data_562
# 
_chem_comp.id                                    562 
_chem_comp.name                                  "N~5~-[N-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-L-ornithine" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C12 H26 N7 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2015-07-31 
_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                        332.379 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     562 
_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        5CUT 
_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 
562 N   N   N 0 1 N N N Y Y N -21.300 20.314 -23.478 5.991  2.257  1.091  N   562 1  
562 CA  CA  C 0 1 N N S Y N N -20.718 20.331 -22.137 6.570  0.982  0.649  CA  562 2  
562 C   C   C 0 1 N N N Y N Y -20.606 21.759 -21.648 7.899  1.236  -0.013 C   562 3  
562 O   O   O 0 1 N N N Y N Y -19.609 22.139 -20.992 8.164  2.338  -0.433 O   562 4  
562 CB  CB  C 0 1 N N N N N N -19.371 19.632 -22.086 5.623  0.311  -0.349 CB  562 5  
562 CG  CG  C 0 1 N N N N N N -19.598 18.165 -22.426 4.318  -0.060 0.357  CG  562 6  
562 CD  CD  C 0 1 N N N N N N -18.302 17.425 -22.259 3.371  -0.731 -0.640 CD  562 7  
562 NE  NE  N 0 1 N N N N N N -18.439 16.005 -22.499 2.121  -1.087 0.036  NE  562 8  
562 CZ  CZ  C 0 1 N N N N N N -17.455 15.146 -21.903 1.113  -1.705 -0.665 CZ  562 9  
562 NH1 NH1 N 0 1 N N N N N N -16.489 15.681 -21.169 1.269  -1.975 -1.930 NH1 562 10 
562 C01 C01 C 0 1 N N N N N N -18.739 11.741 -22.462 -2.320 -2.957 0.156  C01 562 11 
562 NH2 NH2 N 0 1 N N N N N N -17.498 13.835 -22.097 -0.060 -2.039 -0.030 NH2 562 12 
562 N08 N08 N 0 1 N N N N N N -21.781 4.531  -26.990 -9.149 2.404  -1.072 N08 562 13 
562 O01 O01 O 0 1 N N N N N N -19.807 11.166 -23.141 -2.868 -1.709 0.587  O01 562 14 
562 C02 C02 C 0 1 N N N N N N -18.536 13.195 -22.876 -1.135 -2.698 -0.777 C02 562 15 
562 N02 N02 N 0 1 N N N N N N -21.867 5.297  -24.591 -7.159 1.390  -0.818 N02 562 16 
562 O02 O02 O 0 1 N N N N N N -19.946 8.126  -23.602 -4.995 0.221  0.705  O02 562 17 
562 C03 C03 C 0 1 N N N N N N -19.346 10.366 -24.192 -3.986 -1.839 1.468  C03 562 18 
562 N03 N03 N 1 1 N N N N N N -21.823 4.916  -25.793 -8.154 1.897  -0.945 N03 562 19 
562 C04 C04 C 0 1 N N N N N N -20.328 9.224  -24.367 -4.489 -0.449 1.862  C04 562 20 
562 C05 C05 C 0 1 N N N N N N -21.009 7.229  -23.469 -5.492 1.535  0.966  C05 562 21 
562 C06 C06 C 0 1 N N N N N N -20.651 5.879  -24.058 -6.005 2.153  -0.337 C06 562 22 
562 H   H1  H 0 1 N N N Y Y N -22.183 20.783 -23.465 6.566  2.689  1.799  H1  562 23 
562 H2  H2  H 0 1 N Y N Y Y N -20.685 20.779 -24.114 5.849  2.880  0.310  H2  562 24 
562 HA  H4  H 0 1 N N N Y N N -21.398 19.796 -21.457 6.712  0.329  1.510  H4  562 25 
562 OXT OXT O 0 1 N Y N Y N Y -21.397 22.460 -21.868 8.790  0.239  -0.136 OXT 562 26 
562 H6  H6  H 0 1 N N N N N N -18.941 19.721 -21.078 5.411  0.999  -1.167 H6  562 27 
562 H7  H7  H 0 1 N N N N N N -18.686 20.085 -22.818 6.092  -0.591 -0.744 H7  562 28 
562 H8  H8  H 0 1 N N N N N N -19.944 18.076 -23.466 4.530  -0.748 1.176  H8  562 29 
562 H9  H9  H 0 1 N N N N N N -20.356 17.742 -21.750 3.849  0.841  0.753  H9  562 30 
562 H10 H10 H 0 1 N N N N N N -17.940 17.576 -21.231 3.159  -0.043 -1.459 H10 562 31 
562 H11 H11 H 0 1 N N N N N N -17.569 17.834 -22.970 3.840  -1.633 -1.036 H11 562 32 
562 H12 H12 H 0 1 N N N N N N -19.185 15.638 -23.055 2.005  -0.886 0.978  H12 562 33 
562 H13 H13 H 0 1 N N N N N N -15.857 14.989 -20.820 0.557  -2.411 -2.424 H13 562 34 
562 H14 H14 H 0 1 N N N N N N -18.939 11.701 -21.381 -1.982 -3.524 1.024  H14 562 35 
562 H15 H15 H 0 1 N N N N N N -17.824 11.173 -22.687 -3.083 -3.525 -0.375 H15 562 36 
562 H16 H16 H 0 1 N N N N N N -16.784 13.266 -21.689 -0.177 -1.838 0.911  H16 562 37 
562 H17 H17 H 0 1 N N N N N N -22.077 3.581  -27.088 -9.780 2.426  -0.335 H17 562 38 
562 H18 H18 H 0 1 N N N N N N -18.254 13.227 -23.939 -0.773 -3.645 -1.175 H18 562 39 
562 H19 H19 H 0 1 N N N N N N -19.479 13.742 -22.730 -1.453 -2.056 -1.598 H19 562 40 
562 H20 H20 H 0 1 N N N N N N -18.349 9.969  -23.951 -4.784 -2.385 0.964  H20 562 41 
