Figure 5.

A representative top stacking trajectory of the parallel G-quadruplex. (Top) Representative structures with time annotation. 5′ and 3′ are indicated by a red and blue ball, respectively. K⁺ ions are represented in yellow. (Bottom) An order parameter plot depicting number of hydrogen bonds present in first G4 (green), second G4 (red) and third G4 (blue) tetrads of the DNA structure (Figure 2), the drug-base dihedral angle, receptor (red) and ligand (black) RMSD relative to the original crystal pose, center-to-center distance (R/black) and K⁺-K⁺ distance (R/red) and MM-GBSA binding energy (ΔG) (cf. methods section for definition).