Table 5.

Average RMSD Values Calculated during the MD Production Runs^a

ligand	species	run no.	RMSD [Å]
			Cα	ligand	3′Pb	5′Pc/αP	adenine	N-methd
MRS2500	−4	s1	2.428	2.247	2.886	2.871	1.720	1.853
	−4	s2	2.428	1.866	2.047	2.199	1.499	1.870
	−4	s3	2.698	2.696	3.220	3.609	2.082	2.161
	−3a	s1	1.451	1.136	1.920	0.891	0.924	0.622
	−3a	s2	1.569	0.951	1.276	0.776	0.888	0.669
	−3a	s3	1.943	2.992	0.825	1.186	4.390	1.225
	−3b	s1	1.774	1.471	1.824	1.981	1.109	0.782
	−3b	s2	2.294	1.503	1.854	2.000	1.167	0.999
	−3b	s3	1.743	1.965	3.103	2.750	1.131	1.050
	−2	s1	1.566	1.950	2.172	2.111	1.788	1.640
	−2	s2	1.702	1.715	2.314	1.180	1.752	1.275
	−2	s3	1.867	1.887	2.670	1.496	1.974	0.954
MRS2268	−4	s1	1.556	1.239	1.486	1.871	0.800	0.652
	−4	s2	2.018	1.385	1.767	2.025	0.828	0.969
	−4	s3	1.479	1.406	2.073	1.857	0.719	0.990
	−3a	s1e	1.656	1.586	1.824	2.024	1.257	1.216
	−3a	s2e	2.252	1.979	2.873	2.168	1.166	1.848
	−3a	s3e	2.444	1.532	2.38	0.947	1.334	1.209
	−3b	s1	1.909	1.589	1.580	1.930	1.351	1.448
	−3b	s2	1.946	1.135	0.683	2.116	0.794	0.660
	−3b	s3	1.845	1.831	2.205	2.064	1.464	1.553
	−2	s1	2.155	0.938	1.037	0.956	0.920	0.734
	−2	s2	2.063	2.072	2.320	2.880	1.506	1.603
	−2	s3	1.980	1.148	1.381	1.268	0.916	0.959
2MeSADP	−3	s1	1.593	1.247	2.019	1.242	0.889	1.108
	−3	s2	1.575	2.098	2.415	3.619	1.200	1.803
	−3	s3	1.789	1.626	2.161	1.721	1.498	1.295
BPTU	NA	s1e	2.323	1.835
	NA	s2e	3.036	2.197
	NA	s3e	2.355	1.825
	NA	s4e	2.522	1.743
apo	NA	s1	1.905
	NA	s2	1.855
	NA	s3	1.811

^aThe trajectories were aligned on protein Cα, and the first frame coordinates were taken as reference. Selected trajectories for video visualization and detailed visual inspection are highlighted in bold. The simulations were run for 200 ns unless otherwise specified.

^b3′-Phosphate group in MRS2500 and MRS2268 and β-phosphate group in 2MeSADP.

^c5′-Phosphate group in MRS2500 and MRS2268 and α-phosphate group in 2MeSADP.

^d(N)- Methanocarba ring in MRS2500 and MRS2268 and ribose ring in 2MeSADP.

^eSimulation length: 400 ns.