data_bmst000234 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmst000234 _Entry.Title UDP _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 UDP 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. ? bmst000234 2 John Markley L. ? bmst000234 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 bmst000234 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID other_data_list 1 bmst000234 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID 'theoretical chemical shifts' 1 bmst000234 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' bmst000234 2 . . 2008-11-18 2008-11-18 update BMRB 'updated the file to match latest NMR STAR dictionary' bmst000234 3 . . 2008-11-25 2008-11-25 update BMRB 'fixed enumerations: N should be no' bmst000234 4 . . 2010-09-16 2010-09-16 update BMRB 'Removed Shielding_tensor_list_ID and Shielding_tensor_list_label from theoretical_chem_shifts' bmst000234 5 . . 2011-09-14 2011-09-14 update BMRB 'Partially brought up to date with latest Dictionary' bmst000234 6 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmst000234 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 . . UDP_3317_opt.pdb x-chemical/x-pdb 'Name of the file containing the atomic coordinates' bmst000234 2 . . UDP_3317.g03.shifts text/plain 'Name of the file containing theoretical chemical shift data' bmst000234 stop_ save_ ############### # Citations # ############### save_citations _Citation.Sf_category citations _Citation.Sf_framecode citations _Citation.Entry_ID bmst000234 _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. ? bmst000234 1 2 T. Barrett T. ? ? bmst000234 1 3 D. Benson D. A. ? bmst000234 1 4 S. Bryant S. H. ? bmst000234 1 5 K. Canese K. ? ? bmst000234 1 6 V. Chetvenin V. ? ? bmst000234 1 7 D. Church D. M. ? bmst000234 1 8 M. DiCuccio M. ? ? bmst000234 1 9 R. Edgar R. ? ? bmst000234 1 10 S. Federhen S. ? ? bmst000234 1 11 L. Geer L. Y. ? bmst000234 1 12 W. Helmberg W. ? ? bmst000234 1 13 Y. Kapustin Y. ? ? bmst000234 1 14 D. Kenton D. L. ? bmst000234 1 15 O. Khovayko O. ? ? bmst000234 1 16 D. Lipman D. J. ? bmst000234 1 17 T. Madden T. L. ? bmst000234 1 18 D. Maglott D. R. ? bmst000234 1 19 J. Ostell J. ? ? bmst000234 1 20 K. Pruitt K. D. ? bmst000234 1 21 G. Schuler G. D. ? bmst000234 1 22 L. Schriml L. M. ? bmst000234 1 23 E. Sequeira E. ? ? bmst000234 1 24 S. Sherry S. T. ? bmst000234 1 25 K. Sirotkin K. ? ? bmst000234 1 26 A. Souvorov A. ? ? bmst000234 1 27 G. Starchenko G. ? ? bmst000234 1 28 T. Suzek T. O. ? bmst000234 1 29 R. Tatusov R. ? ? bmst000234 1 30 T. Tatusova T. A. ? bmst000234 1 31 L. Bagner L. ? ? bmst000234 1 32 E. Yaschenko E. ? ? bmst000234 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmst000234 _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 $UDP yes native no no ? ? ? bmst000234 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_UDP _Entity.Sf_category entity _Entity.Sf_framecode UDP _Entity.Entry_ID bmst000234 _Entity.ID 1 _Entity.BMRB_code ? _Entity.Name UDP _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 bmst000234 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 bmst000234 _Chem_comp.ID 1 _Chem_comp.Provenance PubChem _Chem_comp.Name UDP _Chem_comp.Type non-polymer _Chem_comp.BMRB_code ? _Chem_comp.PDB_code ? _Chem_comp.InChI_code ; InChI=1/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1/f/h10,16-17,19H ; _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 H14 N2 O12 P2' _Chem_comp.Formula_weight 404.1611820000 _Chem_comp.Formula_mono_iso_wt_nat 404.002196945 _Chem_comp.Formula_mono_iso_wt_13C 413.032390485 _Chem_comp.Formula_mono_iso_wt_15N 405.996266731 _Chem_comp.Formula_mono_iso_wt_13C_15N 413.032390485 _Chem_comp.Image_file_name bmst000234.png _Chem_comp.Image_file_format png _Chem_comp.Topo_file_name ? _Chem_comp.Topo_file_format ? _Chem_comp.Struct_file_name bmst000234.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'-diphosphate" synonym bmst000234 1 'URIDINE DIPHOSPHATE' synonym bmst000234 1 "Uridine 5'-(trihydrogen diphosphate)" synonym bmst000234 1 UDP synonym bmst000234 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]oxyphosphonic acid ; IUPAC bmst000234 1 ; [[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_TRADITIONAL bmst000234 1 ; [[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_OPENEYE bmst000234 1 ; [[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_CAS bmst000234 1 ; [[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxyphosphonic acid ; IUPAC_SYSTEMATIC bmst000234 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)O)O)O bmst000234 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 ? ? ? ? 6.8909 -2.4945 -0.702 -0.940 2.784 1 bmst000234 1 P2 P ? ? ? ? 8.4732 -3.1989 -2.791 0.559 3.804 2 bmst000234 1 O3 O ? ? ? ? 7.4787 -3.3035 -1.618 0.434 2.655 3 bmst000234 1 O4 O ? ? ? ? 6.3031 -1.6854 0.361 -0.828 1.619 4 bmst000234 1 O5 O ? ? ? ? 7.6999 -1.9067 0.200 -0.680 4.067 5 bmst000234 1 O6 O ? ? ? ? 9.4677 -3.0944 -3.865 -0.531 3.379 6 bmst000234 1 O7 O ? ? ? ? 8.5778 -4.1935 -3.544 1.918 3.445 7 bmst000234 1 O8 O ? ? ? ? 2.4607 0.2791 -1.645 0.890 -3.229 8 bmst000234 1 O9 O ? ? ? ? 3.1330 -1.7900 -2.212 -1.364 -1.991 9 bmst000234 1 O10 O ? ? ? ? 5.0298 -0.0299 0.553 0.585 -0.938 10 bmst000234 1 O11 O ? ? ? ? 6.0819 -3.0822 -1.618 -2.115 2.773 11 bmst000234 1 O12 O ? ? ? ? 8.3687 -2.2044 -2.165 0.484 5.152 12 bmst000234 1 O13 O ? ? ? ? 2.4888 1.5579 2.014 -1.413 -2.647 13 bmst000234 1 O14 O ? ? ? ? 4.2208 4.5579 5.801 0.735 -4.034 14 bmst000234 1 N15 N ? ? ? ? 4.2208 1.5579 1.925 0.885 -2.833 15 bmst000234 1 N16 N ? ? ? ? 3.3548 3.0579 3.879 -0.288 -3.335 16 bmst000234 1 C17 C ? ? ? ? 5.3086 -1.7900 0.112 -1.421 0.317 17 bmst000234 1 C18 C ? ? ? ? 4.2208 0.5579 0.553 0.949 -2.304 18 bmst000234 1 C19 C ? ? ? ? 4.7208 -0.9809 -0.443 -0.402 -0.660 19 bmst000234 1 C20 C ? ? ? ? 3.4118 -0.0299 -0.502 0.082 -3.027 20 bmst000234 1 C21 C ? ? ? ? 