Table 1.

Analysis of the channel state in the deprotonated and protonated trajectories. Data was obtained and analyzed in MOLE 2.0 and assigned to specific channels using Wade's nomenclature. The centroid structures of the top five clusters of both trajectories from GROMOS++ clustering (see methods) are reported along with similar analysis of the 3EQM crystal structure in the Protein Databank. The channel widths are reported for each channel in the result (some channels have multiple openings detected by the algorithm).

	S Channel	Channel 5	2d Channel	Channel 1
Crystal Structure	1.57 Å, 0.37 Å	0.87 Å	Closed	Closed
Deprotonated Cluster 1 (67%)	1.94 Å, 0.89 Å	0.46 Å, 1.10 Å	0.86 Å, 0.86 Å	Closed
Deprotonated Cluster 2 (11%)	1.94 Å, 0.89 Å	Closed	0.89 Å, 0.89 Å	Closed
Deprotonated Cluster 3 (6%)	1.36 Å	Closed	0.97 Å, 1.28 Å	Closed
Deprotonated Cluster 4 (4%)	1.03 Å	0.97 Å, 0.95 Å, 0.95 Å	Closed	Closed
Deprotonated Cluster 5 (4%)	1.22 Å, 1.40 Å	1.04 Å	Closed	Closed
Protonated Cluster 1 (61%)	Closed	1.48 Å	Closed	Closed
Protonated Cluster 2 (14%)	Closed	1.37 Å	Closed	Closed
Protonated Cluster 3 (10%)	0.57 Å, 0.57 Å	0.84 Å, 0.84 Å, 0.84 Å	Closed	Closed
Protonated Cluster 4 (6%)	Closed	1.19 Å	1.00 Å	Closed
Protonated Cluster 5 (4%)	Closed	0.83 Å, 0.78 Å	0.90 Å	0.70 Å