The XYZ_Gen.py script uses SMILES.txt to determine the substituents assigned to each tetrazine. Additionally, it uses SMILES_fragments.txt to obtain information about the charge of the substituents and whether a conformational search is required. For simple substituents like phenyl or iodine, a conformational search is not necessary. However, if a substituent requires a conformational search, the script will note this down. Details concerning the charge and the conformational search are annotated as comments in the resulting XYZ file, providing the settings for run.py directly in the geometry file.