data_bmst000001 save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmst000001 _Entry.Title 1_3_diaminopropane _Entry.Submission_date 2006-02-23 _Entry.Accession_date 2006-02-23 _Entry.Last_release_date 2006-02-23 _Entry.Original_release_date 2006-02-23 _Entry.Origination author _Entry.BMRB_internal_directory_name 1_3_diaminopropane _Entry.Version_type original _Entry.NMR_STAR_version 'NMR STAR v3.1' _Entry.Experimental_method NMR _Entry.Experimental_method_subtype theoretical _Entry.Details ? loop_ _Entry_src.Project_name _Entry_src.Organization_full_name _Entry_src.Organization_initials _Entry_src.Entry_ID metabolics 'Madison Metabolomics Consortium' MMC bmst000001 stop_ loop_ _Entry_author.Ordinal _Entry_author.Family_name _Entry_author.Given_name _Entry_author.Middle_initials _Entry_author.Family_title _Entry_author.Entry_ID 1 Westler William M. ? bmst000001 2 Markley John L. ? bmst000001 stop_ save_ save_citations _Citation.Sf_category citations _Citation.Sf_framecode citations _Citation.Entry_ID bmst000001 _Citation.ID 1 _Citation.Class "reference citation" _Citation.Title "Database resources of the National Center for Biotechnology Information." _Citation.Status published _Citation.Type internet _Citation.WWW_URL "http://pubchem.ncbi.nlm.nih.gov/" _Citation.Year 2006 _Citation.Details ? loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 D. Wheeler D. L. ? bmst000001 1 1 T. Barrett T. ? ? bmst000001 1 1 D. Benson D. A. ? bmst000001 1 1 S. Bryant S. H. ? bmst000001 1 1 K. Canese K. ? ? bmst000001 1 1 V. Chetvenin V. ? ? bmst000001 1 1 D. Church D. M. ? bmst000001 1 1 M. DiCuccio M. ? ? bmst000001 1 1 R. Edgar R. ? ? bmst000001 1 1 S. Federhen S. ? ? bmst000001 1 1 L. Geer L. Y. ? bmst000001 1 1 W. Helmberg W. ? ? bmst000001 1 1 Y. Kapustin Y. ? ? bmst000001 1 1 D. Kenton D. L. ? bmst000001 1 1 O. Khovayko O. ? ? bmst000001 1 1 D. Lipman D. J. ? bmst000001 1 1 T. Madden T. L. ? bmst000001 1 1 D. Maglott D. R. ? bmst000001 1 1 J. Ostell J. ? ? bmst000001 1 1 K. Pruitt K. D. ? bmst000001 1 1 G. Schuler G. D. ? bmst000001 1 1 L. Schriml L. M. ? bmst000001 1 1 E. Sequeira E. ? ? bmst000001 1 1 S. Sherry S. T. ? bmst000001 1 1 K. Sirotkin K. ? ? bmst000001 1 1 A. Souvorov A. ? ? bmst000001 1 1 G. Starchenko G. ? ? bmst000001 1 1 T. Suzek T. O. ? bmst000001 1 1 R. Tatusov R. ? ? bmst000001 1 1 T. Tatusova T. A. ? bmst000001 1 1 L. Bagner L. ? ? bmst000001 1 1 E. Yaschenko E. ? ? bmst000001 1 stop_ save_ save_entity _Entity.Sf_category entity _Entity.Sf_framecode entity _Entity.Entry_ID bmst000001 _Entity.ID 1 _Entity.BMRB_code ? _Entity.Name "1-3-diaminopropane" _Entity.Type non-polymer _Entity.Ambiguous_conformational_states N _Entity.Ambiguous_chem_comp_sites N _Entity.Nstd_chirality N _Entity.Nstd_linkage N loop_ _Entity_comp_index.ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 1 $chem_comp_1 bmst000001 1 stop_ save_ save_chem_comp_1 _Chem_comp.Sf_category Chem_comp _Chem_comp.Sf_framecode chem_comp_1 _Chem_comp.Entry_ID bmst000001 _Chem_comp.ID 1 _Chem_comp.Name "1-3-diaminopropane" _Chem_comp.BMRB_code ? _Chem_comp.PDB_code ? _Chem_comp.Type non-polymer _Chem_comp.PDB_NSTD_flag ? _Chem_comp.Std_deriv_one_letter_code ? _Chem_comp.Std_deriv_three_letter_code ? _Chem_comp.Std_deriv_BMRB_code ? _Chem_comp.Std_deriv_PDB_code ? _Chem_comp.InCHi_code InChI=1/C3H10N2/c4-2-1-3-5/h1-5H2 _Chem_comp.Empirical_formula 'C3 H10 N2' _Chem_comp.Formula_weight 74.1249000000 _Chem_comp.Formula_mono_iso_wt_nat 74.0843983314 _Chem_comp.Formula_mono_iso_wt_13C 77.0944628448 _Chem_comp.Formula_mono_iso_wt_15N 76.0784681178 _Chem_comp.Formula_mono_iso_wt_13C_15N 