data_bmst000235 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmst000235 _Entry.Title dAMP _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 dAMP 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. ? bmst000235 2 John Markley L. ? bmst000235 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 bmst000235 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID other_data_list 1 bmst000235 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID 'theoretical chemical shifts' 1 bmst000235 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' bmst000235 2 . . 2008-11-18 2008-11-18 update BMRB 'updated the file to match latest NMR STAR dictionary' bmst000235 3 . . 2008-11-25 2008-11-25 update BMRB 'fixed enumerations: N should be no' bmst000235 4 . . 2010-09-16 2010-09-16 update BMRB 'Removed Shielding_tensor_list_ID and Shielding_tensor_list_label from theoretical_chem_shifts' bmst000235 5 . . 2011-09-14 2011-09-14 update BMRB 'Partially brought up to date with latest Dictionary' bmst000235 6 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmst000235 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 . . dAMP_3651_opt.pdb x-chemical/x-pdb 'Name of the file containing the atomic coordinates' bmst000235 2 . . dAMP_3651.g03.shifts text/plain 'Name of the file containing theoretical chemical shift data' bmst000235 stop_ save_ ############### # Citations # ############### save_citations _Citation.Sf_category citations _Citation.Sf_framecode citations _Citation.Entry_ID bmst000235 _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. ? bmst000235 1 2 T. Barrett T. ? ? bmst000235 1 3 D. Benson D. A. ? bmst000235 1 4 S. Bryant S. H. ? bmst000235 1 5 K. Canese K. ? ? bmst000235 1 6 V. Chetvenin V. ? ? bmst000235 1 7 D. Church D. M. ? bmst000235 1 8 M. DiCuccio M. ? ? bmst000235 1 9 R. Edgar R. ? ? bmst000235 1 10 S. Federhen S. ? ? bmst000235 1 11 L. Geer L. Y. ? bmst000235 1 12 W. Helmberg W. ? ? bmst000235 1 13 Y. Kapustin Y. ? ? bmst000235 1 14 D. Kenton D. L. ? bmst000235 1 15 O. Khovayko O. ? ? bmst000235 1 16 D. Lipman D. J. ? bmst000235 1 17 T. Madden T. L. ? bmst000235 1 18 D. Maglott D. R. ? bmst000235 1 19 J. Ostell J. ? ? bmst000235 1 20 K. Pruitt K. D. ? bmst000235 1 21 G. Schuler G. D. ? bmst000235 1 22 L. Schriml L. M. ? bmst000235 1 23 E. Sequeira E. ? ? bmst000235 1 24 S. Sherry S. T. ? bmst000235 1 25 K. Sirotkin K. ? ? bmst000235 1 26 A. Souvorov A. ? ? bmst000235 1 27 G. Starchenko G. ? ? bmst000235 1 28 T. Suzek T. O. ? bmst000235 1 29 R. Tatusov R. ? ? bmst000235 1 30 T. Tatusova T. A. ? bmst000235 1 31 L. Bagner L. ? ? bmst000235 1 32 E. Yaschenko E. ? ? bmst000235 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmst000235 _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 $dAMP yes native no no ? ? ? bmst000235 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_dAMP _Entity.Sf_category entity _Entity.Sf_framecode dAMP _Entity.Entry_ID bmst000235 _Entity.ID 1 _Entity.BMRB_code ? _Entity.Name dAMP _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 bmst000235 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 bmst000235 _Chem_comp.ID 1 _Chem_comp.Provenance PubChem _Chem_comp.Name dAMP _Chem_comp.Type non-polymer _Chem_comp.BMRB_code ? _Chem_comp.PDB_code ? _Chem_comp.InChI_code ; InChI=1/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1/f/h17-18H,11H2 ; _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 'C10 H14 N5 O6 P' _Chem_comp.Formula_weight 331.2218210000 _Chem_comp.Formula_mono_iso_wt_nat 331.068169718 _Chem_comp.Formula_mono_iso_wt_13C 341.101718096 _Chem_comp.Formula_mono_iso_wt_15N 336.053344184 _Chem_comp.Formula_mono_iso_wt_13C_15N 341.101718096 _Chem_comp.Image_file_name bmst000235.png _Chem_comp.Image_file_format png _Chem_comp.Topo_file_name ? _Chem_comp.Topo_file_format ? _Chem_comp.Struct_file_name bmst000235.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 'Deoxyadenylic acid' synonym bmst000235 1 "2'-Deoxyadenylic acid" synonym bmst000235 1 "2'-Deoxyadenosine monophosphate" synonym bmst000235 1 "Adenosine, 2'-deoxy-, 5'-(dihydrogen phosphate) (8CI)" synonym bmst000235 1 "2'-Deoxyadenosine 5'-(dihydrogen phosphate)" synonym bmst000235 1 "2'-Deoxyadenosine 5'-monophosphate" synonym bmst000235 1 2'-Deoxy-AMP synonym bmst000235 1 'Deoxyadenosine monophosphate' synonym bmst000235 1 dAMP synonym bmst000235 1 'NSC 77680' synonym bmst000235 1 "2'-Deoxy-5'-adenosine monophosphate" synonym bmst000235 1 'PdA (VAN)' synonym bmst000235 1 "5'-Adenylic acid, 2'-deoxy- (9CI)" synonym bmst000235 1 "2'-Deoxyadenosine 5'-phosphate" synonym bmst000235 1 2'-dAMP synonym bmst000235 1 "Deoxy-5'-adenylic acid" synonym bmst000235 1 'NSC 82625' synonym bmst000235 1 "Deoxyadenosine 5'-monophosphate" synonym bmst000235 1 Deoxy-AMP synonym bmst000235 1 "Deoxyadenosine 5'-phosphate" synonym bmst000235 1 "2'-DEOXY-5'-ADENYLIC ACID" synonym bmst000235 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,3R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxyphosphonic acid' IUPAC bmst000235 1 '[(2S,3R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-tetrahydrofuran-2-yl]methoxyphosphonic acid' IUPAC_TRADITIONAL bmst000235 1 '[(2S,3R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-tetrahydrofuran-2-yl]methoxyphosphonic acid' IUPAC_CAS bmst000235 1 '[(2S,3R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-tetrahydrofuran-2-yl]methoxyphosphonic acid' IUPAC_OPENEYE bmst000235 1 '[(2S,3R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxyphosphonic acid' IUPAC_SYSTEMATIC bmst000235 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID Canonical C1C(C(OC1N2C=NC3=C2N=CN=C3N)COP(=O)(O)O)O bmst000235 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 ? ? ? ? 5.0474 3.4584 -0.103 -2.629 -2.609 1 bmst000235 1 O2 O ? ? ? ? 5.3548 2.5068 0.840 -1.752 -1.650 2 bmst000235 1 O3 O ? ? ? ? 5.9990 3.7658 0.284 -1.995 -4.035 3 bmst000235 1 O4 O ? ? ? ? 4.7400 4.4100 -1.575 -2.050 -2.236 4 bmst000235 1 O5 O ? ? ? ? 6.7523 1.0890 3.468 -1.398 2.358 5 bmst000235 1 O6 O ? ? ? ? 4.4025 0.0053 1.942 0.146 0.217 6 bmst000235 1 O7 O ? ? ? ? 4.0958 3.1510 -0.008 -4.100 -2.562 7 bmst000235 1 N8 N ? ? ? ? 2.8660 -4.5600 -3.196 4.217 0.469 8 bmst000235 1 N9 N ? ? ? ? 4.6783 -1.7553 0.669 1.809 1.302 9 bmst000235 1 N10 N ? ? ? ? 4.6783 -3.3648 -0.191 3.877 0.972 10 bmst000235 1 N11 N ? ? ? ? 