The PubChemQC PM6 dataset consists of optimized molecular geometries and electronic properties calculated by the PM6 method for 94.0% of the 91.6 million molecules cataloged in PubChem Compounds retrieved on August 29, 2016. In addition to neutral states, the cationic, anionic, and spin flipped electronic states of respectively 56.2%, 49.7%, and 41.3% of the molecules have also been studied. As such, the grand total of the PM6 calculations amounted to 221 million.