The redocking simulation of the prepared complex allowed the finding of the co-crystallized conformation of the reference ligand with a total energy of -20.395 kcal•mol⁻¹ and RMSD of 0.419 Å. Conversely, the redocking experiments of the complex without the careful preparation protocol produced a top-1 docked pose with a total energy of 12.946 kcal•mol⁻¹ and RMSD of 2.382 Å. The main difference between the predicted binding poses relies on the 5-nitrocatechol moiety, which coordinates the metal ion. In the structure of the ligand provided by PDBbind, the 5-nitrocatechol group contains the enol tautomer consisting of two hydroxyl groups, which led to an inverted orientation pointing out to the metal ion. The Epik predicted the 5-nitrocatechol moiety in a keto-tautomeric form that optimally coordinates the M 2+ ion. For deep learning-based models based on voxels that consider the hydrogen atoms, improper preparation of the protein-ligand complex could impede the accurate identification of pairs involving hydrogen bond acceptors and donors, mainly for heteroatoms such as oxygen that can be either acceptor (e.g., ketone group) or donor (e.g., hydroxyl). Thus, the incorrect assignment of protonation/tautomeric states associated with a non-optimized hydrogen bond network might induce important inaccuracies in binding mode and affinity predictions. In this context, the availability of a prepared PDBbind dataset regarding protonation/tautomeric states would be an invaluable data resource for training and testing new structure-based methods, including deep learning models that depend on the more accurate description of the polar intermolecular interactions.