2.0000 -3.0600 -3.311 1.896 0.585 11 bmst000235 1 N12 N ? ? ? ? 2.8660 -1.5600 -1.397 0.494 1.040 12 bmst000235 1 C13 C ? ? ? ? 4.6844 1.7648 0.771 -1.948 -0.218 13 bmst000235 1 C14 C ? ? ? ? 4.9889 -0.8048 1.707 0.802 1.459 14 bmst000235 1 C15 C ? ? ? ? 4.9917 0.8132 1.993 -1.276 0.395 15 bmst000235 1 C16 C ? ? ? ? 5.9423 0.5026 2.117 -1.502 1.918 16 bmst000235 1 C17 C ? ? ? ? 5.9405 -0.4974 1.374 -0.297 2.481 17 bmst000235 1 C18 C ? ? ? ? 2.8660 -3.5600 -2.576 3.023 0.636 18 bmst000235 1 C19 C ? ? ? ? 3.7321 -2.0600 -0.687 1.633 1.074 19 bmst000235 1 C20 C ? ? ? ? 3.7321 -3.0600 -1.191 2.924 0.884 20 bmst000235 1 C21 C ? ? ? ? 5.2619 -2.5600 0.886 3.174 1.207 21 bmst000235 1 C22 C ? ? ? ? 2.0000 -2.0600 -2.690 0.726 0.787 22 bmst000235 1 H23 H ? ? ? ? 5.1557 4.8700 -2.243 -2.741 -2.378 23 bmst000235 1 H24 H ? ? ? ? 6.4590 3.3501 0.382 -1.029 -3.989 24 bmst000235 1 H25 H ? ? ? ? 7.3182 0.8358 3.984 -2.098 1.929 25 bmst000235 1 H26 H ? ? ? ? 2.3291 -4.8700 -4.149 4.213 0.137 26 bmst000235 1 H27 H ? ? ? ? 3.4030 -4.8700 -2.635 5.045 0.337 27 bmst000235 1 H28 H ? ? ? ? 4.3035 2.2541 0.789 -3.024 -0.005 28 bmst000235 1 H29 H ? ? ? ? 4.1364 1.4747 -0.153 -1.500 0.159 29 bmst000235 1 H30 H ? ? ? ? 5.4266 -1.2439 2.611 1.352 1.745 30 bmst000235 1 H31 H ? ? ? ? 4.3795 0.9113 2.887 -1.640 -0.129 31 bmst000235 1 H32 H ? ? ? ? 6.4942 0.2202 1.674 -2.457 2.234 32 bmst000235 1 H33 H ? ? ? ? 6.0684 -1.1041 1.715 -0.047 3.488 33 bmst000235 1 H34 H ? ? ? ? 6.5572 -0.4337 0.297 -0.481 2.496 34 bmst000235 1 H35 H ? ? ? ? 5.8819 -2.5600 1.882 3.580 1.332 35 bmst000235 1 H36 H ? ? ? ? 1.4631 -1.7500 -3.327 -0.155 0.735 36 bmst000235 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 ? bmst000235 1 O2 O2 ? bmst000235 1 O3 O3 ? bmst000235 1 O4 O4 ? bmst000235 1 O5 O5 ? bmst000235 1 O6 O6 ? bmst000235 1 O7 O7 ? bmst000235 1 N8 N8 ? bmst000235 1 N9 N9 ? bmst000235 1 N10 N10 ? bmst000235 1 N11 N11 ? bmst000235 1 N12 N12 ? bmst000235 1 C13 C13 ? bmst000235 1 C14 C14 ? bmst000235 1 C15 C15 ? bmst000235 1 C16 C16 ? bmst000235 1 C17 C17 ? bmst000235 1 C18 C18 ? bmst000235 1 C19 C19 ? bmst000235 1 C20 C20 ? bmst000235 1 C21 C21 ? bmst000235 1 C22 C22 ? bmst000235 1 H23 H23 ? bmst000235 1 H24 H24 ? bmst000235 1 H25 H25 ? bmst000235 1 H26 H26 ? bmst000235 1 H27 H27 ? bmst000235 1 H28 H28 ? bmst000235 1 H29 H29 ? bmst000235 1 H30 H30 ? bmst000235 1 H31 H31 ? bmst000235 1 H32 H32 ? bmst000235 1 H33 H33 ? bmst000235 1 H34 H34 ? bmst000235 1 H35 H35 ? bmst000235 1 H36 H36 ? bmst000235 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 O2 ? bmst000235 1 2 covalent SING P1 O3 ? bmst000235 1 3 covalent SING P1 O4 ? bmst000235 1 4 covalent DOUB P1 O7 ? bmst000235 1 5 covalent SING O2 C13 ? bmst000235 1 6 covalent SING O3 H24 ? bmst000235 1 7 covalent SING O4 H23 ? bmst000235 1 8 covalent SING C16 O5 ? bmst000235 1 9 covalent SING O5 H25 ? bmst000235 1 10 covalent SING O6 C14 ? bmst000235 1 11 covalent SING O6 C15 ? bmst000235 1 12 covalent SING N8 C18 ? bmst000235 1 13 covalent SING N8 H26 ? bmst000235 1 14 covalent SING N8 H27 ? bmst000235 1 15 covalent SING C14 N9 ? bmst000235 1 16 covalent SING N9 C19 ? bmst000235 1 17 covalent SING N9 C21 ? bmst000235 