data_AG9
# 
_chem_comp.id                                    AG9 
_chem_comp.name                                  AGMATIDINE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H30 N7 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-02-14 
_chem_comp.pdbx_modified_date                    2013-03-29 
_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                        439.404 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     AG9 
_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        3ZN7 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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.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 
AG9 P      P      P 0 1 N N N -124.131 29.092 -23.237 -6.010 -1.599 -1.248 P      AG9 1  
AG9 N1     N1     N 0 1 N N N -120.081 27.891 -26.134 -0.412 1.747  0.401  N1     AG9 2  
AG9 C2     C2     C 0 1 N N N -118.730 27.671 -26.522 0.856  1.894  -0.113 C2     AG9 3  
AG9 N2     N2     N 0 1 N N N -118.418 27.551 -27.842 1.783  0.895  0.073  N2     AG9 4  
AG9 N3     N3     N 0 1 N N N -117.778 27.600 -25.559 1.189  2.961  -0.771 N3     AG9 5  
AG9 C4     C4     C 0 1 N N R -118.112 27.736 -24.272 0.257  4.053  -1.019 C4     AG9 6  
AG9 N4     N4     N 0 1 N N N -117.133 27.667 -23.367 0.945  5.332  -0.795 N4     AG9 7  
AG9 C5     C5     C 0 1 N N N -119.464 27.948 -23.857 -0.937 3.972  -0.112 C5     AG9 8  
AG9 C6     C6     C 0 1 N N N -120.405 28.011 -24.808 -1.227 2.866  0.541  C6     AG9 9  
AG9 CA     CA     C 0 1 N N N -117.847 26.333 -28.402 3.135  1.041  -0.470 CA     AG9 10 
AG9 CB     CB     C 0 1 N N N -116.361 26.185 -28.036 3.960  -0.201 -0.126 CB     AG9 11 
AG9 CD     CD     C 0 1 N N N -115.793 28.334 -29.335 6.197  -1.291 -0.349 CD     AG9 12 
AG9 NE     NE     N 0 1 N N N -114.651 29.193 -29.655 7.554  -1.144 -0.893 NE     AG9 13 
AG9 CG     CG     C 0 1 N N N -115.515 27.465 -28.107 5.373  -0.049 -0.693 CG     AG9 14 
AG9 CZ     CZ     C 0 1 N N N -114.731 30.347 -30.317 8.376  -2.321 -0.581 CZ     AG9 15 
AG9 "C1'"  "C1'"  C 0 1 N N R -121.131 28.032 -27.176 -0.901 0.422  0.793  "C1'"  AG9 16 
AG9 OP1    OP1    O 0 1 N N N -125.547 28.804 -22.858 -6.816 -2.453 -0.347 OP1    AG9 17 
AG9 "C2'"  "C2'"  C 0 1 N N R -121.602 26.816 -27.967 -1.226 0.394  2.303  "C2'"  AG9 18 
AG9 "O2'"  "O2'"  O 0 1 N N N -121.766 27.216 -29.316 -0.147 -0.188 3.036  "O2'"  AG9 19 
AG9 OP2    OP2    O 0 1 N N N -123.483 30.368 -22.789 -5.917 -2.287 -2.700 OP2    AG9 20 
AG9 "C3'"  "C3'"  C 0 1 N N S -122.910 26.499 -27.250 -2.487 -0.495 2.399  "C3'"  AG9 21 
AG9 "O3'"  "O3'"  O 0 1 N N N -123.863 25.827 -28.040 -2.224 -1.652 3.195  "O3'"  AG9 22 
