data_52169
#######################
# Entry information #
#######################
save_entry_information_1
_Entry.Sf_category entry_information
_Entry.Sf_framecode entry_information_1
_Entry.ID 52169
_Entry.Title
;
Clostridioides peptidoglycan fragment dimer
;
_Entry.Type macromolecule
_Entry.Version_type original
_Entry.Submission_date 2023-10-11
_Entry.Accession_date 2023-10-11
_Entry.Last_release_date 2023-10-11
_Entry.Original_release_date 2023-10-11
_Entry.Origination author
_Entry.Format_name .
_Entry.NMR_STAR_version 3.2.14.0
_Entry.NMR_STAR_dict_location .
_Entry.Original_NMR_STAR_version 3.1
_Entry.Experimental_method NMR
_Entry.Experimental_method_subtype solution
_Entry.Source_data_format .
_Entry.Source_data_format_version .
_Entry.Generated_software_name .
_Entry.Generated_software_version .
_Entry.Generated_software_ID 1
_Entry.Generated_software_label $software_1
_Entry.Generated_date .
_Entry.DOI .
_Entry.UUID .
_Entry.Related_coordinate_file_name .
_Entry.Details '1H NMR chemical shifts for the dimer (GlcNAc-rMurNAc-D-Ala-D-isoGlu-meso-DAP)2'
_Entry.BMRB_internal_directory_name .
loop_
_Entry_author.Ordinal
_Entry_author.Given_name
_Entry_author.Family_name
_Entry_author.First_initial
_Entry_author.Middle_initials
_Entry_author.Family_title
_Entry_author.ORCID
_Entry_author.Entry_ID
1 Nicola Galley . F. . . 52169
2 Mike Williamson . P. . . 52169
3 Stephane Mesnage . . . . 52169
stop_
loop_
_Data_set.Type
_Data_set.Count
_Data_set.Entry_ID
assigned_chemical_shifts 1 52169
stop_
loop_
_Datum.Type
_Datum.Count
_Datum.Entry_ID
'1H chemical shifts' 34 52169
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
2 . . 2024-01-16 2023-10-11 update BMRB 'update entry citation' 52169
1 . . 2023-10-17 2023-10-11 original author 'original release' 52169
stop_
save_
###############
# Citations #
###############
save_citations_1
_Citation.Sf_category citations
_Citation.Sf_framecode citations_1
_Citation.Entry_ID 52169
_Citation.ID 1
_Citation.Name 'entry citation'
_Citation.Class 'entry citation'
_Citation.CAS_abstract_code .
_Citation.MEDLINE_UI_code .
_Citation.PubMed_ID 38043796
_Citation.DOI .
_Citation.Full_citation .
_Citation.Title
;
Clostridioides difficile canonical L,D-transpeptidases catalyze a novel type of peptidoglycan cross-links and are not required for beta-lactam resistance
;
_Citation.Status published
_Citation.Type journal
_Citation.Journal_abbrev 'J. Biol. Chem.'
_Citation.Journal_name_full 'The Journal of biological chemistry'
_Citation.Journal_volume 300
_Citation.Journal_issue 1
_Citation.Journal_ASTM .
_Citation.Journal_ISSN 1083-351X
_Citation.Journal_CSD .
_Citation.Book_title .
_Citation.Book_chapter_title .
_Citation.Book_volume .
_Citation.Book_series .
_Citation.Book_publisher .
_Citation.Book_publisher_city .
_Citation.Book_ISBN .
_Citation.Conference_title .
_Citation.Conference_site .
_Citation.Conference_state_province .
_Citation.Conference_country .
_Citation.Conference_start_date .
_Citation.Conference_end_date .
_Citation.Conference_abstract_number .
_Citation.Thesis_institution .
_Citation.Thesis_institution_city .
_Citation.Thesis_institution_country .
_Citation.WWW_URL .
_Citation.Page_first 105529
_Citation.Page_last 105529
_Citation.Year 2023
_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.ORCID
_Citation_author.Entry_ID
_Citation_author.Citation_ID
1 Nicola Galley N. F. . . 52169 1
2 Darren Greetham D. . . . 52169 1
3 Marcel Alaman-Zarate M. G. . . 52169 1
4 Mike Williamson M. P. . . 52169 1
5 Caroline Evans C. A. . . 52169 1
6 William Spittal W. D. . . 52169 1
7 Jessica Buddle J. E. . . 52169 1
8 Jane Freeman J. . . . 52169 1
9 Georgina Davis G. L. . . 52169 1
10 Mark Dickman M. J. . . 52169 1
11 Mark Wilcox M. H. . . 52169 1
12 Andrew Lovering A. L. . . 52169 1
13 Robert Fagan R. P. . . 52169 1
14 Stephane Mesnage S. . . . 52169 1
stop_
save_
#############################################
# Molecular system (assembly) description #
#############################################
save_assembly_1
_Assembly.Sf_category assembly
_Assembly.Sf_framecode assembly_1
_Assembly.Entry_ID 52169
_Assembly.ID 1
_Assembly.Name 'GlcNAc-MurNAc-D-Ala-D-isoGlu-diamino pimelic acid dimer'
_Assembly.BMRB_code .
_Assembly.Number_of_components 1
_Assembly.Organic_ligands 0
_Assembly.Metal_ions 0
_Assembly.Non_standard_bonds no
_Assembly.Ambiguous_conformational_states no
_Assembly.Ambiguous_chem_comp_sites .
_Assembly.Molecules_in_chemical_exchange no
_Assembly.Paramagnetic no
_Assembly.Thiol_state .
_Assembly.Molecular_mass 1704.7
_Assembly.Enzyme_commission_number .
_Assembly.Details .
_Assembly.DB_query_date .
_Assembly.DB_query_revised_last_date .
loop_
_Entity_assembly.ID
_Entity_assembly.Entity_assembly_name
_Entity_assembly.Entity_ID
_Entity_assembly.Entity_label
_Entity_assembly.Asym_ID
_Entity_assembly.PDB_chain_ID
_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 'GlcNAc-MurNAc-D-Ala-D-isoGlu-diamino pimelic acid dimer' 1 $entity_1 . . yes native no no . structural . 52169 1
stop_
loop_
_Assembly_bio_function.Biological_function
_Assembly_bio_function.Entry_ID
_Assembly_bio_function.Assembly_ID
structural 52169 1
stop_
save_
####################################
# Biological polymers and ligands #
####################################
save_entity_1
_Entity.Sf_category entity
_Entity.Sf_framecode entity_1
_Entity.Entry_ID 52169
_Entity.ID 1
_Entity.BMRB_code .
_Entity.Name entity_1
_Entity.Type polymer
_Entity.Polymer_common_type .
_Entity.Polymer_type polypeptide(D)
_Entity.Polymer_type_details .
_Entity.Polymer_strand_ID .
_Entity.Polymer_seq_one_letter_code_can .
_Entity.Polymer_seq_one_letter_code
;
XXXXX
;
_Entity.Target_identifier .
_Entity.Polymer_author_defined_seq .
_Entity.Polymer_author_seq_details .
_Entity.Ambiguous_conformational_states no
_Entity.Ambiguous_chem_comp_sites no
_Entity.Nstd_monomer yes
_Entity.Nstd_chirality yes
_Entity.Nstd_linkage yes
_Entity.Nonpolymer_comp_ID .
_Entity.Nonpolymer_comp_label .
_Entity.Number_of_monomers 5
_Entity.Number_of_nonpolymer_components .
_Entity.Paramagnetic no
_Entity.Thiol_state 'not present'
_Entity.Src_method .
_Entity.Parent_entity_ID 1
_Entity.Fragment .
_Entity.Mutation .
_Entity.EC_number .
_Entity.Calc_isoelectric_point .
_Entity.Formula_weight 1704.7
_Entity.Formula_weight_exptl .
_Entity.Formula_weight_exptl_meth .
_Entity.Details .
_Entity.DB_query_date .
_Entity.DB_query_revised_last_date .
loop_
_Entity_biological_function.Biological_function
_Entity_biological_function.Entry_ID
_Entity_biological_function.Entity_ID
structural 52169 1
stop_
loop_
_Entity_comp_index.ID
_Entity_comp_index.Auth_seq_ID
_Entity_comp_index.Comp_ID
_Entity_comp_index.Comp_label
_Entity_comp_index.Entry_ID
_Entity_comp_index.Entity_ID
1 . NAG . 52169 1
2 . MUR . 52169 1
3 . DAL . 52169 1
4 . DGL . 52169 1
5 . API . 52169 1
stop_
loop_
_Entity_poly_seq.Hetero
_Entity_poly_seq.Mon_ID
_Entity_poly_seq.Num
_Entity_poly_seq.Comp_index_ID
_Entity_poly_seq.Entry_ID
_Entity_poly_seq.Entity_ID
. NAG 1 1 52169 1
. MUR 2 2 52169 1
. DAL 3 3 52169 1
. DGL 4 4 52169 1
. API 5 5 52169 1
stop_
save_
####################
# Natural source #
####################
save_natural_source_1
_Entity_natural_src_list.Sf_category natural_source
_Entity_natural_src_list.Sf_framecode natural_source_1
_Entity_natural_src_list.Entry_ID 52169
_Entity_natural_src_list.ID 1
loop_
_Entity_natural_src.ID
_Entity_natural_src.Entity_ID
_Entity_natural_src.Entity_label
_Entity_natural_src.Entity_chimera_segment_ID
_Entity_natural_src.NCBI_taxonomy_ID
_Entity_natural_src.Type
_Entity_natural_src.Common
_Entity_natural_src.Organism_name_scientific
_Entity_natural_src.Organism_name_common
_Entity_natural_src.Organism_acronym
_Entity_natural_src.ICTVdb_decimal_code
_Entity_natural_src.Superkingdom
_Entity_natural_src.Kingdom
_Entity_natural_src.Genus
_Entity_natural_src.Species
_Entity_natural_src.Strain
_Entity_natural_src.Variant
_Entity_natural_src.Organ
_Entity_natural_src.Tissue
_Entity_natural_src.Tissue_fraction
_Entity_natural_src.Cell_line
_Entity_natural_src.Cell_type
_Entity_natural_src.ATCC_number
_Entity_natural_src.Organelle
_Entity_natural_src.Secretion
_Entity_natural_src.Plasmid
_Entity_natural_src.Gene_mnemonic
_Entity_natural_src.Details
_Entity_natural_src.Entry_ID
_Entity_natural_src.Entity_natural_src_list_ID
1 1 $entity_1 . 1496 organism . 'Clostridioides difficile' 'Clostridioides difficile' . . Bacteria . Clostridioides difficile R20291 027 . . . . . . . . . . . 52169 1
stop_
save_
#########################
# Experimental source #
#########################
save_experimental_source_1
_Entity_experimental_src_list.Sf_category experimental_source
_Entity_experimental_src_list.Sf_framecode experimental_source_1
_Entity_experimental_src_list.Entry_ID 52169
_Entity_experimental_src_list.ID 1
loop_
_Entity_experimental_src.ID
_Entity_experimental_src.Entity_ID
_Entity_experimental_src.Entity_label
_Entity_experimental_src.Entity_chimera_segment_ID
_Entity_experimental_src.Production_method
_Entity_experimental_src.Host_org_scientific_name
_Entity_experimental_src.Host_org_name_common
_Entity_experimental_src.Host_org_details
_Entity_experimental_src.Host_org_NCBI_taxonomy_ID
_Entity_experimental_src.Host_org_genus
_Entity_experimental_src.Host_org_species
_Entity_experimental_src.Host_org_strain
_Entity_experimental_src.Host_org_variant
_Entity_experimental_src.Host_org_ATCC_number
_Entity_experimental_src.Vector_type
_Entity_experimental_src.PDBview_host_org_vector_name
_Entity_experimental_src.PDBview_plasmid_name
_Entity_experimental_src.Vector_name
_Entity_experimental_src.Vector_details
_Entity_experimental_src.Vendor_name
_Entity_experimental_src.Details
_Entity_experimental_src.Entry_ID
_Entity_experimental_src.Entity_experimental_src_list_ID
1 1 $entity_1 . 'purified from the natural source' . . . . . . . . . . . . . . . 'peptidoglycan was digested with mutanolysin and products were purified by hplc' 52169 1
stop_
save_
#################################
# Polymer residues and ligands #
#################################
save_chem_comp_NAG
_Chem_comp.Sf_category chem_comp
_Chem_comp.Sf_framecode chem_comp_NAG
_Chem_comp.Entry_ID 52169
_Chem_comp.ID NAG
_Chem_comp.Provenance PDB
_Chem_comp.Name N-ACETYL-D-GLUCOSAMINE
_Chem_comp.Type 'D-SACCHARIDE, BETA LINKING'
_Chem_comp.BMRB_code NAG
_Chem_comp.PDB_code NAG
_Chem_comp.Ambiguous_flag no
_Chem_comp.Initial_date 2020-07-10
_Chem_comp.Modified_date 2020-07-10
_Chem_comp.Release_status REL
_Chem_comp.Replaced_by .
