Table 3.

C3 model systems and their simulation lengths

Model system	CuA	Heme a	BNC*	His413	Asp51	Glu242	Tyr244	Lys319	Asp364	No. of replica and simulation lengths, ns
C3-I (FR)†	RED	RED	RED	D (0)	D (−1)	P (0)	P (0)	P (+1)	P (0)	1 × 996
										1 × 952
C3-II (FR)‡	RED	RED	RED	D (0)	D (−1)	P (0)	P (0)	P (+1)	P (0)	5 × 30
C3-III (FR)§	RED	RED	RED	D (0)	D (−1)	P (0)	P (0)	P (+1)	P (0)	5 × 15
C3-IV (FR)¶	RED	RED	RED	D (0)	D (−1)	P (0)	P (0)	P (+1)	P (0)	5 × 15

RED, reduced.

^*Reduced BNC structure of Fe[II]……..Cu[I] TyrOH.

^†BNC reduced with Cu_A/heme a reduced.

^‡Simulations started with a fully hydrated lower part of the H channel.

^§Simulations started with a H₃O⁺ modeled below His413.

^¶Simulations started with a H₃O⁺ modeled above His413.