Table 3.

The absolute binding free energy and configurational entropy calculations for a set of biotin analogs and HIV1-RT inhibitors.^a

Enzyme/ligand	$\mathrm{\Delta }{G}_{MM/\mathit{PBSA}}^{{\mathit{calc}}^{\prime }}$ (Entropy values not added)	$-T\mathrm{\Delta }{S}_{MM/\mathit{PBSA}}^{\mathit{calc}}$	$-T\mathrm{\Delta }{S}_{RR}^{\mathit{calc}}$	$\mathrm{\Delta }{G}_{MM/\mathit{PBSA}}^{{\mathit{calc}}^{\prime }}-T\mathrm{\Delta }{S}_{MM/\mathit{PBSA}}$	$\mathrm{\Delta }{G}_{MM/\mathit{PBSA}}^{{\mathit{calc}}^{\prime }}-T\mathrm{\Delta }{S}_{RR}$	${}^b\mathrm{\Delta }{G}_{\mathit{bind}}^{\mathit{calc}}$			$\mathrm{\Delta }{G}_{\mathit{bind}}^{\mathit{exp}}$
						PDLD/S- LRA/β	LRA/β	LIE/β
Avidin (biotin binding protein)32						β=0.33	β=0.55	β=0.81
16	−41.97	16.65	8.40	−25.32	−33.57	−14.05	−13.18	−14.03	−14.01
17	−33.53	22.98	7.57	−10.55	−25.96	−14.50	−14.87	−13.71	−14.29
HIV1-RT inhibitors31						β=0.30	β=0.45	β=0.64
18	−27.60	15.64	4.90	−11.96	−22.70	−11.74	−11.79	−11.85	−11.87
19	−26.28	15.83	4.22	−10.45	−22.06	−11.18	−10.49	−11.37	−11.69
20	−27.28	15.68	5.41	−11.60	−21.87	−10.66	−10.48	−10.43	−10.60
21	−27.72	17.61	6.82	−10.11	−20.90	−11.67	−10.66	−10.74	−10.44
22	−25.58	15.88	5.27	−9.70	−20.31	−9.13	−8.62	−7.75	−7.81

^aAll energy values are in kcal/mol.

^bThe $\mathrm{\Delta }{G}_{MM/\mathit{PBSA}}^{{\mathit{calc}}^{\prime }}$ does not include the relevant entropic contributions, whereas the $\mathrm{\Delta }{G}_{\mathit{bind}}^{\mathit{calc}}$ does include entropic contributions. The calculated $-T\mathrm{\Delta }{S}_{RR}^{\mathit{calc}}$ is only for comparison to that calculated in refs³¹,³² using normal mode (NMODE) analysis. The $\mathrm{\Delta }{G}_{MM/\mathit{PBSA}}^{{\mathit{calc}}^{\prime }}-T\mathrm{\Delta }{S}_{MM/\mathit{PBSA}}$ is the total binding free energy calculated by MM/PBSA with entropy calculated by NMODE analysis where as the $\mathrm{\Delta }{G}_{MM/\mathit{PBSA}}^{{\mathit{calc}}^{\prime }}-T\mathrm{\Delta }{S}_{RR}$ is the total binding free energy with entropy calculated by RR method.