1 18 covalent SING N10 C20 ? bmst000235 1 19 covalent DOUB N10 C21 ? bmst000235 1 20 covalent SING N11 C18 ? bmst000235 1 21 covalent DOUB N11 C22 ? bmst000235 1 22 covalent DOUB N12 C19 ? bmst000235 1 23 covalent SING N12 C22 ? bmst000235 1 24 covalent SING C15 C13 ? bmst000235 1 25 covalent SING C13 H28 ? bmst000235 1 26 covalent SING C13 H29 ? bmst000235 1 27 covalent SING C14 C17 ? bmst000235 1 28 covalent SING C14 H30 ? bmst000235 1 29 covalent SING C15 C16 ? bmst000235 1 30 covalent SING C15 H31 ? bmst000235 1 31 covalent SING C16 C17 ? bmst000235 1 32 covalent SING C16 H32 ? bmst000235 1 33 covalent SING C17 H33 ? bmst000235 1 34 covalent SING C17 H34 ? bmst000235 1 35 covalent DOUB C18 C20 ? bmst000235 1 36 covalent SING C19 C20 ? bmst000235 1 37 covalent SING C21 H35 ? bmst000235 1 38 covalent SING C22 H36 ? bmst000235 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 155929 sid ? dAMP ? 'matching entry' ? bmst000235 1 no PubChem 3651 sid ? dAMP ? 'matching entry' ? bmst000235 1 no PubChem 12599 cid ? dAMP ? 'matching entry' ? bmst000235 1 no KEGG C00360 'compound ID' ? dAMP ? 'matching entry' ? bmst000235 1 no ChemIDplus 000653634 ? ? dAMP ? 'matching entry' ? bmst000235 1 no 'CAS Registry' 653-63-4 'registry number' ? dAMP ? 'matching entry' ? bmst000235 1 no 'CAS Registry' 75688-15-2 'registry number' ? dAMP ? 'matching entry' ? bmst000235 1 no 'CAS Registry' 87578-08-3 'registry number' ? dAMP ? 'matching entry' ? bmst000235 1 no 'CAS Registry' 29576-96-3 'registry number' ? dAMP ? 'matching entry' ? bmst000235 1 no 'CAS Registry' 2922-74-9 'registry number' ? dAMP ? 'matching entry' ? bmst000235 1 no EINECS 211-503-1 ? ? dAMP ? 'matching entry' ? bmst000235 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 bmst000235 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmst000235 _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 bmst000235 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'geometry optimization' bmst000235 1 'chemical shift calculation' bmst000235 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 bmst000235 _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 ? bmst000235 1 C 13 TMS 'methyl carbons' ppm 0.00 na direct ? bmst000235 1 N 15 'ammonia pentamer' nitrogen ppm 0.00 na direct ? bmst000235 1 P 31 'phosphoric acid' phosphorus ppm 0.00 na direct ? bmst000235 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 bmst000235 _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 bmst000235 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 bmst000235 _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 ? 1.487 ? dAMP ? ? bmst000235 1 2 1 1 1 1 N8 N ? 85.074 ? dAMP ? ? bmst000235 1 3 1 1 1 1 N9 N ? 175.429 ? dAMP ? ? bmst000235 1 4 1 1 1 1 N10 N ? 264.022 ? dAMP ? ? bmst000235 1 5 1 1 1 1 N11 N ? 258.362 ? dAMP ? ? bmst000235 1 6 1 1 1 1 N12 N ? 244.510 ? dAMP ? ? bmst000235 1 7 1 1 1 1 C13 C ? 69.277 ? dAMP ? ? bmst000235 1 8 1 1 1 1 C14 C ? 95.864 ? dAMP ? ? bmst000235 1 9 1 1 1 1 C15 C ? 96.027 ? dAMP ? ? bmst000235 1 10 1 1 1 1 C16 C ? 79.775 ? dAMP ? ? bmst000235 1 11 1 1 1 1 C17 C ? 37.329 ? dAMP ? ? bmst000235 1 12 1 1 1 1 C18 C ? 