data_bmst000236 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmst000236 _Entry.Title uridine _Entry.Version_type update _Entry.Submission_date 2006-02-23 _Entry.Accession_date 2006-02-23 _Entry.Last_release_date 2011-09-14 _Entry.Original_release_date 2006-02-23 _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 uridine 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. ? bmst000236 2 John Markley L. ? bmst000236 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 bmst000236 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID other_data_list 1 bmst000236 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID 'theoretical chemical shifts' 1 bmst000236 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 . . 2006-02-23 2006-02-23 original BMRB 'Original theoretical calculations from NMRFAM' bmst000236 2 . . 2008-11-18 2008-11-18 update BMRB 'updated the file to match latest NMR STAR dictionary' bmst000236 3 . . 2008-11-25 2008-11-25 update BMRB 'fixed enumerations: N should be no' bmst000236 4 . . 2010-09-16 2010-09-16 update BMRB 'Removed Shielding_tensor_list_ID and Shielding_tensor_list_label from theoretical_chem_shifts' bmst000236 5 . . 2011-09-14 2011-09-14 update BMRB 'Partially brought up to date with latest Dictionary' bmst000236 6 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmst000236 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 . . uridine_3593_opt.pdb x-chemical/x-pdb 'Name of the file containing the atomic coordinates' bmst000236 2 . . uridine_3593.g03.shifts text/plain 'Name of the file containing theoretical chemical shift data' bmst000236 stop_ save_ ############### # Citations # ############### save_citations _Citation.Sf_category citations _Citation.Sf_framecode citations _Citation.Entry_ID bmst000236 _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. ? bmst000236 1 2 T. Barrett T. ? ? bmst000236 1 3 D. Benson D. A. ? bmst000236 1 4 S. Bryant S. H. ? bmst000236 1 5 K. Canese K. ? ? bmst000236 1 6 V. Chetvenin V. ? ? bmst000236 1 7 D. Church D. M. ? bmst000236 1 8 M. DiCuccio M. ? ? bmst000236 1 9 R. Edgar R. ? ? bmst000236 1 10 S. Federhen S. ? ? bmst000236 1 11 L. Geer L. Y. ? bmst000236 1 12 W. Helmberg W. ? ? bmst000236 1 13 Y. Kapustin Y. ? ? bmst000236 1 14 D. Kenton D. L. ? bmst000236 1 15 O. Khovayko O. ? ? bmst000236 1 16 D. Lipman D. J. ? bmst000236 1 17 T. Madden T. L. ? bmst000236 1 18 D. Maglott D. R. ? bmst000236 1 19 J. Ostell J. ? ? bmst000236 1 20 K. Pruitt K. D. ? bmst000236 1 21 G. Schuler G. D. ? bmst000236 1 22 L. Schriml L. M. ? bmst000236 1 23 E. Sequeira E. ? ? bmst000236 1 24 S. Sherry S. T. ? bmst000236 1 25 K. Sirotkin K. ? ? bmst000236 1 26 A. Souvorov A. ? ? bmst000236 1 27 G. Starchenko G. ? ? bmst000236 1 28 T. Suzek T. O. ? bmst000236 1 29 R. Tatusov R. ? ? bmst000236 1 30 T. Tatusova T. A. ? bmst000236 1 31 L. Bagner L. ? ? bmst000236 1 32 E. Yaschenko E. ? ? bmst000236 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmst000236 _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 $uridine yes native no no ? ? ? bmst000236 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_uridine _Entity.Sf_category entity _Entity.Sf_framecode uridine _Entity.Entry_ID bmst000236 _Entity.ID 1 _Entity.BMRB_code ? _Entity.Name Uridine _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 bmst000236 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 bmst000236 _Chem_comp.ID 1 _Chem_comp.Provenance