_Chem_comp.Replaces .
_Chem_comp.One_letter_code .
_Chem_comp.Three_letter_code NAG
_Chem_comp.Number_atoms_all 30
_Chem_comp.Number_atoms_nh 15
_Chem_comp.Atom_nomenclature_source .
_Chem_comp.PubChem_code .
_Chem_comp.Subcomponent_list .
_Chem_comp.InChI_code InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
_Chem_comp.Mon_nstd_flag no
_Chem_comp.Mon_nstd_class .
_Chem_comp.Mon_nstd_details .
_Chem_comp.Mon_nstd_parent .
_Chem_comp.Mon_nstd_parent_comp_ID .
_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.Std_deriv_chem_comp_name .
_Chem_comp.Synonyms .
_Chem_comp.Formal_charge 0
_Chem_comp.Paramagnetic .
_Chem_comp.Aromatic no
_Chem_comp.Formula 'C8 H15 N O6'
_Chem_comp.Formula_weight 221.208
_Chem_comp.Formula_mono_iso_wt_nat .
_Chem_comp.Formula_mono_iso_wt_13C .
_Chem_comp.Formula_mono_iso_wt_15N .
_Chem_comp.Formula_mono_iso_wt_13C_15N .
_Chem_comp.Image_file_name .
_Chem_comp.Image_file_format .
_Chem_comp.Topo_file_name .
_Chem_comp.Topo_file_format .
_Chem_comp.Struct_file_name .
_Chem_comp.Struct_file_format .
_Chem_comp.Stereochem_param_file_name .
_Chem_comp.Stereochem_param_file_format .
_Chem_comp.Model_details .
_Chem_comp.Model_erf .
_Chem_comp.Model_source .
_Chem_comp.Model_coordinates_details .
_Chem_comp.Model_coordinates_missing_flag no
_Chem_comp.Ideal_coordinates_details Corina
_Chem_comp.Ideal_coordinates_missing_flag no
_Chem_comp.Model_coordinates_db_code 8PCH
_Chem_comp.Processing_site RCSB
_Chem_comp.Vendor .
_Chem_comp.Vendor_product_code .
_Chem_comp.Details .
_Chem_comp.DB_query_date .
_Chem_comp.DB_last_query_revised_last_date .
loop_
_Chem_comp_descriptor.Descriptor
_Chem_comp_descriptor.Type
_Chem_comp_descriptor.Program
_Chem_comp_descriptor.Program_version
_Chem_comp_descriptor.Entry_ID
_Chem_comp_descriptor.Comp_ID
CC(=O)NC1C(C(C(OC1O)CO)O)O SMILES 'OpenEye OEToolkits' 1.7.6 52169 NAG
CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)O)O SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 52169 NAG
CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O SMILES_CANONICAL CACTVS 3.370 52169 NAG
CC(=O)N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O SMILES CACTVS 3.370 52169 NAG
InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1 InChI InChI 1.03 52169 NAG
O=C(NC1C(O)C(O)C(OC1O)CO)C SMILES ACDLabs 12.01 52169 NAG
OVRNDRQMDRJTHS-FMDGEEDCSA-N InChIKey InChI 1.03 52169 NAG
stop_
loop_
_Chem_comp_identifier.Identifier
_Chem_comp_identifier.Type
_Chem_comp_identifier.Program
_Chem_comp_identifier.Program_version
_Chem_comp_identifier.Entry_ID
_Chem_comp_identifier.Comp_ID
2-(acetylamino)-2-deoxy-beta-D-glucopyranose 'SYSTEMATIC NAME' ACDLabs 12.01 52169 NAG
DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 52169 NAG
GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 52169 NAG
N-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 52169 NAG
N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1.0 52169 NAG
b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 52169 NAG
stop_
loop_
_PDBX_chem_comp_feature.Type
_PDBX_chem_comp_feature.Value
_PDBX_chem_comp_feature.Source
_PDBX_chem_comp_feature.Support
_PDBX_chem_comp_feature.Entry_ID
_PDBX_chem_comp_feature.Comp_ID
'CARBOHYDRATE ANOMER' beta PDB . 52169 NAG
'CARBOHYDRATE ISOMER' D PDB . 52169 NAG
'CARBOHYDRATE RING' pyranose PDB . 52169 NAG
stop_
loop_
_Chem_comp_atom.Atom_ID
_Chem_comp_atom.BMRB_code
_Chem_comp_atom.PDB_atom_ID
_Chem_comp_atom.Alt_atom_ID
_Chem_comp_atom.Auth_atom_ID
_Chem_comp_atom.Type_symbol
_Chem_comp_atom.Isotope_number
_Chem_comp_atom.Chirality
_Chem_comp_atom.Stereo_config
_Chem_comp_atom.Charge
_Chem_comp_atom.Partial_charge
_Chem_comp_atom.Oxidation_number
_Chem_comp_atom.Unpaired_electron_number
_Chem_comp_atom.Align
_Chem_comp_atom.Aromatic_flag
_Chem_comp_atom.Leaving_atom_flag
_Chem_comp_atom.Substruct_code
_Chem_comp_atom.Ionizable
_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_x_esd
_Chem_comp_atom.Model_Cartn_y
_Chem_comp_atom.Model_Cartn_y_esd
_Chem_comp_atom.Model_Cartn_z
_Chem_comp_atom.Model_Cartn_z_esd
_Chem_comp_atom.Model_Cartn_x_ideal
_Chem_comp_atom.Model_Cartn_y_ideal
_Chem_comp_atom.Model_Cartn_z_ideal
_Chem_comp_atom.PDBX_ordinal
_Chem_comp_atom.Details
_Chem_comp_atom.Entry_ID
_Chem_comp_atom.Comp_ID
C1 C1 C1 C1 . C . . R 0 . . . 1 N N . . . . 7.396 . 28.163 . 26.662 . 0.185 1.082 -0.421 1 . 52169 NAG
C2 C2 C2 C2 . C . . R 0 . . . 1 N N . . . . 6.973 . 29.233 . 27.644 . 0.790 -0.220 0.112 2 . 52169 NAG
C3 C3 C3 C3 . C . . R 0 . . . 1 N N . . . . 7.667 . 29.055 . 29.000 . -0.124 -1.390 -0.265 3 . 52169 NAG
C4 C4 C4 C4 . C . . S 0 . . . 1 N N . . . . 7.573 . 27.588 . 29.490 . -1.526 -1.129 0.294 4 . 52169 NAG
C5 C5 C5 C5 . C . . R 0 . . . 1 N N . . . . 7.902 . 26.592 . 28.373 . -2.042 0.207 -0.246 5 . 52169 NAG
C6 C6 C6 C6 . C . . N 0 . . . 1 N N . . . . 7.599 . 25.173 . 28.797 . -3.417 0.504 0.355 6 . 52169 NAG
C7 C7 C7 C7 . C . . N 0 . . . 1 N N . . . . 6.291 . 31.299 . 26.595 . 3.197 0.157 0.076 7 . 52169 NAG
C8 C8 C8 C8 . C . . N 0 . . . 1 N N . . . . 6.684 . 32.649 . 26.036 . 4.559 -0.052 -0.533 8 . 52169 NAG
N2 N2 N2 N2 . N . . N 0 . . . 1 N N . . . . 7.268 . 30.545 . 27.089 . 2.114 -0.422 -0.480 9 . 52169 NAG
O1 O1 O1 O1 . O . . N 0 . . . 1 N Y . . . . 6.676 . 28.363 . 25.419 . 1.003 2.185 -0.024 10 . 52169 NAG
O3 O3 O3 O3 . O . . N 0 . . . 1 N N . . . . 7.038 . 29.909 . 29.947 . 0.395 -2.600 0.291 11 . 52169 NAG
O4 O4 O4 O4 . O . . N 0 . . . 1 N N . . . . 8.494 . 27.358 . 30.574 . -2.405 -2.180 -0.114 12 . 52169 NAG
O5 O5 O5 O5 . O . . N 0 . . . 1 N N . . . . 7.104 . 26.875 . 27.206 . -1.130 1.248 0.113 13 . 52169 NAG
O6 O6 O6 O6 . O . . N 0 . . . 1 N N . . . . 6.232 . 25.040 . 29.165 . -3.949 1.691 -0.236 14 . 52169 NAG
O7 O7 O7 O7 . O . . N 0 . . . 1 N N . . . . 5.114 . 30.936 . 26.562 . 3.074 0.845 1.067 15 . 52169 NAG
H1 H1 H1 H1 . H . . N 0 . . . 1 N N . . . . 8.477 . 28.257 . 26.481 . 0.133 1.040 -1.509 16 . 52169 NAG
H2 H2 H2 H2 . H . . N 0 . . . 1 N N . . . . 5.888 . 29.146 . 27.803 . 0.879 -0.163 1.197 17 . 52169 NAG
H3 H3 H3 H3 . H . . N 0 . . . 1 N N . . . . 8.729 . 29.321 . 28.892 . -0.174 -1.478 -1.350 18 . 52169 NAG
H4 H4 H4 H4 . H . . N 0 . . . 1 N N . . . . 6.544 . 27.403 . 29.831 . -1.483 -1.091 1.382 19 . 52169 NAG
H5 H5 H5 H5 . H . . N 0 . . . 1 N N . . . . 8.971 . 26.674 . 28.128 . -2.123 0.154 -1.332 20 . 52169 NAG
H61 H61 H61 H61 . H . . N 0 . . . 1 N N . . . . 7.816 . 24.492 . 27.961 . -4.088 -0.333 0.157 21 . 52169 NAG
H62 H62 H62 H62 . H . . N 0 . . . 1 N N . . . . 8.232 . 24.910 . 29.657 . -3.320 0.645 1.431 22 . 52169 NAG
H81 H81 H81 H81 . H . . N 0 . . . 1 N N . . . . 5.791 . 33.159 . 25.646 . 4.560 0.320 -1.558 23 . 52169 NAG
H82 H82 H82 H82 . H . . N 0 . . . 1 N N . . . . 7.136 . 33.258 . 26.833 . 5.305 0.490 0.050 24 . 52169 NAG
H83 H83 H83 H83 . H . . N 0 . . . 1 N N . . . . 7.411 . 32.511 . 25.222 . 4.799 -1.115 -0.532 25 . 52169 NAG
