Table 2.

Calculated binding free energies in comparison with available experimental data (all in kcal/mol)

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

^aResults 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).

^bDirectly 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).

^cBinding free energies derived from the experimental IC₅₀ values in ref. 36