Skatole | C9H9N | MD Topology | NMR | X-Ray

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Molecule Information

Molecule Typeheteromolecule
Residue Name (RNME)_I0E
FormulaC9H9N
IUPAC InChI Key
ZFRKQXVRDFCRJG-UHFFFAOYSA-N
IUPAC InChI
InChI=1S/C9H9N/c1-7-6-10-9-5-3-2-4-8(7)9/h2-6,10H,1H3
IUPAC Name
3-Methyl-1H-indole
Common NameSkatole
Canonical SMILES (Daylight)
Cc1c[nH]c2c1cccc2
Number of atoms19
Net Charge0
Forcefieldmultiple
Molecule ID14
ChemSpider ID6480
ChEMBL ID 1329793
Visibility Public
Molecule Tags aromatic amine II ATB3.0 validation Gerber Mobley et al. 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

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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) 1000 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 Time10 days, 14:26:17 (hh:mm:ss)

ATB Pipeline Setting

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Experimental Solvation Free Energies (1-2 of 2)

Calculated Solvation Free Energy

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Solvation Free Energy Data

Status Completed
TI Solvent SPC water
Result -27.1 +/- 0.6 kJ.mol-1
Experimental Solvent water
Experimental Value -24.7 +/- NA 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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