HN2 HN2 HN2 HN2 . H . . N 0 . . . 1 N N . . . . 8.210 . 30.881 . 27.079 . 2.212 -0.973 -1.273 26 . 52169 NAG
HO1 HO1 HO1 HO1 . H . . N 0 . . . 1 N Y . . . . 6.933 . 27.696 . 24.793 . 0.679 3.044 -0.328 27 . 52169 NAG
HO3 HO3 HO3 HO3 . H . . N 0 . . . 1 N Y . . . . 7.459 . 29.809 . 30.793 . -0.135 -3.384 0.091 28 . 52169 NAG
HO4 HO4 HO4 HO4 . H . . N 0 . . . 1 N Y . . . . 8.425 . 26.456 . 30.863 . -3.312 -2.079 0.206 29 . 52169 NAG
HO6 HO6 HO6 HO6 . H . . N 0 . . . 1 N Y . . . . 6.060 . 24.143 . 29.428 . -4.822 1.940 0.099 30 . 52169 NAG
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.Aromatic_flag
_Chem_comp_bond.Stereo_config
_Chem_comp_bond.Ordinal
_Chem_comp_bond.Details
_Chem_comp_bond.Entry_ID
_Chem_comp_bond.Comp_ID
1 . SING C1 C2 N N 1 . 52169 NAG
2 . SING C1 O1 N N 2 . 52169 NAG
3 . SING C1 O5 N N 3 . 52169 NAG
4 . SING C1 H1 N N 4 . 52169 NAG
5 . SING C2 C3 N N 5 . 52169 NAG
6 . SING C2 N2 N N 6 . 52169 NAG
7 . SING C2 H2 N N 7 . 52169 NAG
8 . SING C3 C4 N N 8 . 52169 NAG
9 . SING C3 O3 N N 9 . 52169 NAG
10 . SING C3 H3 N N 10 . 52169 NAG
11 . SING C4 C5 N N 11 . 52169 NAG
12 . SING C4 O4 N N 12 . 52169 NAG
13 . SING C4 H4 N N 13 . 52169 NAG
14 . SING C5 C6 N N 14 . 52169 NAG
15 . SING C5 O5 N N 15 . 52169 NAG
16 . SING C5 H5 N N 16 . 52169 NAG
17 . SING C6 O6 N N 17 . 52169 NAG
18 . SING C6 H61 N N 18 . 52169 NAG
19 . SING C6 H62 N N 19 . 52169 NAG
20 . SING C7 C8 N N 20 . 52169 NAG
21 . SING C7 N2 N N 21 . 52169 NAG
22 . DOUB C7 O7 N N 22 . 52169 NAG
23 . SING C8 H81 N N 23 . 52169 NAG
24 . SING C8 H82 N N 24 . 52169 NAG
25 . SING C8 H83 N N 25 . 52169 NAG
26 . SING N2 HN2 N N 26 . 52169 NAG
27 . SING O1 HO1 N N 27 . 52169 NAG
28 . SING O3 HO3 N N 28 . 52169 NAG
29 . SING O4 HO4 N N 29 . 52169 NAG
30 . SING O6 HO6 N N 30 . 52169 NAG
stop_
save_
save_chem_comp_MUR
_Chem_comp.Sf_category chem_comp
_Chem_comp.Sf_framecode chem_comp_MUR
_Chem_comp.Entry_ID 52169
_Chem_comp.ID MUR
_Chem_comp.Provenance PDB
_Chem_comp.Name 'MURAMIC ACID'
_Chem_comp.Type 'D-SACCHARIDE, BETA LINKING'
_Chem_comp.BMRB_code MUR
_Chem_comp.PDB_code MUR
_Chem_comp.Ambiguous_flag no
_Chem_comp.Initial_date 2020-07-10
_Chem_comp.Modified_date 2020-07-10
_Chem_comp.Release_status REL
_Chem_comp.Replaced_by .
_Chem_comp.Replaces .
_Chem_comp.One_letter_code .
_Chem_comp.Three_letter_code MUR
_Chem_comp.Number_atoms_all 34
_Chem_comp.Number_atoms_nh 17
_Chem_comp.Atom_nomenclature_source .
_Chem_comp.PubChem_code .
_Chem_comp.Subcomponent_list .
_Chem_comp.InChI_code InChI=1S/C9H17NO7/c1-3(8(13)14)16-7-5(10)9(15)17-4(2-11)6(7)12/h3-7,9,11-12,15H,2,10H2,1H3,(H,13,14)/t3-,4-,5-,6-,7-,9-/m1/s1
_Chem_comp.Mon_nstd_flag no
_Chem_comp.Mon_nstd_class .
_Chem_comp.Mon_nstd_details .
_Chem_comp.Mon_nstd_parent .
_Chem_comp.Mon_nstd_parent_comp_ID .
_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.Std_deriv_chem_comp_name .
_Chem_comp.Synonyms .
_Chem_comp.Formal_charge 0
_Chem_comp.Paramagnetic .
_Chem_comp.Aromatic no
_Chem_comp.Formula 'C9 H17 N O7'
_Chem_comp.Formula_weight 251.234
_Chem_comp.Formula_mono_iso_wt_nat .
_Chem_comp.Formula_mono_iso_wt_13C .
_Chem_comp.Formula_mono_iso_wt_15N .
_Chem_comp.Formula_mono_iso_wt_13C_15N .
_Chem_comp.Image_file_name .
_Chem_comp.Image_file_format .
_Chem_comp.Topo_file_name .
_Chem_comp.Topo_file_format .
_Chem_comp.Struct_file_name .
_Chem_comp.Struct_file_format .
_Chem_comp.Stereochem_param_file_name .
_Chem_comp.Stereochem_param_file_format .
_Chem_comp.Model_details .
_Chem_comp.Model_erf .
_Chem_comp.Model_source .
_Chem_comp.Model_coordinates_details .
_Chem_comp.Model_coordinates_missing_flag no
_Chem_comp.Ideal_coordinates_details .
_Chem_comp.Ideal_coordinates_missing_flag no
_Chem_comp.Model_coordinates_db_code 1LOD
_Chem_comp.Processing_site RCSB
_Chem_comp.Vendor .
_Chem_comp.Vendor_product_code .
_Chem_comp.Details .
_Chem_comp.DB_query_date .
_Chem_comp.DB_last_query_revised_last_date .
loop_
_Chem_comp_descriptor.Descriptor
_Chem_comp_descriptor.Type
_Chem_comp_descriptor.Program
_Chem_comp_descriptor.Program_version
_Chem_comp_descriptor.Entry_ID
_Chem_comp_descriptor.Comp_ID
CC(C(=O)O)OC1C(C(OC(C1O)CO)O)N SMILES 'OpenEye OEToolkits' 1.5.0 52169 MUR
C[C@@H](O[C@@H]1[C@@H](N)[C@H](O)O[C@H](CO)[C@H]1O)C(O)=O SMILES_CANONICAL CACTVS 3.341 52169 MUR
C[C@H](C(=O)O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H]1O)CO)O)N SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 52169 MUR
C[CH](O[CH]1[CH](N)[CH](O)O[CH](CO)[CH]1O)C(O)=O SMILES CACTVS 3.341 52169 MUR
InChI=1S/C9H17NO7/c1-3(8(13)14)16-7-5(10)9(15)17-4(2-11)6(7)12/h3-7,9,11-12,15H,2,10H2,1H3,(H,13,14)/t3-,4-,5-,6-,7-,9-/m1/s1 InChI InChI 1.03 52169 MUR
MSFSPUZXLOGKHJ-KTZFPWNASA-N InChIKey InChI 1.03 52169 MUR
O=C(O)C(OC1C(O)C(OC(O)C1N)CO)C SMILES ACDLabs 10.04 52169 MUR
stop_
loop_
_Chem_comp_identifier.Identifier
_Chem_comp_identifier.Type
_Chem_comp_identifier.Program
_Chem_comp_identifier.Program_version
_Chem_comp_identifier.Entry_ID
_Chem_comp_identifier.Comp_ID
'(2R)-2-[(2R,3R,4R,5S,6R)-3-amino-2,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxypropanoic acid' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 52169 MUR
2-amino-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranose 'SYSTEMATIC NAME' ACDLabs 10.04 52169 MUR
Mur 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 52169 MUR
b-D-GlcpN3<C3O2> 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 52169 MUR
stop_
loop_
_PDBX_chem_comp_feature.Type
_PDBX_chem_comp_feature.Value
_PDBX_chem_comp_feature.Source
_PDBX_chem_comp_feature.Support
_PDBX_chem_comp_feature.Entry_ID
_PDBX_chem_comp_feature.Comp_ID
'CARBOHYDRATE ANOMER' beta PDB . 52169 MUR
'CARBOHYDRATE ISOMER' D PDB . 52169 MUR
'CARBOHYDRATE RING' pyranose PDB . 52169 MUR
stop_
loop_
_Chem_comp_atom.Atom_ID
_Chem_comp_atom.BMRB_code
_Chem_comp_atom.PDB_atom_ID
_Chem_comp_atom.Alt_atom_ID
_Chem_comp_atom.Auth_atom_ID
_Chem_comp_atom.Type_symbol
_Chem_comp_atom.Isotope_number
_Chem_comp_atom.Chirality
_Chem_comp_atom.Stereo_config
_Chem_comp_atom.Charge
_Chem_comp_atom.Partial_charge
_Chem_comp_atom.Oxidation_number
_Chem_comp_atom.Unpaired_electron_number
_Chem_comp_atom.Align
_Chem_comp_atom.Aromatic_flag
_Chem_comp_atom.Leaving_atom_flag
_Chem_comp_atom.Substruct_code
_Chem_comp_atom.Ionizable
_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_x_esd
_Chem_comp_atom.Model_Cartn_y
_Chem_comp_atom.Model_Cartn_y_esd
_Chem_comp_atom.Model_Cartn_z
_Chem_comp_atom.Model_Cartn_z_esd
_Chem_comp_atom.Model_Cartn_x_ideal
_Chem_comp_atom.Model_Cartn_y_ideal
_Chem_comp_atom.Model_Cartn_z_ideal
_Chem_comp_atom.PDBX_ordinal
_Chem_comp_atom.Details
_Chem_comp_atom.Entry_ID
_Chem_comp_atom.Comp_ID
C1 C1 C1 C1 . C . . R 0 . . . 1 N N . . . . -8.910 . 43.175 . 3.974 . -1.641 0.340 -1.567 1 . 52169 MUR
