Table 2. RMSD (Å) values and cluster population percentages in the absence of electrostatic interactions.

The electrostatic interactions in the force field are removed, and we perform simulations with conformational constraints similar to those in Table 1. Heavy atom RMSD values are given on the first line of each row, and population sizes in terms of percentage are given on the second line, for each protein-peptide complex. We report data for only the largest two clusters. The number of clusters is dependent upon the cluster population distribution; we report the clusters having a significant number of samples (see Table S2). The bolded values are the conformations having RMSD lower than 10 Å.

PDB ID	Fixed receptor		Flexible side-chain		Flexible receptor
	1st cluster	2nd cluster	1st cluster	2nd cluster	1st cluster	2nd cluster
1BFE	12.34	18.12	1.51		6.40	2.96
	29.4%	5.4%	70.2%	--	9.0%	6.7%
1DDW	5.74	9.74	6.25	6.25	7.51	25.76
	26.8%	21.8%	34.1%	18.5%	26.9%	13.2%
1CL5	11.66	21.99	11.25	6.80	7.84	6.40
	24.2%	12.1%	11.9%	11.1%	20%	7.6%
2HPJ	25.51	25.75	18.51	4.70	17.08	24.31
	23.3%	13.7%	25.5%	16.9%	17.7%	9.3%
1X2J	10.72	34.01	9.73	39.93	7.41	39.37
	30.5%	17.1%	19.3%	14.4%	16.9%	11.2%
1SRL	15.59	9.78	20.85	20.96	14.86	19.76
	14.1%	10.3%	6.7%	4.8%	3.6%	3.4%
2ID8	6.69	24.34	9.93	21.24	10.28
	31.7%	18.8%	20.2%	5.2%	72.3%	--
2ZGC	31.18	19.80	33.79	22.25	37.31	24.55
	8.7%	7.3%	35.8%	3.7%	8.9%	4.0%