A dataset of 1843 molecules were extracted from 1000 crystal structures provided by the Cambridge Crystallographic Data Centre (CCDC). These molecules were extracted using the CCDC Python API. For each molecule, the atomic transition charge (ATC) for each atom was computed using density functional theory as described below. Our final data set therefore consisted of 99,784 atoms, each of which was assigned a label according to the molecule where it came from, as well as its calculated ATC value.