data_bmst000284 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmst000284 _Entry.Title S_Adenosyl_L_homocysteine _Entry.Version_type update _Entry.Submission_date 2007-01-05 _Entry.Accession_date 2007-01-05 _Entry.Last_release_date 2011-09-14 _Entry.Original_release_date 2007-01-05 _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 S_Adenosyl_L_homocysteine 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. ? bmst000284 2 John Markley L. ? bmst000284 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 bmst000284 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID other_data_list 1 bmst000284 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID 'theoretical chemical shifts' 1 bmst000284 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 . . 2007-01-05 2007-01-05 original BMRB 'Original theoretical calculations from NMRFAM' bmst000284 2 . . 2008-11-18 2008-11-18 update BMRB 'updated the file to match latest NMR STAR dictionary' bmst000284 3 . . 2008-11-25 2008-11-25 update BMRB 'fixed enumerations: N should be no' bmst000284 4 . . 2010-09-16 2010-09-16 update BMRB 'Removed Shielding_tensor_list_ID and Shielding_tensor_list_label from theoretical_chem_shifts' bmst000284 5 . . 2011-09-14 2011-09-14 update BMRB 'Partially brought up to date with latest Dictionary' bmst000284 6 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmst000284 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 . . S_Adenosyl_L_homocysteine_3323_opt.pdb x-chemical/x-pdb 'Name of the file containing the atomic coordinates' bmst000284 2 . . S_Adenosyl_L_homocysteine_3323.g03.shifts text/plain 'Name of the file containing theoretical chemical shift data' bmst000284 stop_ save_ ############### # Citations # ############### save_citations _Citation.Sf_category citations _Citation.Sf_framecode citations _Citation.Entry_ID bmst000284 _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. ? bmst000284 1 2 T. Barrett T. ? ? bmst000284 1 3 D. Benson D. A. ? bmst000284 1 4 S. Bryant S. H. ? bmst000284 1 5 K. Canese K. ? ? bmst000284 1 6 V. Chetvenin V. ? ? bmst000284 1 7 D. Church D. M. ? bmst000284 1 8 M. DiCuccio M. ? ? bmst000284 1 9 R. Edgar R. ? ? bmst000284 1 10 S. Federhen S. ? ? bmst000284 1 11 L. Geer L. Y. ? bmst000284 1 12 W. Helmberg W. ? ? bmst000284 1 13 Y. Kapustin Y. ? ? bmst000284 1 14 D. Kenton D. L. ? bmst000284 1 15 O. Khovayko O. ? ? bmst000284 1 16 D. Lipman D. J. ? bmst000284 1 17 T. Madden T. L. ? bmst000284 1 18 D. Maglott D. R. ? bmst000284 1 19 J. Ostell J. ? ? bmst000284 1 20 K. Pruitt K. D. ? bmst000284 1 21 G. Schuler G. D. ? bmst000284 1 22 L. Schriml L. M. ? bmst000284 1 23 E. Sequeira E. ? ? bmst000284 1 24 S. Sherry S. T. ? bmst000284 1 25 K. Sirotkin K. ? ? bmst000284 1 26 A. Souvorov A. ? ? bmst000284 1 27 G. Starchenko G. ? ? bmst000284 1 28 T. Suzek T. O. ? bmst000284 1 29 R. Tatusov R. ? ? bmst000284 1 30 T. Tatusova T. A. ? bmst000284 1 31 L. Bagner L. ? ? bmst000284 1 32 E. Yaschenko E. ? ? bmst000284 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmst000284 _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 $S_Adenosyl_L_homocysteine yes native no no ? ? ? bmst000284 