Package name: 1,2,3,4,7,8-hexachlorooxanthrene

Package ID: 123
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:03:21
Modified at 2016-09-03 23:03:21

Abstract

The topology was generated using MOL2FF v0.111, with user-defined charges. These charges were obtained using the protocol P3 from Beckstein et al. (J Comput Aided Mol Des, 2012, 26, 635-645): geometry optimization and CHelpG charges calculation using Gaussian03 (http://www.gaussian.com) at the HF/6-31G* level, then a two-stage RESP fitting using AmberTools (http://ambermd.org).

Chemical structure
General view

 Detailed view

References
Authors: Beckstein O, Iorga BI
Title: Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field.
Journal: J Comput Aided Mol Des
Year: 2012 May
Volume: 26
Pages: 635-45
DOI: 10.1007/s10822-011-9527-9
Pubmed ID:   22187140
Comments:

Reference validation values

These are experimental values or high-level quantum mechanics values, which will be used for comparison with computed values (found in individual versions).

Files and history

All deposited versions are available and can be downloaded individually. Higher version numbers are more recent. Files that changed between versions can be identified by differing SHA1 hash checksums.

Version 1 created at 2016-09-03

Score 1/5 "These parameters are not validated yet"

Computed validation values

grompp
preprocessor output "grompp-compatible"
Created at 2016-09-03 23:03:21 | Modified at 2016-09-03 23:03:21 | [download zip]
Type Description Hash (SHA1)
Topology xfer3-335_3.itp 0df14fbe45c6d9c7bfcc8f05f3dece04de64dff5
Structure xfer3-335_3.pdb 7c17588daa08943a9c6ad4b26f2564d532713515

Compound details
Ligand code UNL
Molecule identifier 54812EBF25F1FDF1
Displayed name 1,2,3,4,7,8-hexachlorooxanthrene
Canonical IUPAC name 1,2,3,4,7,8-hexakis(chloranyl)dibenzo-p-dioxin
Formula C12H2Cl6O2
Molecular weight 390.86
Charge 0
Number of atoms 22
SMILES C3(=CC2=C(OC1=C(C(=C(C(=C1O2)Cl)Cl)Cl)Cl)C=C3Cl)Cl
PubChem CID 38251
CAS RN 39227-28-6
Other names 1,2,3,4,7,8-hexachlorooxanthrene • 39227-28-6 • 1,2,3,4,7,8-HCDD • 1,2,3,4,7,8-Hexachloro-dibenzo[b,e][1,4]dioxin • Dibenzo-p-dioxin, hexachloro- • HEXACHLORODIBENZO-P-DIOXIN • AIDS-105038 • 1,2,3,4,7,8-HEXACHLORODIBENZO-P-DIOXIN • 1,2,3,4,7,8-Hexachlorodibenzo(b,e)(1,4)dioxin • 1,2,3,4,7,8-Hexachlorodibenzo-p-dioxin [Dioxin and dioxin-like compounds] • 1,2,3,4,7,8-Hexachlorodibenzodioxin • D 66 • Dibenzo(b,e)(1,4)dioxin, 1,2,3,4,7,8-hexachloro- • Dibenzo-p-dioxin, 1,2,3,4,7,8-hexachloro- • AIDS105038

License
Type CC BY-SA – Creative Commons Attribution-Share Alike License
Name Bogdan I. Iorga
Email (hidden)
Source MOL2FF (http://mol2ff.icsn.cnrs-gif.fr)

Ligandbook is described in

Jan Domański, Oliver Beckstein, Bogdan I. Iorga; Ligandbook: an online repository for small and drug-like molecule force field parameters, Bioinformatics, Volume 33, Issue 11, 1 June 2017, Pages 1747–1749, https://doi.org/10.1093/bioinformatics/btx037

Actions
Documentation
Support

"Can I have everything louder than everything else?" (Deep Purple)