Table 4.

The protein-ligand binding energy components: potential energies and additive corrections to it. ΔE is the binding potential energy from the MMFF94 force field in vacuum, calculated by the global minima of the protein-ligand complex and the free ligand with energy of the free protein. ΔG _ν is the correction due to vibration degrees of freedom calculated with respective configuration integral Z _ν (2). ΔG _t and ΔG _r are corrections due to translational and rotational degrees of freedom calculated with configuration integrals Z _t (3) and Z _r (4), respectively. Corrections ΔG _ν, ΔG _t, and ΔG _r include both enthalpy and entropy components. ΔG _all is the correction for multiple minima accounting; it is calculated as a difference between binding free energy ΔG _bind, calculated with multiple minima accounting, and binding free energy, calculated with only the global minima of the complex and the ligand. ΔG _exp⁡ is the experimental binding energy calculated from the binding constant.

Protein	PDBID	ΔG exp⁡, kcal/mol	ΔG bind, kcal/mol	ΔE, kcal/mol	ΔG ν, kcal/mol	ΔG t, kcal/mol	ΔG r, kcal/mol	ΔG all, kcal/mol
CHK1	4FT0	−10.1	82.2	63.8	−3.9	10.6	10.3	1.4
	4FT9	−10.9	−48.5	−63.7	−5.0	10.4	9.9	−0.1
	4FSW	−6.8	−44.2	−60.2	−3.7	10.3	9.4	0.0
	4FTA	−9.8	−9.8	−30.4	−0.2	10.6	10.1	0.1
ERK2	4FV5	−10.9	−79.3	−102.1	0.5	10.7	10.6	1.0
	4FV6	−12.3	−74.6	−96.8	−0.4	10.8	10.7	1.1
Thrombin	1DWC	−10.5	−128.5	−144.9	−4.2	10.9	10.5	0.2
	1TOM	−11.8	−224.1	−248.7	2.7	10.7	10.5	0.7
Urokinase	1C5Y	−6.0	−16.3	−34.8	−0.7	10.0	8.7	0.5
	1F5L	−7.5	34.7	17.4	−2.3	10.2	9.3	0.1
	1O3P	−9.4	23.8	3.9	−2.0	10.6	10.2	1.1
	1SQO	−10.6	−4.6	−24.8	−0.4	10.3	9.6	0.7
	1VJ9	−10.7	−25.9	−50.7	2.4	11.0	10.8	0.6
	1VJA	−10.9	−31.0	−51.1	−2.1	10.9	10.5	0.8
Factor Xa	2P94	−13.0	−42.0	−68.2	−5.5	10.9	10.8	0.0
	3CEN	−11.7	−49.2	−69.5	−1.9	10.9	10.6	0.7