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_S_Adenosyl_L_homocysteine _Entity.Sf_category entity _Entity.Sf_framecode S_Adenosyl_L_homocysteine _Entity.Entry_ID bmst000284 _Entity.ID 1 _Entity.BMRB_code ? _Entity.Name S-Adenosyl-L-homocysteine _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 bmst000284 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 bmst000284 _Chem_comp.ID 1 _Chem_comp.Provenance PubChem _Chem_comp.Name S-Adenosyl-L-homocysteine _Chem_comp.Type non-polymer _Chem_comp.BMRB_code ? _Chem_comp.PDB_code ? _Chem_comp.InChI_code ; InChI=1/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1/f/h23H,16H2 ; _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 'C14 H20 N6 O5 S' _Chem_comp.Formula_weight 384.4108000000 _Chem_comp.Formula_mono_iso_wt_nat 384.121588474 _Chem_comp.Formula_mono_iso_wt_13C 398.168556203 _Chem_comp.Formula_mono_iso_wt_15N 390.103797833 _Chem_comp.Formula_mono_iso_wt_13C_15N 398.168556203 _Chem_comp.Image_file_name bmst000284.png _Chem_comp.Image_file_format png _Chem_comp.Topo_file_name ? _Chem_comp.Topo_file_format ? _Chem_comp.Struct_file_name bmst000284.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 ; D-Ribitol, 5-S-(3-amino-3-carboxypropyl)-1-C-(7-amino-1H-pyrazolo(4,3-d)pyrimidin-3-yl)-1,4-anhydro-5-thio-, (1S,5(S))- ; synonym bmst000284 1 'BRN 5166233' synonym bmst000284 1 Formycinylhomocysteine synonym bmst000284 1 S-Adenosylhomocysteine synonym bmst000284 1 S-Adenosyl-L-homocysteine synonym bmst000284 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)-2-amino-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methylsulfanyl]butanoic acid ; IUPAC bmst000284 1 ; (2S)-2-amino-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methylthio]butanoic acid ; IUPAC_TRADITIONAL bmst000284 1 ; (2S)-2-amino-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methylsulfanyl]butanoic acid ; IUPAC_OPENEYE bmst000284 1 ; (2S)-2-amino-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methylthio]butanoic acid ; IUPAC_CAS bmst000284 1 ; (2S)-2-amino-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methylsulfanyl]butanoic acid ; IUPAC_SYSTEMATIC bmst000284 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID Canonical C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)CSCCC(C(=O)O)N)O)O bmst000284 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 S1 S ? ? ? ? 5.3548 1.2890 1.520 -0.988 -1.495 1 bmst000284 1 O2 O ? ? ? ? 6.7485 -2.3044 1.388 0.114 4.554 2 bmst000284 1 O3 O ? ? ? ? 6.7523 -0.1288 3.528 -0.911 3.292 3 bmst000284 1 O4 O ? ? ? ? 5.7735 5.6278 -2.697 -4.208 -4.449 4 bmst000284 1 O5 O ? ? ? ? 4.4025 -1.2125 2.195 0.676 1.087 5 bmst000284 1 O6 O ? ? ? ? 7.0587 4.4666 -2.592 -2.255 -3.389 6 bmst000284 1 N7 N ? ? ? ? 4.4327 4.1438 -0.558 -2.718 -5.925 7 bmst000284 1 N8 N ? ? ? ? 2.8660 -5.7778 -3.070 4.576 0.995 8 bmst000284 1 N9 N ? ? ? ? 4.6783 -2.9731 0.712 2.164 2.149 9 bmst000284 1 N10 N ? ? ? ? 4.6783 -4.5825 -0.163 4.240 1.916 10 bmst000284 1 N11 N ? ? ? ? 2.0000 -4.2778 -3.116 2.254 0.848 11 bmst000284 1 N12 N ? ? ? ? 2.8660 -2.7778 -1.243 0.847 1.436 12 bmst000284 1 C13 C ? ? ? ? 5.4105 3.9342 -0.553 -3.029 -4.485 13 bmst000284 1 C14 C ? ? ? ? 