Table 2.
Compound | Nonpolar contributiona |
Polar contributiona |
MMa | ΔGbindSIEa | ΔGbindGBSAb | ΔGbindexpc | ||
---|---|---|---|---|---|---|---|---|
vdW | np | Coul | RF | |||||
1 | −59.5 | −9.2 | −9.4 | 5.6 | −68.9 | −10.5 (−11.6) | −43.8 (−11.4) | −11.4 |
2 | −55.8 | −8.6 | −8.7 | 5.8 | −64.5 | −9.9 (−10.9) | −42.5 (−10.6) | −10.8 |
3 | −53.6 | −8.9 | −9.2 | 5.86 | −62.8 | −9.8 (−10.7) | −41.6 (−10.1) | −10.7 |
4 | −53.9 | −8.8 | −7.4 | 5.94 | −61.3 | −9.6 (−10.5) | −40.8 (−9.6) | −10.5 |
5 | −52.7 | −8.0 | −6.0 | 6.01 | −58.8 | −9.3 (−10.0) | −41.8 (−10.2) | −10.2 |
6 | −48.2 | −8.4 | −5.1 | 5.8 | −53.3 | −8.8 (−9.5) | −41.1 (−9.8) | −9.7 |
7 | −45.6 | −8.3 | −6.1 | 7.61 | −51.7 | −8.4 (−9.0) | −41.5 (−10.0) | −9.1 |
8 | −45.6 | −8.9 | −2.2 | 6.78 | −47.8 | −8.1 (−8.7) | −40.5 (−9.4) | −8.8 |
9 | −44.9 | −8.9 | −4.7 | 8.71 | −49.6 | −8.1 (−8.7) | −39.4 (−8.8) | −8.7 |
10 | −42.4 | −7.6 | −4.2 | 6.05 | −46.6 | −7.9 (−8.5) | −39.1 (−8.6) | −8.3 |
11 | −39.8 | −8.0 | −2.1 | 4.8 | −41.9 | −7.6 (−8.1) | −37.3 (−7.6) | −7.9 |
Results calculated with the SIE method using the standard parameters. The values in parentheses are the corresponding binding free energies calculated using the new parameter values refined in the present work. The listed individual contributions are intermolecular van der Waals interactions (vdW), intermolecular coulomb interactions (Coul), molecular mechanical energy (MM), change in nonpolar solvation energy (np), and change in reaction field energy (RF).
Directly calculated binding energies with MM/GBSA method neglecting the entropic contribution. The values in parentheses are the binding free energies calculated by using Eq.(8).
Binding free energies derived from the experimental IC50 values in ref. 36