UCSF Chimera was used to deduce bond orders and to add hydrogen atoms to each ligand based on its 3D coordinates. Ligand topologies were manually checked, corrected where necessary, and saved in mol2 format. SwissParam 52 was used to generate the ligand FF topologies and parameters based on the Merck Molecular Force Field. In the new version of the SwissParam, it is possible to parameterize both pre-and post-reactive topologies of a ligand starting from either form.