5.0474 2.2406 0.390 -2.229 -2.243 14 bmst000284 1 C15 C ? ? ? ? 5.7178 2.9826 0.222 -1.939 -3.737 15 bmst000284 1 C16 C ? ? ? ? 4.6844 0.5471 1.312 -1.455 0.272 16 bmst000284 1 C17 C ? ? ? ? 4.9889 -2.0226 1.752 1.170 2.341 17 bmst000284 1 C18 C ? ? ? ? 4.9917 -0.4045 2.359 -0.755 1.140 18 bmst000284 1 C19 C ? ? ? ? 5.9405 -1.7152 1.308 -0.065 3.157 19 bmst000284 1 C20 C ? ? ? ? 5.9423 -0.7152 2.285 -1.121 2.641 20 bmst000284 1 C21 C ? ? ? ? 6.0809 4.6762 -2.022 -3.095 -4.033 21 bmst000284 1 C22 C ? ? ? ? 2.8660 -4.7778 -2.437 3.382 1.126 22 bmst000284 1 C23 C ? ? ? ? 3.7321 -3.2778 -0.587 1.989 1.694 23 bmst000284 1 C24 C ? ? ? ? 3.7321 -4.2778 -1.103 3.283 1.571 24 bmst000284 1 C25 C ? ? ? ? 5.2619 -3.7778 0.891 3.536 2.238 25 bmst000284 1 C26 C ? ? ? ? 2.0000 -3.2778 -2.492 1.080 1.017 26 bmst000284 1 H27 H ? ? ? ? 7.3154 -2.0532 0.575 0.560 4.836 27 bmst000284 1 H28 H ? ? ? ? 7.3182 -0.3820 4.171 -1.532 2.916 28 bmst000284 1 H29 H ? ? ? ? 6.1892 6.0878 -2.086 -4.835 -4.870 29 bmst000284 1 H30 H ? ? ? ? 4.0170 3.6838 0.397 -2.724 -6.277 30 bmst000284 1 H31 H ? ? ? ? 4.2421 4.7338 -1.075 -3.414 -6.457 31 bmst000284 1 H32 H ? ? ? ? 3.4030 -6.0878 -3.949 4.584 0.499 32 bmst000284 1 H33 H ? ? ? ? 2.3291 -6.0878 -2.516 5.419 1.008 33 bmst000284 1 H34 H ? ? ? ? 5.2199 4.5242 -0.093 -4.011 -4.251 34 bmst000284 1 H35 H ? ? ? ? 4.6665 2.7299 0.806 -3.234 -2.086 35 bmst000284 1 H36 H ? ? ? ? 4.4995 1.9505 -0.580 -2.172 -1.744 36 bmst000284 1 H37 H ? ? ? ? 6.2658 3.2727 1.211 -1.851 -4.208 37 bmst000284 1 H38 H ? ? ? ? 6.0987 2.4934 -0.296 -0.987 -3.881 38 bmst000284 1 H39 H ? ? ? ? 4.3035 1.0363 1.443 -2.540 0.364 39 bmst000284 1 H40 H ? ? ? ? 4.1364 0.2569 0.303 -1.182 0.596 40 bmst000284 1 H41 H ? ? ? ? 5.4266 -2.4617 2.571 1.674 2.868 41 bmst000284 1 H42 H ? ? ? ? 4.3795 -0.3065 3.362 -0.981 0.752 42 bmst000284 1 H43 H ? ? ? ? 6.4934 -1.4347 0.298 -0.347 2.842 43 bmst000284 1 H44 H ? ? ? ? 6.4942 -0.9976 1.914 -2.143 2.807 44 bmst000284 1 H45 H ? ? ? ? 5.8819 -3.7778 1.842 3.944 2.559 45 bmst000284 1 H46 H ? ? ? ? 1.4631 -2.9678 -3.084 0.199 0.776 46 bmst000284 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID S1 S1 ? bmst000284 1 O2 O2 ? bmst000284 1 O3 O3 ? bmst000284 1 O4 O4 ? bmst000284 1 O5 O5 ? bmst000284 1 O6 O6 ? bmst000284 1 N7 N7 ? bmst000284 1 N8 N8 ? bmst000284 1 N9 N9 ? bmst000284 1 N10 N10 ? bmst000284 1 N11 N11 ? bmst000284 1 N12 N12 ? bmst000284 1 C13 C13 ? bmst000284 1 C14 C14 ? bmst000284 1 C15 C15 ? bmst000284 1 C16 C16 ? bmst000284 1 C17 C17 ? bmst000284 1 C18 C18 ? bmst000284 1 C19 C19 ? bmst000284 1 C20 C20 ? bmst000284 1 C21 C21 ? bmst000284 1 C22 C22 ? bmst000284 1 C23 C23 ? bmst000284 1 C24 C24 ? bmst000284 1 C25 C25 ? bmst000284 1 C26 C26 ? bmst000284 1 H27 H27 ? bmst000284 1 H28 H28 ? bmst000284 1 H29 H29 ? bmst000284 1 H30 H30 ? bmst000284 1 H31 H31 ? bmst000284 1 H32 H32 ? bmst000284 1 H33 H33 ? bmst000284 1 H34 H34 ? bmst000284 1 H35 H35 ? bmst000284 1 H36 H36 ? bmst000284 1 H37 H37 ? bmst000284 1 H38 H38 ? bmst000284 1 H39 H39 ? bmst000284 1 H40 H40 ? bmst000284 1 H41 H41 ? bmst000284 1 H42 H42 ? bmst000284 1 H43 H43 ? bmst000284 1 H44 H44 ? bmst000284 1 H45 H45 ? bmst000284 1 H46 H46 ? bmst000284 