(color online) Stability of the intermediate state. (a)–(c) Time series of the distance between the side chain of TN i+2 and the -end of DNA–RNA hybrid (black lines) and that between the residue Y639 and the -end of DNA–RNA hybrid (red lines) in the three trajectories. (d) Time series of the non-bond interaction energy between the base of the template DNA nucleotide and the -end of DNA–RNA hybrid (black line) and the non-bond interaction energy between the -end of DNA–RNA hybrid and residue Y639 (red line).