Table 2.

Occurrence of three-centred hydrogen bonds (%) to DNA for netropsin and distamycin

Netropsin			Distamycin
Three-centred hydrogen bond		Occurrence (%)	Three-centred hydrogen bond		Occurrence (%)
N1–H12→	5Ade N3	5	N1–H12→	5Ade N3	11
	6Ade O4′			6Ade O4′
N2–H22→	5Ade N3	9	N1–H12→	5Ade N3	1
	6Ade O4′			10Cyt* O2
N2–H22→	5Ade N3	1	N2–H22→	5Ade N3	7
	10Cyt* O2			6Ade O4′
N3–H3→	6Ade N3	2	N2–H22→	5Ade N3	1
	7Ade O4′			10Cyt* O2
N3–H3→	6Ade N3	3	N3–H3→	6Ade N3	2
	9Thy* O2			7Ade O4′
N7–H7→	8Ade N3	7	N3–H3→	6Ade N3	6
	7Thy* O2			9Thy* O2
N7–H7→	7Thy* O2	2	N7–H7→	7Thy* O2	3
	8Thy* O4′			8Thy* O4′
N9–H92→	9Ade N3	1	N9–H9→	8Ade N3	2
	10Cyt O4′			9Ade O4′
N10–H102→	6Thy* O2	10	N9–H9→	9Ade O4′	2
	7Thy* O4′			9Ade N3
			N9–H9→	9Ade N3	1
				6Thy* O2

The occurrence of hydrogen bonds larger than 1% is given. Nucleotides in the second strand of the DNA duplex are marked with an asterisk after the nucleotide name and ribose atoms with a prime (′) after the atom name. Three-centred hydrogen bonds are defined for a donor atom D, hydrogen atom H, and two acceptor atoms A1 and A2 if (i) the distances H–A1 and H–A2 are within 0.27 nm; (ii) the angles D–H–A1 and D–H–A2 are >90°; (iii) the sum of the angles D–H–A1, D–H–A2 and A1–H–A2 is at least 340°; and (iv) the dihedral angle defined by the planes through the atoms D–A1–A2 and H–A1–A2 is at most 15°.