Biomolecular Modeling Database

Biomolecular Modeling Database (BMOD)

1-(Piperidinomethyl)-1H-Benzo[D]Imidazole (C13H17N3)

Cite this entry: PDF Text

Citation:Dashti, H., Ulrich, E., Wedell, J., Aceti, D., Amarasinghe, G., Westler, W., Markley, J., Eghbalnia, H., Biomolecular Modeling Database doi:10.13018/BMOD0000010401 2025-11-04
Download entry: Compressed file
InChI: InChI=1S/C13H17N3/c1-4-8-15(9-5-1)11-16-10-14-12-6-2-3-7-13(12)16/h2-3,6-7,10H,1,4-5,8-9,11H2
SMILES: c1ccc2c(c1)ncn2CN1CCCCC1
NMR-STAR: BMOD0000010401.str
Compound details: screening fragment

Graphical representations:

Image for 1-(Piperidinomethyl)-1H-Benzo[D]Imidazole

Molecular modeling parameter files

RUNER (Download)

Xplor-NIH (Download)

AMBER (Download)

CHARMM (Download)

Reference citations:

Dashti Hesam, Westler William M., Markley John L., Eghbalnia Hamid R., Unique identifiers for small molecules enable rigorous labeling of their atoms, Scientific Data, 2017, 4, ., doi:10.1038/sdata.2017.73, https://www.nature.com/articles/sdata201773
Dashti Hesam, Wedell Jonathan R., Cornilescu Gabriel, Schwieters Charles D., Westler William M., Markley John L., Eghbalnia Hamid R., Robust nomenclature and software for enhanced reproducibility in molecular modeling of small molecules, biorxiv preprint, 2018, ., ., https://doi.org/10.1101/429530, https://www.biorxiv.org/content/early/2018/09/27/429530
Maybridge Fragment Libraries, http://www.maybridge.com/
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA., Development and testing of a general amber force field., J. Comput Chem., 2004 Jul, 25, 9, doi: 0.1002/jcc.20035
Wang Junmei, Wang Wei, Kollman Peter A., Case David A., Automatic atom type and bond type perception in molecular mechanical calculations., Journal of Molecular Graphics and Modelling, 2006, 25, 2, https://doi.org/10.1016/j.jmgm.2005.12.005
TopSpin V.4, Bruker; https://www.bruker.com/products/mr/nmr/nmr-software/nmr-software/topspin/overview.html
Thain Douglas, Tannenbaum Todd, Livny Miron , Distributed computing in practice: the Condor experience, CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE, 2005, 17, ., DOI:10.1002/cpe.938
RDKit: Open-source cheminformatics; http://www.rdkit.org

Disclaimer:

BMOD is available to the public as a web-service via our web server. This work is copyrighted under the terms of GPL. The data entries are provided on an "as is" basis without warranty of any kind, either expressed or implied. Any usage of BMOD data entries, or modification and application of the data are free for academic use when BMOD publications are cited.
The chemical compounds archived in this database are aggregated from several different databases and have been processed with different software packages. For appropriate citation of the data entries please check the PDF description files provided for every entry.
The majority of the aggregated compounds are provided in 2D structure and with implicit hydrogen atoms. We utilized the Open Babel (The Open Source Chemistry Toolbox) software package to add explicit hydrogen atoms and to generate 3D structure of the compounds; please comply with the Open Babel license agreements.

Contact:

For any question or concern please contact Hesam Dashti (hdashti@bwh.harvard.edu).

