To isolate the influence resulting from the presence of N in the molecule, we directly compared molecules containing the same atom types but with and without N (Figure ). Median scores and ion match rates are lower for every group of molecules, except for those contain- Similarly, the presence of P negatively influences prediction accuracy using our chosen methodology (Figure ). P often serves as a central atom, resulting in a more flexible structure. Within our dataset, P containing molecules have an average number of rotatable bonds of 8.4 over 2.9 for all other molecules respectively. This is further supported by the negative correlation of the rotatable bond count and cosine similarity and number of matching ions (Figure ).