For rs3DDPDs, coordinate statistics and partial charges per atom were collected for each target and standardized between 0 and 1. Subsequently, dimensionality reduction was applied in the form of PCA. A number of PCs for each atom were selected and grouped per residue as average and SD. A second dimensionality reduction step was applied on residue data and the selected PCs were placed in their matching sections corresponding to a MSA of the targets of interest.