data_bmst000239 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmst000239 _Entry.Title UTP _Entry.Version_type update _Entry.Submission_date 2006-04-13 _Entry.Accession_date 2006-04-13 _Entry.Last_release_date 2011-09-14 _Entry.Original_release_date 2006-04-13 _Entry.Origination author _Entry.NMR_STAR_version 3.1.1.7 _Entry.Original_NMR_STAR_version 'NMR STAR v3.1' _Entry.Experimental_method NMR _Entry.Experimental_method_subtype theoretical _Entry.Details ? _Entry.BMRB_internal_directory_name UTP loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.Middle_initials _Entry_author.Family_title _Entry_author.Entry_ID 1 William Westler M. ? bmst000239 2 John Markley L. ? bmst000239 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Organization_full_name _Entry_src.Organization_initials _Entry_src.Entry_ID 1 metabolics 'Madison Metabolomics Consortium' MMC bmst000239 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID other_data_list 1 bmst000239 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID 'theoretical chemical shifts' 1 bmst000239 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 1 . . 2006-04-13 2006-04-13 original BMRB 'Original theoretical calculations from NMRFAM' bmst000239 2 . . 2008-11-18 2008-11-18 update BMRB 'updated the file to match latest NMR STAR dictionary' bmst000239 3 . . 2008-11-25 2008-11-25 update BMRB 'fixed enumerations: N should be no' bmst000239 4 . . 2010-09-16 2010-09-16 update BMRB 'Removed Shielding_tensor_list_ID and Shielding_tensor_list_label from theoretical_chem_shifts' bmst000239 5 . . 2011-09-14 2011-09-14 update BMRB 'Partially brought up to date with latest Dictionary' bmst000239 6 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmst000239 stop_ loop_ _Auxiliary_files.ID _Auxiliary_files.URI _Auxiliary_files.DOI _Auxiliary_files.Path _Auxiliary_files.Format _Auxiliary_files.Details _Auxiliary_files.Entry_ID 1 . . UTP_3375_opt.pdb x-chemical/x-pdb 'Name of the file containing the atomic coordinates' bmst000239 2 . . UTP_3375.g03.shifts text/plain 'Name of the file containing theoretical chemical shift data' bmst000239 stop_ save_ ############### # Citations # ############### save_citations _Citation.Sf_category citations _Citation.Sf_framecode citations _Citation.Entry_ID bmst000239 _Citation.ID 1 _Citation.Class 'reference citation' _Citation.PubMed_ID 18940862 _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. ? bmst000239 1 2 T. Barrett T. ? ? bmst000239 1 3 D. Benson D. A. ? bmst000239 1 4 S. Bryant S. H. ? bmst000239 1 5 K. Canese K. ? ? bmst000239 1 6 V. Chetvenin V. ? ? bmst000239 1 7 D. Church D. M. ? bmst000239 1 8 M. DiCuccio M. ? ? bmst000239 1 9 R. Edgar R. ? ? bmst000239 1 10 S. Federhen S. ? ? bmst000239 1 11 L. Geer L. Y. ? bmst000239 1 12 W. Helmberg W. ? ? bmst000239 1 13 Y. Kapustin Y. ? ? bmst000239 1 14 D. Kenton D. L. ? bmst000239 1 15 O. Khovayko O. ? ? bmst000239 1 16 D. Lipman D. J. ? bmst000239 1 17 T. Madden T. L. ? bmst000239 1 18 D. Maglott D. R. ? bmst000239 1 19 J. Ostell J. ? ? bmst000239 1 20 K. Pruitt K. D. ? bmst000239 1 21 G. Schuler G. D. ? bmst000239 1 22 L. Schriml