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 S1 C14 ? bmst000284 1 2 covalent SING S1 C16 ? bmst000284 1 3 covalent SING C19 O2 ? bmst000284 1 4 covalent SING O2 H27 ? bmst000284 1 5 covalent SING C20 O3 ? bmst000284 1 6 covalent SING O3 H28 ? bmst000284 1 7 covalent SING O4 C21 ? bmst000284 1 8 covalent SING O4 H29 ? bmst000284 1 9 covalent SING O5 C17 ? bmst000284 1 10 covalent SING O5 C18 ? bmst000284 1 11 covalent DOUB O6 C21 ? bmst000284 1 12 covalent SING C13 N7 ? bmst000284 1 13 covalent SING N7 H30 ? bmst000284 1 14 covalent SING N7 H31 ? bmst000284 1 15 covalent SING N8 C22 ? bmst000284 1 16 covalent SING N8 H32 ? bmst000284 1 17 covalent SING N8 H33 ? bmst000284 1 18 covalent SING C17 N9 ? bmst000284 1 19 covalent SING N9 C23 ? bmst000284 1 20 covalent SING N9 C25 ? bmst000284 1 21 covalent SING N10 C24 ? bmst000284 1 22 covalent DOUB N10 C25 ? bmst000284 1 23 covalent SING N11 C22 ? bmst000284 1 24 covalent DOUB N11 C26 ? bmst000284 1 25 covalent DOUB N12 C23 ? bmst000284 1 26 covalent SING N12 C26 ? bmst000284 1 27 covalent SING C13 C15 ? bmst000284 1 28 covalent SING C13 C21 ? bmst000284 1 29 covalent SING C13 H34 ? bmst000284 1 30 covalent SING C14 C15 ? bmst000284 1 31 covalent SING C14 H35 ? bmst000284 1 32 covalent SING C14 H36 ? bmst000284 1 33 covalent SING C15 H37 ? bmst000284 1 34 covalent SING C15 H38 ? bmst000284 1 35 covalent SING C18 C16 ? bmst000284 1 36 covalent SING C16 H39 ? bmst000284 1 37 covalent SING C16 H40 ? bmst000284 1 38 covalent SING C17 C19 ? bmst000284 1 39 covalent SING C17 H41 ? bmst000284 1 40 covalent SING C18 C20 ? bmst000284 1 41 covalent SING C18 H42 ? bmst000284 1 42 covalent SING C19 C20 ? bmst000284 1 43 covalent SING C19 H43 ? bmst000284 1 44 covalent SING C20 H44 ? bmst000284 1 45 covalent DOUB C22 C24 ? bmst000284 1 46 covalent SING C23 C24 ? bmst000284 1 47 covalent SING C25 H45 ? bmst000284 1 48 covalent SING C26 H46 ? bmst000284 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 3862936 sid ? S-Adenosyl-L-homocysteine ? 'matching entry' ? bmst000284 1 no PubChem 3323 sid ? S-Adenosyl-L-homocysteine ? 'matching entry' ? bmst000284 1 no PubChem 439155 cid ? S-Adenosyl-L-homocysteine ? 'matching entry' ? bmst000284 1 no KEGG C00021 'compound ID' ? S-Adenosyl-L-homocysteine ? 'matching entry' ? bmst000284 1 no ChemIDplus 075899148 ? ? S-Adenosyl-L-homocysteine ? 'matching entry' ? bmst000284 1 no 'CAS Registry' 979-92-0 'registry number' ? S-Adenosyl-L-homocysteine ? 'matching entry' ? bmst000284 1 no 'CAS Registry' 75899-14-8 'registry number' ? S-Adenosyl-L-homocysteine ? 'matching entry' ? bmst000284 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 bmst000284 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmst000284 _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 bmst000284 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'geometry optimization' bmst000284 1 'chemical shift calculation' bmst000284 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 bmst000284 _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 ? bmst000284 1 C 13 TMS 'methyl carbons' ppm 0.00 na direct ? bmst000284 1 N 15 'ammonia pentamer' nitrogen ppm 0.00 na direct ? bmst000284 1 P 31 'phosphoric acid' phosphorus ppm 0.00 na direct ? bmst000284 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 bmst000284 _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 bmst000284 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 bmst000284 _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 N7 N ? 