The QMrebind method involves several steps to calculate the charges of the ligand at its binding site (see QMrebind protocol). Initially, a protein data bank (PDB) file of the receptor-ligand complex and its topology file are provided as inputs to the QMrebind software. The user defines a distance cut-off value, which delineates a region of receptor atoms encompassing the ligand within the cut-off distance, typically including only the residues in the binding site. Once the binding site is identified, the ligand is defined as the high-level QM region of the ONIOM method.