77.0944628448 _Chem_comp.Image_file_name standards/1_3_diaminopropane/lit/4233.png _Chem_comp.Image_file_format png _Chem_comp.Formal_charge ? _Chem_comp.Paramagnetic ? _Chem_comp.Aromatic ? _Chem_comp.Topo_file_name ? _Chem_comp.Topo_file_format ? _Chem_comp.Struct_file_name standards/1_3_diaminopropane/lit/4233.mol _Chem_comp.Struct_file_format mol _Chem_comp.Stereochem_param_file_name ? _Chem_comp.Details ? _Chem_comp.DB_query_date ? _Chem_comp.DB_last_query_revised_last_date ? loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID Isomeric C(CN)CN bmst000001 1 Canonical C(CN)CN bmst000001 1 stop_ loop_ _Chem_comp_common_name.Name _Chem_comp_common_name.Type _Chem_comp_common_name.Entry_ID _Chem_comp_common_name.Comp_ID Propane-1,3-diamine synonym bmst000001 1 DAP synonym bmst000001 1 1,3-Propylenediamine synonym bmst000001 1 1,3-Diaminopropane synonym bmst000001 1 1,3-Propanediamine synonym bmst000001 1 "BRN 0605277" synonym bmst000001 1 1,3-DIAMINOPROPANE synonym bmst000001 1 TMEDA synonym bmst000001 1 AI3-25358 synonym bmst000001 1 Trimethylenediamine synonym bmst000001 1 alpha,omega-Propanediamine synonym bmst000001 1 stop_ loop_ _Chem_comp_systematic_name.Name _Chem_comp_systematic_name.Naming_system _Chem_comp_systematic_name.Entry_ID _Chem_comp_systematic_name.Comp_ID "propane-1,3-diamine" IUPAC bmst000001 1 "propane-1,3-diamine" IUPAC_TRADITIONAL bmst000001 1 "propane-1,3-diamine" IUPAC_CAS bmst000001 1 "propane-1,3-diamine" IUPAC_OPENEYE bmst000001 1 "propane-1,3-diamine" IUPAC_SYSTEMATIC bmst000001 1 stop_ loop_ _Chem_comp_db_link.Author_supplied _Chem_comp_db_link.Database_code _Chem_comp_db_link.Accession_code_type _Chem_comp_db_link.Accession_code _Chem_comp_db_link.Entry_mol_code _Chem_comp_db_link.Entry_mol_name _Chem_comp_db_link.Entry_experimental_method _Chem_comp_db_link.Entry_relation_type _Chem_comp_db_link.Entry_details _Chem_comp_db_link.Entry_ID _Chem_comp_db_link.Comp_ID no PubChem sid 151124 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no PubChem cid 428 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no PubChem sid 4233 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no KEGG 'compound ID' C00986 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no 'CAS Registry' 'registry number' 10517-44-9 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no 'CAS Registry' 'registry number' 109-76-2 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no 'CAS Registry' 'registry number' 54018-94-9 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no CHEBI ? 15725 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no NSC ? 8154 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no 'Beilstein Handbook Reference' ? 4-04-00-01258 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no CCRIS ? 4054 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 no EINECS ? 203-702-7 ? "1-3-diaminopropane" ? 'matching entry' ? bmst000001 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID C1 C1 ? bmst000001 1 C2 C2 ? bmst000001 1 C3 C3 ? bmst000001 1 N4 N4 ? bmst000001 1 H5 H5 ? bmst000001 1 N6 N6 ? bmst000001 1 H7 H7 ? bmst000001 1 H8 H8 ? bmst000001 1 H9 H9 ? bmst000001 1 H10 H10 ? bmst000001 1 H11 H11 ? bmst000001 1 H12 H12 ? bmst000001 1 H13 H13 ? bmst000001 1 H14 H14 ? bmst000001 1 H15 H15 ? bmst000001 1 stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Details _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 covalent SING C1 C2 ? bmst000001 1 2 covalent SING C1 N6 ? bmst000001 1 3 covalent SING C1 H10 ? bmst000001 1 4 covalent SING C1 H11 ? bmst000001 1 5 covalent SING C2 C3 ? bmst000001 1 