L. M. ? bmst000239 1 23 E. Sequeira E. ? ? bmst000239 1 24 S. Sherry S. T. ? bmst000239 1 25 K. Sirotkin K. ? ? bmst000239 1 26 A. Souvorov A. ? ? bmst000239 1 27 G. Starchenko G. ? ? bmst000239 1 28 T. Suzek T. O. ? bmst000239 1 29 R. Tatusov R. ? ? bmst000239 1 30 T. Tatusova T. A. ? bmst000239 1 31 L. Bagner L. ? ? bmst000239 1 32 E. Yaschenko E. ? ? bmst000239 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmst000239 _Assembly.ID 1 _Assembly.Name ASSEMBLY_NAME _Assembly.Number_of_components 1 _Assembly.Organic_ligands 0 _Assembly.Metal_ions ? _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state 'not reported' loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 ENT_NAME 1 $UTP yes native no no ? ? ? bmst000239 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_UTP _Entity.Sf_category entity _Entity.Sf_framecode UTP _Entity.Entry_ID bmst000239 _Entity.ID 1 _Entity.BMRB_code ? _Entity.Name UTP _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality no _Entity.Nstd_linkage no _Entity.Paramagnetic no _Entity.Thiol_state 'not reported' 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 bmst000239 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_1 _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_1 _Chem_comp.Entry_ID bmst000239 _Chem_comp.ID 1 _Chem_comp.Provenance PubChem _Chem_comp.Name UTP _Chem_comp.Type non-polymer _Chem_comp.BMRB_code ? _Chem_comp.PDB_code ? _Chem_comp.InChI_code ; InChI=1/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1/f/h10,16-17,19,21H ; _Chem_comp.Mon_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.Formal_charge ? _Chem_comp.Paramagnetic no _Chem_comp.Aromatic yes _Chem_comp.Formula 'C9 H15 N2 O15 P3' _Chem_comp.Formula_weight 484.1410830000 _Chem_comp.Formula_mono_iso_wt_nat 483.968527353 _Chem_comp.Formula_mono_iso_wt_13C 492.998720894 _Chem_comp.Formula_mono_iso_wt_15N 485.96259714 _Chem_comp.Formula_mono_iso_wt_13C_15N 492.998720894 _Chem_comp.Image_file_name bmst000239.png _Chem_comp.Image_file_format png _Chem_comp.Topo_file_name ? _Chem_comp.Topo_file_format ? _Chem_comp.Struct_file_name bmst000239.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_common_name.Name _Chem_comp_common_name.Type _Chem_comp_common_name.Entry_ID _Chem_comp_common_name.Comp_ID "URIDINE 5'-TRIPHOSPHATE" synonym bmst000239 1 'Uridine triphosphate' synonym bmst000239 1 "Uridine 5'-(tetrahydrogen triphosphate)" synonym bmst000239 1 "Uridine 5'-triphosphoric acid" synonym bmst000239 1 UTP synonym bmst000239 1 Uteplex synonym bmst000239 1 'BRN 0071520' synonym bmst000239 1 5'-UTP synonym bmst000239 1 "Uridine 5'-triphosphate" synonym bmst000239 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 ; [[[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC bmst000239 1 ; [[[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_TRADITIONAL bmst000239 1 ; [[[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_OPENEYE bmst000239 1 ; [[[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_CAS bmst000239 1 ; [[[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_SYSTEMATIC bmst000239 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID Canonical C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O bmst000239 1 stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Oxidation_number _Chem_comp_atom.Unpaired_electron_number _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.Model_Cartn_x _Chem_comp_atom.Model_Cartn_y _Chem_comp_atom.Model_Cartn_z _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID P1 P ? ? ? ? 