562 H21 H21 H 0 1 N N N N N N -19.291 10.958 -25.117 -3.683 -2.383 2.362  H21 562 42 
562 H22 H22 H 0 1 N N N N N N -21.328 9.555  -24.049 -3.667 0.128  2.286  H22 562 43 
562 H23 H23 H 0 1 N N N N N N -20.358 8.933  -25.427 -5.284 -0.546 2.602  H23 562 44 
562 H24 H24 H 0 1 N N N N N N -21.888 7.630  -23.995 -6.307 1.479  1.687  H24 562 45 
562 H25 H25 H 0 1 N N N N N N -21.245 7.106  -22.402 -4.691 2.153  1.370  H25 562 46 
562 H26 H26 H 0 1 N N N N N N -20.235 5.227  -23.276 -5.214 2.128  -1.087 H26 562 47 
562 H27 H27 H 0 1 N N N N N N -19.911 6.005  -24.863 -6.302 3.186  -0.156 H27 562 48 
562 HXT HXT H 0 1 N Y N Y N Y -21.182 23.308 -21.497 9.629  0.451  -0.568 HXT 562 49 
# 
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 
562 N08 N03 DOUB N N 1  
562 N03 N02 DOUB N N 2  
562 N02 C06 SING N N 3  
562 C04 C03 SING N N 4  
562 C04 O02 SING N N 5  
562 C03 O01 SING N N 6  
562 C06 C05 SING N N 7  
562 O02 C05 SING N N 8  
562 N   CA  SING N N 9  
562 O01 C01 SING N N 10 
562 C02 C01 SING N N 11 
562 C02 NH2 SING N N 12 
562 NE  CD  SING N N 13 
562 NE  CZ  SING N N 14 
562 CG  CD  SING N N 15 
562 CG  CB  SING N N 16 
562 CA  CB  SING N N 17 
562 CA  C   SING N N 18 
562 NH2 CZ  SING N N 19 
562 CZ  NH1 DOUB N N 20 
562 C   O   DOUB N N 21 
562 N   H   SING N N 22 
562 N   H2  SING N N 23 
562 CA  HA  SING N N 24 
562 C   OXT SING N N 25 
562 CB  H6  SING N N 26 
562 CB  H7  SING N N 27 
562 CG  H8  SING N N 28 
562 CG  H9  SING N N 29 
562 CD  H10 SING N N 30 
562 CD  H11 SING N N 31 
562 NE  H12 SING N N 32 
562 NH1 H13 SING N N 33 
562 C01 H14 SING N N 34 
562 C01 H15 SING N N 35 
562 NH2 H16 SING N N 36 
562 N08 H17 SING N N 37 
562 C02 H18 SING N N 38 
562 C02 H19 SING N N 39 
562 C03 H20 SING N N 40 
562 C03 H21 SING N N 41 
562 C04 H22 SING N N 42 
562 C04 H23 SING N N 43 
562 C05 H24 SING N N 44 
562 C05 H25 SING N N 45 
562 C06 H26 SING N N 46 
562 C06 H27 SING N N 47 
562 OXT HXT SING N N 48 
# 
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 
562 SMILES           ACDLabs              12.01 "NC(CCCN\C(=N)NCCOCCOCC\N=[N+]=N)C(=O)O"                                                                                                
562 InChI            InChI                1.03  "InChI=1S/C12H25N7O4/c13-10(11(20)21)2-1-3-16-12(14)17-4-6-22-8-9-23-7-5-18-19-15/h10,15H,1-9,13H2,(H3-,14,16,17,20,21)/p+1/t10-/m0/s1" 
562 InChIKey         InChI                1.03  LSTVCWRTCOJGHW-JTQLQIEISA-O                                                                                                             
562 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCCNC(=N)NCCOCCOCCN=[N+]=N)C(O)=O"                                                                                             
562 SMILES           CACTVS               3.385 "N[CH](CCCNC(=N)NCCOCCOCCN=[N+]=N)C(O)=O"                                                                                               
562 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "[H]/N=C(/NCCC[C@@H](C(=O)O)N)\NCCOCCOCCN=[N+]=N"                                                                                       
562 SMILES           "OpenEye OEToolkits" 1.9.2 "C(CC(C(=O)O)N)CNC(=N)NCCOCCOCCN=[N+]=N"                                                                                                
# 
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 
562 "SYSTEMATIC NAME" ACDLabs              12.01 "N~5~-[N-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-L-ornithine"                                    
562 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "azanylidene-[2-[2-[2-[[N-[(4S)-4-azanyl-5-oxidanyl-5-oxidanylidene-pentyl]carbamimidoyl]amino]ethoxy]ethoxy]ethylimino]azanium" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
562 "Create component" 2015-07-31 RCSB 
562 "Initial release"  2018-03-14 RCSB 
562 "Modify backbone"  2023-11-03 PDBE 
562 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            562 
_pdbx_chem_comp_pcm.modified_residue_id                ? 
_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      ? 
# 
