B3LYP/6-31G(d,p) optimized geometries of base:base (B:B) type of base:ligand interactions that resemble the cis Watson Crick–Hoogsteen (cWH), trans Watson Crick–Hoogsteen (tWH), cis Hoogsteen–Sugar (cHS), cis Watson Crick–Sugar (cWS) or cis Sugar–Watson Crick (cSW) RNA base pairs. Structure number (#), base:ligand interaction identity, and base pair type (cWH, tWH, cHS, cWS or cSW) are provided against each structure for identification from tables. Base-pairing interaction code and PDB code of the crystal structure used for optimization, as well as the MP2/aug-cc-pVDZ interaction energy (kcal/mol) are provided for each structure in parentheses. Hydrogen bonding donor–acceptor (D–A) distance (Å), acceptor–hydrogen (A–H) distance (Å), and D–H–A (deg) are provided for each hydrogen bond (dotted lines) in Supplemental Tables S4–S8. For structures #47 and #56, only the positions of hydrogen atoms were optimized, whereas full optimization was carried out for all other structures. Structures #43, #44, #49, and #57 contain positively charged ligand moieties.