160.699 ? dAMP ? ? bmst000235 1 13 1 1 1 1 C19 C ? 156.330 ? dAMP ? ? bmst000235 1 14 1 1 1 1 C20 C ? 127.199 ? dAMP ? ? bmst000235 1 15 1 1 1 1 C21 C ? 147.796 ? dAMP ? ? bmst000235 1 16 1 1 1 1 C22 C ? 160.948 ? dAMP ? ? bmst000235 1 17 1 1 1 1 H23 H ? 3.659 ? dAMP ? ? bmst000235 1 18 1 1 1 1 H24 H ? 3.782 ? dAMP ? ? bmst000235 1 19 1 1 1 1 H25 H ? 0.427 ? dAMP ? ? bmst000235 1 20 1 1 1 1 H26 H ? 5.425 ? dAMP ? ? bmst000235 1 21 1 1 1 1 H27 H ? 6.202 ? dAMP ? ? bmst000235 1 22 1 1 1 1 H28 H ? 4.867 ? dAMP ? ? bmst000235 1 23 1 1 1 1 H29 H ? 6.545 ? dAMP ? ? bmst000235 1 24 1 1 1 1 H30 H ? 7.396 ? dAMP ? ? bmst000235 1 25 1 1 1 1 H31 H ? 5.155 ? dAMP ? ? bmst000235 1 26 1 1 1 1 H32 H ? 5.160 ? dAMP ? ? bmst000235 1 27 1 1 1 1 H33 H ? 3.292 ? dAMP ? ? bmst000235 1 28 1 1 1 1 H34 H ? 5.140 ? dAMP ? ? bmst000235 1 29 1 1 1 1 H35 H ? 8.690 ? dAMP ? ? bmst000235 1 30 1 1 1 1 H36 H ? 10.069 ? dAMP ? ? bmst000235 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 bmst000235 _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 bmst000235 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 -0.103 -2.629 -2.609 bmst000235 1 1 2 1 1 1 1 O2 1 1 O2 O 0.840 -1.752 -1.650 bmst000235 1 1 3 1 1 1 1 O3 1 1 O3 O 0.284 -1.995 -4.035 bmst000235 1 1 4 1 1 1 1 O4 1 1 O4 O -1.575 -2.050 -2.236 bmst000235 1 1 5 1 1 1 1 O5 1 1 O5 O 3.468 -1.398 2.358 bmst000235 1 1 6 1 1 1 1 O6 1 1 O6 O 1.942 0.146 0.217 bmst000235 1 1 7 1 1 1 1 O7 1 1 O7 O -0.008 -4.100 -2.562 bmst000235 1 1 8 1 1 1 1 N8 1 1 N8 N -3.196 4.217 0.469 bmst000235 1 1 9 1 1 1 1 N9 1 1 N9 N 0.669 1.809 1.302 bmst000235 1 1 10 1 1 1 1 N10 1 1 N10 N -0.191 3.877 0.972 bmst000235 1 1 11 1 1 1 1 N11 1 1 N11 N -3.311 1.896 0.585 bmst000235 1 1 12 1 1 1 1 N12 1 1 N12 N -1.397 0.494 1.040 bmst000235 1 1 13 1 1 1 1 C13 1 1 C13 C 0.771 -1.948 -0.218 bmst000235 1 1 14 1 1 1 1 C14 1 1 C14 C 1.707 0.802 1.459 bmst000235 1 1 15 1 1 1 1 C15 1 1 C15 C 1.993 -1.276 0.395 bmst000235 1 1 16 1 1 1 1 C16 1 1 C16 C 2.117 -1.502 1.918 bmst000235 1 1 17 1 1 1 1 C17 1 1 C17 C 1.374 -0.297 2.481 bmst000235 1 1 18 1 1 1 1 C18 1 1 C18 C -2.576 3.023 0.636 bmst000235 1 1 19 1 1 1 1 C19 1 1 C19 C -0.687 1.633 1.074 bmst000235 1 1 20 1 1 1 1 C20 1 1 C20 C -1.191 2.924 0.884 bmst000235 1 1 21 1 1 1 1 C21 1 1 C21 C 0.886 3.174 1.207 bmst000235 1 1 22 1 1 1 1 C22 1 1 C22 C -2.690 0.726 0.787 bmst000235 1 1 23 1 1 1 1 H23 1 1 H23 H -2.243 -2.741 -2.378 bmst000235 1 1 24 1 1 1 1 H24 1 1 H24 H 0.382 -1.029 -3.989 bmst000235 1 1 25 1 1 1 1 H25 1 1 H25 H 3.984 -2.098 1.929 bmst000235 1 1 26 1 1 1 1 H26 1 1 H26 H -4.149 4.213 0.137 bmst000235 1 1 27 1 1 1 1 H27 1 1 H27 H -2.635 5.045 0.337 bmst000235 1 1 28 1 1 1 1 H28 1 1 H28 H 0.789 -3.024 -0.005 bmst000235 1 1 29 1 1 1 1 H29 1 1 H29 H -0.153 -1.500 0.159 bmst000235 1 1 30 1 1 1 1 H30 1 1 H30 H 2.611 1.352 1.745 bmst000235 1 1 31 1 1 1 1 H31 1 1 H31 H 2.887 -1.640 -0.129 bmst000235 1 1 32 1 1 1 1 H32 1 1 H32 H 1.674 -2.457 2.234 bmst000235 1 1 33 1 1 1 1 H33 1 1 H33 H 1.715 -0.047 3.488 bmst000235 1 1 34 1 1 1 1 H34 1 1 H34 H 0.297 -0.481 2.496 bmst000235 1 1 35 1 1 1 1 H35 1 1 H35 H 1.882 3.580 1.332 bmst000235 1 1 36 1 1 1 1 H36 1 1 H36 H -3.327 -0.155 0.735 bmst000235 1 stop_ save_