Package name: (2E)-3,7-dimethylocta-2,6-dien-1-ol

Package ID: 140
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:03:27
Modified at 2016-09-03 23:03:27

Abstract

The topology was generated using MOL2FF, with user-defined charges. These charges were obtained using the protocol P3 from Beckstein et al. (J Comput Aided Mol Des, 2014, 28, 265-276): 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, 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 23:03:27 | Modified at 2016-09-03 23:03:27 | [download zip]
Type Description Hash (SHA1)
Topology SAMPL4_004_3.itp 0b8d5596eda664d80e2dcf55ee94f8eea0fd9d83
Structure SAMPL4_004_3.pdb d0546317b3d0457b5439674c0616b0feb4eadb6e

Compound details
Ligand code 64Z
Molecule identifier C19F81A72CBAE674
Displayed name (2E)-3,7-dimethylocta-2,6-dien-1-ol
Canonical IUPAC name (2E)-3,7-dimethylocta-2,6-dien-1-ol
Formula C10H18O
Molecular weight 154.25
Charge 0
Number of atoms 29
SMILES C(O)\C=C(/C)CCC=C(C)C
PubChem CID 637566
CAS RN 106-24-1
Other names (2E)-3,7-dimethylocta-2,6-dien-1-ol • 3,7-dimethylocta-2,6-dien-1-ol • 624-15-7 • 106-24-1 • 8007-13-4 • 68311-14-8 • SBB007719 • AIDS-032464 • AIDS032464 • 163333_ALDRICH • NCI60_042058 • SPECTRUM1501132 • 48799_FLUKA • 1-Octanol, 3,7-dimethyl-, tetradehydro deriv. • 3,7-Dimethyloctan-1-ol, tetradehydro derivative • EINECS 269-750-6 • InChI=1/C10H18O/c1-9(2)5-4-6-10(3)7-8-11/h5,7,11H,4,6,8H2,1-3H3/b10-7 • (2E)-3,7-dimethyl-2,6-octadien-1-ol • CHEBI:17447 • t-geraniol • DivK1c_000193 • KBioSS_000881 • 3,7-Dimethyl-2,6-octadien-1-ol • 3,7-Dimethyl-2,6-octadienol • Citrol • EINECS 210-831-2 • NCI9279 • W250708_ALDRICH • W250716_ALDRICH • C01500 • Geraniol • NCGC00013095 • NSC-9279 • 2,6-Dimethyl-2,6-octadien-8-ol • 2-trans-3,7-dimethyl-2,6-octadiene-1-ol • Octadien-1-ol, 3,7-dimethyl-, (E)- • c1043 • trans-2,6-Dimethyl-2,6-octadien-8-ol • Spectrum5_001513 • 2E-geraniol • LMPR01020001 • CHEBI:24221 • Spectrum_000401 • Spectrum2_000784 • KBio1_000193 • BSPBio_002919 • 48798_FLUKA • NCGC00094905-04 • KBioGR_000822 • Guaniol • 2,6-Dimethyl-trans-2,6-octadien-8-ol • 2,6-Octadien-1-ol, 3,7-dimethyl-, (E)- • 2,6-Octadien-1-ol, 3,7-dimethyl-, trans- • 3,7-Dimethyl-trans-2,6-octadien-1-ol • Geraniol alcohol • Geraniol extra • Geranyl alcohol • 2,6-octadien-1-ol, 3,7-dimethyl- • NSC9279 • WLN: Q2UY1&3UY1&1 -T • trans-3,7-Dimethyl-2,6-octadien-1-ol • trans-Geraniol • Lemonol • NCIStruc1_000041 • Spectrum3_001450 • SMP1_000212 • NINDS_000193 • SPBio_000888 • 2,6-Octadien-1-ol, 3,7-dimethyl-,(Z)- • NSC46105 • WLN: Q2UY1 & 3UY1 & 1-C • WLN: Q2UY1 & 3YU1 & 1-Z • KBio2_000881 • KBio2_003449 • KBio2_006017 • KBio3_002419 • Spectrum4_000441 • IDI1_000193 • ZINC01529210 • (E)-3,7-Dimethyl-2,6-octadien-1-ol • (E)-Geraniol • (E)-Nerol • 2,6-Octadien-1-ol, 3,7-dimethyl-, (2E)- • 2-trans-3,7-Dimethyl-2,6-octadien-1-ol • 3,7-Dimethyl-2,6-octadien-1-ol, (E)- • 4-01-00-02277 (Beilstein Handbook Reference) • AI3-00206 • BRN 1722456 • CCRIS 7243 • EINECS 203-377-1 • EPA Pesticide Chemical Code 597501 • FEMA No. 2507 • Geraniol (natural) • HSDB 484 • NSC 9279 • beta-Geraniol • (Z)-Geraniol • 2,6-Octadien-1-ol, 3,7-dimethyl-, (2Z)- • 2,6-Octadien-1-ol, 3,7-dimethyl-, (Z)- • 2-cis-3,7-Dimethyl-2,6-octadien-1-ol • 3,7-DIMETHYL-(Z)-2,6-OCTADIEN-1-OL • 3,7-Dimethyl-2,6-octadien-1-ol, (Z)- • 3,7-Dimethyl-2,6-octadien-1-ol, cis- • AI3-28202 • EINECS 203-378-7 • FEMA No. 2770 • NSC-46105 • Nerol (natural) • Neryl alcohol • cis-Geraniol • NCIStruc2_000251 • NCGC00094905-01 • NCGC00094905-02

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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