	Biomolecular Modeling Database (BMOD)
Home Source Databases BMOD's NMR-STAR dictionary Complete NMR-STAR dictionary NMRFAM Servers Search:	1-(Piperidinomethyl)-1H-Benzo[D]Imidazole (C13H17N3) Cite this entry: PDF Text Citation:Dashti, H., Ulrich, E., Wedell, J., Aceti, D., Amarasinghe, G., Westler, W., Markley, J., Eghbalnia, H., Biomolecular Modeling Database doi:10.13018/BMOD0000010401 2025-11-04 Download entry: Compressed file InChI: InChI=1S/C13H17N3/c1-4-8-15(9-5-1)11-16-10-14-12-6-2-3-7-13(12)16/h2-3,6-7,10H,1,4-5,8-9,11H2 SMILES: c1ccc2c(c1)ncn2CN1CCCCC1 NMR-STAR: BMOD0000010401.str Compound details: screening fragment Graphical representations: Molecular modeling parameter files RUNER (Download) inchi_complete.inchi updated_alatis_output_09_H06_mol.prmtop updated_alatis_output_09_H06_mol.pdb updated_alatis_output_09_H06_mol_ALATIS.top updated_alatis_output_09_H06_mol_ALATIS.par Xplor-NIH (Download) updated_alatis_output_09_H06_mol.pdb updated_alatis_output_09_H06_mol_ALATIS.top updated_alatis_output_09_H06_mol_ALATIS.par double_bonds.bo AMBER (Download) alatis_output_09_H06_mol.xyz ANTECHAMBER_AC.AC ANTECHAMBER_AC.AC0 ANTECHAMBER_AM1BCC.AC ANTECHAMBER_AM1BCC_PRE.AC ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_BOND_TYPE.AC0 ANTECHAMBER_PREP.AC ANTECHAMBER_PREP.AC0 ATOMTYPE.INF updated_alatis_output_09_H06_mol.frcmod updated_alatis_output_09_H06_mol.inpcrd updated_alatis_output_09_H06_mol.lib updated_alatis_output_09_H06_mol.mol2 updated_alatis_output_09_H06_mol.prmtop updated_alatis_output_09_H06_mol.pdb CHARMM (Download) updated_alatis_output_09_H06_mol.charmm.inp updated_alatis_output_09_H06_mol.charmm.prm updated_alatis_output_09_H06_mol.charmm.rtf updated_alatis_output_09_H06_mol.pdb Reference citations: Dashti Hesam, Westler William M., Markley John L., Eghbalnia Hamid R., Unique identifiers for small molecules enable rigorous labeling of their atoms, Scientific Data, 2017, 4, ., doi:10.1038/sdata.2017.73, https://www.nature.com/articles/sdata201773 Dashti Hesam, Wedell Jonathan R., Cornilescu Gabriel, Schwieters Charles D., Westler William M., Markley John L., Eghbalnia Hamid R., Robust nomenclature and software for enhanced reproducibility in molecular modeling of small molecules, biorxiv preprint, 2018, ., ., https://doi.org/10.1101/429530, https://www.biorxiv.org/content/early/2018/09/27/429530 Maybridge Fragment Libraries, http://www.maybridge.com/ Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA., Development and testing of a general amber force field., J. Comput Chem., 2004 Jul, 25, 9, doi: 0.1002/jcc.20035 Wang Junmei, Wang Wei, Kollman Peter A., Case David A., Automatic atom type and bond type perception in molecular mechanical calculations., Journal of Molecular Graphics and Modelling, 2006, 25, 2, https://doi.org/10.1016/j.jmgm.2005.12.005 TopSpin V.4, Bruker; https://www.bruker.com/products/mr/nmr/nmr-software/nmr-software/topspin/overview.html Thain Douglas, Tannenbaum Todd, Livny Miron , Distributed computing in practice: the Condor experience, CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE, 2005, 17, ., DOI:10.1002/cpe.938 RDKit: Open-source cheminformatics; http://www.rdkit.org
Disclaimer: BMOD is available to the public as a web-service via our web server. This work is copyrighted under the terms of GPL. The data entries are provided on an "as is" basis without warranty of any kind, either expressed or implied. Any usage of BMOD data entries, or modification and application of the data are free for academic use when BMOD publications are cited. The chemical compounds archived in this database are aggregated from several different databases and have been processed with different software packages. For appropriate citation of the data entries please check the PDF description files provided for every entry. The majority of the aggregated compounds are provided in 2D structure and with implicit hydrogen atoms. We utilized the Open Babel (The Open Source Chemistry Toolbox) software package to add explicit hydrogen atoms and to generate 3D structure of the compounds; please comply with the Open Babel license agreements. Contact: For any question or concern please contact Hesam Dashti (hdashti@bwh.harvard.edu).