6 covalent SING C2 H12 ? bmst000001 1 7 covalent SING C2 H13 ? bmst000001 1 8 covalent SING C3 N4 ? bmst000001 1 9 covalent SING C3 H14 ? bmst000001 1 10 covalent SING C3 H15 ? bmst000001 1 11 covalent SING N4 H5 ? bmst000001 1 12 covalent SING N4 H9 ? bmst000001 1 13 covalent SING N6 H7 ? bmst000001 1 14 covalent SING N6 H8 ? bmst000001 1 stop_ loop_ _Chem_comp_citation.Citation_ID _Chem_comp_citation.Citation_label _Chem_comp_citation.Entry_ID _Chem_comp_citation.Comp_ID 1 $citations bmst000001 1 stop_ save_ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmst000001 _Software.ID 1 _Software.Name Gaussian _Software.Version ? _Software.Details ? loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID "Gaussian, Inc." ? "http://www.gaussian.com/home.htm" bmst000001 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'geometry optimization' bmst000001 1 'chemical shift calculation' bmst000001 1 stop_ save_ save_chem_shift_reference _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference _Chem_shift_reference.Entry_ID bmst000001 _Chem_shift_reference.ID 1 _Chem_shift_reference.Details ? loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _Chem_shift_ref.Mol_common_name _Chem_shift_ref.Atom_group _Chem_shift_ref.Chem_shift_units _Chem_shift_ref.Chem_shift_val _Chem_shift_ref.Ref_type _Chem_shift_ref.Indirect_shift_ratio _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID H 1 TMS 'methyl protons' ppm 0.00 direct ? bmst000001 1 C 13 TMS 'methyl carbons' ppm 0.00 direct ? bmst000001 1 N 15 'ammonia pentamer' nitrogen ppm 0.00 direct ? bmst000001 1 P 31 'phosphoric acid' phosphorus ppm 0.00 direct ? bmst000001 1 stop_ save_ save_chem_shifts_calc_type _Chem_shifts_calc_type.Sf_category chem_shifts_calc_type _Chem_shifts_calc_type.Sf_framecode chem_shifts_calc_type _Chem_shifts_calc_type.Entry_ID bmst000001 _Chem_shifts_calc_type.ID 1 _Chem_shifts_calc_type.Calculation_level 'Density Functional Theory' _Chem_shifts_calc_type.Quantum_mechanical_method GIAO _Chem_shifts_calc_type.Quantum_mechanical_theory_level B3LYP _Chem_shifts_calc_type.Quantum_mechanical_basis_set 3-21g** _Chem_shifts_calc_type.Chem_shift_nucleus ? _Chem_shifts_calc_type.Chem_shift_reference_ID 1 _Chem_shifts_calc_type.Chem_shift_reference_label $chem_shift_reference _Chem_shifts_calc_type.Details ; Theoretical Chemical shift referencing and correction: 1H chemical shifts Tetramethylsilane (TMS) was geometry optimized at the B3LYP/6-311+g* level of theory. The chemical shielding of TMS was calculated at the pbe1pbe/3-21g* level of theory using the GIAO method. The chemical shielding of TMS was used as the reference (0 ppm) to obtain all other chemical shifts. A series of small organic molecules were optimized and the chemical shieldings were calculated in the same manner as that for TMS. To correct for biases arising from the applied level of theory, especially the bias from the small basis set size, a linear regression analysis was used. The slope and intercept from this regression was used to correct the calculated chemical shifts. The chemical shift was calculated by subtracting the chemical shielding value of the compound of interest from that of TMS and applying the slope and intercept corrections obtained from the regression analysis. corrected_shift=((TMS_shielding - uncorrected_shielding)+1.006)/0.963 13C chemical shifts: Tetramethylsilane (TMS) was geometry optimized at the B3LYP/6-311+g* level of theory. The chemical shielding of TMS was calculated at the pbe1pbe/3-21g* level of theory using the GIAO method. The chemical shielding of TMS was used as the reference (0 ppm) to obtain all other chemical shifts. A series of small organic molecules were optimized and the chemical shieldings were calculated in the same manner as that for TMS. To correct for biases arising from the applied level of theory, especially the bias from the small basis set size, a linear regression analysis of theoretical versus experimental chemical shifts was used. The slope and intercept from this regression was used to correct the calculated chemical shifts. The chemical shift was calculated by subtracting the chemical shielding value of the compound of interest from that of TMS and applying the slope and intercept corrections obtained from the regression analysis. Corrected_shift=((TMS_shielding - uncorrected shielding) -4.53)/0.85 15N chemical shifts: A cyclic pentamer of ammonia (NH3_5) was geometry optimized at the B3LYP/6-311+g* level of theory. The chemical shielding of NH3_5 was calculated at the pbe1pbe/3-21g* level of theory using the GIAO method. The chemical shielding of NH3_5 was used as the reference (0 ppm) to obtain all other chemical shifts. A series of small organic molecules were optimized and the chemical shieldings were calculated in the same manner as that for NH3_5. To correct for biases arising from the applied level of theory, especially the bias from the small basis set size, a linear regression analysis was used. The slope and intercept from this regression was used to correct the calculated chemical shifts. The chemical shift was calculated by subtracting the chemical shielding value of the compound of interest from that of NH3_5 and applying the slope and intercept corrections obtained from the regression analysis. Corrected_shift=((NH_3_5_shielding - uncorrected_shielding)+10.2)/0.9088 31P chemical shifts: Phosphoric acid (H3PO4) was geometry optimized at the B3LYP/6-311+g* level of theory. The chemical shielding of H3PO4 was calculated at the pbe1pbe/3-21g* level of theory using the GIAO method. The chemical shielding of H3PO4 was used as the reference (0 ppm) to obtain all other chemical shifts. No correction for linear bias or offset was applied to calculated 31P chemical shifts. The chemical shift was calculated by subtracting the chemical shielding value of the compound of interest from that of H3PO4. Shift=(H3PO4_shielding - shielding) ; loop_ _Chem_shifts_calc_software.Software_ID _Chem_shifts_calc_software.Software_label _Chem_shifts_calc_software.Entry_ID _Chem_shifts_calc_software.Chem_shifts_calc_type_ID 1 $software_1 bmst000001 1 stop_ save_ save_theoretical_chem_shifts _Theoretical_chem_shift_list.Sf_category theoretical_chem_shifts _Theoretical_chem_shift_list.Sf_framecode theoretical_chem_shifts _Theoretical_chem_shift_list.Entry_ID bmst000001 _Theoretical_chem_shift_list.ID 1 _Theoretical_chem_shift_list.Data_file_name 1_3_diaminopropane_4233.g03.shifts _Theoretical_chem_shift_list.Chem_shifts_calc_type_ID 1 _Theoretical_chem_shift_list.Chem_shifts_calc_type_label $chem_shifts_calc_type _Theoretical_chem_shift_list.Model_atomic_coordinates_ID 1 _Theoretical_chem_shift_list.Model_atomic_coordinates_label $conformer_family_coord_set_1 _Theoretical_chem_shift_list.Chem_shielding_tensor_list_ID ? _Theoretical_chem_shift_list.Chem_shielding_tensor_list_label ? _Theoretical_chem_shift_list.Fermi_contact_spin_density_units ? _Theoretical_chem_shift_list.Chem_shift_1H_err ? _Theoretical_chem_shift_list.Chem_shift_2H_err ? _Theoretical_chem_shift_list.Chem_shift_13C_err ? _Theoretical_chem_shift_list.Chem_shift_15N_err ? _Theoretical_chem_shift_list.Chem_shift_19F_err ? _Theoretical_chem_shift_list.Chem_shift_31P_err ? _Theoretical_chem_shift_list.Details ? _Theoretical_chem_shift_list.Text_data_format ? _Theoretical_chem_shift_list.Text_data ? loop_ _Theoretical_chem_shift.ID _Theoretical_chem_shift.Entity_ID _Theoretical_chem_shift.Comp_index_ID _Theoretical_chem_shift.Comp_ID _Theoretical_chem_shift.Atom_ID _Theoretical_chem_shift.Atom_type _Theoretical_chem_shift.Fermi_contact_spin_density _Theoretical_chem_shift.Val _Theoretical_chem_shift.Val_err _Theoretical_chem_shift.Auth_seq_ID _Theoretical_chem_shift.Auth_comp_ID _Theoretical_chem_shift.Auth_atom_ID _Theoretical_chem_shift.Entry_ID _Theoretical_chem_shift.Theoretical_chem_shift_list_ID 1 1 1 1_3_diaminopropane C1 C ? 44.226 ? 1_3_diaminopropane ? ? bmst000001 1 2 1 1 1_3_diaminopropane C2 C ? 36.162 ? 1_3_diaminopropane ? ? bmst000001 1 3 1 1 1_3_diaminopropane C3 C ? 44.226 ? 1_3_diaminopropane ? ? bmst000001 1 4 1 1 1_3_diaminopropane N4 N ? 36.898 ? 1_3_diaminopropane ? ? bmst000001 1 5 1 1 1_3_diaminopropane H5 H ? 0.798 ? 1_3_diaminopropane ? ? bmst000001 1 6 1 1 1_3_diaminopropane N6 N ? 36.898 ? 1_3_diaminopropane ? ? bmst000001 1 7 1 1 1_3_diaminopropane H7 H ? 0.798 ? 1_3_diaminopropane ? ? bmst000001 1 8 1 1 1_3_diaminopropane H8 H ? 0.226 ? 1_3_diaminopropane ? ? bmst000001 1 9 1 1 1_3_diaminopropane H9 H ? 0.226 ? 1_3_diaminopropane ? ? bmst000001 1 10 1 1 1_3_diaminopropane H10 H ? 3.556 ? 1_3_diaminopropane ? ? bmst000001 1 11 1 1 1_3_diaminopropane H11 H ? 3.575 ? 1_3_diaminopropane ? ? bmst000001 1 12 1 1 1_3_diaminopropane H12 H ? 3.241 ? 1_3_diaminopropane ? ? bmst000001 1 13 1 1 1_3_diaminopropane H13 H ? 2.046 ? 1_3_diaminopropane ? ? bmst000001 1 14 1 1 1_3_diaminopropane H14 H ? 3.556 ? 1_3_diaminopropane ? ? bmst000001 1 15 1 1 1_3_diaminopropane H15 H ? 3.575 ? 1_3_diaminopropane ? ? bmst000001 1 stop_ save_ save_conformer_family_coord_set_1 _Conformer_family_coord_set.Sf_category conformer_family_coord_set _Conformer_family_coord_set.Sf_framecode conformer_family_coord_set_1 _Conformer_family_coord_set.Entry_ID bmst000001 _Conformer_family_coord_set.ID 1 _Conformer_family_coord_set.File_name 1_3_diaminopropane_4233_opt.pdb _Conformer_family_coord_set.Details ? loop_ _Conformer_family_software.Software_ID _Conformer_family_software.Software_label _Conformer_family_software.Entry_ID _Conformer_family_software.Conformer_family_coord_set_ID 1 $software_1 bmst000001 1 stop_ loop_ _Atom_site.Model_ID _Atom_site.ID _Atom_site.Label_entity_ID _Atom_site.Label_comp_index_ID _Atom_site.Label_comp_ID _Atom_site.Label_atom_ID _Atom_site.Auth_seq_ID _Atom_site.Auth_comp_ID _Atom_site.Auth_atom_ID _Atom_site.Type_symbol _Atom_site.Cartn_x _Atom_site.Cartn_y _Atom_site.Cartn_z _Atom_site.Entry_ID _Atom_site.Conformer_family_coord_set_ID 1 1 1 1 1 C1 1 1 C1 C 1.330 -0.331 -0.017 bmst000001 1 1 2 1 1 1 C2 1 1 C2 C -0.198 -0.281 -0.034 bmst000001 1 1 3 1 1 1 C3 1 1 C3 C -0.755 1.144 -0.017 bmst000001 1 1 4 1 1 1 N4 1 1 N4 N -2.223 1.124 -0.062 bmst000001 1 1 5 1 1 1 H5 1 1 H5 H -2.580 2.078 -0.070 bmst000001 1 1 6 1 1 1 N6 1 1 N6 N 1.800 -1.721 -0.062 bmst000001 1 1 7 1 1 1 H7 1 1 H7 H 2.819 -1.739 -0.070 bmst000001 1 1 8 1 1 1 H8 1 1 H8 H 1.520 -2.200 0.794 bmst000001 1 1 9 1 1 1 H9 1 1 H9 H -2.581 0.700 0.794 bmst000001 1 1 10 1 1 1 H10 1 1 H10 H 1.718 0.178 -0.909 bmst000001 1 1 11 1 1 1 H11 1 1 H11 H 1.704 0.240 0.855 bmst000001 1 1 12 1 1 1 H12 1 1 H12 H -0.571 -0.808 -0.918 bmst000001 1 1 13 1 1 1 H13 1 1 H13 H -0.585 -0.827 0.843 bmst000001 1 1 14 1 1 1 H14 1 1 H14 H -0.405 1.679 -0.909 bmst000001 1 1 15 1 1 1 H15 1 1 H15 H -0.342 1.687 0.855 bmst000001 1 stop_ save_