Package name: (E)-oct-5-enoic acid
| Package ID: 221 |
| Force-field: OPLS-AA | Code: Gromacs |
| Created by |
Bogdan Iorga (biorga)
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| Created at | 2016-09-03 23:03:59 |
| Modified at | 2016-09-03 23:03:59 |
Abstract
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| 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
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General view
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Detailed view
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References
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| 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
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| Pubmed ID: |
24557853 |
| Comments: |
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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 23:04:00 |
Modified at 2016-09-03 23:04:00 |
[download zip]
| Type |
Description |
Hash (SHA1) |
| Topology |
SAMPL4_031_3.itp
|
22ce159aa2ae616f2389164a58064639b32056ec |
| Structure |
SAMPL4_031_3.pdb
|
4b3c533e15b29a90f7444609de06adf236893558 |
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| Ligand code |
UNL
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| Molecule identifier | 4355F98908921619 |
| Displayed name | (E)-oct-5-enoic acid |
| Canonical IUPAC name | (E)-oct-5-enoic acid |
| Formula | C8H14O2 |
| Molecular weight | 142.20 |
| Charge | 0 |
| Number of atoms | 24 |
| SMILES | C(=O)(O)CCC/C=C/CC |
| PubChem CID | 5282719
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| CAS RN | —
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| Other names | (E)-oct-5-enoic acid • trans-5-octenoic acid • trans-delta-octenoic acid • 5E-octenoic acid • LMFA01030023 |