O1 O1 O1 O1 . O . . N 0 . . . 1 N Y . . . . -9.329 . 44.498 . 4.094 . -3.020 0.063 -1.818 2 . 52169 MUR
C2 C2 C2 C2 . C . . R 0 . . . 1 N N . . . . -7.460 . 43.205 . 4.105 . -1.258 -0.193 -0.184 3 . 52169 MUR
N2 N2 N2 N2 . N . . N 0 . . . 1 N N . . . . -7.013 . 44.132 . 3.179 . -2.102 0.437 0.838 4 . 52169 MUR
C3 C3 C3 C3 . C . . R 0 . . . 1 N N . . . . -6.867 . 41.855 . 3.836 . 0.212 0.137 0.088 5 . 52169 MUR
O3 O3 O3 O3 . O . . N 0 . . . 1 N N . . . . -5.452 . 42.018 . 4.006 . 0.625 -0.485 1.306 6 . 52169 MUR
C4 C4 C4 C4 . C . . S 0 . . . 1 N N . . . . -7.562 . 40.960 . 4.874 . 1.061 -0.391 -1.073 7 . 52169 MUR
O4 O4 O4 O4 . O . . N 0 . . . 1 N N . . . . -7.218 . 39.597 . 4.743 . 2.416 0.035 -0.917 8 . 52169 MUR
C5 C5 C5 C5 . C . . R 0 . . . 1 N N . . . . -9.112 . 41.052 . 4.797 . 0.501 0.154 -2.388 9 . 52169 MUR
O5 O5 O5 O5 . O . . N 0 . . . 1 N N . . . . -9.506 . 42.393 . 4.967 . -0.842 -0.289 -2.566 10 . 52169 MUR
C6 C6 C6 C6 . C . . N 0 . . . 1 N N . . . . -9.932 . 40.245 . 5.800 . 1.360 -0.345 -3.552 11 . 52169 MUR
O6 O6 O6 O6 . O . . N 0 . . . 1 N N . . . . -9.876 . 40.879 . 7.067 . 0.845 0.172 -4.780 12 . 52169 MUR
C7 C7 C7 C7 . C . . R 0 . . . 1 N N . . . . -4.436 . 41.999 . 3.000 . 0.372 0.450 2.355 13 . 52169 MUR
C8 C8 C8 C8 . C . . N 0 . . . 1 N N . . . . -3.978 . 43.438 . 2.739 . 0.069 -0.293 3.630 14 . 52169 MUR
O8 O8 O8 O8 . O . . N 0 . . . 1 N N . . . . -3.000 . 43.900 . 3.345 . 0.069 -1.501 3.639 15 . 52169 MUR
O9 O9 O9 O9 . O . . N 0 . . . 1 N N . . . . -4.695 . 44.183 . 2.051 . -0.201 0.386 4.756 16 . 52169 MUR
C9 C9 C9 C9 . C . . N 0 . . . 1 N N . . . . -3.262 . 41.312 . 3.700 . 1.606 1.332 2.561 17 . 52169 MUR
H1 H1 H1 H1 . H . . N 0 . . . 1 N N . . . . -9.205 . 42.723 . 2.998 . -1.476 1.417 -1.597 18 . 52169 MUR
HO1 HO1 HO1 HO1 . H . . N 0 . . . 1 N Y . . . . -10.274 . 44.478 . 4.008 . -3.220 0.415 -2.696 19 . 52169 MUR
H2 H2 H2 H2 . H . . N 0 . . . 1 N N . . . . -7.154 . 43.482 . 5.140 . -1.400 -1.273 -0.159 20 . 52169 MUR
HN21 HN21 HN21 1HN2 . H . . N 0 . . . 0 N N . . . . -5.997 . 44.153 . 3.270 . -3.056 0.193 0.618 21 . 52169 MUR
HN22 HN22 HN22 2HN2 . H . . N 0 . . . 0 N Y . . . . -7.449 . 45.048 . 3.277 . -1.882 -0.013 1.714 22 . 52169 MUR
H3 H3 H3 H3 . H . . N 0 . . . 1 N N . . . . -7.010 . 41.406 . 2.825 . 0.336 1.217 0.169 23 . 52169 MUR
H4 H4 H4 H4 . H . . N 0 . . . 1 N N . . . . -7.200 . 41.348 . 5.854 . 1.021 -1.480 -1.083 24 . 52169 MUR
HO4 HO4 HO4 HO4 . H . . N 0 . . . 1 N Y . . . . -7.647 . 39.043 . 5.384 . 2.909 -0.316 -1.671 25 . 52169 MUR
H5 H5 H5 H5 . H . . N 0 . . . 1 N N . . . . -9.329 . 40.611 . 3.796 . 0.522 1.244 -2.364 26 . 52169 MUR
H61 H61 H61 1H6 . H . . N 0 . . . 1 N N . . . . -10.979 . 40.080 . 5.455 . 2.387 -0.006 -3.417 27 . 52169 MUR
H62 H62 H62 2H6 . H . . N 0 . . . 1 N N . . . . -9.612 . 39.177 . 5.846 . 1.337 -1.434 -3.578 28 . 52169 MUR
HO6 HO6 HO6 HO6 . H . . N 0 . . . 1 N Y . . . . -10.386 . 40.376 . 7.691 . 1.413 -0.165 -5.486 29 . 52169 MUR
H7 H7 H7 H7 . H . . N 0 . . . 1 N N . . . . -4.776 . 41.518 . 2.053 . -0.479 1.075 2.087 30 . 52169 MUR
HO9 HO9 HO9 HO9 . H . . N 0 . . . 1 N N . . . . -4.411 . 45.075 . 1.889 . -0.396 -0.090 5.574 31 . 52169 MUR
H91 H91 H91 1H9 . H . . N 0 . . . 1 N N . . . . -2.469 . 41.297 . 2.915 . 2.458 0.708 2.829 32 . 52169 MUR
H92 H92 H92 2H9 . H . . N 0 . . . 1 N N . . . . -2.953 . 41.785 . 4.661 . 1.826 1.870 1.638 33 . 52169 MUR
H93 H93 H93 3H9 . H . . N 0 . . . 1 N N . . . . -3.501 . 40.314 . 4.135 . 1.413 2.046 3.361 34 . 52169 MUR
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.Aromatic_flag
_Chem_comp_bond.Stereo_config
_Chem_comp_bond.Ordinal
_Chem_comp_bond.Details
_Chem_comp_bond.Entry_ID
_Chem_comp_bond.Comp_ID
1 . SING C1 O1 N N 1 . 52169 MUR
2 . SING C1 C2 N N 2 . 52169 MUR
3 . SING C1 O5 N N 3 . 52169 MUR
4 . SING C1 H1 N N 4 . 52169 MUR
5 . SING O1 HO1 N N 5 . 52169 MUR
6 . SING C2 N2 N N 6 . 52169 MUR
7 . SING C2 C3 N N 7 . 52169 MUR
8 . SING C2 H2 N N 8 . 52169 MUR
9 . SING N2 HN21 N N 9 . 52169 MUR
10 . SING N2 HN22 N N 10 . 52169 MUR
11 . SING C3 O3 N N 11 . 52169 MUR
12 . SING C3 C4 N N 12 . 52169 MUR
13 . SING C3 H3 N N 13 . 52169 MUR
14 . SING O3 C7 N N 14 . 52169 MUR
15 . SING C4 O4 N N 15 . 52169 MUR
16 . SING C4 C5 N N 16 . 52169 MUR
17 . SING C4 H4 N N 17 . 52169 MUR
18 . SING O4 HO4 N N 18 . 52169 MUR
19 . SING C5 O5 N N 19 . 52169 MUR
20 . SING C5 C6 N N 20 . 52169 MUR
21 . SING C5 H5 N N 21 . 52169 MUR
22 . SING C6 O6 N N 22 . 52169 MUR
23 . SING C6 H61 N N 23 . 52169 MUR
24 . SING C6 H62 N N 24 . 52169 MUR
25 . SING O6 HO6 N N 25 . 52169 MUR
26 . SING C7 C8 N N 26 . 52169 MUR
27 . SING C7 C9 N N 27 . 52169 MUR
28 . SING C7 H7 N N 28 . 52169 MUR
29 . DOUB C8 O8 N N 29 . 52169 MUR
30 . SING C8 O9 N N 30 . 52169 MUR
31 . SING O9 HO9 N N 31 . 52169 MUR
32 . SING C9 H91 N N 32 . 52169 MUR
33 . SING C9 H92 N N 33 . 52169 MUR
34 . SING C9 H93 N N 34 . 52169 MUR
stop_
save_
save_chem_comp_DAL
_Chem_comp.Sf_category chem_comp
_Chem_comp.Sf_framecode chem_comp_DAL
_Chem_comp.Entry_ID 52169
_Chem_comp.ID DAL
_Chem_comp.Provenance PDB
_Chem_comp.Name D-ALANINE
_Chem_comp.Type 'D-PEPTIDE LINKING'
_Chem_comp.BMRB_code DAL
_Chem_comp.PDB_code DAL
_Chem_comp.Ambiguous_flag no
_Chem_comp.Initial_date 2020-07-10
_Chem_comp.Modified_date 2020-07-10
_Chem_comp.Release_status REL
_Chem_comp.Replaced_by .
_Chem_comp.Replaces .
_Chem_comp.One_letter_code A
_Chem_comp.Three_letter_code DAL
_Chem_comp.Number_atoms_all 13
_Chem_comp.Number_atoms_nh 6
_Chem_comp.Atom_nomenclature_source .
_Chem_comp.PubChem_code .
_Chem_comp.Subcomponent_list .
_Chem_comp.InChI_code InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1
_Chem_comp.Mon_nstd_flag no
_Chem_comp.Mon_nstd_class .
_Chem_comp.Mon_nstd_details .
_Chem_comp.Mon_nstd_parent .
_Chem_comp.Mon_nstd_parent_comp_ID .
_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.Std_deriv_chem_comp_name .
_Chem_comp.Synonyms .
_Chem_comp.Formal_charge 0
_Chem_comp.Paramagnetic .
_Chem_comp.Aromatic no
_Chem_comp.Formula 'C3 H7 N O2'
_Chem_comp.Formula_weight 89.093
_Chem_comp.Formula_mono_iso_wt_nat .
_Chem_comp.Formula_mono_iso_wt_13C .
_Chem_comp.Formula_mono_iso_wt_15N .
_Chem_comp.Formula_mono_iso_wt_13C_15N .
_Chem_comp.Image_file_name .
_Chem_comp.Image_file_format .
_Chem_comp.Topo_file_name .
_Chem_comp.Topo_file_format .
_Chem_comp.Struct_file_name .
_Chem_comp.Struct_file_format .
_Chem_comp.Stereochem_param_file_name .
_Chem_comp.Stereochem_param_file_format .
_Chem_comp.Model_details .
_Chem_comp.Model_erf .
_Chem_comp.Model_source .
_Chem_comp.Model_coordinates_details .
_Chem_comp.Model_coordinates_missing_flag no
_Chem_comp.Ideal_coordinates_details .
_Chem_comp.Ideal_coordinates_missing_flag no
_Chem_comp.Model_coordinates_db_code .
_Chem_comp.Processing_site RCSB
_Chem_comp.Vendor .
_Chem_comp.Vendor_product_code .
_Chem_comp.Details .
_Chem_comp.DB_query_date .