42.367 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 2 1 1 1 1 N8 N ? 85.072 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 3 1 1 1 1 N9 N ? 172.637 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 4 1 1 1 1 N10 N ? 265.486 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 5 1 1 1 1 N11 N ? 259.942 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 6 1 1 1 1 N12 N ? 245.634 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 7 1 1 1 1 C13 C ? 58.880 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 8 1 1 1 1 C14 C ? 28.378 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 9 1 1 1 1 C15 C ? 30.172 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 10 1 1 1 1 C16 C ? 36.463 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 11 1 1 1 1 C17 C ? 93.380 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 12 1 1 1 1 C18 C ? 87.778 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 13 1 1 1 1 C19 C ? 73.232 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 14 1 1 1 1 C20 C ? 79.819 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 15 1 1 1 1 C21 C ? 171.854 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 16 1 1 1 1 C22 C ? 153.963 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 17 1 1 1 1 C23 C ? 149.618 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 18 1 1 1 1 C24 C ? 121.489 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 19 1 1 1 1 C25 C ? 142.046 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 20 1 1 1 1 C26 C ? 154.185 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 21 1 1 1 1 H27 H ? 0.584 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 22 1 1 1 1 H28 H ? 0.574 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 23 1 1 1 1 H29 H ? 6.407 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 24 1 1 1 1 H30 H ? 0.840 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 25 1 1 1 1 H31 H ? 0.766 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 26 1 1 1 1 H32 H ? 5.426 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 27 1 1 1 1 H33 H ? 6.163 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 28 1 1 1 1 H34 H ? 3.863 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 29 1 1 1 1 H35 H ? 2.666 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 30 1 1 1 1 H36 H ? 3.563 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 31 1 1 1 1 H37 H ? 1.934 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 32 1 1 1 1 H38 H ? 3.442 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 33 1 1 1 1 H39 H ? 2.763 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 34 1 1 1 1 H40 H ? 4.890 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 35 1 1 1 1 H41 H ? 7.084 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 36 1 1 1 1 H42 H ? 4.866 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 37 1 1 1 1 H43 H ? 