Package name: (2R,5R)-2-methyl-5-prop-1-en-2-ylcyclohexan-1-one

Package ID: 164
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:03:36
Modified at 2016-09-03 23:03:36

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 23:03:37 | Modified at 2016-09-03 23:03:37 | [download zip]
Type Description Hash (SHA1)
Topology SAMPL4_012_3.itp 5912ae173ca534421e6d3ea9db6f638b33fe14b6
Structure SAMPL4_012_3.pdb 92906e87674f4ad8468328c872400d16c0b57ab7

Compound details
Ligand code UNL
Molecule identifier 91F6139B26A383B7
Displayed name (2R,5R)-2-methyl-5-prop-1-en-2-ylcyclohexan-1-one
Canonical IUPAC name (2R,5R)-2-methyl-5-prop-1-en-2-yl-cyclohexan-1-one
Formula C10H16O
Molecular weight 152.24
Charge 0
Number of atoms 27
SMILES C1(=O)[C@H](C)CC[C@@H](C(=C)C)C1
PubChem CID 22227
CAS RN 112163702400
Other names (2R,5R)-2-methyl-5-prop-1-en-2-ylcyclohexan-1-one • (2R,5R)-5-isopropenyl-2-methyl-cyclohexan-1-one • (2R,5R)-5-isopropenyl-2-methyl-1-cyclohexanone • (2R,5R)-2-methyl-5-prop-1-en-2-yl-cyclohexan-1-one • 5524-05-0 • 5948-04-9 • ZINC00967816 • (2R-trans)-2-Methyl-5-(1-methylvinyl)cyclohexan-1-one • Cyclohexanone, 2-methyl-5-(1-methylethenyl)-, (2R,5R)- • Cyclohexanone, 2-methyl-5-(1-methylethenyl)-, (2theta-trans)- • EINECS 226-872-4 • d-Dihydrocarvone • Cyclohexanone, 2-methyl-5-(1-methylethenyl)-, trans- • p-MENTH-8-EN-2-ONE, E- • trans-2-Methyl-5-(1-methylethenyl)cyclohexanone • LMPR01020081 • C11398 • (1R,4R)-Dihydrocarvone • (E)-dihydrocarvone

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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