The PDBbind database is extensively used in the development and benchmarking of molecular modelling tools, such as molecular docking, scoring functions, and other machine learning-based models for drug discovery . The goal of PDBbind is to provide a comprehensive collection of experimentally determined binding affinity data for as many biomolecular complexes as possible deposited in the Protein Data Bank (PDB) . Despite the extensive scope of the PDBbind v.2020 refined set, the preparation of its protein-ligand complexes, especially in terms of their protonation/tautomeric states, which are vital for accurately depicting protein-ligand interactions , can be considerably improved. Consequently, incorrect protonation or tautomeric states in protein-ligand complexes within the PDBbind dataset, depending on the molecular representation employed, can lead to erroneous descriptions of protein-ligand interactions.