Table 3. Binding free energies (kJ/mol) and its components between protein and protein, protein and ligand, respectively.
| complex | Van der Waal (kJ/mol) | Electrostatic (kJ/mol) | Polar solvation (kJ/mol) | Non-polar solvation (kJ/mol) | Binding energy (kJ/mol) |
|---|---|---|---|---|---|
| CDC25B:CDK2/Cyclin Aa | −725.772 | −1146.987 | 1778.599 | −77.645 | −171.806 |
| CDC25B:CDK2/Cyclin A (binding with comp#1)b | −844.393 | −1164.718 | 2097.316 | −91.844 | −3.638 |
| CDC25B:CDK2/Cyclin A (binding with compound 7)c | −870.918 | −1415.664 | 2333.299 | −89.165 | −42.449 |
| CDC25B:CDK2/Cyclin A-comp#1d | −311.415 | −11.098 | 127.710 | −21.527 | −216.329 |
| CDC25B:CDK2/Cyclin A-compound 7e | −121.681 | −445.412 | 538.187 | −13.864 | −42.770 |
aCDC25B:CDK2/Cyclin A: the binding free energy between CDC25B and CDK2/Cyclin A.
bCDC25B:CDK2/Cyclin A (binding with comp#1): the binding free energy between CDC25B and CDK2/Cyclin A when comp#1 bound to CDC25B.
cCDC25B:CDK2/Cyclin A (binding with compound 7): the binding free energy between CDC25B and CDK2/Cyclin A when compound7 bound to CDC25B:CDK2/Cyclin A.
dCDC25B:CDK2/Cyclin A-comp#1: the binding free energy between comp#1 and CDC25B:CDK2/Cyclin A.
eCDC25B:CDK2/Cyclin A-compound 7: the binding free energy between compound 7 and CDC25B:CDK2/Cyclin A.