Fig. 2.

A schematic view of the cubic grid C used for deriving the potential for two [P, OP2] pairs. Only one layer of grid cells is represented and for simplicity we consider that all atoms are within this single layer. The potential W⁽ⁿ⁾ is additive for cells <9Å from more than one OP2 atom. (the darker the area, the more negative value of the potential for the given grid cell). MetalionRNA places the center of a predicted cation in the grid cell with the lowest value, calculates the sum of W⁽ⁿ⁾ of cells covered by the cation introduced and removes these cells from further consideration.