data_bmst000232
#######################
# Entry information #
#######################
save_entry_information
_Entry.Sf_category entry_information
_Entry.Sf_framecode entry_information
_Entry.ID bmst000232
_Entry.Title dTMP
_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 dTMP
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. ? bmst000232
2 John Markley L. ? bmst000232
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 bmst000232
stop_
loop_
_Data_set.Type
_Data_set.Count
_Data_set.Entry_ID
other_data_list 1 bmst000232
stop_
loop_
_Datum.Type
_Datum.Count
_Datum.Entry_ID
'theoretical chemical shifts' 1 bmst000232
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' bmst000232
2 . . 2008-11-18 2008-11-18 update BMRB 'updated the file to match latest NMR STAR dictionary' bmst000232
3 . . 2008-11-25 2008-11-25 update BMRB 'fixed enumerations: N should be no' bmst000232
4 . . 2010-09-16 2010-09-16 update BMRB 'Removed Shielding_tensor_list_ID and Shielding_tensor_list_label from theoretical_chem_shifts' bmst000232
5 . . 2011-09-14 2011-09-14 update BMRB 'Partially brought up to date with latest Dictionary' bmst000232
6 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmst000232
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 . . dTMP_3655_opt.pdb x-chemical/x-pdb 'Name of the file containing the atomic coordinates' bmst000232
2 . . dTMP_3655.g03.shifts text/plain 'Name of the file containing theoretical chemical shift data' bmst000232
stop_
save_
###############
# Citations #
###############
save_citations
_Citation.Sf_category citations
_Citation.Sf_framecode citations
_Citation.Entry_ID bmst000232
_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. ? bmst000232 1
2 T. Barrett T. ? ? bmst000232 1
3 D. Benson D. A. ? bmst000232 1
4 S. Bryant S. H. ? bmst000232 1
5 K. Canese K. ? ? bmst000232 1
6 V. Chetvenin V. ? ? bmst000232 1
7 D. Church D. M. ? bmst000232 1
8 M. DiCuccio M. ? ? bmst000232 1
9 R. Edgar R. ? ? bmst000232 1
10 S. Federhen S. ? ? bmst000232 1
11 L. Geer L. Y. ? bmst000232 1
12 W. Helmberg W. ? ? bmst000232 1
13 Y. Kapustin Y. ? ? bmst000232 1
14 D. Kenton D. L. ? bmst000232 1
15 O. Khovayko O. ? ? bmst000232 1
16 D. Lipman D. J. ? bmst000232 1
17 T. Madden T. L. ? bmst000232 1
18 D. Maglott D. R. ? bmst000232 1
19 J. Ostell J. ? ? bmst000232 1
20 K. Pruitt K. D. ? bmst000232 1
21 G. Schuler G. D. ? bmst000232 1
22 L. Schriml L. M. ? bmst000232 1
23 E. Sequeira E. ? ? bmst000232 1
24 S. Sherry S. T. ? bmst000232 1
25 K. Sirotkin K. ? ? bmst000232 1
26 A. Souvorov A. ? ? bmst000232 1
27 G. Starchenko G. ? ? bmst000232 1
28 T. Suzek T. O. ? bmst000232 1
29 R. Tatusov R. ? ? bmst000232 1
30 T. Tatusova T. A. ? bmst000232 1
31 L. Bagner L. ? ? bmst000232 1
32 E. Yaschenko E. ? ? bmst000232 1
stop_
save_
#############################################
# Molecular system (assembly) description #
#############################################
save_assembly
_Assembly.Sf_category assembly
_Assembly.Sf_framecode assembly
_Assembly.Entry_ID bmst000232
_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 $dTMP yes native no no ? ? ? bmst000232 1
stop_
save_
####################################
# Biological polymers and ligands #
####################################
save_dTMP
_Entity.Sf_category entity
_Entity.Sf_framecode dTMP
_Entity.Entry_ID bmst000232
_Entity.ID 1
_Entity.BMRB_code ?