8.4732 -3.1217 -1.327 1.170 3.069 1 bmst000239 1 P2 P ? ? ? ? 6.8909 -2.4172 -0.026 -1.183 2.033 2 bmst000239 1 P3 P ? ? ? ? 10.0555 -3.8262 -3.826 1.759 4.087 3 bmst000239 1 O4 O ? ? ? ? 7.4787 -3.2262 -0.693 0.368 1.858 4 bmst000239 1 O5 O ? ? ? ? 9.4677 -3.0171 -2.944 0.996 2.914 5 bmst000239 1 O6 O ? ? ? ? 6.3031 -1.6082 0.989 -1.213 0.816 6 bmst000239 1 O7 O ? ? ? ? 8.5778 -4.1162 -1.039 2.682 2.689 7 bmst000239 1 O8 O ? ? ? ? 7.6999 -1.8294 0.971 -0.991 3.257 8 bmst000239 1 O9 O ? ? ? ? 10.8645 -3.2384 -3.638 0.840 5.366 9 bmst000239 1 O10 O ? ? ? ? 10.6433 -4.6352 -5.337 1.457 3.692 10 bmst000239 1 O11 O ? ? ? ? 2.4607 0.3564 -1.065 0.187 -4.099 11 bmst000239 1 O12 O ? ? ? ? 3.1330 -1.7127 -1.701 -1.930 -2.672 12 bmst000239 1 O13 O ? ? ? ? 5.0298 0.0474 1.207 -0.066 -1.863 13 bmst000239 1 O14 O ? ? ? ? 8.3687 -2.1271 -0.901 0.680 4.420 14 bmst000239 1 O15 O ? ? ? ? 6.0819 -3.0050 -1.083 -2.207 2.084 15 bmst000239 1 O16 O ? ? ? ? 9.2465 -4.4139 -3.414 3.187 4.138 16 bmst000239 1 O17 O ? ? ? ? 2.4888 1.6352 2.493 -2.245 -3.490 17 bmst000239 1 O18 O ? ? ? ? 4.2208 4.6352 6.331 -0.383 -5.128 18 bmst000239 1 N19 N ? ? ? ? 4.2208 1.6352 2.509 0.038 -3.822 19 bmst000239 1 N20 N ? ? ? ? 3.3548 3.1352 4.386 -1.262 -4.308 20 bmst000239 1 C21 C ? ? ? ? 5.3086 -1.7127 0.660 -1.908 -0.414 21 bmst000239 1 C22 C ? ? ? ? 4.2208 0.6352 1.165 0.204 -3.251 22 bmst000239 1 C23 C ? ? ? ? 4.7208 -0.9037 0.153 -0.950 -1.474 23 bmst000239 1 C24 C ? ? ? ? 3.4118 0.0474 0.043 -0.662 -3.869 24 bmst000239 1 C25 C ? ? ? ? 3.7208 -0.9037 -0.298 -1.679 -2.752 25 bmst000239 1 C26 C ? ? ? ? 3.3548 2.1352 3.088 -1.236 -3.841 26 bmst000239 1 C27 C ? ? ? ? 4.2208 3.6352 5.193 -0.184 -4.741 27 bmst000239 1 C28 C ? ? ? ? 5.0868 2.1352 3.236 1.151 -4.202 28 bmst000239 1 C29 C ? ? ? ? 5.0868 3.1352 4.506 1.095 -4.654 29 bmst000239 1 H30 H ? ? ? ? 8.0762 -4.4806 -1.698 3.261 3.148 30 bmst000239 1 H31 H ? ? ? ? 7.6351 -1.2128 0.514 -0.552 4.013 31 bmst000239 1 H32 H ? ? ? ? 11.2599 -4.5704 -5.749 2.229 3.268 32 bmst000239 1 H33 H ? ? ? ? 10.7997 -2.6218 -2.688 0.601 5.470 33 bmst000239 1 H34 H ? ? ? ? 2.0000 -0.0585 -1.845 -0.314 -3.788 34 bmst000239 1 H35 H ? ? ? ? 3.3852 -2.2791 -1.898 -2.739 -3.168 35 bmst000239 1 H36 H ? ? ? ? 2.8179 3.4452 4.815 -2.181 -4.333 36 bmst000239 1 H37 H ? ? ? ? 4.7514 -1.9845 -0.095 -2.674 -0.211 37 bmst000239 1 H38 H ? ? ? ? 5.4795 -2.3087 1.591 -2.371 -0.747 38 bmst000239 1 H39 H ? ? ? ? 3.6684 0.9166 0.902 1.252 -3.423 39 bmst000239 1 H40 H ? ? ? ? 5.3332 -0.8067 -0.695 -0.369 -1.086 40 bmst000239 1 H41 H ? ? ? ? 2.9734 -0.3910 0.367 -1.148 -4.797 41 bmst000239 1 H42 H ? ? ? ? 3.1085 -0.8067 0.266 -2.602 -2.897 42 bmst000239 1 H43 H ? ? ? ? 