Simulation report

Technical information

General information

Name: Lysophosphatidic acid receptor 1 in complex with ono9780307

PDB id: 4Z34.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 (159 mM), Chloride (191 mM)

Number of molecules:

Water: 17482

POPC: 175

Chloride: 60

Sodium ion: 50

ONO9780307: 1

Lysophosphatidic acid receptor 1: 1

Total number of atoms: 81088

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: 1.5 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

Ligands

Orthosteric ligand(s)

Ono9780307

(1 molecule)


Receptor

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Mutations

No mutations found



Other molecules



Sodium ion

Specific State ID: 5016

(50 molecules)

Na+


Chloride

Specific State ID: 5017

(60 molecules)

Cl-


POPC

Specific State ID: 5018

(175 molecules)


Water

Specific State ID: 5019

(17482 molecules)

H2O


ONO9780307 (orthosteric lig.)

Specific State ID: 5112

(1 molecule)