Table 4.

Comparison of AutoDock-Vina poses of O₂N-[HoPhe]-Ala-COOH obtained by XPLOR-NIH minimization with PRE-derived distance constraints ^*

2R5D	Ligand fixeda				Ligand allowed to moveb
pose	RMSD PRE / s−1	PRE Q factor†	RMSD Dist. / Å c	Ligand positional RMSD d	RMSD PRE / s−1	PRE Q factor†	RMSD Dist. / Å c	Ligand positional RMSD d
1	11.78	0.27	1.174	0.379	2.63	0.058	0.139	1.01
2	11.91	0.26	1.414	0.424	3.44	0.077	0.151	1.764
3	27.23	0.61	4.431	0.506	16.51	0.37	2.198	3.899
4	23.16	0.52	3.558	0.956	12.65	0.28	1.428	2.31
5	21.44	0.48	3.259	1.434	17.38	0.39	2.545	1.315
6	12.36	0.28	0.843	0.408	3.31	0.043	0.102	1.798
7	16.11	0.36	1.535	1.181	1.93	0.020	0.036	2.351
8	24.75	0.56	3.924	0.745	22.32	0.50	2.969	2.491
9	19.06	0.42	3.06	0.837	1.73	0.035	0.073	1.923
3P7K	Fixeda				Movedb
1	20.57	0.46	2.714	0.301	3.47	0.056	0.139	1.657
2	10.41	0.23	1.209	0.565	3.07	0.068	0.181	1.855
3	17.98	0.41	2.235	1.435	11.91	0.27	1.706	1.415
4	10.53	0.24	0.817	0.49	4.49	0.042	0.116	0.946
5	21.26	0.48	2.324	1.278	13.80	0.31	1.253	2.737
6	28.84	0.65	4.515	1.718	26.91	0.61	4.301	1.71
7	16.75	0.38	2.266	0.628	16.47	0.37	2.117	0.84
8	25.49	0.57	3.77	2.033	12.81	0.29	1.282	2.702
9	20.96	0.47	2.914	0.699	18.74	0.42	2.418	0.626

^*Experimental error range included in calculation of RMSD and Q factors; low values are shaded in gray; PRE Q factor measures the agreement between observed and calculated PRE according to the equation [Σ_i = [PRE_obs(i)- PRE_calc(i)]²/[Σ _iPRE_obs(i)²]^½.

^aXPLOR-optimized ligand position fixed during PRE-derived distance - constrained minimization, protein side chains and MTSL allowed to move;

^bLigand allowed to move during PRE-derived distance - constrained minimization, weak harmonic constraints (scaling factor 0.2 – 0.8) applied to protein side chains, MTSL side chain unconstrained;

^cPRE-derived distances calculated at τ_c=12ns;

^dCompared to original docked structure, all heavy atom RMSD, in Å