5.6238 1.8252 2.699 2.090 -4.116 43 bmst000239 1 H44 H ? ? ? ? 5.6238 3.4452 5.040 1.987 -4.952 44 bmst000239 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID P1 P1 ? bmst000239 1 P2 P2 ? bmst000239 1 P3 P3 ? bmst000239 1 O4 O4 ? bmst000239 1 O5 O5 ? bmst000239 1 O6 O6 ? bmst000239 1 O7 O7 ? bmst000239 1 O8 O8 ? bmst000239 1 O9 O9 ? bmst000239 1 O10 O10 ? bmst000239 1 O11 O11 ? bmst000239 1 O12 O12 ? bmst000239 1 O13 O13 ? bmst000239 1 O14 O14 ? bmst000239 1 O15 O15 ? bmst000239 1 O16 O16 ? bmst000239 1 O17 O17 ? bmst000239 1 O18 O18 ? bmst000239 1 N19 N19 ? bmst000239 1 N20 N20 ? bmst000239 1 C21 C21 ? bmst000239 1 C22 C22 ? bmst000239 1 C23 C23 ? bmst000239 1 C24 C24 ? bmst000239 1 C25 C25 ? bmst000239 1 C26 C26 ? bmst000239 1 C27 C27 ? bmst000239 1 C28 C28 ? bmst000239 1 C29 C29 ? bmst000239 1 H30 H30 ? bmst000239 1 H31 H31 ? bmst000239 1 H32 H32 ? bmst000239 1 H33 H33 ? bmst000239 1 H34 H34 ? bmst000239 1 H35 H35 ? bmst000239 1 H36 H36 ? bmst000239 1 H37 H37 ? bmst000239 1 H38 H38 ? bmst000239 1 H39 H39 ? bmst000239 1 H40 H40 ? bmst000239 1 H41 H41 ? bmst000239 1 H42 H42 ? bmst000239 1 H43 H43 ? bmst000239 1 H44 H44 ? bmst000239 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 P1 O4 ? bmst000239 1 2 covalent SING P1 O5 ? bmst000239 1 3 covalent SING P1 O7 ? bmst000239 1 4 covalent DOUB P1 O14 ? bmst000239 1 5 covalent SING P2 O4 ? bmst000239 1 6 covalent SING P2 O6 ? bmst000239 1 7 covalent SING P2 O8 ? bmst000239 1 8 covalent DOUB P2 O15 ? bmst000239 1 9 covalent SING P3 O5 ? bmst000239 1 10 covalent SING P3 O9 ? bmst000239 1 11 covalent SING P3 O10 ? bmst000239 1 12 covalent DOUB P3 O16 ? bmst000239 1 13 covalent SING O6 C21 ? bmst000239 1 14 covalent SING O7 H30 ? bmst000239 1 15 covalent SING O8 H31 ? bmst000239 1 16 covalent SING O9 H33 ? bmst000239 1 17 covalent SING O10 H32 ? bmst000239 1 18 covalent SING C24 O11 ? bmst000239 1 19 covalent SING O11 H34 ? bmst000239 1 20 covalent SING C25 O12 ? bmst000239 1 21 covalent SING O12 H35 ? bmst000239 1 22 covalent SING O13 C22 ? bmst000239 1 23 covalent SING O13 C23 ? bmst000239 1 24 covalent DOUB O17 C26 ? bmst000239 1 25 covalent DOUB O18 C27 ? bmst000239 1 26 covalent SING C22 N19 ? bmst000239 1 27 covalent SING N19 C26 ? bmst000239 1 28 covalent SING N19 C28 ? bmst000239 1 29 covalent SING N20 C26 ? bmst000239 1 30 covalent SING N20 C27 ? bmst000239 1 31 covalent SING N20 H36 ? bmst000239 1 32 covalent SING C23 C21 ? bmst000239 1 33 covalent SING C21 H37 ? bmst000239 1 34 covalent SING C21 H38 ? bmst000239 1 35 covalent SING C22 C24 ? bmst000239 1 36 covalent SING C22 H39 ? bmst000239 1 37 covalent SING C23 C25 ? bmst000239 1 38 covalent SING C23 H40 ? bmst000239 1 39 covalent SING C24 C25 ? bmst000239 1 40 covalent SING C24 H41 ? bmst000239 1 41 covalent SING C25 H42 ? bmst000239 1 42 covalent SING C27 C29 ? bmst000239 1 43 covalent DOUB C28 C29 ? bmst000239 1 44 covalent SING C28 H43 ? bmst000239 1 45 covalent SING C29 H44 ? bmst000239 1 stop_ loop_ _Chem_comp_db_link.Author_supplied _Chem_comp_db_link.Database_code _Chem_comp_db_link.Accession_code _Chem_comp_db_link.Accession_code_type _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 149028 sid ? UTP ? 