Simulation report

Technical information

General information

Name: Nociceptin receptor in complex with 1-benzyl-n-[3-(1'h,3h-spiro[2-benzofuran-1,4'-piperidin]-1'-y...

PDB id: 4EA3.A

Activation state: Inactive

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

Submitted by: GPCRmd community

System setup

Solvent type: TIP3P

Membrane type: Homogeneous

Membrane composition: POPC

Ionic composition: Sodium ion (163 mM), Chloride (194 mM)

Number of molecules:

Water: 13997

POPC: 152

Chloride: 49

Sodium ion: 41

1-benzyl-n-[3-(1'h,3h-spiro[2-benzofuran-1,4'-piperidin]-1'-yl)propyl]-d-prolinamide: 1

Nociceptin receptor: 1

Total number of atoms: 67103

Simulation details

Software and version: ACEMD, GPUGRID

Forcefield and version: CHARMM, 36m Feb 2016

Time step : 4.0 fs

Delta : 0.2 ns

Replicates: 3

Accumulated simulation time: 1.45 µs

Additonal parameters: Available at "Simulation protocol & starting files"



References

Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, et al.. 2020. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature methods 17 (8). doi: 10.1038/s41592-020-0884-y. (http://doi.org/10.1038/s41592-020-0884-y)


Simulation components

Receptor

PDB id: 4EA3.A
Nociceptin receptor

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Open with GPCRmd Workbench

Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(41 molecules)

Na+


Chloride

Specific State ID: 5017

(49 molecules)

Cl-


POPC

Specific State ID: 5018

(152 molecules)


1-benzyl-n-[3-(1'h,3h-spiro[2-benzofuran-1,4'-piperidin]-1'-yl)propyl]-d-prolinamide (orthosteric lig.)

Specific State ID: 5051

(1 molecule)


Water

Specific State ID: 5019

(13997 molecules)

H2O