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

Package ID: 175
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:03:40
Modified at 2016-09-03 23:03:40

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 23:03:41 | Modified at 2016-09-03 23:03:41 | [download zip]
Type Description Hash (SHA1)
Topology SAMPL4_016_2.itp 64a8af75c1ac4bbc29d336492401f0cc4b07093e
Structure SAMPL4_016_2.pdb 271f240a0654d5420e8f72c427db17401e690091

Compound details
Ligand code UNL
Molecule identifier D3B710034538A540
Displayed name (1R,2S,5R)-5-methyl-2-propan-2-ylcyclohexan-1-ol
Canonical IUPAC name (1R,2S,5R)-5-methyl-2-propan-2-yl-cyclohexan-1-ol
Formula C10H20O
Molecular weight 156.27
Charge 0
Number of atoms 31
SMILES [C@@H]1(O)C[C@H](C)CC[C@H]1C(C)C
PubChem CID 16666
CAS RN 89-78-1
Other names (1R,2S,5R)-5-methyl-2-propan-2-ylcyclohexan-1-ol • (1R,2S,5R)-2-isopropyl-5-methyl-cyclohexan-1-ol • (1R,2S,5R)-2-isopropyl-5-methyl-1-cyclohexanol • (1R,2S,5R)-5-methyl-2-propan-2-yl-cyclohexan-1-ol • 98167-53-4 • 2216-51-5 • 89-78-1 • W266558_ALDRICH • LMPR01020015 • IDI1_000820 • KBioSS_000785 • 15785_RIEDEL • KBio1_000820 • KBio3_002562 • (1R,2S,5R)-2-Isopropyl-5-methylcyclohexanol • BB_NC-0057 • (1R,2S,5R)-(-)-menthol • (-)-Menthol • C00400 • L-Menthol • SPECTRUM1503134 • (−)-Menthol • ZINC01482164 • KBio2_000785 • D00064 • l-Menthol (JP15) • l-Menthol (TN) • KBio2_005921 • W266523_ALDRICH • (1R,2S,5R)-5-methyl-2-(propan-2-yl)cyclohexan-1-ol • (1alpha,2beta,5alpha)-5-methyl-2(1-methylethyl)cyclohexanol • CHEBI:15409 • (1R,2S,5R)-5-methyl-2-(1-methylethyl)cyclohexanol • DivK1c_000820 • 5-Methyl-2-(1-methylethyl)cyclohexanol • Cyclohexanol, 2-isopropyl-5-methyl- • Cyclohexanol, 5-methyl-2-(1-methylethyl)-, (1.alpha.,2.beta.,5.alpha.)- • Hexahydrothymol • MENTHOL • Menthacamphor • Menthol, cis-1,3,trans-1,4- • Menthomenthol • NCI-C50000 • NSC2603 • Peppermint camphor • WLN: L6TJ AY1&1 BQ D1 • p-Menthan-3-ol • SDCCGMLS-0066659.P001 • Spectrum5_001060 • Spectrum2_000855 • W266590_ALDRICH • 63660_FLUKA • Spectrum_000305 • (R)-(-)-Menthol • Cyclohexanol, 5-methyl-2-(1-methylethyl)-, [1R-(1.alpha.,2.beta.,5.alpha.)]- • L-(-)-Menthol • Menthol, (1R,3R,4S)-(-)- • NSC62788 • U.s.p. menthol • WLN: L6TJ AY1&1 DQ D1 -L • Spectrum3_001561 • KBio2_003353 • (1R,2S,5R)-(−)-Menthol • 588733_ALDRICH • nchembio862-comp1 • M2780_SIAL • SPBio_000869 • NINDS_000820 • L-Menthol crystals • (-)-(1R,3R,4S)-Menthol • (-)-Menthyl alcohol • (-)-trans-p-Menthan-cis-ol • (1R)-(-)-Menthol • (1R-(1-alpha,2-beta,5-alpha))-5-Methyl-2-(1-methylethyl)cyclohexanol • (L)-MENTHOL • AI3-52408 • CCRIS 3728 • Cyclohexanol, 5-methyl-2-(1-methylethyl)-, (1R,2S,5R)- • Cyclohexanol, 5-methyl-2-(1-methylethyl)-, (1R,3R,4S)- • Cyclohexanol, 5-methyl-2-(1-methylethyl)-, (1R-(1alpha,2beta,5alpha))- (9CI) • D-(-)-Menthol • EINECS 218-690-9 • HSDB 5662 • Levomenthol • Levomenthol [BAN:INN] • Levomentholum [INN-Latin] • Menthol, l- • NSC 62788 • l-Menthol (natural) • BSPBio_003062

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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