PubChem _Chem_comp.Name Uridine _Chem_comp.Type non-polymer _Chem_comp.BMRB_code ? _Chem_comp.PDB_code ? _Chem_comp.InChI_code ; InChI=1/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1/f/h10H ; _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 H12 N2 O6' _Chem_comp.Formula_weight 244.2013800000 _Chem_comp.Formula_mono_iso_wt_nat 244.069536128 _Chem_comp.Formula_mono_iso_wt_13C 253.099729668 _Chem_comp.Formula_mono_iso_wt_15N 246.063605915 _Chem_comp.Formula_mono_iso_wt_13C_15N 253.099729668 _Chem_comp.Image_file_name bmst000236.png _Chem_comp.Image_file_format png _Chem_comp.Topo_file_name ? _Chem_comp.Topo_file_format ? _Chem_comp.Struct_file_name bmst000236.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 'Uracil, 1-beta-D-ribofuranosyl-' synonym bmst000236 1 1-beta-D-Ribofuranosyluracil synonym bmst000236 1 URIDINE synonym bmst000236 1 AI3-52690 synonym bmst000236 1 Uridin synonym bmst000236 1 'Uracil riboside' synonym bmst000236 1 Uridine synonym bmst000236 1 Urd synonym bmst000236 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 1-[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione IUPAC bmst000236 1 1-[(2R,3R,4R,5R)-3,4-dihydroxy-5-methylol-tetrahydrofuran-2-yl]pyrimidine-2,4-quinone IUPAC_TRADITIONAL bmst000236 1 1-[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidine-2,4-dione IUPAC_CAS bmst000236 1 1-[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidine-2,4-dione IUPAC_OPENEYE bmst000236 1 1-[(2R,3R,4R,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione IUPAC_SYSTEMATIC bmst000236 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID Isomeric C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O bmst000236 1 Canonical C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O bmst000236 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 H1 H ? ? ? ? 5.6238 2.2671 3.985 -1.628 -1.103 1 bmst000236 1 H2 H ? ? ? ? 5.6238 0.6471 1.622 -2.315 -0.747 2 bmst000236 1 H3 H ? ? ? ? 3.1085 -1.9847 -3.062 -0.309 1.885 3 bmst000236 1 H4 H ? ? ? ? 2.9734 -1.5691 -0.653 0.106 1.795 4 bmst000236 1 H5 H ? ? ? ? 5.3332 -1.9847 -3.389 -0.297 -0.887 5 bmst000236 1 H6 H ? ? ? ? 3.6684 -0.2614 -0.392 -1.975 -0.395 6 bmst000236 1 H7 H ? ? ? ? 4.7514 -3.1625 -2.188 1.833 0.954 7 bmst000236 1 H8 H ? ? ? ? 5.4795 -3.4867 -3.793 1.773 0.205 8 bmst000236 1 H9 H ? ? ? ? 2.8179 2.2671 2.704 2.301 -0.250 9 bmst000236 1 H10 H ? ? ? ? 3.3852 -3.4571 -3.851 -2.190 0.802 10 bmst000236 1 H11 H ? ? ? ? 2.0000 -1.2365 -1.219 -2.610 1.981 11 bmst000236 1 H12 H ? ? ? ? 6.6676 -3.2878 -1.340 2.247 -1.063 12 bmst000236 1 C13 C ? ? ? ? 5.0868 1.9571 3.221 -0.910 -0.837 13 bmst000236 1 C14 C ? ? ? ? 5.0868 0.9571 1.938 -1.282 -0.645 14 bmst000236 1 C15 C ? ? ? ? 4.2208 2.4571 3.601 0.487 -0.699 15 bmst000236 1 C16 C ? ? ? ? 3.3548 0.9571 1.188 0.960 -0.146 16 bmst000236 1 C17 C ? ? ? ? 3.7208 -2.0817 -2.504 -0.772 1.061 17 bmst000236 1 C18 C ? ? ? ? 3.4118 -1.1307 -0.989 -0.824 1.333 18 bmst000236 1 C19 C ? ? ? ? 4.7208 -2.0817 -2.578 0.046 -0.233 19 bmst000236 1 C20 C ? ? ? ? 4.2208 -0.5429 -0.442 -0.916 -0.113 20 bmst000236 1 C21 C ? ? ? ? 5.3086 -2.8907 -2.730 1.558 0.037 21 bmst000236 1 N22 N ? ? ? ? 3.3548 1.9571 2.504 1.312 -0.360 22 bmst000236 1 N23 N ? ? ? ? 4.2208 0.4571 0.926 -0.405 -0.303 23 bmst000236 1 O24 O ? ? ? ? 4.2208 3.4571 4.712 0.966 -0.846 24 bmst000236 1 O25 O ? ? ? ? 2.4888 0.4571 0.334 1.784 0.161 25 bmst000236 1 O26 O ? ? ? ? 