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. Author manuscript; available in PMC: 2013 Oct 25.
Published in final edited form as: J Phys Chem B. 2012 Oct 12;116(42):12721–12734. doi: 10.1021/jp309230v

Table 1.

Overview of MD simulationsa

Simulation
label		 Ligand C7 prot.
State		 Time

(µs)		 Force-Field Initial
Structure		 RMSDb

(Å)		 Rgc

(Å)
GCA-Q0del removed C7H+ 3.3 ff99bsc0χOL3 3GCA 2.3 ± 0.4 13.2 ± 0.3
GCA-Q0 preQ0 C7H+ 3.4 ff99bsc0χOL3 3GCA 1.7 ± 0.3 13.3 ± 0.2
GCA-Q1 preQ1 C7H+ 3.1 ff99bsc0χOL3 3GCA 2.1 ± 0.7 13.4 ± 0.3
GCA-Q1+ preQ1+ C7H+ 3.4 ff99bsc0χOL3 3GCA 2.0 ± 0.4 13.3 ± 0.2
Q51-free-1 no C7H+ 3.5 ff99bsc0χOL3 3Q51 2.2 ± 0.3 13.3 ± 0.2
Q51-free-2 no C7H+ 3.5 ff99bsc0χOL3 3Q51 2.4 ± 0.3 13.2 ± 0.2
a

Some additional MD simulations are listed in Table S1 in the Supporting Information.

b

Mean RMSD (mass-weighted) of nucleotides 1–33 (all atoms) calculated with respect to initial (X-ray) structure and over entire trajectory of a given simulation.

c

Mean radius of gyration of nucleotides 1–33 (all atoms) calculated over entire trajectory of a given simulation. The X-ray Rgs of the ligand-bound (PDB ID 3GCA) and ligand-free (PDB ID 3Q51) PQA are equal to 12.9 Å and 13.2 Å, respectively.