Package name: (2S,5R)-5-methyl-2-propan-2-ylcyclohexan-1-one

Package ID: 178
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:03:43
Modified at 2016-09-03 23:03:43

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 23:03:43 | Modified at 2016-09-03 23:03:43 | [download zip]
Type Description Hash (SHA1)
Topology SAMPL4_017_2.itp a3816615154155373b52836d56af1dfbb1b2761d
Structure SAMPL4_017_2.pdb 7c201bdc8c46fa9c3402ad1c09845722ac9be391

Compound details
Ligand code UNL
Molecule identifier 83C84A9D0A336183
Displayed name (2S,5R)-5-methyl-2-propan-2-ylcyclohexan-1-one
Canonical IUPAC name (2S,5R)-5-methyl-2-propan-2-yl-cyclohexan-1-one
Formula C10H18O
Molecular weight 154.25
Charge 0
Number of atoms 29
SMILES C1(=O)C[C@H](C)CC[C@H]1C(C)C
PubChem CID 26447
CAS RN 14073-97-3
Other names (2S,5R)-5-methyl-2-propan-2-ylcyclohexan-1-one • (2S,5R)-2-isopropyl-5-methyl-cyclohexan-1-one • (2S,5R)-2-isopropyl-5-methyl-1-cyclohexanone • (2S,5R)-5-methyl-2-propan-2-yl-cyclohexan-1-one • 21060-23-1 • 14073-97-3 • ZINC00967796 • KBio2_001779 • KBio1_001477 • KBio2_006915 • 63677_FLUKA • Spectrum2_000691 • (1R,4S)-p-menthan-3-one • (2S,5R)-2-isopropyl-5-methylcyclohexanone • C00843 • l-Menthone • (2S-trans)-5-methyl-2-(1-methylethyl)cyclohexanone • CHEBI:15410 • W266701_ALDRICH • (-)-(2S,5R)-Menthone • (-)-5-Methyl-2-(1-methylethyl)cyclohexanone • c1067 • trans-p-Menthan-3-one • 63678_FLUKA • DivK1c_006533 • Spectrum3_001272 • KBio2_004347 • SPECTRUM300564 • KBioGR_002115 • LMPR01020019 • (-)-Menthone • InChI=1/C10H18O/c1-7(2)9-5-4-8(3)6-10(9)11/h7-9H,4-6H2,1-3H3/t8-,9+/m1/s • rel-(2R,5S)-2-isopropyl-5-methylcyclohexanone • (2S,5R)-5-methyl-2-(1-methylethyl)cyclohexanone • SPBio_000841 • (2S,5R)-5-methyl-2-(propan-2-yl)cyclohexanone • KBio3_002364 • Spectrum_001299 • BSPBio_002864 • AIDS-032329 • SpecPlus_000437 • AIDS032329 • Cyclohexanone, 5-methyl-2-(1-methylethyl)-, (2S,5R)- • Cyclohexanone, 5-methyl-2-(1-methylethyl)-, (2S-trans)- • EINECS 237-926-1 • L-Menthan-3-one • KBioSS_001779 • SDCCGMLS-0066582.P001 • 1/C10H18O/c1-7(2)9-5-4-8(3)6-10(9)11/h7-9H,4-6H2,1-3H3/t8-,9+/m1/s • (−)-Menthone • 218235_ALDRICH • Spectrum4_001648 • BB_NC-0294 • Spectrum5_000495

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

"Count the Bubbles In Your Hair" (The Breeders)