TABLE 5.

Summary of computed energies of critical atoms on drug molecules in drug-DNA complex structures

			Energies
			Clustering		Local density		Global density
NBD_ID	Drug_ID*	Critical atoms	<5	<10	<5	<10	<5	<10
2:1 Drug-DNA complexes
bdd002	ImHpPyPy I	6	3	5	5	6	5	5
	II	6	4	5	5	5	5	6
bdd003	ImPyPyPy I	5	5	5	5	5	5	5
	II	5	5	5	5	5	5	5
gdj057	ImImPyPy I	6	5	6	6	6	6	6
	II	6	6	6	6	6	6	6
dd0020	ImPyHpPy I	6	5	6	5	6	6	6
	II	6	3	6	4	6	6	6
dd0021	ImPyPyPy I	5	2	5	5	5	4	5
	II	5	4	5	5	5	5	5
gdj054	ImIm I	6	5	6	6	6	5	6
	II	6	5	6	4	6	4	6
gdh060	PyPyPy I	5	4	5	5	5	4	5
(unit 1)	II	5	5	5	5	5	4	5
gdh060	PyPyPy I	5	4	5	5	5	5	5
(unit 2)	II	5	5	5	5	5	3	5
1:1 Drug-DNA complexes
dd0014	PlBiBiBiBz	3	3	3	3	3	3	3
gd1003	PyPyPy	5	4	4	4	5	3	4
gd1004	PyPy	6	4	5	5	6	5	5
gd1008	IdBz	3	2	3	3	3	3	3
gd1018	PyPy	6	5	5	6	6	5	6
gd1030	PyPy	6	5	6	6	6	6	6
gd1033	PlBiBiBz	3	3	3	3	3	3	3
gd1038	ImPy	6	6	6	6	6	6	6
gd1039	PlBiBiBiBz	3	3	3	3	3	3	3
gd1047	PrIpIpBz	3	3	3	3	3	3	3
gd1052	IpIpBz	4	3	3	4	4	3	3
Total		136	111	130	127	135	121	132

^*Drug_ID refers to the chemical name and number of a polyamide ligand according to the nomenclature in Fig. 3; critical atoms to the number of hydrogen-bond forming atoms on the drug; <5 and <10 to the number of critical atoms with calculated average binding scores <5 or 10, i.e., within 3.2 or 4.5 standard deviations of the preferred positions of water molecules on the minor-groove edges of the DNA bases. See legend to Table 1.