Table 2.

Absolute binding free energies of the quindoline at the two binding sites from computation and experiment. (in kcal/mol.)

Binding Site	$\mathrm{\Delta }{\mathrm{G}}_{\mathit{bind}}^{°}$ PMF approach	$\mathrm{\Delta }{\mathrm{G}}_{\mathit{bind}}^{°}$ DDM, no-ligand-intramoleculara	$\mathrm{\Delta }{\mathrm{G}}_{\mathit{bind}}^{°}$ DDM, with-ligand-intramolecularb	$\mathrm{\Delta }{\mathrm{G}}_{\mathit{bind}}^{°}$ Experimentc
5′-end	−8.8 (±0.6)	−11.2 (±1.3)	−12.4 (±1.7)	−8.94
3′-end	−7.7 (±0.7)	−9.6 (±0.6)	−7.5 (±0.3)

^aThe intramolecular nonbonded interactions in the decoupled ligand are turned off.

^bThe intramolecular interactions in the decoupled state of the ligand are left unchanged.

^cDerived from SPR.