Table 1. Predicted binding free energy change for the CDC25c phosphopeptide and peptide from dynamic and static structure calculations.
| CDC25c Phosphopeptide (MMPBSA) | CDC25c Peptide (MMPBSA) | CDC25c Phosphopeptide (Static) | CDC25c Peptide (Static) | |
| VDW (kcal/mol) | −41.3±1.2 | −36.0±0.8 | −56.0 | −53.0 |
| Electrostatic Interaction (kcal/mol) | −187.5±3.4 | −25.6±1.2 | −241.0 | −72.6 |
| Desolvation Penalty (kcal/mol) | 208.3±2.6 | 50.3±1.7 | 252.4 | 87.7 |
| SASA(kcal/mol) | −2.8±0.0 | −2.7±0.0 | −5.6 | −5.1 |
| Ligand Deformation (kcal/mol) | −9.3 | −7.9 | 5.9 | 10.1 |
| Δ H (kcal/mol) | −32.7 | −21.9 | −44.2 | −32.9 |
| ΔΔ H (kcal/mol) | 10.8 | 11.3 | ||
| Unbound Peptide TS (kcal/mol) | 71.8±1.1 | 62.5±1.0 | NA | NA |
| Bound Peptide TS (kcal/mol) | 58.1±0.7 | 53.3±1.1 | NA | NA |
| −TΔ S Peptide (kcal/mol) | 13.7 | 9.2 | NA | NA |
| −ΔTΔ S Peptide (kcal/mol) | −4.5 | NA | ||
| Δ G (kcal/mol) | −19.0 | −12.7 | NA | NA |
| ΔΔ G (kcal/mol) | 6.2 | NA |
The predicted binding free energy change for the CDC25c phosphopeptide and the CDC25c peptide from the MM-PBSA and static structure calculations. The separate contributions to the binding free energy change are also reported. The ligand deformation is the difference between the internal energy of the ligand in the bound and the unbound states. The entropic contribution to the binding free energy from the peptide is the difference between the entropy in the bound and unbound states calculated by normal mode analysis. The standard errors of the mean are estimated from twenty equally sized blocks.