3.7208 -0.9809 -0.822 -1.040 -2.008 21 bmst000234 1 C22 C ? ? ? ? 3.3548 2.0579 2.569 -0.355 -2.913 22 bmst000234 1 C23 C ? ? ? ? 4.2208 3.5579 4.643 0.853 -3.674 23 bmst000234 1 C24 C ? ? ? ? 5.0868 2.0579 2.606 2.054 -3.119 24 bmst000234 1 C25 C ? ? ? ? 5.0868 3.0579 3.890 2.090 -3.530 25 bmst000234 1 H26 H ? ? ? ? 7.6351 -1.2901 -0.369 -0.321 4.790 26 bmst000234 1 H27 H ? ? ? ? 9.8322 -3.5960 -3.389 -1.370 3.153 27 bmst000234 1 H28 H ? ? ? ? 8.0762 -4.5579 -3.281 2.625 4.058 28 bmst000234 1 H29 H ? ? ? ? 2.0000 -0.1357 -2.407 0.336 -2.971 29 bmst000234 1 H30 H ? ? ? ? 3.3852 -2.3564 -2.358 -2.122 -2.577 30 bmst000234 1 H31 H ? ? ? ? 2.8179 3.3679 4.355 -1.181 -3.404 31 bmst000234 1 H32 H ? ? ? ? 4.7514 -2.0618 -0.584 -2.258 0.424 32 bmst000234 1 H33 H ? ? ? ? 5.4795 -2.3859 1.082 -1.779 -0.032 33 bmst000234 1 H34 H ? ? ? ? 3.6684 0.8394 0.249 1.994 -2.414 34 bmst000234 1 H35 H ? ? ? ? 5.3332 -0.8840 -1.334 0.082 -0.237 35 bmst000234 1 H36 H ? ? ? ? 3.3148 0.5825 -0.124 -0.310 -3.980 36 bmst000234 1 H37 H ? ? ? ? 3.1085 -0.8840 -0.209 -1.919 -2.212 37 bmst000234 1 H38 H ? ? ? ? 5.6238 1.7479 2.020 2.958 -2.993 38 bmst000234 1 H39 H ? ? ? ? 5.6238 3.3679 4.387 3.024 -3.753 39 bmst000234 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 ? bmst000234 1 P2 P2 ? bmst000234 1 O3 O3 ? bmst000234 1 O4 O4 ? bmst000234 1 O5 O5 ? bmst000234 1 O6 O6 ? bmst000234 1 O7 O7 ? bmst000234 1 O8 O8 ? bmst000234 1 O9 O9 ? bmst000234 1 O10 O10 ? bmst000234 1 O11 O11 ? bmst000234 1 O12 O12 ? bmst000234 1 O13 O13 ? bmst000234 1 O14 O14 ? bmst000234 1 N15 N15 ? bmst000234 1 N16 N16 ? bmst000234 1 C17 C17 ? bmst000234 1 C18 C18 ? bmst000234 1 C19 C19 ? bmst000234 1 C20 C20 ? bmst000234 1 C21 C21 ? bmst000234 1 C22 C22 ? bmst000234 1 C23 C23 ? bmst000234 1 C24 C24 ? bmst000234 1 C25 C25 ? bmst000234 1 H26 H26 ? bmst000234 1 H27 H27 ? bmst000234 1 H28 H28 ? bmst000234 1 H29 H29 ? bmst000234 1 H30 H30 ? bmst000234 1 H31 H31 ? bmst000234 1 H32 H32 ? bmst000234 1 H33 H33 ? bmst000234 1 H34 H34 ? bmst000234 1 H35 H35 ? bmst000234 1 H36 H36 ? bmst000234 1 H37 H37 ? bmst000234 1 H38 H38 ? bmst000234 1 H39 H39 ? bmst000234 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 O3 ? bmst000234 1 2 covalent SING P1 O4 ? bmst000234 1 3 covalent SING P1 O5 ? bmst000234 1 4 covalent DOUB P1 O11 ? bmst000234 1 5 covalent SING P2 O3 ? bmst000234 1 6 covalent SING P2 O6 ? bmst000234 1 7 covalent SING P2 O7 ? bmst000234 1 8 covalent DOUB P2 O12 ? bmst000234 1 9 covalent SING O4 C17 ? bmst000234 1 10 covalent SING O5 H26 ? bmst000234 1 11 covalent SING O6 H27 ? bmst000234 1 12 covalent SING O7 H28 ? bmst000234 1 13 covalent SING C20 O8 ? bmst000234 1 14 covalent SING O8 H29 ? bmst000234 1 15 covalent SING C21 O9 ? bmst000234 1 16 covalent SING O9 H30 ? bmst000234 1 17 covalent SING O10 C18 ? bmst000234 1 18 covalent SING O10 C19 ? bmst000234 1 19 covalent DOUB O13 C22 ? bmst000234 1 20 covalent DOUB O14 C23 ? bmst000234 1 21 covalent SING C18 N15 ? bmst000234 1 22 