hannahbaumann
commented
1 year ago Compared both isomers with the structures deposited in the PLB from Hahn et al as well as with the structures in the structures deposited by Schrodinger (https://github.com/schrodinger/public_binding_free_energy_benchmark/tree/main/fep_benchmark_inputs/structure_inputs/merck). Kept the same isomer as was used in the other two sets. commit f7cf58eba0d86fd5d7e98a96825b323f5911b0a6
ligand lig_CHEMBL1084935 has a charged tertiary amine and therefore also a "stereocenter". Both "stereo isomers" are deposited . Both have the same name which makes it difficult to separate them from each other in e.g. a ligand network. Here the question I have is whether to always include both in the calculations, or whether it makes sense to run a transformation between them, figure out which is the more favorable one and only include that one in future benchmark studies.