In this study, we have used an alchemical nonequilibrium free energy calculation approach to calculate absolute protein-ligand binding free energies for 128 complexes. We have developed a novel way of treating the decoupled state of the ligand (see Methods section for details). The large set of investigated systems allows us to have an extensive evaluation of the accuracy that can be achieved with the first principles based calculations. Figure shows the calculated values for the binding free energy plotted against the experimental measurements. When compared to the experimental values, the absolute unsigned error (AUE) of 4.9 ± 0.5 kJ/mol (1.2 ± 0.1 kcal/mol) only marginally exceeds the state-of-the-art accuracy threshold of 1 kcal/mol achievable for relative binding free energy calculations. Accuracies for jnk1 and p38α are exceptionally good with AUEs of 3.0 ± 0.8 and 3.1 ± 0.7 kJ/mol (0.7 ± 0.2 kcal/mol for both), respectively. Some systems, however, have a considerably lower accuracy (AUE of 10.8 ± 1.5 kJ/mol for tyk2, 5.5±1.4 kJ/mol for pde2), revealing a particular challenge for affinity estimation in these systems. An accurate evaluation of the offset in the ∆G is critical for obtaining reliable absolute ∆G values: inaccuracies in this case manifest as large shifts of the calculated values with respect to the experimental measurements, e.g. tyk2 in Fig 1 . Interestingly, even such offsets do not significantly deteriorate the relative free energy difference estimates (Fig ).