covalent SING N15 C22 ? bmst000234 1 23 covalent SING N15 C24 ? bmst000234 1 24 covalent SING N16 C22 ? bmst000234 1 25 covalent SING N16 C23 ? bmst000234 1 26 covalent SING N16 H31 ? bmst000234 1 27 covalent SING C19 C17 ? bmst000234 1 28 covalent SING C17 H32 ? bmst000234 1 29 covalent SING C17 H33 ? bmst000234 1 30 covalent SING C18 C20 ? bmst000234 1 31 covalent SING C18 H34 ? bmst000234 1 32 covalent SING C19 C21 ? bmst000234 1 33 covalent SING C19 H35 ? bmst000234 1 34 covalent SING C20 C21 ? bmst000234 1 35 covalent SING C20 H36 ? bmst000234 1 36 covalent SING C21 H37 ? bmst000234 1 37 covalent SING C23 C25 ? bmst000234 1 38 covalent DOUB C24 C25 ? bmst000234 1 39 covalent SING C24 H38 ? bmst000234 1 40 covalent SING C25 H39 ? bmst000234 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 148892 sid ? UDP ? 'matching entry' ? bmst000234 1 no PubChem 3317 sid ? UDP ? 'matching entry' ? bmst000234 1 no PubChem 6031 cid ? UDP ? 'matching entry' ? bmst000234 1 no KEGG C00015 'compound ID' ? UDP ? 'matching entry' ? bmst000234 1 no ChemIDplus 000058980 ? ? UDP ? 'matching entry' ? bmst000234 1 no 'CAS Registry' 58-98-0 'registry number' ? UDP ? 'matching entry' ? bmst000234 1 no EINECS 200-409-6 ? ? UDP ? 'matching entry' ? bmst000234 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 bmst000234 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmst000234 _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 bmst000234 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'geometry optimization' bmst000234 1 'chemical shift calculation' bmst000234 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 bmst000234 _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 ? bmst000234 1 C 13 TMS 'methyl carbons' ppm 0.00 na direct ? bmst000234 1 N 15 'ammonia pentamer' nitrogen ppm 0.00 na direct ? bmst000234 1 P 31 'phosphoric acid' phosphorus ppm 0.00 na direct ? bmst000234 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 bmst000234 _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 bmst000234 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 bmst000234 _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 ? 8.551 ? UDP ? ? bmst000234 1 2 1 1 1 1 P2 P ? 8.007 ? UDP ? ? bmst000234 1 3 1 1 1 1 N15 N ? 157.579 ? UDP ? ? bmst000234 1 4 1 1 1 1 N16 N ? 166.194 ? UDP ? ? bmst000234 1 5 1 1 1 1 C17 C ? 74.776 ? UDP ? ? bmst000234 1 6 1 1 1 1 C18 C ? 110.749 ? UDP ? ? bmst000234 1 7 1 1 1 1 C19 C ? 90.197 ? UDP ? ? bmst000234 1 8 1 1 1 1 C20 C ? 78.259 ? UDP ? ? bmst000234 1 9 1 1 1 1 C21 C ? 78.180 ? UDP ? ? bmst000234 1 10 1 1 1 1 C22 C ? 157.277 ? UDP ? ? bmst000234 1 11 1 1 1 1 C23 C ? 166.967 ? UDP ? ? bmst000234 1 12 1 1 1 1 C24 C ? 151.695 ? UDP ? ? bmst000234 1 13 1 1 1 1 C25 C ? 108.934 ? UDP ? ? bmst000234 1 14 1 1 1 1 H26 H ? 7.299 ? UDP ? ? bmst000234 1 15 1 1 1 1 H27 H ? 7.581 ? UDP ? ? bmst000234 1 16 1 1 1 1 H28 H ? 4.499 ? UDP ? ? bmst000234 1 17 1 1 1 1 H29 H ? 