'matching entry' ? bmst000239 1 no PubChem 3375 sid ? UTP ? 'matching entry' ? bmst000239 1 no PubChem 6133 cid ? UTP ? 'matching entry' ? bmst000239 1 no KEGG C00075 'compound ID' ? UTP ? 'matching entry' ? bmst000239 1 no ChemIDplus 000063398 ? ? UTP ? 'matching entry' ? bmst000239 1 no 'CAS Registry' 63-39-8 'registry number' ? UTP ? 'matching entry' ? bmst000239 1 no EINECS 200-558-7 ? ? UTP ? 'matching entry' ? bmst000239 1 no 'Beilstein Handbook Reference' 4-24-00-01222 ? ? UTP ? 'matching entry' ? bmst000239 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 bmst000239 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmst000239 _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 bmst000239 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'geometry optimization' bmst000239 1 'chemical shift calculation' bmst000239 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ 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 bmst000239 _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_method _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 na direct ? bmst000239 1 C 13 TMS 'methyl carbons' ppm 0.00 na direct ? bmst000239 1 N 15 'ammonia pentamer' nitrogen ppm 0.00 na direct ? bmst000239 1 P 31 'phosphoric acid' phosphorus ppm 0.00 na direct ? bmst000239 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 bmst000239 _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 bmst000239 1 stop_ save_ ################################# # Theoretical chemical shifts # ################################# 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 bmst000239 _Theoretical_chem_shift_list.ID 1 _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.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_assembly_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 1 P1 P ? -2.621 ? UTP ? ? bmst000239 1 2 1 1 1 1 P2 P ? 1.367 ? UTP ? ? bmst000239 1 3 1 1 1 1 P3 P ? 6.052 ? UTP ? ? bmst000239 1 4 1 1 1 1 N19 N ? 157.580 ? UTP ? ? bmst000239 1 5 1 1 1 1 N20 N ? 166.106 ? UTP ? ? bmst000239 1 6 1 1 1 1 C21 C ? 74.600 ? UTP ? ? bmst000239 1 7 1 1 1 1 C22 C ? 110.369 ? UTP ? ? bmst000239 1 8 1 1 1 1 C23 C ? 89.877 ? UTP ? ? bmst000239 1 9 1 1 1 1 C24 C ? 77.957 ? UTP ? ? bmst000239 1 10 1 1 1 1 C25 C ? 77.892 ? UTP ? ? bmst000239 1 11 1 1 1 1 C26 C ? 157.080 ? UTP ? ? bmst000239 1 12 1 1 1 1 C27 C ? 166.995 ? UTP ? ? bmst000239 1 13 1 1 1 1 C28 C ? 151.807 ? UTP ? ? bmst000239 1 14 1 1 1 1 C29 C ? 108.749 ? UTP ? ? bmst000239 1 15 1 1 1 1 H30 H ? 7.737 ? UTP ? ? bmst000239 1 16 1 1 1 1 H31 H ? 7.355 ? UTP ? ? bmst000239 1 17 1 1 1 1 H32 H ? 4.736 ? UTP ? ? bmst000239 1 18 1 1 1 1 H33 H ? 6.845 ? UTP ? ? bmst000239 1 19 1 1 1 1 H34 H ? 3.590 ? UTP ? ? bmst000239 1 20 1 1 1 1 H35 H ? 0.990 ? UTP ? ? bmst000239 1 21 1 1 1 1 H36 H ? 7.235 ? UTP ? ? bmst000239 1 22 1 1 1 1 H37 H ? 5.745 ? UTP ? ? bmst000239 1 23 1 1 1 1 H38 H ? 5.751 ? UTP ? ? bmst000239 1 24 1 1 1 1 H39 H ? 6.061 ? UTP ? ? bmst000239 1 25 1 1 1 1 H40 H ? 5.421 ? UTP ? ? bmst000239 1 26 1 1 1 1 H41 H ? 4.920 ? UTP ? ? bmst000239 1 27 1 1 1 1 H42 H ? 