Package name: 1,4-Dioxane

Package ID: 259
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:04:13
Modified at 2016-09-03 23:04:13

Abstract

The topology was generated using MOL2FF, with user-defined charges. These charges were obtained using the protocol P2 from Beckstein et al. (J Comput Aided Mol Des, 2014, 28, 265-276): geometry optimization and electrostatic potential (ESP) fitting, using Jaguar (http:// www.schrodinger.com) at the LMP2/cc-pVTZ(-F) level; the charges for chemically equivalent atoms obtained from the Jaguar calculations output were generally not identical, and they were adjusted manually before further use.

Chemical structure
General view

 Detailed view

References
Authors: Beckstein O, Fourrier A, Iorga BI
Title: Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field.
Journal: J Comput Aided Mol Des
Year: 2014 Mar
Volume: 28
Pages: 265-76
DOI: 10.1007/s10822-014-9727-1
Pubmed ID:   24557853
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 23:04:13 | Modified at 2016-09-03 23:04:13 | [download zip]
Type Description Hash (SHA1)
Topology SAMPL4_044_2.itp 584a0478e3b4b99dd318f882b8f21773f97f5e45
Structure SAMPL4_044_2.pdb 152170ab6df3cf87b5e2e4beab7e4aab4f70f672

Compound details
Ligand code DIO
Molecule identifier 288FE4ADD757D868
Displayed name 1,4-Dioxane
Canonical IUPAC name 1,4-dioxane
Formula C4H8O2
Molecular weight 88.11
Charge 0
Number of atoms 14
SMILES C1OCCOC1
PubChem CID 31275
CAS RN 123-91-1
Other names 1,4-Dioxane • 28347-88-8 • 28347-91-3 • 39449-24-6 • 54841-74-6 • 123-91-1 • Dioxane, technical grade • Dioxanne [French] • DIO • Glycolethylenether • HSDB 81 • NE 220 • NSC 8728 • RCRA waste no. U108 • RCRA waste number U108 • Tetrahydro-para-dioxin • UN 1165 • UN1165 • p-Dioxan [Czech] • EINECS 204-661-8 • para-Dioxane • 33147_RIEDEL • 154822_ALDRICH • 42502_FLUKA • 42512_FLUKA • 4M8367_SUPELCO • 631868_ALDRICH • 42510_FLUKA • 48367_SUPELCO • 539538_ALDRICH • 611905_ALDRICH • 34944_RIEDEL • 631876_ALDRICH • InChI=1/C4H8O2/c1-2-6-4-3-5-1/h1-4H • 442251_SUPELCO • 1,4-Diethylene dioxide • 1,4-Dioxan • Di(ethylene oxide) • Diethylene dioxide • Diethylene ether • Diethylene oxide • Diokan • Dioksan • Diossano-1,4 • Dioxaan-1,4 • Dioxan • Dioxan-1,4 • Dioxane • Dioxane-1,4 • Dioxanne • Dioxyethylene ether • Glycol ethylene ether • NCI-C03689 • NSC8728 • Tetrahydro-1,4-dioxin • Tetrahydro-p-dioxin • WLN: T6O DOTJ • p-Dioxan • p-Dioxane • 533971_ALDRICH • D201863_ALDRICH • p-Dioxin, tetrahydro- • 676934_SIAL • 631841_ALDRICH • 1,4-Dioxane solution • 296309_ALDRICH • CHEBI:47032 • 76887_FLUKA • 34857_SIAL • 612073_ALDRICH • 551368_ALDRICH • C14440 • 631833_ALDRICH • ZINC01648204 • 360481_SIAL • 1,4-Diethylenedioxide • 1,4-Dioxacyclohexane • 1,4-Dioxanne [French] • 5-19-01-00016 (Beilstein Handbook Reference) • AI3-01055 • BRN 0102551 • CCRIS 269 • Dioksan [Polish] • Diossano-1,4 [Italian] • Dioxaan-1,4 [Dutch] • Dioxan-1,4 [German] • Dioxane [UN1165] [Flammable liquid]

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

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