FIG. 4.
Displayed is a schematic of the six variables necessary to represent the configuration of a guanidinium cation with respect to a phosphate group. Coordinates are chosen so that phosphorus lies at the origin, OP1 and OP2 lie in the y–z plane at equal and opposite values of y, and O5′ lies in the x–z plane, with positive x and negative z. With this choice of coordinate frame, the translational parameters of the guanidinium are specified by the vector describing the displacement of the guanidinium carbon C from the phosphorus atom P. The position of this carbon is then taken to be the origin of a new set of coordinates x′, y′, and z′. These coordinates are defined such that the non-end-group nitrogen N lies on the positive z′-axis, the x′-axis is set by the cross product of the x- and z′-axes, and the y′-axis is set by the cross product of the z′- and x′-axes. With this set of coordinates, the rotational degrees of freedom are given by the Euler angles θ and ϕ that the z′-axis makes with respect to the z-axis, and the angle ω that the NH1-NH2 vector makes with the x′-axis. Images created with Pymol.