_Entity.Name dTMP
_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 bmst000232 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 bmst000232
_Chem_comp.ID 1
_Chem_comp.Provenance PubChem
_Chem_comp.Name dTMP
_Chem_comp.Type non-polymer
_Chem_comp.BMRB_code ?
_Chem_comp.PDB_code ?
_Chem_comp.InChI_code
;
InChI=1/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1/f/h11,16-17H
;
_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 H15 N2 O8 P'
_Chem_comp.Formula_weight 322.2084610000
_Chem_comp.Formula_mono_iso_wt_nat 322.056601979
_Chem_comp.Formula_mono_iso_wt_13C 332.090150357
_Chem_comp.Formula_mono_iso_wt_15N 324.050671765
_Chem_comp.Formula_mono_iso_wt_13C_15N 332.090150357
_Chem_comp.Image_file_name bmst000232.png
_Chem_comp.Image_file_format png
_Chem_comp.Topo_file_name ?
_Chem_comp.Topo_file_format ?
_Chem_comp.Struct_file_name bmst000232.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
'Deoxy TMP' synonym bmst000232 1
"Deoxythymidine 5'-phosphate" synonym bmst000232 1
'Thymidine monophosphate' synonym bmst000232 1
"Thymidine 5'-phosphate" synonym bmst000232 1
'Deoxyribosylthymine monophosphate' synonym bmst000232 1
5-Methyl-dUMP synonym bmst000232 1
'Thymidine mononucleotide' synonym bmst000232 1
'Thymidine phosphate' synonym bmst000232 1
dTMP synonym bmst000232 1
"Thymidine 5'-phosphoric acid" synonym bmst000232 1
'Deoxythymidine monophosphate' synonym bmst000232 1
'TMP (VAN)' synonym bmst000232 1
5'-TMP synonym bmst000232 1
"Thymidine-5'-monophosphoric acid" synonym bmst000232 1
"5'-Thymidylic acid" synonym bmst000232 1
'NSC 46713' synonym bmst000232 1
"Deoxythymidine 5'-monophosphate" synonym bmst000232 1
'Deoxythymidylic acid' synonym bmst000232 1
"2'-Deoxythymidine 5'-monophosphate" synonym bmst000232 1
'Thymidine, mono(dihydrogen phosphate) (ester)' synonym bmst000232 1
"Thymidine 5'-monophosphate" synonym bmst000232 1
'THYMIDYLIC ACID' synonym bmst000232 1
'Deoxythymydilic acid' synonym bmst000232 1
5'-dTMP synonym bmst000232 1
'Thymidylic acid' synonym bmst000232 1
Thymidylate synonym bmst000232 1
'TMP (nucleotide)' synonym bmst000232 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)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid' IUPAC bmst000232 1
;
[(2S,3R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)tetrahydrofuran-2-yl]methoxyphosphonic acid
;
IUPAC_TRADITIONAL bmst000232 1
;
[(2S,3R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)tetrahydrofuran-2-yl]methoxyphosphonic acid
;
IUPAC_OPENEYE bmst000232 1
;
[(2S,3R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)tetrahydrofuran-2-yl]methoxyphosphonic acid
;
IUPAC_CAS bmst000232 1
