We developed heuristics for automatically picking suitable atoms for Boresch-style restraints. The orientational restraints used here restrain 3 atoms in the protein and 3 atoms in the ligand through 1 distance, 2 angle, and 3 dihedral restraints. Although the binding free energy should be independent of the atom selection, the selection can impact convergence and (numerical) stability of the simulations. Therefore, we implemented a tool that selects suitable atoms for the restraints.