Figure 1.

The thermodynamics cycle used in calculating the binding entropy. ℓ and ℓ' represents the charged and uncharged forms of the ligand, respectively, while ℓ" represents the ligand being reduced to “nothing”. p and w designate protein and water, respectively. The calculations use K_cage= 0.22 kcal mol⁻¹ Å⁻² throughout the cycle, except when it is set to K⁰ = 0.026 kcal mol⁻¹ Å⁻², that corresponds to a molar volume (1660 Ų). Also, note that the calculations of the polarization and hydrophobic entropies involve a strong constraint on the ligand.