'[(2S,3R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphonic acid' IUPAC_SYSTEMATIC bmst000232 1
stop_
loop_
_Chem_comp_SMILES.Type
_Chem_comp_SMILES.String
_Chem_comp_SMILES.Entry_ID
_Chem_comp_SMILES.Comp_ID
Canonical CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O bmst000232 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 ? ? ? ? 6.4021 -3.1217 -1.979 -1.407 3.299 1 bmst000232 1
O2 O ? ? ? ? 5.8144 -2.3126 -2.045 -0.833 1.801 2 bmst000232 1
O3 O ? ? ? ? 7.2112 -2.5339 -2.855 -0.300 4.068 3 bmst000232 1
O4 O ? ? ? ? 6.9899 -3.9307 -0.429 -1.109 3.688 4 bmst000232 1
O5 O ? ? ? ? 2.6443 -2.4172 -2.160 -2.477 -2.418 5 bmst000232 1
O6 O ? ? ? ? 4.5411 -0.6571 -1.110 0.421 -0.642 6 bmst000232 1
O7 O ? ? ? ? 5.5931 -3.7095 -2.408 -2.795 3.555 7 bmst000232 1
O8 O ? ? ? ? 2.0000 0.9307 1.569 -0.966 -0.882 8 bmst000232 1
O9 O ? ? ? ? 3.7321 3.9307 4.666 2.390 -0.907 9 bmst000232 1
N10 N ? ? ? ? 3.7321 0.9307 0.905 1.093 -1.689 10 bmst000232 1
N11 N ? ? ? ? 2.8660 2.4307 3.079 0.746 -0.930 11 bmst000232 1
C12 C ? ? ? ? 4.8198 -2.4172 -1.342 -1.534 0.750 12 bmst000232 1
C13 C ? ? ? ? 5.4641 2.9307 2.833 4.375 -1.963 13 bmst000232 1
C14 C ? ? ? ? 3.7321 -0.0693 -0.495 0.660 -1.889 14 bmst000232 1
C15 C ? ? ? ? 4.2321 -1.6082 -1.687 -0.893 -0.579 15 bmst000232 1
C16 C ? ? ? ? 3.2321 -1.6082 -1.151 -1.695 -1.791 16 bmst000232 1
C17 C ? ? ? ? 2.9230 -0.6571 -0.690 -0.598 -2.755 17 bmst000232 1
C18 C ? ? ? ? 2.8660 1.4307 1.827 0.201 -1.143 18 bmst000232 1
C19 C ? ? ? ? 3.7321 2.9307 3.516 2.064 -1.158 19 bmst000232 1
C20 C ? ? ? ? 4.5981 2.4307 2.476 2.941 -1.696 20 bmst000232 1
C21 C ? ? ? ? 4.5981 1.4307 1.250 2.417 -1.917 21 bmst000232 1
H22 H ? ? ? ? 7.1464 -1.9173 -2.638 0.603 3.780 22 bmst000232 1
H23 H ? ? ? ? 7.6065 -3.8659 -0.118 -1.773 4.326 23 bmst000232 1
H24 H ? ? ? ? 2.0277 -2.3524 -2.242 -3.313 -1.935 24 bmst000232 1
H25 H ? ? ? ? 2.3291 2.7407 3.765 0.108 -0.541 25 bmst000232 1
H26 H ? ? ? ? 4.2626 -2.6890 -1.664 -2.583 0.750 26 bmst000232 1
H27 H ? ? ? ? 4.9907 -3.0132 -0.264 -1.477 0.923 27 bmst000232 1
H28 H ? ? ? ? 5.1541 3.4676 3.657 4.443 -2.682 28 bmst000232 1
H29 H ? ? ? ? 6.0010 3.2407 3.178 4.867 -1.046 29 bmst000232 1
H30 H ? ? ? ? 5.7741 2.3937 1.978 4.932 -2.358 30 bmst000232 1
H31 H ? ? ? ? 4.2845 0.2122 -0.971 1.528 -2.358 31 bmst000232 1
H32 H ? ? ? ? 4.8444 -1.5112 -2.777 -0.807 -0.674 32 bmst000232 1
H33 H ? ? ? ? 3.5135 -2.1606 -0.302 -2.317 -1.493 33 bmst000232 1
H34 H ? ? ? ? 2.6130 -0.1202 -1.500 -0.420 -3.471 34 bmst000232 1
H35 H ? ? ? ? 2.3566 -0.9093 0.207 -0.869 -3.313 35 bmst000232 1