_Chem_comp.DB_last_query_revised_last_date .
loop_
_Chem_comp_descriptor.Descriptor
_Chem_comp_descriptor.Type
_Chem_comp_descriptor.Program
_Chem_comp_descriptor.Program_version
_Chem_comp_descriptor.Entry_ID
_Chem_comp_descriptor.Comp_ID
CC(C(=O)O)N SMILES 'OpenEye OEToolkits' 1.5.0 52169 DAL
C[C@@H](N)C(O)=O SMILES_CANONICAL CACTVS 3.341 52169 DAL
C[C@H](C(=O)O)N SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 52169 DAL
C[CH](N)C(O)=O SMILES CACTVS 3.341 52169 DAL
InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1 InChI InChI 1.03 52169 DAL
O=C(O)C(N)C SMILES ACDLabs 10.04 52169 DAL
QNAYBMKLOCPYGJ-UWTATZPHSA-N InChIKey InChI 1.03 52169 DAL
stop_
loop_
_Chem_comp_identifier.Identifier
_Chem_comp_identifier.Type
_Chem_comp_identifier.Program
_Chem_comp_identifier.Program_version
_Chem_comp_identifier.Entry_ID
_Chem_comp_identifier.Comp_ID
'(2R)-2-aminopropanoic acid' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 52169 DAL
D-alanine 'SYSTEMATIC NAME' ACDLabs 10.04 52169 DAL
stop_
loop_
_Chem_comp_atom.Atom_ID
_Chem_comp_atom.BMRB_code
_Chem_comp_atom.PDB_atom_ID
_Chem_comp_atom.Alt_atom_ID
_Chem_comp_atom.Auth_atom_ID
_Chem_comp_atom.Type_symbol
_Chem_comp_atom.Isotope_number
_Chem_comp_atom.Chirality
_Chem_comp_atom.Stereo_config
_Chem_comp_atom.Charge
_Chem_comp_atom.Partial_charge
_Chem_comp_atom.Oxidation_number
_Chem_comp_atom.Unpaired_electron_number
_Chem_comp_atom.Align
_Chem_comp_atom.Aromatic_flag
_Chem_comp_atom.Leaving_atom_flag
_Chem_comp_atom.Substruct_code
_Chem_comp_atom.Ionizable
_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_x_esd
_Chem_comp_atom.Model_Cartn_y
_Chem_comp_atom.Model_Cartn_y_esd
_Chem_comp_atom.Model_Cartn_z
_Chem_comp_atom.Model_Cartn_z_esd
_Chem_comp_atom.Model_Cartn_x_ideal
_Chem_comp_atom.Model_Cartn_y_ideal
_Chem_comp_atom.Model_Cartn_z_ideal
_Chem_comp_atom.PDBX_ordinal
_Chem_comp_atom.Details
_Chem_comp_atom.Entry_ID
_Chem_comp_atom.Comp_ID
N N N N . N . . N 0 . . . 1 N N . . . . 17.005 . 31.325 . 27.552 . -1.564 -0.992 0.101 1 . 52169 DAL
CA CA CA CA . C . . R 0 . . . 1 N N . . . . 17.495 . 30.650 . 26.346 . -0.724 0.176 0.402 2 . 52169 DAL
CB CB CB CB . C . . N 0 . . . 1 N N . . . . 16.859 . 31.287 . 25.124 . -1.205 1.374 -0.420 3 . 52169 DAL
C C C C . C . . N 0 . . . 1 N N . . . . 17.165 . 29.151 . 26.377 . 0.709 -0.132 0.051 4 . 52169 DAL
O O O O . O . . N 0 . . . 1 N N . . . . 16.244 . 28.758 . 27.139 . 1.001 -1.213 -0.403 5 . 52169 DAL
OXT OXT OXT OXT . O . . N 0 . . . 1 N Y . . . . 17.840 . 28.394 . 25.631 . 1.660 0.795 0.243 6 . 52169 DAL
H H H H . H . . N 0 . . . 1 N N . . . . 16.893 . 30.656 . 28.287 . -1.281 -1.723 0.736 7 . 52169 DAL
H2 H2 H2 HN2 . H . . N 0 . . . 1 N Y . . . . 17.663 . 32.023 . 27.834 . -2.509 -0.741 0.351 8 . 52169 DAL
HA HA HA HA . H . . N 0 . . . 1 N N . . . . 18.589 . 30.759 . 26.304 . -0.796 0.411 1.464 9 . 52169 DAL
HB1 HB1 HB1 1HB . H . . N 0 . . . 1 N N . . . . 16.705 . 32.361 . 25.308 . -1.133 1.139 -1.481 10 . 52169 DAL
HB2 HB2 HB2 2HB . H . . N 0 . . . 1 N N . . . . 17.521 . 31.155 . 24.255 . -2.241 1.597 -0.166 11 . 52169 DAL
HB3 HB3 HB3 3HB . H . . N 0 . . . 1 N N . . . . 15.890 . 30.807 . 24.923 . -0.582 2.240 -0.197 12 . 52169 DAL
HXT HXT HXT HXT . H . . N 0 . . . 1 N Y . . . . 17.544 . 27.498 . 25.738 . 2.580 0.598 0.018 13 . 52169 DAL
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.Aromatic_flag
_Chem_comp_bond.Stereo_config
_Chem_comp_bond.Ordinal
_Chem_comp_bond.Details
_Chem_comp_bond.Entry_ID
_Chem_comp_bond.Comp_ID
1 . SING N CA N N 1 . 52169 DAL
2 . SING N H N N 2 . 52169 DAL
3 . SING N H2 N N 3 . 52169 DAL
4 . SING CA CB N N 4 . 52169 DAL
5 . SING CA C N N 5 . 52169 DAL
6 . SING CA HA N N 6 . 52169 DAL
7 . SING CB HB1 N N 7 . 52169 DAL
8 . SING CB HB2 N N 8 . 52169 DAL
9 . SING CB HB3 N N 9 . 52169 DAL
10 . DOUB C O N N 10 . 52169 DAL
11 . SING C OXT N N 11 . 52169 DAL
12 . SING OXT HXT N N 12 . 52169 DAL
stop_
save_
save_chem_comp_DGL
_Chem_comp.Sf_category chem_comp
_Chem_comp.Sf_framecode chem_comp_DGL
_Chem_comp.Entry_ID 52169
_Chem_comp.ID DGL
_Chem_comp.Provenance PDB
_Chem_comp.Name 'D-GLUTAMIC ACID'
_Chem_comp.Type 'D-PEPTIDE LINKING'
_Chem_comp.BMRB_code DGL
_Chem_comp.PDB_code DGL
_Chem_comp.Ambiguous_flag no
_Chem_comp.Initial_date 2020-07-10
_Chem_comp.Modified_date 2020-07-10
_Chem_comp.Release_status REL
_Chem_comp.Replaced_by .
_Chem_comp.Replaces .
_Chem_comp.One_letter_code E
_Chem_comp.Three_letter_code DGL
_Chem_comp.Number_atoms_all 19
_Chem_comp.Number_atoms_nh 10
_Chem_comp.Atom_nomenclature_source .
_Chem_comp.PubChem_code .
_Chem_comp.Subcomponent_list .
_Chem_comp.InChI_code InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1
_Chem_comp.Mon_nstd_flag no
_Chem_comp.Mon_nstd_class .
_Chem_comp.Mon_nstd_details .
_Chem_comp.Mon_nstd_parent .
_Chem_comp.Mon_nstd_parent_comp_ID .
_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.Std_deriv_chem_comp_name .
_Chem_comp.Synonyms .
_Chem_comp.Formal_charge 0
_Chem_comp.Paramagnetic .
_Chem_comp.Aromatic no
_Chem_comp.Formula 'C5 H9 N O4'
_Chem_comp.Formula_weight 147.129
_Chem_comp.Formula_mono_iso_wt_nat .
_Chem_comp.Formula_mono_iso_wt_13C .
_Chem_comp.Formula_mono_iso_wt_15N .
_Chem_comp.Formula_mono_iso_wt_13C_15N .
_Chem_comp.Image_file_name .
_Chem_comp.Image_file_format .
_Chem_comp.Topo_file_name .
_Chem_comp.Topo_file_format .
_Chem_comp.Struct_file_name .
_Chem_comp.Struct_file_format .
_Chem_comp.Stereochem_param_file_name .
_Chem_comp.Stereochem_param_file_format .
_Chem_comp.Model_details .
_Chem_comp.Model_erf .
_Chem_comp.Model_source .
_Chem_comp.Model_coordinates_details .
_Chem_comp.Model_coordinates_missing_flag no
_Chem_comp.Ideal_coordinates_details Corina
_Chem_comp.Ideal_coordinates_missing_flag no
_Chem_comp.Model_coordinates_db_code 1CZQ
_Chem_comp.Processing_site RCSB
_Chem_comp.Vendor .
_Chem_comp.Vendor_product_code .
_Chem_comp.Details .
_Chem_comp.DB_query_date .
_Chem_comp.DB_last_query_revised_last_date .
