Biomolecular Modeling Database

Biomolecular Modeling Database (BMOD)

3-(1H-Indol-3-Yl)-2-Oxopropanoic Acid (C11H9NO3)

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/BMOD0000101898 2025-04-04
Download entry: Compressed file
InChI: InChI=1S/C11H9NO3/c13-10(11(14)15)5-7-6-12-9-4-2-1-3-8(7)9/h1-4,6,12H,5H2,(H,14,15)
SMILES: O=C(O)C(=O)Cc1c[nH]c2ccccc12
NMR-STAR: BMOD0000101898.str
Compound details: PDB Ligand Expo small molecules

Graphical representations:

Image for 3-(1H-Indol-3-Yl)-2-Oxopropanoic Acid

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
Feng Z., Chen L., Maddula H., Akcan O., Oughtred R., Berman H.M., Westbrook J., Ligand Depot: a data warehouse for ligands bound to macromolecules, Bioinformatics, 2004., 20, 13, DOI:10.1093/bioinformatics/bth214
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
Maciejewski, M.W., Schuyler, A.D., Gryk, M.R., Moraru, I.I., Romero, P.R., Ulrich, E.L., Eghbalnia, H.R., Livny, M., Delaglio, F., Hoch, J.C. (2017) NMRbox: A Resource for Biomolecular NMR Computation. Biophysical Journal, 112, 1529-1534. http://dx.doi.org/10.1016/j.bpj.2017.03.011
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:	3-(1H-Indol-3-Yl)-2-Oxopropanoic Acid (C11H9NO3) 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/BMOD0000101898 2025-04-04 Download entry: Compressed file InChI: InChI=1S/C11H9NO3/c13-10(11(14)15)5-7-6-12-9-4-2-1-3-8(7)9/h1-4,6,12H,5H2,(H,14,15) SMILES: O=C(O)C(=O)Cc1c[nH]c2ccccc12 NMR-STAR: BMOD0000101898.str Compound details: PDB Ligand Expo small molecules Graphical representations: Molecular modeling parameter files RUNER (Download) inchi_complete.inchi updated_alatis_output_compound_3D_h_sdf.prmtop updated_alatis_output_compound_3D_h_sdf.pdb updated_alatis_output_compound_3D_h_sdf_ALATIS.top updated_alatis_output_compound_3D_h_sdf_ALATIS.par Xplor-NIH (Download) updated_alatis_output_compound_3D_h_sdf.pdb updated_alatis_output_compound_3D_h_sdf_ALATIS.top updated_alatis_output_compound_3D_h_sdf_ALATIS.par double_bonds.bo AMBER (Download) alatis_output_compound_3D_h_sdf.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_compound_3D_h_sdf.frcmod updated_alatis_output_compound_3D_h_sdf.inpcrd updated_alatis_output_compound_3D_h_sdf.lib updated_alatis_output_compound_3D_h_sdf.mol2 updated_alatis_output_compound_3D_h_sdf.prmtop updated_alatis_output_compound_3D_h_sdf.pdb CHARMM (Download) updated_alatis_output_compound_3D_h_sdf.charmm.inp updated_alatis_output_compound_3D_h_sdf.charmm.prm updated_alatis_output_compound_3D_h_sdf.charmm.rtf updated_alatis_output_compound_3D_h_sdf.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 Feng Z., Chen L., Maddula H., Akcan O., Oughtred R., Berman H.M., Westbrook J., Ligand Depot: a data warehouse for ligands bound to macromolecules, Bioinformatics, 2004., 20, 13, DOI:10.1093/bioinformatics/bth214 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 Maciejewski, M.W., Schuyler, A.D., Gryk, M.R., Moraru, I.I., Romero, P.R., Ulrich, E.L., Eghbalnia, H.R., Livny, M., Delaglio, F., Hoch, J.C. (2017) NMRbox: A Resource for Biomolecular NMR Computation. Biophysical Journal, 112, 1529-1534. http://dx.doi.org/10.1016/j.bpj.2017.03.011 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).