H36 H ? ? ? ? 5.1350 1.1207 0.441 3.028 -2.307 36 bmst000232 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 ? bmst000232 1
O2 O2 ? bmst000232 1
O3 O3 ? bmst000232 1
O4 O4 ? bmst000232 1
O5 O5 ? bmst000232 1
O6 O6 ? bmst000232 1
O7 O7 ? bmst000232 1
O8 O8 ? bmst000232 1
O9 O9 ? bmst000232 1
N10 N10 ? bmst000232 1
N11 N11 ? bmst000232 1
C12 C12 ? bmst000232 1
C13 C13 ? bmst000232 1
C14 C14 ? bmst000232 1
C15 C15 ? bmst000232 1
C16 C16 ? bmst000232 1
C17 C17 ? bmst000232 1
C18 C18 ? bmst000232 1
C19 C19 ? bmst000232 1
C20 C20 ? bmst000232 1
C21 C21 ? bmst000232 1
H22 H22 ? bmst000232 1
H23 H23 ? bmst000232 1
H24 H24 ? bmst000232 1
H25 H25 ? bmst000232 1
H26 H26 ? bmst000232 1
H27 H27 ? bmst000232 1
H28 H28 ? bmst000232 1
H29 H29 ? bmst000232 1
H30 H30 ? bmst000232 1
H31 H31 ? bmst000232 1
H32 H32 ? bmst000232 1
H33 H33 ? bmst000232 1
H34 H34 ? bmst000232 1
H35 H35 ? bmst000232 1
H36 H36 ? bmst000232 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 ? bmst000232 1
2 covalent SING P1 O3 ? bmst000232 1
3 covalent SING P1 O4 ? bmst000232 1
4 covalent DOUB P1 O7 ? bmst000232 1
5 covalent SING O2 C12 ? bmst000232 1
6 covalent SING O3 H22 ? bmst000232 1
7 covalent SING O4 H23 ? bmst000232 1
8 covalent SING C16 O5 ? bmst000232 1
9 covalent SING O5 H24 ? bmst000232 1
10 covalent SING O6 C14 ? bmst000232 1
11 covalent SING O6 C15 ? bmst000232 1
12 covalent DOUB O8 C18 ? bmst000232 1
13 covalent DOUB O9 C19 ? bmst000232 1
14 covalent SING C14 N10 ? bmst000232 1
15 covalent SING N10 C18 ? bmst000232 1
16 covalent SING N10 C21 ? bmst000232 1
17 covalent SING N11 C18 ? bmst000232 1
18 covalent SING N11 C19 ? bmst000232 1
19 covalent SING N11 H25 ? bmst000232 1
20 covalent SING C15 C12 ? bmst000232 1
21 covalent SING C12 H26 ? bmst000232 1
22 covalent SING C12 H27 ? bmst000232 1
23 covalent SING C13 C20 ? bmst000232 1
24 covalent SING C13 H28 ? bmst000232 1
25 covalent SING C13 H29 ? bmst000232 1
26 covalent SING C13 H30 ? bmst000232 1
27 covalent SING C14 C17 ? bmst000232 1
28 covalent SING C14 H31 ? bmst000232 1
29 covalent SING C15 C16 ? bmst000232 1
30 covalent SING C15 H32 ? bmst000232 1
31 covalent SING C16 C17 ? bmst000232 1
32 covalent SING C16 H33 ? bmst000232 1
33 covalent SING C17 H34 ? bmst000232 1
34 covalent SING C17 H35 ? bmst000232 1
35 covalent SING C19 C20 ? bmst000232 1
36 covalent DOUB C20 C21 ? bmst000232 1
37 covalent SING C21 H36 ? bmst000232 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 152914 sid ? dTMP ? 'matching entry' ? bmst000232 1
no PubChem 3655 sid ? dTMP ? 'matching entry' ? bmst000232 1
no PubChem 9700 cid ? dTMP ? 'matching entry' ? bmst000232 1
no KEGG C00364 'compound ID' ? dTMP ? 'matching entry' ? bmst000232 1
