C 6 H 9 | MD Topology | NMR | X-Ray

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C6H9 | MD Topology | NMR | X-Ray

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Go back to Topology Fragment-Based Parametrisation with OFraMP Shell Size 1 2 3 4 Repository ATB3

• Molecule Information
• Molecular Dynamics (MD) Files
• X-Ray - Docking Files
• NMR Refinement Files
• 1H NMR Spectrum

Molecule Information

Molecule Type	heteromolecule
Residue Name (RNME)	J38J
Formula	C6H9
IUPAC InChI Key	PRBHEGAFLDMLAL-GQCTYLIASA-N
IUPAC InChI	InChI=1S/C6H10/c1-3-5-6-4-2/h3-4,6H,1,5H2,2H3/b6-4+
IUPAC Name	(4E)-hexa-1,4-diene hexa-1,4-diene
Common Name
Canonical SMILES (Daylight)	C=CC/C=C/C
Number of atoms	15
Net Charge	1
Forcefield	multiple
Molecule ID	762491
Visibility	Public
Molecule Tags

Format

Gromos 54A7 GROMACS GROMOS11 GROMOS96 LAMMPS

Molecular Dynamics (MD) Files

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X-Ray - Docking Files

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NMR Parameters

Solvent CDCL3 DMSO H2O/D2O Frequency (MHz) Submit

1H NMR Spectrum

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Fragment-Based Charges

No charge assignments available. Use the button above to use OFraMP fragment-based charge assignment.

Topology History

Processing Information

QM Processing Stage

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Processing Stage		Template	Semi-Empirical QM (QM0)	DFT QM (QM1)	DFT Hessian QM (QM2)
Calculation		None	Energy Minization	Energy Minization	Hessian
Level of Theory		None	Semi-Empirical / SCF	DFT (B3LYP/6-31G*)	DFT (B3LYP/6-31G*)
Default Size Limit (Atoms)		2000	500	50	40
Content of MD Topology
Charges Derived From		None	MOPAC	Merz-Singh-Kollman	Merz-Singh-Kollman
Geometry		User Provided	Optimized	Optimized	Optimized
Non-Bonded Interactions	Bonds	Rule Based: Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.			Hessian Based: Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.
	Angles
	Dihedrals

Data

Current Processing State	Completed
Total Processing Time	1:00:09 (hh:mm:ss)

ATB Pipeline Setting

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Maximum qm_level Resubmit molecule Update (admin only)

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Calculated Solvation Free Energy

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Submit New Solvation Free Energy Computation

Method TI Solvent SPC water ATB3.0 hexane Target Uncertainty (kJ.mol-1)

Conditions of Use

The Automated Topology Builder (ATB) and Repository has been developed and is currently maintained with support from the University of Queensland (UQ), the Australian Research Council (ARC) and the Queensland Cyber Infrastructure Foundation (QCIF). Access to the ATB is provided free to academic users from publically funded teaching or research institutions. Access for academic use is conditional on: i) any molecule submitted to the ATB being made publically available and ii) the source of any material downloaded from the ATB being appropriately acknowledged in any publications or other forms in which research using this material is disseminated.

Use of the ATB by other parties, or academic users wishing to restrict the access of others to specific molecules, is considered to be commercial in nature. Commercial access is available by licence or collaborative agreement. Parties interested in commercial licencing or other arrangements should contact Prof Alan E. Mark at the address provided at the bottom of the page.

Contact

For queries regarding the ATB, please contact:

UQ MD Group Website

Contributors

Scientific Development:

• Alan E. Mark
• Martin Stroet
• Alpesh K. Malde
• Josef Holownia
• Callum Macfarlane
• Jordan Yee

Collaborating Groups:

• Mehdi Mobli
• Biochemical and Biophysical Systems Group, LLNL
• Gunnar Klau
• Chris Oostenbrink
• Daan Geerke

Current Developers:

• Martin Stroet
• Sharif Nada
• Josef Holownia
• Callum Macfarlane
• Jordan Yee

Previous Developers:

• Bertrand Caron
• Le Zuo
• Matthew Breeze
• Mohammed El-Kebir
• David Warne
• Richard Hammond
• Wenhan Chen
• Thomas Lee

Contributors:

• David Poger
• Phil Hünenberger
• Bruno Horta
• Katarzyna Koziara
• Yik Chang Jonathan Ting
• Martina Setz
• Zihan Zhou
• Pramod C. Nair
• Purvi Gupta
• Nikhil Biyani

Supported By

This project is supported by the Australian Research Data Commons (ARDC). The ARDC is enabled by NCRIS.