. Author manuscript; available in PMC: 2019 May 31.

Published in final edited form as: J Phys Chem B. 2017 Dec 26;122(21):5336–5346. doi: 10.1021/acs.jpcb.7b10340

Table 1.

Summary of Simulated Systems and Events and Corresponding Outputs

run #	method	duration (ns)	initial conformation	initially bound substrate/ions	transition	output
1	aMD	200	OFo	2 Na⁺, 1 Cl⁻, and no DA binding	OFo → OFc/IFc	energy landscape Figure 6
2		200
3^a	aMD	450	OFo	2 Na⁺, 1 Cl⁻, 1 DA ~15 Å away from site S1	OFo/OFo* → OFc* → occluded* → IFo*	transport events in Figure 5
4^a		400	OFo*	2 Na⁺/1 Cl⁻/1 DA
5	aMD	200	IFo* D79 protonated	1 Na⁺/1 DA	IFo* → IFo
6	aMD	200	IFo D79 protonated	none	fluctuating near IFo	energy landscape Figure 6
7		200			IFo → IFc/OFc
8	aMD	200	IFo D79 deprotonated		fluctuating near IFo
9		200			fluctuating near IFo
10–12	FEP	2–10	OFo*	2 Na⁺/1 Cl⁻/1 DA	bound/unbound	EC DA-binding affinity Figure 2
13–15	FEP	2–10	OFc*	2 Na⁺/1 Cl⁻/1 DA
16–18	FEP	2–10	IFo₃*	2 Na⁺/1 Cl⁻/1 DA		IC DA binding with different ion occupancy Figure 3
19–21	FEP	2–10	IFo₁*	1 Na⁺/1 DA
22–23	FEP	2–10	IFo₀*	1 DA
24	ABF	100	IFo₁*	1 Na⁺/1 DA	IFo* → IFo	IC DA release Figure 4

Trajectory generated in earlier work,³⁷ used here for generating the outputs listed in the same column.