While in this work we have highlighted the importance of the proper apo state ensemble for the accurate absolute binding free energy predictions, it is essential to reliably represent the holo state as well. Here, we relied on the crystallographic protein holo states and carefully modeled ligand binding poses from previous investigation . Naturally, the ligand modelling step introduces additional uncertainy in defining the starting structure for initializing the simulations Accurate binding ∆G estimates suggest that the holo state representation was proper for most of the investigated cases. The tyk2 kinase, however, is an exception, as the calculated ∆G values significantly underestimate the experimentally measured binding affinities (Fig ). The apo state representation is unlikely to be solely responsible, as identification of any deeper free energy minima for the apo state would only impose an additional penalty on the ∆G of binding, thus reducing the predicted affinity even further, as illustrated in Fig S6 . A deeper free energy minimum for the holo state can lead to the prediction of a lower binding ∆G. This prompts us to assume that the holo state representation for the tyk2 kinase could be improved by exploring additional ligand poses, protein conformations, internal water placement or a combination of these components. This way, tyk2 could serve as an interesting candidate for future investigations possibly presenting a challenging case for the holo state description.