loop_
_Chem_comp_descriptor.Descriptor
_Chem_comp_descriptor.Type
_Chem_comp_descriptor.Program
_Chem_comp_descriptor.Program_version
_Chem_comp_descriptor.Entry_ID
_Chem_comp_descriptor.Comp_ID
C(CC(=O)O)C(C(=O)O)N SMILES 'OpenEye OEToolkits' 1.7.0 52169 DGL
C(CC(=O)O)[C@H](C(=O)O)N SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 52169 DGL
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1 InChI InChI 1.03 52169 DGL
N[C@H](CCC(O)=O)C(O)=O SMILES_CANONICAL CACTVS 3.370 52169 DGL
N[CH](CCC(O)=O)C(O)=O SMILES CACTVS 3.370 52169 DGL
O=C(O)C(N)CCC(=O)O SMILES ACDLabs 12.01 52169 DGL
WHUUTDBJXJRKMK-GSVOUGTGSA-N InChIKey InChI 1.03 52169 DGL
stop_
loop_
_Chem_comp_identifier.Identifier
_Chem_comp_identifier.Type
_Chem_comp_identifier.Program
_Chem_comp_identifier.Program_version
_Chem_comp_identifier.Entry_ID
_Chem_comp_identifier.Comp_ID
'(2R)-2-azanylpentanedioic acid' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.0 52169 DGL
'D-glutamic acid' 'SYSTEMATIC NAME' ACDLabs 12.01 52169 DGL
stop_
loop_
_Chem_comp_atom.Atom_ID
_Chem_comp_atom.BMRB_code
_Chem_comp_atom.PDB_atom_ID
_Chem_comp_atom.Alt_atom_ID
_Chem_comp_atom.Auth_atom_ID
_Chem_comp_atom.Type_symbol
_Chem_comp_atom.Isotope_number
_Chem_comp_atom.Chirality
_Chem_comp_atom.Stereo_config
_Chem_comp_atom.Charge
_Chem_comp_atom.Partial_charge
_Chem_comp_atom.Oxidation_number
_Chem_comp_atom.Unpaired_electron_number
_Chem_comp_atom.Align
_Chem_comp_atom.Aromatic_flag
_Chem_comp_atom.Leaving_atom_flag
_Chem_comp_atom.Substruct_code
_Chem_comp_atom.Ionizable
_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_x_esd
_Chem_comp_atom.Model_Cartn_y
_Chem_comp_atom.Model_Cartn_y_esd
_Chem_comp_atom.Model_Cartn_z
_Chem_comp_atom.Model_Cartn_z_esd
_Chem_comp_atom.Model_Cartn_x_ideal
_Chem_comp_atom.Model_Cartn_y_ideal
_Chem_comp_atom.Model_Cartn_z_ideal
_Chem_comp_atom.PDBX_ordinal
_Chem_comp_atom.Details
_Chem_comp_atom.Entry_ID
_Chem_comp_atom.Comp_ID
N N N N . N . . N 0 . . . 1 N N . . . . 15.813 . -4.736 . 28.474 . -1.198 1.861 -0.122 1 . 52169 DGL
CA CA CA CA . C . . R 0 . . . 1 N N . . . . 14.782 . -5.702 . 28.834 . -1.130 0.510 0.451 2 . 52169 DGL
C C C C . C . . N 0 . . . 1 N N . . . . 14.875 . -6.180 . 30.276 . -2.352 -0.272 0.040 3 . 52169 DGL
O O O O . O . . N 0 . . . 1 N N . . . . 14.832 . -7.381 . 30.553 . -2.999 0.079 -0.918 4 . 52169 DGL
CB CB CB CB . C . . N 0 . . . 1 N N . . . . 13.397 . -5.090 . 28.574 . 0.125 -0.199 -0.062 5 . 52169 DGL
CG CG CG CG . C . . N 0 . . . 1 N N . . . . 13.060 . -4.844 . 27.093 . 1.368 0.525 0.460 6 . 52169 DGL
CD CD CD CD . C . . N 0 . . . 1 N N . . . . 13.663 . -3.568 . 26.500 . 2.605 -0.173 -0.045 7 . 52169 DGL
OE1 OE1 OE1 OE1 . O . . N 0 . . . 1 N N . . . . 14.422 . -2.859 . 27.182 . 2.502 -1.149 -0.750 8 . 52169 DGL
OE2 OE2 OE2 OE2 . O . . N 0 . . . 1 N N . . . . 13.367 . -3.264 . 25.323 . 3.820 0.290 0.289 9 . 52169 DGL
OXT OXT OXT OXT . O . . N 0 . . . 1 N Y . . . . 15.022 . -5.237 . 31.196 . -2.720 -1.357 0.738 10 . 52169 DGL
H H H H . H . . N 0 . . . 1 N N . . . . 15.696 . -4.464 . 27.519 . -1.236 1.826 -1.129 11 . 52169 DGL
H2 H2 H2 HN2 . H . . N 0 . . . 1 N Y . . . . 15.735 . -3.931 . 29.062 . -1.984 2.373 0.252 12 . 52169 DGL
HA HA HA HA . H . . N 0 . . . 1 N N . . . . 14.940 . -6.589 . 28.203 . -1.091 0.577 1.538 13 . 52169 DGL
HB2 HB2 HB2 HB1 . H . . N 0 . . . 1 N N . . . . 12.645 . -5.785 . 28.976 . 0.130 -1.230 0.291 14 . 52169 DGL
HB3 HB3 HB3 HB2 . H . . N 0 . . . 1 N N . . . . 13.359 . -4.119 . 29.090 . 0.129 -0.188 -1.152 15 . 52169 DGL
HG2 HG2 HG2 HG1 . H . . N 0 . . . 1 N N . . . . 13.446 . -5.697 . 26.516 . 1.363 1.556 0.107 16 . 52169 DGL
HG3 HG3 HG3 HG2 . H . . N 0 . . . 1 N N . . . . 11.966 . -4.769 . 27.006 . 1.364 0.514 1.550 17 . 52169 DGL
HE2 HE2 HE2 HE2 . H . . N 0 . . . 1 N N . . . . 13.804 . -2.455 . 25.085 . 4.583 -0.191 -0.059 18 . 52169 DGL
HXT HXT HXT HXT . H . . N 0 . . . 1 N Y . . . . 15.084 . -5.639 . 32.055 . -3.510 -1.826 0.436 19 . 52169 DGL
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.Aromatic_flag
_Chem_comp_bond.Stereo_config
_Chem_comp_bond.Ordinal
_Chem_comp_bond.Details
_Chem_comp_bond.Entry_ID
_Chem_comp_bond.Comp_ID
1 . SING N CA N N 1 . 52169 DGL
2 . SING N H N N 2 . 52169 DGL
3 . SING N H2 N N 3 . 52169 DGL
4 . SING CA C N N 4 . 52169 DGL
5 . SING CA CB N N 5 . 52169 DGL
6 . SING CA HA N N 6 . 52169 DGL
7 . DOUB C O N N 7 . 52169 DGL
8 . SING C OXT N N 8 . 52169 DGL
9 . SING CB CG N N 9 . 52169 DGL
10 . SING CB HB2 N N 10 . 52169 DGL
11 . SING CB HB3 N N 11 . 52169 DGL
12 . SING CG CD N N 12 . 52169 DGL
13 . SING CG HG2 N N 13 . 52169 DGL
14 . SING CG HG3 N N 14 . 52169 DGL
15 . DOUB CD OE1 N N 15 . 52169 DGL
16 . SING CD OE2 N N 16 . 52169 DGL
17 . SING OE2 HE2 N N 17 . 52169 DGL
18 . SING OXT HXT N N 18 . 52169 DGL
stop_
save_
save_chem_comp_API
_Chem_comp.Sf_category chem_comp
_Chem_comp.Sf_framecode chem_comp_API
_Chem_comp.Entry_ID 52169
_Chem_comp.ID API
_Chem_comp.Provenance PDB
_Chem_comp.Name '2,6-DIAMINOPIMELIC ACID'
_Chem_comp.Type 'L-PEPTIDE LINKING'
_Chem_comp.BMRB_code API
_Chem_comp.PDB_code API
_Chem_comp.Ambiguous_flag no
_Chem_comp.Initial_date 2020-07-10
_Chem_comp.Modified_date 2020-07-10
_Chem_comp.Release_status REL
_Chem_comp.Replaced_by .
_Chem_comp.Replaces .
_Chem_comp.One_letter_code K
_Chem_comp.Three_letter_code API
_Chem_comp.Number_atoms_all 27
_Chem_comp.Number_atoms_nh 13
_Chem_comp.Atom_nomenclature_source .
_Chem_comp.PubChem_code .
_Chem_comp.Subcomponent_list .
_Chem_comp.InChI_code InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
_Chem_comp.Mon_nstd_flag no
_Chem_comp.Mon_nstd_class .
_Chem_comp.Mon_nstd_details .
_Chem_comp.Mon_nstd_parent .
_Chem_comp.Mon_nstd_parent_comp_ID LYS
_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.Std_deriv_chem_comp_name .
_Chem_comp.Synonyms .
_Chem_comp.Formal_charge 0
_Chem_comp.Paramagnetic .
_Chem_comp.Aromatic no
_Chem_comp.Formula 'C7 H14 N2 O4'
_Chem_comp.Formula_weight 190.197
_Chem_comp.Formula_mono_iso_wt_nat .
_Chem_comp.Formula_mono_iso_wt_13C .
_Chem_comp.Formula_mono_iso_wt_15N .
_Chem_comp.Formula_mono_iso_wt_13C_15N .
_Chem_comp.Image_file_name .
_Chem_comp.Image_file_format .
_Chem_comp.Topo_file_name .
_Chem_comp.Topo_file_format .
_Chem_comp.Struct_file_name .
_Chem_comp.Struct_file_format .
_Chem_comp.Stereochem_param_file_name .
_Chem_comp.Stereochem_param_file_format .
_Chem_comp.Model_details .
_Chem_comp.Model_erf .
_Chem_comp.Model_source .
_Chem_comp.Model_coordinates_details .
_Chem_comp.Model_coordinates_missing_flag no
_Chem_comp.Ideal_coordinates_details Corina
_Chem_comp.Ideal_coordinates_missing_flag no
_Chem_comp.Model_coordinates_db_code 2DAP
_Chem_comp.Processing_site EBI
_Chem_comp.Vendor .
_Chem_comp.Vendor_product_code .
_Chem_comp.Details .
_Chem_comp.DB_query_date .
_Chem_comp.DB_last_query_revised_last_date .
loop_
_Chem_comp_descriptor.Descriptor
_Chem_comp_descriptor.Type
_Chem_comp_descriptor.Program
_Chem_comp_descriptor.Program_version
_Chem_comp_descriptor.Entry_ID
_Chem_comp_descriptor.Comp_ID
C(CC(C(=O)O)N)CC(C(=O)O)N SMILES 'OpenEye OEToolkits' 1.7.2 52169 API
C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.2 52169 API
GMKMEZVLHJARHF-SYDPRGILSA-N InChIKey InChI 1.03 52169 API
InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+ InChI InChI 1.03 52169 API
N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O SMILES_CANONICAL CACTVS 3.370 52169 API
N[CH](CCC[CH](N)C(O)=O)C(O)=O SMILES CACTVS 3.370 52169 API
O=C(O)C(N)CCCC(C(=O)O)N SMILES ACDLabs 12.01 52169 API
stop_
loop_
_Chem_comp_identifier.Identifier
_Chem_comp_identifier.Type
_Chem_comp_identifier.Program
_Chem_comp_identifier.Program_version
_Chem_comp_identifier.Entry_ID
_Chem_comp_identifier.Comp_ID
'(2R,6S)-2,6-diaminoheptanedioic acid' 'SYSTEMATIC NAME' ACDLabs 12.01 52169 API
'(2S,6R)-2,6-bis(azanyl)heptanedioic acid' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.2 52169 API
stop_
loop_
_Chem_comp_atom.Atom_ID
_Chem_comp_atom.BMRB_code
_Chem_comp_atom.PDB_atom_ID
_Chem_comp_atom.Alt_atom_ID
_Chem_comp_atom.Auth_atom_ID
_Chem_comp_atom.Type_symbol
