Table 5.

Binding energies (in kcal/mol) calculated as E ₀ ¹(PL)  −  E(P)  −  E ₀ ¹(L), where E ₀ ¹(PL) and E ₀ ¹(L) are energies of the protein-ligand complex and the free ligand in their global minima, respectively, and E(P) is energy of the protein in its configuration prepared as it is described in Section 2. The global energies of complexes and ligands were taken from respective minima sets (see Section 2.2). ΔG _exp⁡ is the experimental binding energy calculated from the binding constant. “Energy range” is the difference between the highest and the lowest energies among all 16 protein-ligand complexes. “Energy correlation” is Pearson correlation coefficient between experimental and calculated binding energies. Autodock and SOL scoring functions are also given to compare (in kcal/mol).

PDB ID	ΔG exp⁡	{1}MMFF94	{1}MMFF94 + PCM	{1}PM7	{1}PM7 + COSMO	{2}MMFF94	{2}MMFF94 + PCM	{2}MMFF94 + SGB	Sol Score	Autodock score
4FT0	−10.1	63.84	0.04	−39.48	−48.67	58.64	−0.08	3.03	−5.20	−7.15
4FT9	−10.9	−63.72	−9.98	−111.64	−48.77	−64.83	−10.05	−16.34	−4.29	−4.9
4FSW	−6.8	−60.20	−5.89	−108.48	−46.41	−60.19	−6.53	−7.72	−4.78	−6.08
4FTA	−9.8	−30.36	−5.44	−126.54	−58.61	−30.35	−15.04	−14.05	−4.35	−4.7
4FV5	−10.9	−102.01	−7.42	−168.44	−54.37	−102.01	−4.64	−11.16	−6.05	−8.25
4FV6	−12.3	−96.92	−7.75	−164.91	−72.68	−89.27	−13.42	−13.87	−5.26	−5.6
1DWC	−10.5	−146.16	−33.43	−194.69	−70.12	−144.88	−32.93	−36.77	−2.86	−4.24
1TOM	−11.8	−248.29	−49.66	−258.10	−73.67	−248.28	−49.89	−51.59	−8.11	−7.88
1C5Y	−6.0	−34.83	−79.15	−33.81	−52.84	−34.83	−79.34	−80.85	−6.83	−5.28
1F5L	−7.5	17.40	−52.26	−29.98	−81.95	17.40	−52.54	−52.88	−4.41	−6.62
1O3P	−9.4	3.59	−40.30	−32.53	−64.60	3.59	−40.59	−42.54	−6.95	−8.43
1SQO	−10.6	−24.78	−50.42	−58.75	−69.56	−24.78	−51.30	−52.22	−6.75	−8.68
1VJ9	−10.7	−49.57	−50.03	−91.69	−76.58	−49.20	−43.77	−49.18	−4.53	−3.17
1VJA	−10.9	−49.87	−51.91	−95.43	−81.40	−47.97	−38.86	−41.85	−4.47	−1.82
2P94	−13.0	−68.20	−15.74	−153.53	−68.94	−67.28	−15.79	−20.87	−6.53	−13.09
3CEN	−11.7	−69.48	−18.17	−133.10	−63.12	−69.47	−18.43	−26.62	−5.48	−11.68
Energy range	7.0	312	79.2	228	35.5	306.93	79.26	83.89	5.25	11.27
Energy correlation		0.41	−0.36	0.60	0.33	0.40	−0.39	−0.35	0.09	0.13