FIG. 3.

The detailed parameters specifying the conformation of the sugar-phosphate backbone in the model complex. (Top) From left to right are a stick image with selected non-hydrogen atoms labeled, an all-atom molecular graphic, and a stick image with the dihedral angles and pseudorotation phase angles labeled. In the all-atom molecular graphic, oxygen is colored red, phosphorus orange, carbon beige, and nitrogen blue, with hydrogens not shown for clarity. (Bottom) Displayed is the chosen positive sign convention for the dihedral angle ϕ between four atoms A-B-C-D, defined to be the angle between the planes formed by A-B-C and by B-C-D, with the angle taken to be zero when the atoms are in a planar, cis conformation.