5.0298 -1.1307 -1.346 -0.230 -0.943 26 bmst000236 1 O27 O ? ? ? ? 3.1330 -2.8907 -2.888 -2.139 0.892 27 bmst000236 1 O28 O ? ? ? ? 2.4607 -0.8216 -0.586 -1.889 2.155 28 bmst000236 1 O29 O ? ? ? ? 6.3031 -2.7862 -2.309 2.338 -1.053 29 bmst000236 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID H1 H1 ? bmst000236 1 H2 H2 ? bmst000236 1 H3 H3 ? bmst000236 1 H4 H4 ? bmst000236 1 H5 H5 ? bmst000236 1 H6 H6 ? bmst000236 1 H7 H7 ? bmst000236 1 H8 H8 ? bmst000236 1 H9 H9 ? bmst000236 1 H10 H10 ? bmst000236 1 H11 H11 ? bmst000236 1 H12 H12 ? bmst000236 1 C13 C13 ? bmst000236 1 C14 C14 ? bmst000236 1 C15 C15 ? bmst000236 1 C16 C16 ? bmst000236 1 C17 C17 ? bmst000236 1 C18 C18 ? bmst000236 1 C19 C19 ? bmst000236 1 C20 C20 ? bmst000236 1 C21 C21 ? bmst000236 1 N22 N22 ? bmst000236 1 N23 N23 ? bmst000236 1 O24 O24 ? bmst000236 1 O25 O25 ? bmst000236 1 O26 O26 ? bmst000236 1 O27 O27 ? bmst000236 1 O28 O28 ? bmst000236 1 O29 O29 ? bmst000236 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 H1 C13 ? bmst000236 1 2 covalent SING H2 C14 ? bmst000236 1 3 covalent SING H3 C17 ? bmst000236 1 4 covalent SING H4 C18 ? bmst000236 1 5 covalent SING H5 C19 ? bmst000236 1 6 covalent SING H6 C20 ? bmst000236 1 7 covalent SING H7 C21 ? bmst000236 1 8 covalent SING H8 C21 ? bmst000236 1 9 covalent SING H9 N22 ? bmst000236 1 10 covalent SING H10 O27 ? bmst000236 1 11 covalent SING H11 O28 ? bmst000236 1 12 covalent SING H12 O29 ? bmst000236 1 13 covalent DOUB C13 C14 ? bmst000236 1 14 covalent SING C13 C15 ? bmst000236 1 15 covalent SING C14 N23 ? bmst000236 1 16 covalent SING C15 N22 ? bmst000236 1 17 covalent DOUB C15 O24 ? bmst000236 1 18 covalent SING C16 N22 ? bmst000236 1 19 covalent SING C16 N23 ? bmst000236 1 20 covalent DOUB C16 O25 ? bmst000236 1 21 covalent SING C17 C18 ? bmst000236 1 22 covalent SING C17 C19 ? bmst000236 1 23 covalent SING C17 O27 ? bmst000236 1 24 covalent SING C18 C20 ? bmst000236 1 25 covalent SING C18 O28 ? bmst000236 1 26 covalent SING C19 C21 ? bmst000236 1 27 covalent SING C19 O26 ? bmst000236 1 28 covalent SING C20 N23 ? bmst000236 1 29 covalent SING C20 O26 ? bmst000236 1 30 covalent SING C21 O29 ? bmst000236 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 148890 sid ? Uridine ? 'matching entry' ? bmst000236 1 no PubChem 6029 cid ? Uridine ? 'matching entry' ? bmst000236 1 no PubChem 3593 sid ? Uridine ? 'matching entry' ? bmst000236 1 no KEGG C00299 'compound ID' ? Uridine ? 'matching entry' ? bmst000236 1 no 'CAS Registry' 12693-39-9 'registry number' ? Uridine ? 'matching entry' ? bmst000236 1 no 'CAS Registry' 58-96-8 'registry number' ? Uridine ? 'matching entry' ? bmst000236 1 no 'CAS Registry' 68184-15-6 'registry number' ? Uridine ? 'matching entry' ? bmst000236 1 no CHEBI 16704 ? ? Uridine ? 'matching entry' ? bmst000236 1 no EINECS 200-407-5 ? ? Uridine ? 'matching entry' ? bmst000236 1 no NSC 20256 ? ? Uridine ? 'matching entry' ? bmst000236 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 bmst000236 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmst000236 _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 bmst000236 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'geometry optimization' bmst000236 1 'chemical shift calculation' bmst000236 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 bmst000236 _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 ? bmst000236 1 C 13 TMS 'methyl carbons' ppm 0.00 na direct ? bmst000236 1 N 15 'ammonia pentamer' nitrogen ppm 0.00 na direct ? bmst000236 1 P 31 'phosphoric acid' phosphorus ppm 0.00 na direct ? bmst000236 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 bmst000236 _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 bmst000236 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 bmst000236 _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 H1 H ? 