All-atom molecular dynamics (MD) simulations in both explicit and implicit solvent, followed by MM-GBSA energy analysis, have been used to estimate binding free energies of four pyrimidine dicarboxamide inhibitors with human collagenase-3 (MMP-13) for comparison with experimental activities. Energetic analysis reveals that affinity is driven primarily by favorable van der Waals interactions and burial of total surface area. The computed effects of desolvation, as a function of ligand structure, quantitatively show that hydrophilic derivatives pay greater penalties upon binding than their related more hydrophobic analogs.