7.353 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 38 1 1 1 1 H44 H ? 5.020 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 39 1 1 1 1 H45 H ? 8.689 ? S_Adenosyl_L_homocysteine ? ? bmst000284 1 40 1 1 1 1 H46 H ? 10.177 ? S_Adenosyl_L_homocysteine ? ? bmst000284 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 bmst000284 _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 bmst000284 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 S1 1 1 S1 S 1.520 -0.988 -1.495 bmst000284 1 1 2 1 1 1 1 O2 1 1 O2 O 1.388 0.114 4.554 bmst000284 1 1 3 1 1 1 1 O3 1 1 O3 O 3.528 -0.911 3.292 bmst000284 1 1 4 1 1 1 1 O4 1 1 O4 O -2.697 -4.208 -4.449 bmst000284 1 1 5 1 1 1 1 O5 1 1 O5 O 2.195 0.676 1.087 bmst000284 1 1 6 1 1 1 1 O6 1 1 O6 O -2.592 -2.255 -3.389 bmst000284 1 1 7 1 1 1 1 N7 1 1 N7 N -0.558 -2.718 -5.925 bmst000284 1 1 8 1 1 1 1 N8 1 1 N8 N -3.070 4.576 0.995 bmst000284 1 1 9 1 1 1 1 N9 1 1 N9 N 0.712 2.164 2.149 bmst000284 1 1 10 1 1 1 1 N10 1 1 N10 N -0.163 4.240 1.916 bmst000284 1 1 11 1 1 1 1 N11 1 1 N11 N -3.116 2.254 0.848 bmst000284 1 1 12 1 1 1 1 N12 1 1 N12 N -1.243 0.847 1.436 bmst000284 1 1 13 1 1 1 1 C13 1 1 C13 C -0.553 -3.029 -4.485 bmst000284 1 1 14 1 1 1 1 C14 1 1 C14 C 0.390 -2.229 -2.243 bmst000284 1 1 15 1 1 1 1 C15 1 1 C15 C 0.222 -1.939 -3.737 bmst000284 1 1 16 1 1 1 1 C16 1 1 C16 C 1.312 -1.455 0.272 bmst000284 1 1 17 1 1 1 1 C17 1 1 C17 C 1.752 1.170 2.341 bmst000284 1 1 18 1 1 1 1 C18 1 1 C18 C 2.359 -0.755 1.140 bmst000284 1 1 19 1 1 1 1 C19 1 1 C19 C 1.308 -0.065 3.157 bmst000284 1 1 20 1 1 1 1 C20 1 1 C20 C 2.285 -1.121 2.641 bmst000284 1 1 21 1 1 1 1 C21 1 1 C21 C -2.022 -3.095 -4.033 bmst000284 1 1 22 1 1 1 1 C22 1 1 C22 C -2.437 3.382 1.126 bmst000284 1 1 23 1 1 1 1 C23 1 1 C23 C -0.587 1.989 1.694 bmst000284 1 1 24 1 1 1 1 C24 1 1 C24 C -1.103 3.283 1.571 bmst000284 1 1 25 1 1 1 1 C25 1 1 C25 C 0.891 3.536 2.238 bmst000284 1 1 26 1 1 1 1 C26 1 1 C26 C -2.492 1.080 1.017 bmst000284 1 1 27 1 1 1 1 H27 1 1 H27 H 0.575 0.560 4.836 bmst000284 1 1 28 1 1 1 1 H28 1 1 H28 H 4.171 -1.532 2.916 bmst000284 1 1 29 1 1 1 1 H29 1 1 H29 H -2.086 -4.835 -4.870 bmst000284 1 1 30 1 1 1 1 H30 1 1 H30 H 0.397 -2.724 -6.277 bmst000284 1 1 31 1 1 1 1 H31 1 1 H31 H -1.075 -3.414 -6.457 bmst000284 1 1 32 1 1 1 1 H32 1 1 H32 H -3.949 4.584 0.499 bmst000284 1 1 33 1 1 1 1 H33 1 1 H33 H -2.516 5.419 1.008 bmst000284 1 1 34 1 1 1 1 H34 1 1 H34 H -0.093 -4.011 -4.251 bmst000284 1 1 35 1 1 1 1 H35 1 1 H35 H 0.806 -3.234 -2.086 bmst000284 1 1 36 1 1 1 1 H36 1 1 H36 H -0.580 -2.172 -1.744 bmst000284 1 1 37 1 1 1 1 H37 1 1 H37 H 1.211 -1.851 -4.208 bmst000284 1 1 38 1 1 1 1 H38 1 1 H38 H -0.296 -0.987 -3.881 bmst000284 1 1 39 1 1 1 1 H39 1 1 H39 H 1.443 -2.540 0.364 bmst000284 1 1 40 1 1 1 1 H40 1 1 H40 H 0.303 -1.182 0.596 bmst000284 1 1 41 1 1 1 1 H41 1 1 H41 H 2.571 1.674 2.868 bmst000284 1 1 42 1 1 1 1 H42 1 1 H42 H 3.362 -0.981 0.752 bmst000284 1 1 43 1 1 1 1 H43 1 1 H43 H 0.298 -0.347 2.842 bmst000284 1 1 44 1 1 1 1 H44 1 1 H44 H 1.914 -2.143 2.807 bmst000284 1 1 45 1 1 1 1 H45 1 1 H45 H 1.842 3.944 2.559 bmst000284 1 1 46 1 1 1 1 H46 1 1 H46 H -3.084 0.199 0.776 bmst000284 1 stop_ save_