For example, inaccurate protonation state predictions impair the accuracy of predicted distribution coefficients such as those from free energy calculations. Similarly, binding calculations can be affected by a change in protonation state . If a ligand in a protein-ligand system has a different protonation state in the binding pocket compared to when the molecule is in the aqueous phase, then this needs to be taken into account in the thermodynamic cycle when computing protein-ligand binding affinities.