Table 1.

Summary table of equilibrium simulations performed

SystemEquilibrationProduction
NavAb expanded α-model (PDB ID 5VB8) 30 ns 185 ns (unrestrained) 
NavAb expanded α-model I217C (PDB ID 5VB8) 30 ns 250 ns (Cα restrained) 
Expanded π-model 30 ns 154 ns (unrestrained) 
NavAb expanded α-model (PDB ID 5VB8) 30 ns 200 ns (Cα restrained) 
NavAb expanded α-model (+750 mV) 30 ns 200 ns (Cα restrained) 
NavAb expanded α-model (−750 mV) 30 ns 200 ns (Cα restrained) 
NavAb expanded π-model (PDB ID 5VB8) 30 ns 200 ns (Cα restrained) 
NavAb expanded π-model (PDB ID 5VB8) 30 ns 154 ns (unrestrained) 
NavAb expanded α-model + lidocaine 30 ns 200 ns (Cα restrained) 
NavAb asymmetric α model + lidocaine 30 ns 200 ns (unrestrained) 
NavAb resting α model + lidocaine 30 ns 200 ns (unrestrained) 
NavAb expanded π-model + lidocaine 30 ns 200 ns (Cα restrained) 
NavAb expanded π-model N1211L 30 ns 200 ns (Cα restrained) 
NavAb contracted α-model (PDB ID 5VB2) with CTD—300 K—Charmm36m 36 ns 200 ns (unrestrained) 
NavAb contracted α-model (PDB ID 5VB2) with CTD—320 K—Charmm36m 36 ns 308 ns (unrestrained) 
NavAb contracted α-model (PDB ID 5VB2) with CTD—360 K—Charmm36m 36 ns 309 ns (unrestrained) 
NavAb contracted α-model (PDB ID 5VB2) with CTD—400 K—Charmm36m 36 ns 215 ns, 223 ns, 232 ns (unrestrained) 
NavAb contracted π-model (PDB ID 5VB2) with CTD 36 ns 200 ns (unrestrained) 
NavAb contracted π-model (PDB ID 5VB2 WT) without CTD 36 ns Equilibrated structure used for ABMD simulation × 3 
NavAb contracted α-model (PDB ID 5VB2) without CTD 36 ns Equilibrated structure used for ABMD simulation × 3 
NavAb contracted α-model (PDB ID 5VB2 N1211L) without CTD 36 ns Equilibrated structure used for ABMD simulation × 3 

Restrained production simulations (where indicated) were used to prevent pore collapse in the absence of CTD. Ion permeation and drug permeation free energy calculations.

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