data_C6D
# 
_chem_comp.id                                    C6D 
_chem_comp.name                                  "N~5~-[N-(3-hydroxypropyl)carbamimidoyl]-L-ornithine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H20 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ARG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-09-13 
_chem_comp.pdbx_modified_date                    2024-09-27 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        232.280 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     C6D 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        6AZK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
C6D N   N   N 0 1 N N N Y Y N -28.513 35.798 -31.121 4.290  1.821  -0.439 N   C6D 1  
C6D CA  CA  C 0 1 N N S Y N N -28.428 35.652 -29.670 4.283  0.587  0.358  CA  C6D 2  
C6D C   C   C 0 1 N N N Y N Y -27.737 34.336 -29.315 5.576  -0.156 0.144  C   C6D 3  
C6D O   O   O 0 1 N N N Y N Y -28.080 33.692 -28.330 6.251  0.073  -0.832 O   C6D 4  
C6D CB  CB  C 0 1 N N N N N N -29.825 35.718 -29.014 3.110  -0.294 -0.076 CB  C6D 5  
C6D CG  CG  C 0 1 N N N N N N -30.617 36.967 -29.378 1.793  0.410  0.257  CG  C6D 6  
C6D CD  CD  C 0 1 N N N N N N -31.655 37.242 -28.315 0.620  -0.471 -0.177 CD  C6D 7  
C6D NE  NE  N 0 1 N N N N N N -32.472 38.399 -28.634 -0.641 0.204  0.141  NE  C6D 8  
C6D CZ  CZ  C 0 1 N N N N N N -33.499 38.788 -27.898 -1.839 -0.401 -0.159 CZ  C6D 9  
C6D NH1 NH1 N 0 1 N N N N N N -33.784 38.068 -26.824 -1.852 -1.574 -0.727 NH1 C6D 10 
C6D NH2 NH2 N 0 1 N N N N N N -34.232 39.853 -28.204 -3.022 0.232  0.140  NH2 C6D 11 
C6D C01 C01 C 0 1 N N N N N N -35.188 41.461 -29.706 -5.451 0.496  0.252  C01 C6D 12 
C6D C02 C02 C 0 1 N N N N N N -33.955 40.667 -29.381 -4.298 -0.412 -0.180 C02 C6D 13 
C6D C03 C03 C 0 1 N N N N N N -34.897 42.474 -30.770 -6.784 -0.177 -0.082 C03 C6D 14 
C6D O2  O2  O 0 1 N N N N N N -35.047 43.753 -30.236 -7.860 0.672  0.322  O2  C6D 15 
C6D H   H1  H 0 1 N N N Y Y N -28.966 36.661 -31.344 5.017  2.448  -0.128 H1  C6D 16 
C6D H2  H2  H 0 1 N Y N Y Y N -27.592 35.795 -31.511 4.386  1.616  -1.422 H2  C6D 17 
C6D HA  H4  H 0 1 N N N Y N N -27.824 36.476 -29.263 4.179  0.838  1.414  H4  C6D 18 
C6D H6  H6  H 0 1 N N N N N N -30.400 34.837 -29.334 3.167  -0.471 -1.150 H6  C6D 19 
C6D H7  H7  H 0 1 N N N N N N -29.697 35.695 -27.922 3.156  -1.246 0.452  H7  C6D 20 
C6D H8  H8  H 0 1 N N N N N N -29.933 37.825 -29.451 1.737  0.587  1.331  H8  C6D 21 
C6D H9  H9  H 0 1 N N N N N N -31.117 36.813 -30.346 1.747  1.363  -0.271 H9  C6D 22 
C6D H10 H10 H 0 1 N N N N N N -32.308 36.362 -28.221 0.676  -0.648 -1.251 H10 C6D 23 
C6D H11 H11 H 0 1 N N N N N N -31.143 37.422 -27.358 0.666  -1.423 0.351  H11 C6D 24 
C6D H12 H12 H 0 1 N N N N N N -32.246 38.928 -29.452 -0.631 1.077  0.564  H12 C6D 25 
C6D H13 H13 H 0 1 N N N N N N -34.573 38.431 -26.329 -2.697 -2.001 -0.939 H13 C6D 26 
C6D H14 H14 H 0 1 N N N N N N -34.996 40.103 -27.609 -3.012 1.105  0.562  H14 C6D 27 
C6D H15 H15 H 0 1 N N N N N N -35.534 41.978 -28.799 -5.392 0.672  1.326  H15 C6D 28 
C6D H16 H16 H 0 1 N N N N N N -35.974 40.779 -30.062 -5.381 1.447  -0.276 H16 C6D 29 
C6D H17 H17 H 0 1 N N N N N N -33.696 40.017 -30.230 -4.358 -0.588 -1.255 H17 C6D 30 
