Since the Stk core library does not consider the chemical validity of the generated structures and relies on the external library Stko for structure optimization Stko, we compared BuildAMol's outputs to both the raw and optimized structures from Stk or Stk+Stko. In each case we optimized Stk-raw structures using Stko's UFF Force Field implementation. In most cases Stk+Stko structure outputs were on par with those of BuildAMol. In case of the metal complex (3) the Nitrogen atoms were properly aligned but at the cost of bond distortions in the ligands. In the case of the rotaxane (5), after optimization with Stko, the axle molecule's distorted bonds were fixed, but the cycles were colliding with the main axle.