After the constrained optimization of the remaining sets of indistinguishable atoms (according to the auxiliary assignment problem) and all sets of monovalent atoms, the number N of formed and broken bonds is evaluated for all atom maps in order to perform an unconstrained optimization for the atom maps with the lowest N, i.e. permutations between all atoms of the same element are allowed according to the optimization scheme described above. Subsequently, the squared error of dihedrals [Eq. ( )] is determined for all those atom maps that yield the lowest number of formed and broken bonds to find the atom map with the minimum SE θ , i.e. the final atom map used in the following to construct orbital maps.