It is known that phototoxicity is related to chemical structure. We have previously reported a prediction method of chemical structure-based in silico phototoxicity for in vitro 3T3 NRU-PT assay. To improve the concordance of the method, here we added new descriptors related to another mechanism of phototoxicity. We focused on potential energy, which certainly contributes to chemical reactivity regardless of photo-irradiation. As a result, stretch-bend, a form of potential energy, was found as a new descriptor of phototoxicity. Our analysis strongly indicates that chemical reactivity is an important factor for phototoxic outcome.