Table 1.

Summary of simulation systems

System	Protonation state of E210	Occupied Cl− sites	Initial protein structure	Simulation length (ns)	External potential Kcal/(mol Å e)
1 (APBP)	Protonated A B	Sext and Sint	X-ray	100	After 80 ns, −0.1
2 (AdBd)	Deprotonated A B	Sext and Sint	X-ray	100	After 80 ns, −0.1
3	Deprotonated A B	Scen	84 ns of ApBp	8	−0.1
4	AdBp∗	Sext and Sint	80 ns of ApBp	50	−0.1
5	AdBp∗	Scen and Sext	Snapshot from 4‡	20	−0.1
6	AdBp∗	Sint Scen and Sext	Snapshot from 4‡	40	−0.1
7	Deprotonated A B	Scen	Snapshot from 5	40	−0.1
8	Deprotonated A B	Scen	Snapshot from 5	30	−0.1
Y265A	Deprotonated A B	Sext and Sint	X-ray	14 ns	0.0

^∗Deprotonated E210 in subunit A and protonated E210 in subunit B.

^‡Cl⁻ ion at S_ext was docked manually.