An additional source of error introduced by the QM/MM PHVA is the structural differences, which we quantified by calculating the root-mean-square deviations (RMSD) of nuclear positions. Although larger RMSDs could be observed for two of the systems, which most likely contributed substantially to the overall errors of these systems, they were not necessarily the most critical factor since the systems with low RMSDs had higher errors than the ones with high RMSDs. The angular deviations revealed that many normal modes from the QM/MM Hessians were dissimilar in direction compared to the normal modes from the partial QM Hessians, potentially due to the aforementioned difference in geometries. Nonetheless, we