. 2019 Apr 22;20(8):1970. doi: 10.3390/ijms20081970

Table 3.

Clustering of the multiple walker metadynamics trajectories around the free energy minima. The table contains the percentages of those frames within 3 Å around the minima, for which the calculated clusters are representative, and the RMSD values of the cluster structures compared to the reference binding modes. The RMSD values refer to heavy atoms and were calculated both for the ligand and for the residues of the orthosteric binding site, i.e., the residues which are located within 5 Å of the ligand in the reference structure.

System	Cluster Number	Percentage of Frames	RMSD Compared to Reference [Å]
System	Cluster Number	Percentage of Frames	Ligand	Receptor Binding Pocket
H₁R + histamine	1	91.7	1.35	1.78
	2	5.3	5.29	1.81
	3	2.3	3.46	1.75
	4	0.6	5.39	1.92
	5	0.2	8.33	1.77
$β_{2}$ AR + adrenaline	1	74.0	0.42	0.40
	2	21.0	1.96	0.48
	3	4.6	3.06	0.62
	4	0.4	4.38	0.72
	5	0.1	3.75	0.57
$β_{2}$ AR + alprenolol	1	69.1	0.99	0.70
	2	20.6	2.43	0.61
	3	8.5	3.40	0.70
	4	1.7	3.43	0.48
	5	0.1	8.20	0.61