Table 1.

Binding free energy (kcal/mol), obtained by MM-PBSA method, for Hoechst 34580 and Hoechst 33342 using the AMBER-f99SB-ILDN force field

Receptor	Complex	$\mathrm{\Delta }{\text{G}}_{\text{elec}}$	$\mathrm{\Delta }{\text{G}}_{\text{vdW}}$	$\mathrm{\Delta }{\text{G}}_{\text{PB}}$	$\mathrm{\Delta }{\text{G}}_{\text{sur}}$	$\text{T}\mathrm{\Delta }\text{S}$	$\mathrm{\Delta }{\text{G}}_{\text{bind}}$
2LMN	Hoechst 34580	−14.94	−61.94	31.56	−7.47	−25.87	−26.93 ± 1.89
	Hoechst 33342	−8.28	−58.66	32.47	−5.60	−23.30	−16.77 ± 2.43
2M4J	Hoechst 34580	−10.66	−41.19	23.26	−4.56	−23.07	−10.07 ± 6.24
	Hoechst 33342	−8.00	−36.33	14.19	−5.76	−21.81	−14.08 ± 2.27
2BEG	Hoechst 34580	−3.89	−49.78	15.51	−7.11	−21.61	−23.66 ± 4.47
	Hoechst 33342	−10.92	−51.31	22.68	−5.43	−22.91	−22.08 ± 5.73
2MXU	Hoechst 34580	−4.65	−65.32	29.06	−5.89	−23.21	−23.59 ± 1.12
	Hoechst 33342	−4.51	−52.23	21.43	−8.38	−23.11	−20.57 ± 4.37

Results were averaged over 4 MD trajectories