5.778 ? UTP ? ? bmst000239 1 28 1 1 1 1 H43 H ? 8.368 ? UTP ? ? bmst000239 1 29 1 1 1 1 H44 H ? 6.822 ? UTP ? ? bmst000239 1 stop_ save_ ##################################### # Conformer family coordinate set # ##################################### 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 bmst000239 _Conformer_family_coord_set.ID 1 _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 bmst000239 1 stop_ loop_ _Atom_site.Model_ID _Atom_site.ID _Atom_site.Label_entity_assembly_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 1 P1 1 1 P1 P -1.327 1.170 3.069 bmst000239 1 1 2 1 1 1 1 P2 1 1 P2 P -0.026 -1.183 2.033 bmst000239 1 1 3 1 1 1 1 P3 1 1 P3 P -3.826 1.759 4.087 bmst000239 1 1 4 1 1 1 1 O4 1 1 O4 O -0.693 0.368 1.858 bmst000239 1 1 5 1 1 1 1 O5 1 1 O5 O -2.944 0.996 2.914 bmst000239 1 1 6 1 1 1 1 O6 1 1 O6 O 0.989 -1.213 0.816 bmst000239 1 1 7 1 1 1 1 O7 1 1 O7 O -1.039 2.682 2.689 bmst000239 1 1 8 1 1 1 1 O8 1 1 O8 O 0.971 -0.991 3.257 bmst000239 1 1 9 1 1 1 1 O9 1 1 O9 O -3.638 0.840 5.366 bmst000239 1 1 10 1 1 1 1 O10 1 1 O10 O -5.337 1.457 3.692 bmst000239 1 1 11 1 1 1 1 O11 1 1 O11 O -1.065 0.187 -4.099 bmst000239 1 1 12 1 1 1 1 O12 1 1 O12 O -1.701 -1.930 -2.672 bmst000239 1 1 13 1 1 1 1 O13 1 1 O13 O 1.207 -0.066 -1.863 bmst000239 1 1 14 1 1 1 1 O14 1 1 O14 O -0.901 0.680 4.420 bmst000239 1 1 15 1 1 1 1 O15 1 1 O15 O -1.083 -2.207 2.084 bmst000239 1 1 16 1 1 1 1 O16 1 1 O16 O -3.414 3.187 4.138 bmst000239 1 1 17 1 1 1 1 O17 1 1 O17 O 2.493 -2.245 -3.490 bmst000239 1 1 18 1 1 1 1 O18 1 1 O18 O 6.331 -0.383 -5.128 bmst000239 1 1 19 1 1 1 1 N19 1 1 N19 N 2.509 0.038 -3.822 bmst000239 1 1 20 1 1 1 1 N20 1 1 N20 N 4.386 -1.262 -4.308 bmst000239 1 1 21 1 1 1 1 C21 1 1 C21 C 0.660 -1.908 -0.414 bmst000239 1 1 22 1 1 1 1 C22 1 1 C22 C 1.165 0.204 -3.251 bmst000239 1 1 23 1 1 1 1 C23 1 1 C23 C 0.153 -0.950 -1.474 bmst000239 1 1 24 1 1 1 1 C24 1 1 C24 C 0.043 -0.662 -3.869 bmst000239 1 1 25 1 1 1 1 C25 1 1 C25 C -0.298 -1.679 -2.752 bmst000239 1 1 26 1 1 1 1 C26 1 1 C26 C 3.088 -1.236 -3.841 bmst000239 1 1 27 1 1 1 1 C27 1 1 C27 C 5.193 -0.184 -4.741 bmst000239 1 1 28 1 1 1 1 C28 1 1 C28 C 3.236 1.151 -4.202 bmst000239 1 1 29 1 1 1 1 C29 1 1 C29 C 4.506 1.095 -4.654 bmst000239 1 1 30 1 1 1 1 H30 1 1 H30 H -1.698 3.261 3.148 bmst000239 1 1 31 1 1 1 1 H31 1 1 H31 H 0.514 -0.552 4.013 bmst000239 1 1 32 1 1 1 1 H32 1 1 H32 H -5.749 2.229 3.268 bmst000239 1 1 33 1 1 1 1 H33 1 1 H33 H -2.688 0.601 5.470 bmst000239 1 1 34 1 1 1 1 H34 1 1 H34 H -1.845 -0.314 -3.788 bmst000239 1 1 35 1 1 1 1 H35 1 1 H35 H -1.898 -2.739 -3.168 bmst000239 1 1 36 1 1 1 1 H36 1 1 H36 H 4.815 -2.181 -4.333 bmst000239 1 1 37 1 1 1 1 H37 1 1 H37 H -0.095 -2.674 -0.211 bmst000239 1 1 38 1 1 1 1 H38 1 1 H38 H 1.591 -2.371 -0.747 bmst000239 1 1 39 1 1 1 1 H39 1 1 H39 H 0.902 1.252 -3.423 bmst000239 1 1 40 1 1 1 1 H40 1 1 H40 H -0.695 -0.369 -1.086 bmst000239 1 1 41 1 1 1 1 H41 1 1 H41 H 0.367 -1.148 -4.797 bmst000239 1 1 42 1 1 1 1 H42 1 1 H42 H 0.266 -2.602 -2.897 bmst000239 1 1 43 1 1 1 1 H43 1 1 H43 H 2.699 2.090 -4.116 bmst000239 1 1 44 1 1 1 1 H44 1 1 H44 H 5.040 1.987 -4.952 bmst000239 1 stop_ save_