no ChemIDplus 000365071 ? ? dTMP ? 'matching entry' ? bmst000232 1
no 'CAS Registry' 365-07-1 'registry number' ? dTMP ? 'matching entry' ? bmst000232 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 bmst000232 1
stop_
save_
############################
# Computer software used #
############################
save_software_1
_Software.Sf_category software
_Software.Sf_framecode software_1
_Software.Entry_ID bmst000232
_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 bmst000232 1
stop_
loop_
_Task.Task
_Task.Entry_ID
_Task.Software_ID
'geometry optimization' bmst000232 1
'chemical shift calculation' bmst000232 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 bmst000232
_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 ? bmst000232 1
C 13 TMS 'methyl carbons' ppm 0.00 na direct ? bmst000232 1
N 15 'ammonia pentamer' nitrogen ppm 0.00 na direct ? bmst000232 1
P 31 'phosphoric acid' phosphorus ppm 0.00 na direct ? bmst000232 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 bmst000232
_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 bmst000232 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 bmst000232
_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 ? 0.895 ? dTMP ? ? bmst000232 1
2 1 1 1 1 N10 N ? 159.624 ? dTMP ? ? bmst000232 1
3 1 1 1 1 N11 N ? 164.657 ? dTMP ? ? bmst000232 1
4 1 1 1 1 C12 C ? 70.630 ? dTMP ? ? bmst000232 1
5 1 1 1 1 C13 C ? 15.357 ? dTMP ? ? bmst000232 1
6 1 1 1 1 C14 C ? 102.056 ? dTMP ? ? bmst000232 1
7 1 1 1 1 C15 C ? 94.834 ? dTMP ? ? bmst000232 1
8 1 1 1 1 C16 C ? 78.394 ? dTMP ? ? bmst000232 1
9 1 1 1 1 C17 C ? 42.289 ? dTMP ? ? bmst000232 1
10 1 1 1 1 C18 C ? 156.365 ? dTMP ? ? bmst000232 1
11 1 1 1 1 C19 C ? 168.822 ? dTMP ? ? bmst000232 1
12 1 1 1 1 C20 C ? 116.845 ? dTMP ? ? bmst000232 1
13 1 1 1 1 C21 C ? 147.412 ? dTMP ? ? bmst000232 1
14 1 1 1 1 H22 H ? 3.909 ? dTMP ? ? bmst000232 1
15 1 1 1 1 H23 H ? 3.675 ? dTMP ? ? bmst000232 1
16 1 1 1 1 H24 H ? 0.799 ? dTMP ? ? bmst000232 1
17 1 1 1 1 H25 H ? 7.220 ? dTMP ? ? bmst000232 1
18 1 1 1 1 H26 H ? 5.003 ? dTMP ? ? bmst000232 1
19 1 1 1 1 H27 H ? 5.548 ? dTMP ? ? bmst000232 1
20 1 1 1 1 H28 H ? 3.244 ? dTMP ? ? bmst000232 1
21 1 1 1 1 H29 H ? 3.267 ? dTMP ? ? bmst000232 1
22 1 1 1 1 H30 H ? 2.389 ? dTMP ? ? bmst000232 1
23 1 1 1 1 H31 H ? 6.005 ? dTMP ? ? bmst000232 1
24 1 1 1 1 H32 H ? 5.234 ? dTMP ? ? bmst000232 1
25 1 1 1 1 H33 H ? 5.980 ? dTMP ? ? bmst000232 1
26 1 1 1 1 H34 H ? 3.641 ? dTMP ? ? bmst000232 1
27 1 1 1 1 H35 H ? 3.722 ? dTMP ? ? bmst000232 1
28 1 1 1 1 H36 H ? 7.913 ? dTMP ? ? bmst000232 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 bmst000232
