Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

Table 4

The protein-ligand binding energy components: potential energies and additive corrections to it. 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. is the correction due to vibration degrees of freedom calculated with respective configuration integral (2). and are corrections due to translational and rotational degrees of freedom calculated with configuration integrals (3) and (4), respectively. Corrections , , and include both enthalpy and entropy components. is the correction for multiple minima accounting; it is calculated as a difference between binding free energy , calculated with multiple minima accounting, and binding free energy, calculated with only the global minima of the complex and the ligand. is the experimental binding energy calculated from the binding constant.

Protein	PDBID	, kcal/mol	, kcal/mol	, kcal/mol	, kcal/mol	, kcal/mol	, kcal/mol	, 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