Fig. 4.9 Illustration of thermodynamic contributions to the free binding energy ΔG. Before binding, the ligand can move freely in water. It has a certain translational and rotational entropy. In addition, the ligand is usually flexible and adopts different conformations in solution. Protein and ligand are solvated, forming H-bonds to water molecules (blue spheres). Some water molecules are in loose contact with the protein or ligand others are forming strong H-bonds. Translational and rotational degrees of freedom are lost during binding. The associated decrease in entropy is unfavorable for binding. In addition, the protein and ligand must shed some of their hydrate shell, also a process unfavorable for binding. The binding of the ligand leads to the formation of new direct interactions with the protein and releases water molecules from the protein pocket. Both are contributions that favor binding. In part, water molecules can mediate binding to the protein. The complex formed establishes a new surface that is re-solvated. H-bonds are shown as blue dashed lines, hydrophobic contacts analogously in yellow.