The MD simulations were analyzed using the CPPTRAJ 60 suite of AMBER. These analyses include RMSD, RMSF, dynamic cross-correlation and NMA. Various python and R libraries were used to organize and analyze the raw data, as well as tools such as Gnuplot and Matplotlib were used to visualize the data. AMBER-EDA (Energy Decomposition Analysis) was carried out to determine the stabilizing/destabilizing effects of residues on the active site based on non-bonded (Coulomb and van der Waals) interactions using Amber-EDA . K-means clustering analysis was carried out on all the 1,50,000 trajectories of the two systems, with the O3'-P distance and O3'-P-O3 angle as the two dimensions. Distances less than 3.2 Å and angles greater than 160° were considered to be catalytically viable, and 5 representatives were chosen from each of the systems for further QM/MM calculations. Multi-sequence alignment (MSA) was performed using consurf .