Benzene | C6H6 | MD Topology | NMR | X-Ray

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Molecule Information

Molecule Typeheteromolecule
Residue Name (RNME)G058
FormulaC6H6
IUPAC InChI Key
UHOVQNZJYSORNB-UHFFFAOYSA-N
IUPAC InChI
InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
IUPAC Name
BENZENE
Common NameBenzene
Canonical SMILES (Daylight)
c1ccccc1
Number of atoms12
Net Charge0
Forcefieldmultiple
Molecule ID804
ChemSpider ID236
ChEMBL ID 277500
PDB hetId BNZ
Visibility Public
Molecule Tags ATB3.0 validation Boulanger et al. Dodda et al. Gerber Marenich et al. Mobley et al. phenyl Shivakumar et al.

Format

Molecular Dynamics (MD) Files

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X-Ray - Docking Files

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NMR Parameters

1H NMR Spectrum

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Fragment-Based Charges

Available charge assignments

OFraMP_ID: 43

OFraMP_hash: 3b2e6

Total charge: 0.0
C1: -0.126
C2: -0.126
C3: -0.126
C4: -0.126
C5: -0.126
C6: -0.126
H1: 0.126
H2: 0.126
H3: 0.126
H4: 0.126
H5: 0.126
H6: 0.126
Equivalent atoms within the molecule as predicted by the ATB algorithm. Atom name and unique equivalence class integer code (in brackets) is given for each atom. Node color also maps to the equivalence class.<br>Click to toggle size.

Fig 1. Equivalent atoms within the molecule as predicted by the ATB algorithm. Atom name and unique equivalence class integer code (in brackets) is given for each atom. Node color also maps to the equivalence class.
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Coordinate and Topology Files

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 StateCompleted
Total Processing Time3 days, 0:00:00 (hh:mm:ss)

Calculated Solvation Free Energy

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Solvation Free Energy Data

Status Completed
TI Solvent ATB3.0 hexane
Result -17.3 +/- 1.5 kJ.mol-1
Experimental Solvent hexane
Experimental Value -16.6 +/- 0.8 kJ.mol-1
ATB Version 3.0
Completion Date 2018-10-12

Solvation Free Energy Plot

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Calculated Solvation Free Energy

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Solvation Free Energy Data

Status Completed
TI Solvent SPC water
Result -3.2 +/- 0.5 kJ.mol-1
Experimental Solvent water
Experimental Value -3.8 +/- 0.8 kJ.mol-1
ATB Version 3.0
Completion Date 2018-10-12

Solvation Free Energy Plot

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Calculated Solvation Free Energy

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