6.826 ? uridine ? ? bmst000236 1 2 1 1 1 1 H2 H ? 8.222 ? uridine ? ? bmst000236 1 3 1 1 1 1 H3 H ? 4.368 ? uridine ? ? bmst000236 1 4 1 1 1 1 H4 H ? 5.767 ? uridine ? ? bmst000236 1 5 1 1 1 1 H5 H ? 4.963 ? uridine ? ? bmst000236 1 6 1 1 1 1 H6 H ? 5.794 ? uridine ? ? bmst000236 1 7 1 1 1 1 H7 H ? 4.791 ? uridine ? ? bmst000236 1 8 1 1 1 1 H8 H ? 4.485 ? uridine ? ? bmst000236 1 9 1 1 1 1 H9 H ? 7.364 ? uridine ? ? bmst000236 1 10 1 1 1 1 H10 H ? 0.862 ? uridine ? ? bmst000236 1 11 1 1 1 1 H11 H ? 2.839 ? uridine ? ? bmst000236 1 12 1 1 1 1 H12 H ? 2.776 ? uridine ? ? bmst000236 1 13 1 1 1 1 C13 C ? 109.221 ? uridine ? ? bmst000236 1 14 1 1 1 1 C14 C ? 151.590 ? uridine ? ? bmst000236 1 15 1 1 1 1 C15 C ? 166.584 ? uridine ? ? bmst000236 1 16 1 1 1 1 C16 C ? 157.648 ? uridine ? ? bmst000236 1 17 1 1 1 1 C17 C ? 78.244 ? uridine ? ? bmst000236 1 18 1 1 1 1 C18 C ? 77.412 ? uridine ? ? bmst000236 1 19 1 1 1 1 C19 C ? 91.495 ? uridine ? ? bmst000236 1 20 1 1 1 1 C20 C ? 108.445 ? uridine ? ? bmst000236 1 21 1 1 1 1 C21 C ? 64.172 ? uridine ? ? bmst000236 1 22 1 1 1 1 N22 N ? 168.738 ? uridine ? ? bmst000236 1 23 1 1 1 1 N23 N ? 150.211 ? uridine ? ? bmst000236 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 bmst000236 _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 bmst000236 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 H1 1 1 H1 H 3.985 -1.628 -1.103 bmst000236 1 1 2 1 1 1 1 H2 1 1 H2 H 1.622 -2.315 -0.747 bmst000236 1 1 3 1 1 1 1 H3 1 1 H3 H -3.062 -0.309 1.885 bmst000236 1 1 4 1 1 1 1 H4 1 1 H4 H -0.653 0.106 1.795 bmst000236 1 1 5 1 1 1 1 H5 1 1 H5 H -3.389 -0.297 -0.887 bmst000236 1 1 6 1 1 1 1 H6 1 1 H6 H -0.392 -1.975 -0.395 bmst000236 1 1 7 1 1 1 1 H7 1 1 H7 H -2.188 1.833 0.954 bmst000236 1 1 8 1 1 1 1 H8 1 1 H8 H -3.793 1.773 0.205 bmst000236 1 1 9 1 1 1 1 H9 1 1 H9 H 2.704 2.301 -0.250 bmst000236 1 1 10 1 1 1 1 H10 1 1 H10 H -3.851 -2.190 0.802 bmst000236 1 1 11 1 1 1 1 H11 1 1 H11 H -1.219 -2.610 1.981 bmst000236 1 1 12 1 1 1 1 H12 1 1 H12 H -1.340 2.247 -1.063 bmst000236 1 1 13 1 1 1 1 C13 1 1 C13 C 3.221 -0.910 -0.837 bmst000236 1 1 14 1 1 1 1 C14 1 1 C14 C 1.938 -1.282 -0.645 bmst000236 1 1 15 1 1 1 1 C15 1 1 C15 C 3.601 0.487 -0.699 bmst000236 1 1 16 1 1 1 1 C16 1 1 C16 C 1.188 0.960 -0.146 bmst000236 1 1 17 1 1 1 1 C17 1 1 C17 C -2.504 -0.772 1.061 bmst000236 1 1 18 1 1 1 1 C18 1 1 C18 C -0.989 -0.824 1.333 bmst000236 1 1 19 1 1 1 1 C19 1 1 C19 C -2.578 0.046 -0.233 bmst000236 1 1 20 1 1 1 1 C20 1 1 C20 C -0.442 -0.916 -0.113 bmst000236 1 1 21 1 1 1 1 C21 1 1 C21 C -2.730 1.558 0.037 bmst000236 1 1 22 1 1 1 1 N22 1 1 N22 N 2.504 1.312 -0.360 bmst000236 1 1 23 1 1 1 1 N23 1 1 N23 N 0.926 -0.405 -0.303 bmst000236 1 1 24 1 1 1 1 O24 1 1 O24 O 4.712 0.966 -0.846 bmst000236 1 1 25 1 1 1 1 O25 1 1 O25 O 0.334 1.784 0.161 bmst000236 1 1 26 1 1 1 1 O26 1 1 O26 O -1.346 -0.230 -0.943 bmst000236 1 1 27 1 1 1 1 O27 1 1 O27 O -2.888 -2.139 0.892 bmst000236 1 1 28 1 1 1 1 O28 1 1 O28 O -0.586 -1.889 2.155 bmst000236 1 1 29 1 1 1 1 O29 1 1 O29 O -2.309 2.338 -1.053 bmst000236 1 stop_ save_