C6D H18 H18 H 0 1 N N N N N N -33.117 41.349 -29.173 -4.368 -1.363 0.348  H18 C6D 31 
C6D H19 H19 H 0 1 N N N N N N -35.598 42.340 -31.607 -6.843 -0.352 -1.156 H19 C6D 32 
C6D H20 H20 H 0 1 N N N N N N -33.866 42.344 -31.130 -6.853 -1.128 0.446  H20 C6D 33 
C6D H21 H21 H 0 1 N N N N N N -34.864 44.400 -30.907 -8.737 0.308  0.140  H21 C6D 34 
C6D OXT O1  O 0 1 N Y N Y N Y -26.762 33.949 -30.124 5.979  -1.074 1.037  O1  C6D 35 
C6D HXT H3  H 0 1 N Y N Y N Y -26.401 33.127 -29.814 6.815  -1.525 0.857  H3  C6D 36 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
C6D N   CA  SING N N 1  
C6D C03 O2  SING N N 2  
C6D C03 C01 SING N N 3  
C6D C01 C02 SING N N 4  
C6D CA  C   SING N N 5  
C6D CA  CB  SING N N 6  
C6D C02 NH2 SING N N 7  
C6D CG  CB  SING N N 8  
C6D CG  CD  SING N N 9  
C6D C   O   DOUB N N 10 
C6D NE  CD  SING N N 11 
C6D NE  CZ  SING N N 12 
C6D NH2 CZ  SING N N 13 
C6D CZ  NH1 DOUB N N 14 
C6D N   H   SING N N 15 
C6D N   H2  SING N N 16 
C6D CA  HA  SING N N 17 
C6D CB  H6  SING N N 18 
C6D CB  H7  SING N N 19 
C6D CG  H8  SING N N 20 
C6D CG  H9  SING N N 21 
C6D CD  H10 SING N N 22 
C6D CD  H11 SING N N 23 
C6D NE  H12 SING N N 24 
C6D NH1 H13 SING N N 25 
C6D NH2 H14 SING N N 26 
C6D C01 H15 SING N N 27 
C6D C01 H16 SING N N 28 
C6D C02 H17 SING N N 29 
C6D C02 H18 SING N N 30 
C6D C03 H19 SING N N 31 
C6D C03 H20 SING N N 32 
C6D O2  H21 SING N N 33 
C6D C   OXT SING N N 34 
C6D OXT HXT SING N N 35 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
C6D SMILES           ACDLabs              12.01 "NC(C(=O)O)CCCN\C(=N)NCCCO"                                                                                   
C6D InChI            InChI                1.03  "InChI=1S/C9H20N4O3/c10-7(8(15)16)3-1-4-12-9(11)13-5-2-6-14/h7,14H,1-6,10H2,(H,15,16)(H3,11,12,13)/t7-/m0/s1" 
C6D InChIKey         InChI                1.03  YCHONDWDFOKMRR-ZETCQYMHSA-N                                                                                   
C6D SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCCNC(=N)NCCCO)C(O)=O"                                                                               
C6D SMILES           CACTVS               3.385 "N[CH](CCCNC(=N)NCCCO)C(O)=O"                                                                                 
C6D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "[H]/N=C(\NCCC[C@@H](C(=O)O)N)/NCCCO"                                                                         
C6D SMILES           "OpenEye OEToolkits" 2.0.6 "C(CC(C(=O)O)N)CNC(=N)NCCCO"                                                                                  
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
C6D "SYSTEMATIC NAME" ACDLabs              12.01 "N~5~-[N-(3-hydroxypropyl)carbamimidoyl]-L-ornithine"                            
C6D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-2-azanyl-5-[[~{N}-(3-oxidanylpropyl)carbamimidoyl]amino]pentanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
C6D "Create component" 2017-09-13 RCSB 
C6D "Initial release"  2017-12-13 RCSB 
C6D "Modify backbone"  2023-11-03 PDBE 
C6D "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            C6D 
_pdbx_chem_comp_pcm.modified_residue_id                ARG 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
