We subjected the 90783 filtered molecules of the 10 starting molecule recombinant set to the ETGK algorithm. In this set, 89880 molecular graphs (99.0%) were successfully embedded, while 1.0% showed at least one violation. Among the 903 embedding errors, the most common issue is that planar arrangements of atoms (e.g. in aromatic systems) cannot be achieved in the minimization step of the embedding. In about a third of the non-embeddable molecules the method was unable to find an initial embedding. More details on the types of embedding violations can be found in Additional file 3.