The first step in the protocol performs the validation of the chosen molecules. This step checks that the OpenFF Toolkit can sufficiently interpret each molecule, and for molecules that it can, a unique identifier is then assigned to each. Conformers are aligned during this step, and if a subsequently-loaded conformer has an RMSD of less than 0.5 Å from an existing conformer, it will be discarded as a duplicate. In the Public OpenFF Industry Dataset 85 out of 10,226 initial molecules were filtered by validation, hence 10,141 successfully passed this step.