# columns: # pair_type saenger paired_bases hydrogen_flag atom_pair [atom_pair ...] # atom_pair = atom1, atom2, bond_length, standard_deviation, slack # # Canonical Watson-Crick base pairings WWT _ A-T + H61,O4,_,_,_ N1,H3,_,_,_ WWT _ A-T - N6,O4,_,_,_ N1,N3,_,_,_ WWT _ DC-DG + H42,O6,_,_,_ N3,H1,_,_,_ O2,H22,_,_,_ WWT _ DA-DT + H61,O4,_,_,_ N1,H3,_,_,_ WWT _ DC-DG - N4,O6,_,_,_ N3,N1,_,_,_ O2,N2,_,_,_ WWT _ DA-DT - N6,O4,_,_,_ N1,N3,_,_,_ #homo purine _ I A-A + H61,N1,_,_,_ N1,H61,_,_,_ # pairing is symmetric, but distances are not (2.92, 3.06) # set target value to the average and balanced with a slack of 0.07 _ I A-A - N6,N1,2.99,0.14,0.07 N1,N6,2.99,0.14,0.07 _ II A-A + H62,N7,_,_,_ N7,H62,_,_,_ # pairing is symmetric, but distances are not (3.01, 2.89) # set target value to the average and balanced with a slack of 0.06 _ II A-A - N6,N7,2.95,0.20,0.06 N7,N6,2.95,0.20,0.06 _ III G-G + H1,O6,_,_,_ O6,H1,_,_,_ # pairing is symmetric, but distances are not (2.85, 2.88) # set target value to the average and balanced with a slack of _ III G-G - N1,O6,2.86,0.12,0.01 O6,N1,2.86,0.12,0.01 _ IV G-G + H21,N3,_,_,_ N3,H21,_,_,_ # pairing is symmetric, but distances are not (2.96, 3.23) # set target value to the average and balanced with a slack of 0.13 _ IV G-G - N2,N3,3.10,0.22,0.13 N3,N2,3.10,0.22,0.13 _ V A-A + H62,N1,_,_,_ N7,H61,_,_,_ _ V A-A - N6,N1,2.93,0.18,_ N7,N6,3.07,0.17,_ _ VI G-G + O6,H1,_,_,_ N7,H22,_,_,_ _ VI G-G - O6,N1,2.88,0.16,_ N7,N2,2.91,0.15,_ _ VII G-G + N7,H1,_,_,_ O6,H22,_,_,_ _ VII G-G - N7,N1,2.93,0.17,_ O6,N2,2.76,0.24,_ #hetero purine _ VIII A-G + H61,O6,_,_,_ N1,H1,_,_,_ _ VIII A-G - N6,O6,2.95,0.21,_ N1,N1,2.88,0.15,_ _ IX A-G + H62,O6,_,_,_ N7,H1,_,_,_ _ IX A-G - N6,O6,2.70,0.08,_ N7,N1,3.08,0.08,_ _ X A-G + H61,N3,_,_,_ N1,H21,_,_,_ _ X A-G - N6,N3,3.15,0.11,_ N1,N2,3.02,0.19,_ _ XI A-G + H62,N3,_,_,_ N7,H21,_,_,_ _ XI A-G - N6,N3,3.23,0.15,_ N7,N2,3.00,0.16,_ #homo pyrimidine _ XII U-U + H3,O4,_,_,_ O4,H3,_,_,_ # pairing is symmetric, but distances are not (2.98, 2.74) # set target value to the average and balanced with a slack of 0.12 _ XII U-U - N3,O4,2.86,0.05,0.12 O4,N3,2.86,0.05,0.12 _ XIII U-U + O2,H3,_,_,_ H3,O2,_,_,_ # pairing is symmetric, but distances are not (2.70, 2.77) # set target value to the average and balanced with a slack of 0.03 _ XIII U-U - O2,N3,2.74,0.05,0.03 N3,O2,2.74,0.05,0.03 _ XIV C-C + N3,H42,_,_,_ H42,N3,_,_,_ # pairing is symmetric, but distances are not (3.34, 2.09) # set target value to the average and balanced with a slack of 0.6 _ XIV C-C - N3,N4,2.72,0.05,0.6 N4,N3,2.72,0.05,0.6 _ XV C-C + O2,H42,_,_,_ H42,O2,_,_,_ _ XV C-C - O2,N4,2.83,0.01,_ N4,O2,3.12,0.07,_ _ XVI U-U + H3,O4,_,_,_ O2,H3,_,_,_ _ XVI U-U - N3,O4,_,_,_ O2,N3,_,_,_ #hetero pyrimidine _ XVII C-U + N3,H3,_,_,_ H42,O2,_,_,_ _ XVII C-U - N3,N3,2.98,0.05,_ N4,O2,2.91,0.07,_ _ XVIII C-U + H42,O4,_,_,_ N3,H3,_,_,_ _ XVIII C-U - N4,O4,3.19,0.07,_ N3,N3,3.16,0.06,_ #purine - pyrimidine WWT XIX C-G + H42,O6,_,_,_ N3,H1,_,_,_ O2,H22,_,_,_ WWT XIX C-G - N4,O6,2.96,0.17,_ N3,N1,2.89,0.11,_ O2,N2,2.77,0.15,_ WWT XX A-U + H61,O4,_,_,_ N1,H3,_,_,_ WWT XX A-U - N6,O4,3.00,0.17,_ N1,N3,2.84,0.12,_ _ XXI A-U + H61,O2,_,_,_ N1,H3,_,_,_ _ XXI A-U - N6,O2,2.94,0.17,_ N1,N3,2.84,0.13,_ _ XXII C-G + O2,H1,_,_,_ N3,H22,_,_,_ _ XXII C-G - O2,N1,2.80,0.17,_ N3,N2,2.86,0.18,_ _ XXIII A-U + H62,O4,_,_,_ N7,H3,_,_,_ _ XXIII A-U - N6,O4,3.05,0.15,_ N7,N3,2.96,0.15,_ _ XXIV A-U + H62,O2,_,_,_ N7,H3,_,_,_ _ XXIV A-U - N6,O2,2.91,0.19,_ N7,N3,2.87,0.13,_ _ XXV A-C + H62,N3,_,_,_ N7,H42,_,_,_ _ XXV A-C - N6,N3,3.13,0.15,_ N7,N4,3.08,0.18,_ _ XXVI A-C + H61,N3,_,_,_ N1,H42,_,_,_ _ XXVI A-C - N6,N3,3.09,0.14,_ N1,N4,3.01,0.08,_ _ XXVII G-U + O6,H3,_,_,_ H1,O4,_,_,_ _ XXVII G-U - O6,N3,2.99,0.15,_ N1,O4,2.99,0.07,_ WWT XXVIII G-U + O6,H3,_,_,_ H1,O2,_,_,_ WWT XXVIII G-U - O6,N3,2.83,0.13,_ N1,O2,2.79,0.13,_