44.26 (0.11) | − 45.62 (0.30) | 62.87 (0.22) | − 6.34 (0.01) | − 89.88 (0.32) | 56.53 (0.21) | − 33.35 (0.14) | 28.01 (0.67) | − 5.34 (0.68) |
| Complex3 | − 32.39 (0.10) | − 79.24 (0.32) | 87.79 (0.29) | − 5.40 (0.01) | − 111.64 (0.35) | 82.79 (0.29) | − 29.25 (0.10) | 30.43 (0.70) | 1.18 (0.71) |
| Complex4 | − 29.93 (0.09) | − 23.86 (0.20) | 38.44 (0.16) | − 4.46 (0.01) | − 53.80 (0.23) | 33.98 (0.15) | − 19.82 (0.11) | 23.99 (0.61) | 4.17 (0.62) |
| Complex5 | − 37.50 (0.11) | − 20.02 (0.30) | 33.29 (0.26) | − 4.59 (0.01) | − 57.52 (0.34) | 28.70 (0.25) | − 28.82 (0.13) | 20.07 (0.57) | − 8.75 (0.58) |
| Complex6 | − 48.53 (0.05) | − 27.72 (0.10) | 48.09 (0.07) | − 5.89 (0.00) | − 76.25 (0.10) | 42.20 (0.07) | − 34.05 (0.05) | 23.67 (0.46) | − 10.33 (0.46) |
| Complex7 | − 44.14 (0.11) | − 32.75 (0.22) | 47.63 (0.16) | − 5.95 (0.01) | − 76.89 (0.28) | 41.68 (0.15) | − 35.21 (0.16) | 25.68 (0.84) | − 9.53 (0.85) |
| Complex8 | − 33.95 (0.06) | − 17.63 (0.17) | 28.26 (0.15) | − 4.18 (0.01) | − 51.58 (0.17) | 24.09 (0.15) | − 27.49 (0.06) | 17.21 (0.58) | − 10.28 (0.58) |
Standard errors of the mean (SEM) are provided in parentheses
aΔEvdW + ΔEelec
bΔGpol+ ΔGnp
cΔEvdW + ΔEelec + ΔGpol+ ΔGnp
dΔEvdW + ΔEelec + ΔGpol+ ΔGnp − TΔS