_Chem_comp_atom.Isotope_number
_Chem_comp_atom.Chirality
_Chem_comp_atom.Stereo_config
_Chem_comp_atom.Charge
_Chem_comp_atom.Partial_charge
_Chem_comp_atom.Oxidation_number
_Chem_comp_atom.Unpaired_electron_number
_Chem_comp_atom.Align
_Chem_comp_atom.Aromatic_flag
_Chem_comp_atom.Leaving_atom_flag
_Chem_comp_atom.Substruct_code
_Chem_comp_atom.Ionizable
_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_x_esd
_Chem_comp_atom.Model_Cartn_y
_Chem_comp_atom.Model_Cartn_y_esd
_Chem_comp_atom.Model_Cartn_z
_Chem_comp_atom.Model_Cartn_z_esd
_Chem_comp_atom.Model_Cartn_x_ideal
_Chem_comp_atom.Model_Cartn_y_ideal
_Chem_comp_atom.Model_Cartn_z_ideal
_Chem_comp_atom.PDBX_ordinal
_Chem_comp_atom.Details
_Chem_comp_atom.Entry_ID
_Chem_comp_atom.Comp_ID
C1 C1 C1 C1 . C . . N 0 . . . 1 N N . . . . -18.775 . 53.345 . 11.610 . 3.726 -0.379 -0.101 1 . 52169 API
C2 C2 C2 C2 . C . . S 0 . . . 1 N N . . . . -18.550 . 51.842 . 11.972 . 2.498 0.269 0.486 2 . 52169 API
C3 C3 C3 C3 . C . . N 0 . . . 1 N N . . . . -17.378 . 51.807 . 12.955 . 1.249 -0.295 -0.194 3 . 52169 API
C4 C4 C4 C4 . C . . N 0 . . . 1 N N . . . . -16.911 . 50.796 . 13.800 . -0.000 0.269 0.486 4 . 52169 API
C5 C5 C5 C5 . C . . N 0 . . . 1 N N . . . . -15.893 . 50.989 . 14.763 . -1.250 -0.295 -0.193 5 . 52169 API
C6 C6 C6 C6 . C . . R 0 . . . 1 N N . . . . -14.434 . 50.921 . 14.610 . -2.499 0.269 0.486 6 . 52169 API
C7 C7 C7 C7 . C . . N 0 . . . 1 N N . . . . -13.979 . 52.098 . 13.839 . -3.726 -0.379 -0.100 7 . 52169 API
O1 O1 O1 O1 . O . . N 0 . . . 1 N N . . . . -18.650 . 54.295 . 12.271 . 4.374 0.203 -0.938 8 . 52169 API
O2 O2 O2 O2 . O . . N 0 . . . 1 N Y . . . . -19.098 . 53.467 . 10.459 . 4.101 -1.600 0.309 9 . 52169 API
O3 O3 O3 O3 . O . . N 0 . . . 1 N N . . . . -13.556 . 52.079 . 12.777 . -4.375 0.203 -0.937 10 . 52169 API
O4 O4 O4 O4 . O . . N 0 . . . 1 N Y . . . . -14.096 . 53.163 . 14.385 . -4.098 -1.602 0.307 11 . 52169 API
N2 N2 N2 N2 . N . . N 0 . . . 1 N N . . . . -18.248 . 51.116 . 10.708 . 2.560 1.721 0.269 12 . 52169 API
N6 N6 N6 N6 . N . . N 0 . . . 1 N N . . . . -14.192 . 49.753 . 13.787 . -2.560 1.721 0.270 13 . 52169 API
H2 H2 H2 H2 . H . . N 0 . . . 1 N Y . . . . -19.425 . 51.363 . 12.437 . 2.455 0.063 1.555 14 . 52169 API
H31 H31 H31 H31 . H . . N 0 . . . 1 N N . . . . -16.511 . 52.000 . 12.306 . 1.249 -0.012 -1.246 15 . 52169 API
H32 H32 H32 H32 . H . . N 0 . . . 1 N N . . . . -17.627 . 52.615 . 13.658 . 1.249 -1.382 -0.109 16 . 52169 API
H41 H41 H41 H41 . H . . N 0 . . . 1 N N . . . . -17.792 . 50.477 . 14.377 . -0.000 -0.013 1.539 17 . 52169 API
H42 H42 H42 H42 . H . . N 0 . . . 1 N N . . . . -16.522 . 50.018 . 13.126 . -0.000 1.356 0.402 18 . 52169 API
H51 H51 H51 H51 . H . . N 0 . . . 1 N N . . . . -16.062 . 52.021 . 15.105 . -1.250 -0.012 -1.246 19 . 52169 API
H52 H52 H52 H52 . H . . N 0 . . . 1 N N . . . . -16.104 . 50.211 . 15.512 . -1.250 -1.382 -0.109 20 . 52169 API
H6 H6 H6 H6 . H . . N 0 . . . 1 N N . . . . -13.922 . 50.885 . 15.583 . -2.455 0.063 1.556 21 . 52169 API
HO2 HO2 HO2 HO2 . H . . N 0 . . . 1 N N . . . . -19.208 . 54.389 . 10.257 . 4.895 -1.975 -0.096 22 . 52169 API
HO4 HO4 HO4 HO4 . H . . N 0 . . . 1 N N . . . . -13.798 . 53.852 . 13.803 . -4.893 -1.977 -0.098 23 . 52169 API
HN21 HN21 HN21 HN21 . H . . N 0 . . . 0 N N . . . . -18.098 . 50.147 . 10.907 . 2.601 1.938 -0.715 24 . 52169 API
HN22 HN22 HN22 HN22 . H . . N 0 . . . 0 N N . . . . -19.018 . 51.211 . 10.077 . 1.781 2.186 0.710 25 . 52169 API
HN61 HN61 HN61 HN61 . H . . N 0 . . . 0 N N . . . . -13.209 . 49.645 . 13.641 . -1.781 2.186 0.711 26 . 52169 API
HN62 HN62 HN62 HN62 . H . . N 0 . . . 0 N N . . . . -14.552 . 48.941 . 14.247 . -2.602 1.939 -0.714 27 . 52169 API
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.Aromatic_flag
_Chem_comp_bond.Stereo_config
_Chem_comp_bond.Ordinal
_Chem_comp_bond.Details
_Chem_comp_bond.Entry_ID
_Chem_comp_bond.Comp_ID
1 . SING C1 C2 N N 1 . 52169 API
2 . DOUB C1 O1 N N 2 . 52169 API
3 . SING C1 O2 N N 3 . 52169 API
4 . SING C2 C3 N N 4 . 52169 API
5 . SING C2 N2 N N 5 . 52169 API
6 . SING C2 H2 N N 6 . 52169 API
7 . SING C3 C4 N N 7 . 52169 API
8 . SING C3 H31 N N 8 . 52169 API
9 . SING C3 H32 N N 9 . 52169 API
10 . SING C4 C5 N N 10 . 52169 API
11 . SING C4 H41 N N 11 . 52169 API
12 . SING C4 H42 N N 12 . 52169 API
13 . SING C5 C6 N N 13 . 52169 API
14 . SING C5 H51 N N 14 . 52169 API
15 . SING C5 H52 N N 15 . 52169 API
16 . SING C6 C7 N N 16 . 52169 API
17 . SING C6 N6 N N 17 . 52169 API
18 . SING C6 H6 N N 18 . 52169 API
19 . DOUB C7 O3 N N 19 . 52169 API
20 . SING C7 O4 N N 20 . 52169 API
21 . SING O2 HO2 N N 21 . 52169 API
22 . SING O4 HO4 N N 22 . 52169 API
23 . SING N2 HN21 N N 23 . 52169 API
24 . SING N2 HN22 N N 24 . 52169 API
25 . SING N6 HN61 N N 25 . 52169 API
26 . SING N6 HN62 N N 26 . 52169 API
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_sample_1
_Sample.Sf_category sample
_Sample.Sf_framecode sample_1
_Sample.Entry_ID 52169
_Sample.ID 1
_Sample.Name 'GlcNAc-MurNAc-D-Ala-D-isoGlu-diamino pimelic acid dimer'
_Sample.Type solution
_Sample.Sub_type .
_Sample.Details .
_Sample.Aggregate_sample_number .
_Sample.Solvent_system '90% H2O/10% D2O'
_Sample.Preparation_date .
_Sample.Preparation_expiration_date .
_Sample.Polycrystallization_protocol .
_Sample.Single_crystal_protocol .
_Sample.Crystal_grow_apparatus .
_Sample.Crystal_grow_atmosphere .
_Sample.Crystal_grow_details .
_Sample.Crystal_grow_method .
_Sample.Crystal_grow_method_cit_ID .
_Sample.Crystal_grow_pH .
_Sample.Crystal_grow_pH_range .
_Sample.Crystal_grow_pressure .
_Sample.Crystal_grow_pressure_esd .
_Sample.Crystal_grow_seeding .
_Sample.Crystal_grow_seeding_cit_ID .
_Sample.Crystal_grow_temp .
_Sample.Crystal_grow_temp_details .
_Sample.Crystal_grow_temp_esd .
_Sample.Crystal_grow_time .
_Sample.Oriented_sample_prep_protocol .
_Sample.Lyophilization_cryo_protectant .
_Sample.Storage_protocol .
loop_
_Sample_component.ID
_Sample_component.Mol_common_name
_Sample_component.Isotopic_labeling
_Sample_component.Assembly_ID
_Sample_component.Assembly_label
_Sample_component.Entity_ID
_Sample_component.Entity_label
_Sample_component.Product_ID
_Sample_component.Type
_Sample_component.Concentration_val
_Sample_component.Concentration_val_min
_Sample_component.Concentration_val_max
_Sample_component.Concentration_val_units
_Sample_component.Concentration_val_err
_Sample_component.Vendor
_Sample_component.Vendor_product_name
_Sample_component.Vendor_product_code
_Sample_component.Entry_ID
_Sample_component.Sample_ID
1 'GlcNAc-MurNAc-D-Ala-D-isoGlu-diamino pimelic acid dimer' 'natural abundance' . . 1 $entity_1 . . 0.1 . . mM 0.03 . . . 52169 1
stop_
save_
#######################
# Sample conditions #
#######################
save_sample_conditions_1
_Sample_condition_list.Sf_category sample_conditions
_Sample_condition_list.Sf_framecode sample_conditions_1
_Sample_condition_list.Entry_ID 52169
_Sample_condition_list.ID 1
_Sample_condition_list.Name 'conditions 1'
_Sample_condition_list.Details .
loop_
_Sample_condition_variable.Type
_Sample_condition_variable.Val
_Sample_condition_variable.Val_err
_Sample_condition_variable.Val_units
_Sample_condition_variable.Entry_ID
_Sample_condition_variable.Sample_condition_list_ID
pH 6.5 0.1 pH 52169 1
temperature 298 1 K 52169 1
stop_
save_
############################
# Computer software used #
############################
save_software_1
_Software.Sf_category software
_Software.Sf_framecode software_1
_Software.Entry_ID 52169
_Software.ID 1
_Software.Type .
_Software.Name TOPSPIN
_Software.Version 4.0.5
_Software.DOI .
_Software.Details .
loop_
_Task.Task
_Task.Software_module
_Task.Entry_ID
_Task.Software_ID
'data analysis' . 52169 1
stop_
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_NMR_spectrometer_1
_NMR_spectrometer.Sf_category NMR_spectrometer
_NMR_spectrometer.Sf_framecode NMR_spectrometer_1
_NMR_spectrometer.Entry_ID 52169
_NMR_spectrometer.ID 1
_NMR_spectrometer.Name spectrometer
_NMR_spectrometer.Details .
_NMR_spectrometer.Manufacturer Bruker
_NMR_spectrometer.Model DRX
_NMR_spectrometer.Serial_number .
