Simulation report

Technical information

General information

Name: Delta opioid with naltrindole

PDB id: 4N6H

Activation state: Inactive

Description: Classical unbiased (NVT ensemble) complex flexibility assay.

Submitted by: GPCR drug discovery group (Pompeu Fabra University)

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Sodium ion (129 mM), Chloride (195 mM)

Number of molecules:

Water: 13363

POPC: 160

Chloride: 47

Sodium ion: 31

Naltrindole: 1

Delta-type opioid receptor: 1

Total number of atoms: 66513

Simulation details

Software and version: ACEMD, 3203

Forcefield and version: CHARMM, 36

Time step : 4.0 fs

Delta : 4.0 ns

Replicates: 1

Accumulated simulation time: 6.144 µs



Simulation components

Ligands

Orthosteric ligand(s)

Naltrindole

(1 molecule)


Experimental Data:
Ki: 0.199 nM More details

Receptor

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Open with GPCRmd Workbench

Mutations

Table of simulated mutations

(Mutations shown in blue at the viewer)

Residue Generic num. From To
37 - P S


Other molecules



Sodium ion

Specific State ID: 5016

(31 molecules)

Na+


Chloride

Specific State ID: 5017

(47 molecules)

Cl-


POPC

Specific State ID: 5018

(160 molecules)


Water

Specific State ID: 5019

(13363 molecules)

H2O


Naltrindole (orthosteric lig.)

Specific State ID: 5020

(1 molecule)