Table 4.

Energy ranks, interaction energies, RMSD relative to the native structure, RMSD relative to the coarse grain optimized structures, GCD relative to the native structure and cluster population for the four lowest energy geometries obtained by systematic docking simulations.

complex	energy rank	interaction energy [RT]	RMSD [Å]/native	RMSD [Å]/CG opt.	GCD [Å]/native	cluster population
1K79	1	−38.6	1.3	0.0	0.7	27
	2‡	−36.9	29.1	29.1	5.8	9
	3‡	−36.6	28.7	28.7	2.6	9
	4	−36.2	6.4	6.2	3.9	3
1PAR	1	−74.6	0.6	0.0	0.5	20
	2†	−73.4	43.2	43.2	0.8	14
	3	−54.9	44.2	44.2	9.0	4
	4	−54.4	9.3	9.2	8.8	2
2BOP*	1	−55.4	0.2	0.0	0.1	17
	2†	−55.4	32.5	32.5	0.1	14
	3	−41.0	6.2	6.1	3.4	31
	4	−41.0	32.5	32.5	3.4	45
1A74*	1	−68.7	0.7	0.0	0.4	20
	2†	−68.5	37.5	37.5	0.5	23
	3	−43.6	38.3	38.4	9.6	1
	4	−43.5	37.6	37.6	5.0	1
1YTB	1	−58.5	3.8	3.7	0.4	3
	2	−55.7	0.4	0.0	0.3	3
	3	−51.4	3.5	3.6	2.7	12
	4	−47.6	28.4	28.4	12.9	10
1A66	1	−35.6	1.2	0.0	1.0	21
	2	−31.9	14.7	14.1	10.4	4
	3‡	−30.4	25.5	25.3	6.8	8
	4	−29.9	22.6	22.7	8.4	7

^*The symbol pinpoints complexes with palindromic DNA.

^†The symbol shows head-to-tail configurations and

^‡indicates a screwing along the DNA helical axis.