3.623 ? UDP ? ? bmst000234 1 18 1 1 1 1 H30 H ? 0.964 ? UDP ? ? bmst000234 1 19 1 1 1 1 H31 H ? 7.255 ? UDP ? ? bmst000234 1 20 1 1 1 1 H32 H ? 5.701 ? UDP ? ? bmst000234 1 21 1 1 1 1 H33 H ? 5.844 ? UDP ? ? bmst000234 1 22 1 1 1 1 H34 H ? 6.094 ? UDP ? ? bmst000234 1 23 1 1 1 1 H35 H ? 5.516 ? UDP ? ? bmst000234 1 24 1 1 1 1 H36 H ? 4.882 ? UDP ? ? bmst000234 1 25 1 1 1 1 H37 H ? 5.779 ? UDP ? ? bmst000234 1 26 1 1 1 1 H38 H ? 8.364 ? UDP ? ? bmst000234 1 27 1 1 1 1 H39 H ? 6.834 ? UDP ? ? bmst000234 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 bmst000234 _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 bmst000234 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 -0.702 -0.940 2.784 bmst000234 1 1 2 1 1 1 1 P2 1 1 P2 P -2.791 0.559 3.804 bmst000234 1 1 3 1 1 1 1 O3 1 1 O3 O -1.618 0.434 2.655 bmst000234 1 1 4 1 1 1 1 O4 1 1 O4 O 0.361 -0.828 1.619 bmst000234 1 1 5 1 1 1 1 O5 1 1 O5 O 0.200 -0.680 4.067 bmst000234 1 1 6 1 1 1 1 O6 1 1 O6 O -3.865 -0.531 3.379 bmst000234 1 1 7 1 1 1 1 O7 1 1 O7 O -3.544 1.918 3.445 bmst000234 1 1 8 1 1 1 1 O8 1 1 O8 O -1.645 0.890 -3.229 bmst000234 1 1 9 1 1 1 1 O9 1 1 O9 O -2.212 -1.364 -1.991 bmst000234 1 1 10 1 1 1 1 O10 1 1 O10 O 0.553 0.585 -0.938 bmst000234 1 1 11 1 1 1 1 O11 1 1 O11 O -1.618 -2.115 2.773 bmst000234 1 1 12 1 1 1 1 O12 1 1 O12 O -2.165 0.484 5.152 bmst000234 1 1 13 1 1 1 1 O13 1 1 O13 O 2.014 -1.413 -2.647 bmst000234 1 1 14 1 1 1 1 O14 1 1 O14 O 5.801 0.735 -4.034 bmst000234 1 1 15 1 1 1 1 N15 1 1 N15 N 1.925 0.885 -2.833 bmst000234 1 1 16 1 1 1 1 N16 1 1 N16 N 3.879 -0.288 -3.335 bmst000234 1 1 17 1 1 1 1 C17 1 1 C17 C 0.112 -1.421 0.317 bmst000234 1 1 18 1 1 1 1 C18 1 1 C18 C 0.553 0.949 -2.304 bmst000234 1 1 19 1 1 1 1 C19 1 1 C19 C -0.443 -0.402 -0.660 bmst000234 1 1 20 1 1 1 1 C20 1 1 C20 C -0.502 0.082 -3.027 bmst000234 1 1 21 1 1 1 1 C21 1 1 C21 C -0.822 -1.040 -2.008 bmst000234 1 1 22 1 1 1 1 C22 1 1 C22 C 2.569 -0.355 -2.913 bmst000234 1 1 23 1 1 1 1 C23 1 1 C23 C 4.643 0.853 -3.674 bmst000234 1 1 24 1 1 1 1 C24 1 1 C24 C 2.606 2.054 -3.119 bmst000234 1 1 25 1 1 1 1 C25 1 1 C25 C 3.890 2.090 -3.530 bmst000234 1 1 26 1 1 1 1 H26 1 1 H26 H -0.369 -0.321 4.790 bmst000234 1 1 27 1 1 1 1 H27 1 1 H27 H -3.389 -1.370 3.153 bmst000234 1 1 28 1 1 1 1 H28 1 1 H28 H -3.281 2.625 4.058 bmst000234 1 1 29 1 1 1 1 H29 1 1 H29 H -2.407 0.336 -2.971 bmst000234 1 1 30 1 1 1 1 H30 1 1 H30 H -2.358 -2.122 -2.577 bmst000234 1 1 31 1 1 1 1 H31 1 1 H31 H 4.355 -1.181 -3.404 bmst000234 1 1 32 1 1 1 1 H32 1 1 H32 H -0.584 -2.258 0.424 bmst000234 1 1 33 1 1 1 1 H33 1 1 H33 H 1.082 -1.779 -0.032 bmst000234 1 1 34 1 1 1 1 H34 1 1 H34 H 0.249 1.994 -2.414 bmst000234 1 1 35 1 1 1 1 H35 1 1 H35 H -1.334 0.082 -0.237 bmst000234 1 1 36 1 1 1 1 H36 1 1 H36 H -0.124 -0.310 -3.980 bmst000234 1 1 37 1 1 1 1 H37 1 1 H37 H -0.209 -1.919 -2.212 bmst000234 1 1 38 1 1 1 1 H38 1 1 H38 H 2.020 2.958 -2.993 bmst000234 1 1 39 1 1 1 1 H39 1 1 H39 H 4.387 3.024 -3.753 bmst000234 1 stop_ save_