_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 bmst000232 1
stop_
loop_
_Atom_site.Model_ID
_Atom_site.ID
_Atom_site.Label_entity_assembly_ID
_Atom_site.Label_entity_ID
_Atom_site.Label_comp_index_ID
_Atom_site.Label_comp_ID
_Atom_site.Label_atom_ID
_Atom_site.Auth_seq_ID
_Atom_site.Auth_comp_ID
_Atom_site.Auth_atom_ID
_Atom_site.Type_symbol
_Atom_site.Cartn_x
_Atom_site.Cartn_y
_Atom_site.Cartn_z
_Atom_site.Entry_ID
_Atom_site.Conformer_family_coord_set_ID
1 1 1 1 1 1 P1 1 1 P1 P -1.979 -1.407 3.299 bmst000232 1
1 2 1 1 1 1 O2 1 1 O2 O -2.045 -0.833 1.801 bmst000232 1
1 3 1 1 1 1 O3 1 1 O3 O -2.855 -0.300 4.068 bmst000232 1
1 4 1 1 1 1 O4 1 1 O4 O -0.429 -1.109 3.688 bmst000232 1
1 5 1 1 1 1 O5 1 1 O5 O -2.160 -2.477 -2.418 bmst000232 1
1 6 1 1 1 1 O6 1 1 O6 O -1.110 0.421 -0.642 bmst000232 1
1 7 1 1 1 1 O7 1 1 O7 O -2.408 -2.795 3.555 bmst000232 1
1 8 1 1 1 1 O8 1 1 O8 O 1.569 -0.966 -0.882 bmst000232 1
1 9 1 1 1 1 O9 1 1 O9 O 4.666 2.390 -0.907 bmst000232 1
1 10 1 1 1 1 N10 1 1 N10 N 0.905 1.093 -1.689 bmst000232 1
1 11 1 1 1 1 N11 1 1 N11 N 3.079 0.746 -0.930 bmst000232 1
1 12 1 1 1 1 C12 1 1 C12 C -1.342 -1.534 0.750 bmst000232 1
1 13 1 1 1 1 C13 1 1 C13 C 2.833 4.375 -1.963 bmst000232 1
1 14 1 1 1 1 C14 1 1 C14 C -0.495 0.660 -1.889 bmst000232 1
1 15 1 1 1 1 C15 1 1 C15 C -1.687 -0.893 -0.579 bmst000232 1
1 16 1 1 1 1 C16 1 1 C16 C -1.151 -1.695 -1.791 bmst000232 1
1 17 1 1 1 1 C17 1 1 C17 C -0.690 -0.598 -2.755 bmst000232 1
1 18 1 1 1 1 C18 1 1 C18 C 1.827 0.201 -1.143 bmst000232 1
1 19 1 1 1 1 C19 1 1 C19 C 3.516 2.064 -1.158 bmst000232 1
1 20 1 1 1 1 C20 1 1 C20 C 2.476 2.941 -1.696 bmst000232 1
1 21 1 1 1 1 C21 1 1 C21 C 1.250 2.417 -1.917 bmst000232 1
1 22 1 1 1 1 H22 1 1 H22 H -2.638 0.603 3.780 bmst000232 1
1 23 1 1 1 1 H23 1 1 H23 H -0.118 -1.773 4.326 bmst000232 1
1 24 1 1 1 1 H24 1 1 H24 H -2.242 -3.313 -1.935 bmst000232 1
1 25 1 1 1 1 H25 1 1 H25 H 3.765 0.108 -0.541 bmst000232 1
1 26 1 1 1 1 H26 1 1 H26 H -1.664 -2.583 0.750 bmst000232 1
1 27 1 1 1 1 H27 1 1 H27 H -0.264 -1.477 0.923 bmst000232 1
1 28 1 1 1 1 H28 1 1 H28 H 3.657 4.443 -2.682 bmst000232 1
1 29 1 1 1 1 H29 1 1 H29 H 3.178 4.867 -1.046 bmst000232 1
1 30 1 1 1 1 H30 1 1 H30 H 1.978 4.932 -2.358 bmst000232 1
1 31 1 1 1 1 H31 1 1 H31 H -0.971 1.528 -2.358 bmst000232 1
1 32 1 1 1 1 H32 1 1 H32 H -2.777 -0.807 -0.674 bmst000232 1
1 33 1 1 1 1 H33 1 1 H33 H -0.302 -2.317 -1.493 bmst000232 1
1 34 1 1 1 1 H34 1 1 H34 H -1.500 -0.420 -3.471 bmst000232 1
1 35 1 1 1 1 H35 1 1 H35 H 0.207 -0.869 -3.313 bmst000232 1
1 36 1 1 1 1 H36 1 1 H36 H 0.441 3.028 -2.307 bmst000232 1
stop_
save_