_NMR_spectrometer.Field_strength 600
save_
#############################
# NMR applied experiments #
#############################
save_experiment_list_1
_Experiment_list.Sf_category experiment_list
_Experiment_list.Sf_framecode experiment_list_1
_Experiment_list.Entry_ID 52169
_Experiment_list.ID 1
_Experiment_list.Details .
loop_
_Experiment.ID
_Experiment.Name
_Experiment.Raw_data_flag
_Experiment.NUS_flag
_Experiment.Interleaved_flag
_Experiment.NMR_spec_expt_ID
_Experiment.NMR_spec_expt_label
_Experiment.MS_expt_ID
_Experiment.MS_expt_label
_Experiment.SAXS_expt_ID
_Experiment.SAXS_expt_label
_Experiment.FRET_expt_ID
_Experiment.FRET_expt_label
_Experiment.EMR_expt_ID
_Experiment.EMR_expt_label
_Experiment.Sample_ID
_Experiment.Sample_label
_Experiment.Sample_state
_Experiment.Sample_volume
_Experiment.Sample_volume_units
_Experiment.Sample_condition_list_ID
_Experiment.Sample_condition_list_label
_Experiment.Sample_spinning_rate
_Experiment.Sample_angle
_Experiment.NMR_tube_type
_Experiment.NMR_spectrometer_ID
_Experiment.NMR_spectrometer_label
_Experiment.NMR_spectrometer_probe_ID
_Experiment.NMR_spectrometer_probe_label
_Experiment.NMR_spectral_processing_ID
_Experiment.NMR_spectral_processing_label
_Experiment.Mass_spectrometer_ID
_Experiment.Mass_spectrometer_label
_Experiment.Xray_instrument_ID
_Experiment.Xray_instrument_label
_Experiment.Fluorescence_instrument_ID
_Experiment.Fluorescence_instrument_label
_Experiment.EMR_instrument_ID
_Experiment.EMR_instrument_label
_Experiment.Chromatographic_system_ID
_Experiment.Chromatographic_system_label
_Experiment.Chromatographic_column_ID
_Experiment.Chromatographic_column_label
_Experiment.Details
_Experiment.Entry_ID
_Experiment.Experiment_list_ID
1 '2D 1H-1H TOCSY' no no no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 52169 1
2 '2D 1H-1H NOESY' no no no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 52169 1
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chem_shift_reference_1
_Chem_shift_reference.Sf_category chem_shift_reference
_Chem_shift_reference.Sf_framecode chem_shift_reference_1
_Chem_shift_reference.Entry_ID 52169
_Chem_shift_reference.ID 1
_Chem_shift_reference.Name 'chemical shift referencing'
_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.Concentration_val
_Chem_shift_ref.Concentration_units
_Chem_shift_ref.Solvent
_Chem_shift_ref.Rank
_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.External_ref_loc
_Chem_shift_ref.External_ref_sample_geometry
_Chem_shift_ref.External_ref_axis
_Chem_shift_ref.Ref_correction_type
_Chem_shift_ref.Correction_val
_Chem_shift_ref.Entry_ID
_Chem_shift_ref.Chem_shift_reference_ID
H 1 TSP 'methyl protons' . . . . ppm 0 internal direct 1 . . . . . 52169 1
stop_
save_
###################################
# Assigned chemical shift lists #
###################################
###################################################################
# Chemical Shift Ambiguity Index Value Definitions #
# #
# The values other than 1 are used for those atoms with different #
# chemical shifts that cannot be assigned to stereospecific atoms #
# or to specific residues or chains. #
# #
# Index Value Definition #
# #
# 1 Unique (including isolated methyl protons, #
# geminal atoms, and geminal methyl #
# groups with identical chemical shifts) #
# (e.g. ILE HD11, HD12, HD13 protons) #
# 2 Ambiguity of geminal atoms or geminal methyl #
# proton groups (e.g. ASP HB2 and HB3 #
# protons, LEU CD1 and CD2 carbons, or #
# LEU HD11, HD12, HD13 and HD21, HD22, #
# HD23 methyl protons) #
# 3 Aromatic atoms on opposite sides of #
# symmetrical rings (e.g. TYR HE1 and HE2 #
# protons) #
# 4 Intraresidue ambiguities (e.g. LYS HG and #
# HD protons or TRP HZ2 and HZ3 protons) #
# 5 Interresidue ambiguities (LYS 12 vs. LYS 27) #
# 6 Intermolecular ambiguities (e.g. ASP 31 CA #
# in monomer 1 and ASP 31 CA in monomer 2 #
# of an asymmetrical homodimer, duplex #
# DNA assignments, or other assignments #
# that may apply to atoms in one or more #
# molecule in the molecular assembly) #
# 9 Ambiguous, specific ambiguity not defined #
# #
###################################################################
save_assigned_chemical_shifts_1
_Assigned_chem_shift_list.Sf_category assigned_chemical_shifts
_Assigned_chem_shift_list.Sf_framecode assigned_chemical_shifts_1
_Assigned_chem_shift_list.Entry_ID 52169
_Assigned_chem_shift_list.ID 1
_Assigned_chem_shift_list.Name 'GlcNAc-MurNAc-D-Ala-D-isoGlu-diamino pimelic acid dimer'
_Assigned_chem_shift_list.Sample_condition_list_ID 1
_Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1
_Assigned_chem_shift_list.Chem_shift_reference_ID 1
_Assigned_chem_shift_list.Chem_shift_reference_label $chem_shift_reference_1
_Assigned_chem_shift_list.Chem_shift_1H_err 0.03
_Assigned_chem_shift_list.Chem_shift_13C_err .
_Assigned_chem_shift_list.Chem_shift_15N_err .
_Assigned_chem_shift_list.Chem_shift_31P_err .
_Assigned_chem_shift_list.Chem_shift_2H_err .
_Assigned_chem_shift_list.Chem_shift_19F_err .
_Assigned_chem_shift_list.Error_derivation_method .
_Assigned_chem_shift_list.Details .
_Assigned_chem_shift_list.Text_data_format .
_Assigned_chem_shift_list.Text_data .
loop_
_Chem_shift_experiment.Experiment_ID
_Chem_shift_experiment.Experiment_name
_Chem_shift_experiment.Sample_ID
_Chem_shift_experiment.Sample_label
_Chem_shift_experiment.Sample_state
_Chem_shift_experiment.Entry_ID
_Chem_shift_experiment.Assigned_chem_shift_list_ID
1 '2D 1H-1H TOCSY' . . . 52169 1
2 '2D 1H-1H NOESY' . . . 52169 1
stop_
loop_
_Chem_shift_software.Software_ID
_Chem_shift_software.Software_label
_Chem_shift_software.Method_ID
_Chem_shift_software.Method_label
_Chem_shift_software.Entry_ID
_Chem_shift_software.Assigned_chem_shift_list_ID
1 $software_1 . . 52169 1
stop_
loop_
_Atom_chem_shift.ID
_Atom_chem_shift.Assembly_atom_ID
_Atom_chem_shift.Entity_assembly_ID
_Atom_chem_shift.Entity_assembly_asym_ID
_Atom_chem_shift.Entity_ID
_Atom_chem_shift.Comp_index_ID
_Atom_chem_shift.Seq_ID
_Atom_chem_shift.Comp_ID
_Atom_chem_shift.Atom_ID
_Atom_chem_shift.Atom_type
_Atom_chem_shift.Atom_isotope_number
_Atom_chem_shift.Val
_Atom_chem_shift.Val_err
_Atom_chem_shift.Assign_fig_of_merit
_Atom_chem_shift.Ambiguity_code
_Atom_chem_shift.Ambiguity_set_ID
_Atom_chem_shift.Occupancy
_Atom_chem_shift.Resonance_ID
_Atom_chem_shift.Auth_entity_assembly_ID
_Atom_chem_shift.Auth_asym_ID
_Atom_chem_shift.Auth_seq_ID
_Atom_chem_shift.Auth_comp_ID
_Atom_chem_shift.Auth_atom_ID
_Atom_chem_shift.Details
_Atom_chem_shift.Entry_ID
_Atom_chem_shift.Assigned_chem_shift_list_ID
1 . 1 . 1 1 1 NAG H1 H 1 4.67 0.03 . 1 . . . . . 1 NAG H1 . 52169 1
2 . 1 . 1 1 1 NAG H2 H 1 3.74 0.03 . 4 . . . . . 1 NAG H2 . 52169 1
3 . 1 . 1 1 1 NAG H3 H 1 3.58 0.03 . 4 . . . . . 1 NAG H3 . 52169 1
4 . 1 . 1 1 1 NAG H4 H 1 3.48 0.03 . 4 . . . . . 1 NAG H4 . 52169 1
5 . 1 . 1 1 1 NAG H5 H 1 3.44 0.03 . 4 . . . . . 1 NAG H5 . 52169 1
6 . 1 . 1 1 1 NAG HH2 H 1 8.35 0.03 . 1 . . . . . 1 NAG HH2 . 52169 1
7 . 1 . 1 1 1 NAG H8 H 1 2.08 0.03 . 1 . . . . . 1 NAG H8 . 52169 1
8 . 1 . 1 2 2 MUR H1 H 1 4.43 0.03 . 4 . . . . . 2 MUR H1 . 52169 1
9 . 1 . 1 2 2 MUR H2 H 1 4.32 0.03 . 4 . . . . . 2 MUR H2 . 52169 1
10 . 1 . 1 2 2 MUR HH2 H 1 8.11 0.03 . 1 . . . . . 2 MUR HH2 . 52169 1
11 . 1 . 1 2 2 MUR H8 H 1 2.01 0.03 . 1 . . . . . 2 MUR H8 . 52169 1
12 . 1 . 1 2 2 MUR H9 H 1 4.28 0.03 . 1 . . . . . 2 MUR H9 . 52169 1
13 . 1 . 1 2 2 MUR H11 H 1 1.42 0.03 . 1 . . . . . 2 MUR H11 . 52169 1
14 . 1 . 1 3 3 DAL H H 1 8.41 0.03 . 1 . . . . . 3 ALA HN . 52169 1
15 . 1 . 1 3 3 DAL HA H 1 4.32 0.03 . 1 . . . . . 3 ALA HA . 52169 1
16 . 1 . 1 3 3 DAL HB1 H 1 1.43 0.03 . 1 . . . . . 3 ALA HB# . 52169 1
17 . 1 . 1 3 3 DAL HB2 H 1 1.43 0.03 . 1 . . . . . 3 ALA HB# . 52169 1
18 . 1 . 1 3 3 DAL HB3 H 1 1.43 0.03 . 1 . . . . . 3 ALA HB# . 52169 1
19 . 1 . 1 4 4 DGL H H 1 7.92 0.03 . 1 . . . . . 4 DGL H . 52169 1
20 . 1 . 1 4 4 DGL HA H 1 4.20 0.03 . 1 . . . . . 4 DGL HA . 52169 1
21 . 1 . 1 4 4 DGL HB2 H 1 2.10 0.03 . 2 . . . . . 4 DGL HB2 . 52169 1
22 . 1 . 1 4 4 DGL HB3 H 1 1.90 0.03 . 2 . . . . . 4 DGL HB3 . 52169 1
23 . 1 . 1 4 4 DGL HG2 H 1 2.26 0.03 . 1 . . . . . 4 DGL HG2 . 52169 1
24 . 1 . 1 4 4 DGL HG3 H 1 2.26 0.03 . 1 . . . . . 4 DGL HG3 . 52169 1
25 . 1 . 1 5 5 API H H 1 8.11 0.03 . 1 . . . . . 5 API HN . 52169 1
26 . 1 . 1 5 5 API HA H 1 4.43 0.03 . 1 . . . . . 5 API HA . 52169 1
27 . 1 . 1 5 5 API HB2 H 1 1.74 0.03 . 1 . . . . . 5 API HB2 . 52169 1
28 . 1 . 1 5 5 API HB3 H 1 1.74 0.03 . 1 . . . . . 5 API HB3 . 52169 1
29 . 1 . 1 5 5 API HG2 H 1 1.69 0.03 . 1 . . . . . 5 API HG2 . 52169 1
30 . 1 . 1 5 5 API HG3 H 1 1.69 0.03 . 1 . . . . . 5 API HG3 . 52169 1
31 . 1 . 1 5 5 API HD2 H 1 1.95 0.03 . 1 . . . . . 5 API HD2 . 52169 1
32 . 1 . 1 5 5 API HD3 H 1 1.95 0.03 . 1 . . . . . 5 API HD3 . 52169 1
33 . 1 . 1 5 5 API HE H 1 4.26 0.03 . 1 . . . . . 5 API HE . 52169 1
34 . 1 . 1 5 5 API HH H 1 8.04 0.03 . 1 . . . . . 5 API HN . 52169 1
stop_
save_