The largest effect from using an experimen-Figure : Overview of the accuracy of calculated absolute binding free energies ∆G Calc. . Error bars represent standard errors for free energies, absolute unsigned errors (AUE, units of kJ/mol), and the Pearson correlation coefficients (Cor). Apo states were initialized with X-ray crystal structures for all systems except pde2 and tyk2 where holo X-ray structures with the ligand removed were used. Dark and light shaded areas represent regions deviating from experiment by at most 1 and 2 kcal/mol. tally resolved apo structure is observed in the galectin, p38α and cdk2 protein-ligand complexes, while for the other cases the differences in accuracy are less affected. To understand what structural features are responsible for such pronounced effects, we have further explored the p38α system for which ∆G had the largest difference among the systems depicted in Fig 2.