(a.iii) Mapping of the template onto the metal site: Achieving the correct atom order involves an exhaustive exploration of all possible permutations of ligand and atom numbering, the most time-consuming part of the process. For efficiency, the process is divided into two stages. Firstly, the order of all non-hydrogen atoms is determined by exhaustively exploring permutations of the reduced metal site and selecting the one with the lowest root mean square displacement (RMSD) with the template with reordered atoms (Figure ). Subsequently, hydrogen atoms are reconstructed by finding an isomorphism between the template's and the metal site's linkers graphs, constraining the order of heavy atoms. Successful mapping is defined as RMSD < 2Å. If RMSD > 2 Å, the next template from the library is evaluated; if unavailable, the procedure for parametrizing new template is followed (Figure ). (a.iv) Adjusting input topology: If the steps above are successful, the structure's topology is updated by substituting its bonded parameters with those from the reordered template. This topology is further updated by adding residual partial charges from the template, which account for charge transfer effects (Figure ; for comparison with RESP charges see Figure ). These partial charges are obtained from the differences in charges between the complex and separate species (vide infra, Figure ). Since the sum of residual charges of the template is zero, the result of its addition to the new topology only results in the redistribution of partial charges.