AG9 OP3    OP3    O 0 1 N Y N -123.207 27.853 -22.763 -6.708 -0.154 -1.383 OP3    AG9 23 
AG9 "C4'"  "C4'"  C 0 1 N N R -123.428 27.856 -26.819 -2.774 -0.898 0.936  "C4'"  AG9 24 
AG9 "O4'"  "O4'"  O 0 1 N N N -122.255 28.656 -26.589 -2.158 0.138  0.140  "O4'"  AG9 25 
AG9 "C5'"  "C5'"  C 0 1 N N N -124.226 27.809 -25.546 -4.282 -0.939 0.681  "C5'"  AG9 26 
AG9 "O5'"  "O5'"  O 0 1 N N N -124.075 29.049 -24.830 -4.529 -1.425 -0.640 "O5'"  AG9 27 
AG9 NH1    NH1    N 0 1 N N N -113.630 31.052 -30.562 9.580  -2.314 -1.423 NH1    AG9 28 
AG9 NH2    NH2    N 0 1 N N N -115.909 30.812 -30.716 8.768  -2.283 0.834  NH2    AG9 29 
AG9 HN2    HN2    H 0 1 N N N -118.587 28.327 -28.449 1.541  0.094  0.563  HN2    AG9 30 
AG9 H1N4   H1N4   H 0 0 N N N -117.517 27.784 -22.451 1.736  5.430  -1.414 H1N4   AG9 31 
AG9 H2N4   H2N4   H 0 0 N N N -116.684 26.776 -23.429 0.308  6.108  -0.897 H2N4   AG9 32 
AG9 H5     H5     H 0 1 N N N -119.718 28.054 -22.813 -1.571 4.838  0.005  H5     AG9 33 
AG9 H6     H6     H 0 1 N N N -121.437 28.159 -24.525 -2.094 2.828  1.184  H6     AG9 34 
AG9 H1A    H1A    H 0 1 N N N -117.944 26.364 -29.497 3.082  1.153  -1.553 H1A    AG9 35 
AG9 H2A    H2A    H 0 1 N N N -118.399 25.466 -28.010 3.608  1.922  -0.037 H2A    AG9 36 
AG9 H1B    H1B    H 0 1 N N N -116.305 25.803 -27.006 4.013  -0.313 0.957  H1B    AG9 37 
AG9 H2B    H2B    H 0 1 N N N -115.917 25.451 -28.724 3.487  -1.082 -0.559 H2B    AG9 38 
AG9 H1D    H1D    H 0 1 N N N -116.670 28.966 -29.134 5.725  -2.172 -0.782 H1D    AG9 39 
AG9 H2D    H2D    H 0 1 N N N -116.001 27.681 -30.195 6.251  -1.402 0.734  H2D    AG9 40 
AG9 HNE    HNE    H 0 1 N N N -114.027 28.621 -30.188 7.989  -0.299 -0.556 HNE    AG9 41 
AG9 H1G    H1G    H 0 1 N N N -114.454 27.176 -28.122 5.319  0.063  -1.776 H1G    AG9 42 
AG9 H2G    H2G    H 0 1 N N N -115.720 28.064 -27.207 5.845  0.833  -0.260 H2G    AG9 43 
AG9 "H1'"  "H1'"  H 0 1 N N N -120.728 28.733 -27.922 -0.164 -0.342 0.547  "H1'"  AG9 44 
AG9 "H2'"  "H2'"  H 0 1 N N N -120.890 25.984 -27.861 -1.439 1.399  2.667  "H2'"  AG9 45 
AG9 "HO2'" "HO2'" H 0 0 N N N -120.916 27.397 -29.699 -0.321 -0.286 3.982  "HO2'" AG9 46 
AG9 "H3'"  "H3'"  H 0 1 N N N -122.681 25.909 -26.351 -3.322 0.071  2.810  "H3'"  AG9 47 
AG9 "HO3'" "HO3'" H 0 0 N N N -124.645 25.666 -27.525 -1.978 -1.454 4.109  "HO3'" AG9 48 
AG9 "H4'"  "H4'"  H 0 1 N N N -124.040 28.289 -27.624 -2.325 -1.866 0.713  "H4'"  AG9 49 
AG9 "H15'" "H15'" H 0 0 N N N -125.288 27.653 -25.786 -4.756 -1.601 1.406  "H15'" AG9 50 
AG9 "H25'" "H25'" H 0 0 N N N -123.866 26.979 -24.920 -4.695 0.065  0.782  "H25'" AG9 51 
AG9 H1H1   H1H1   H 0 0 N N N -112.835 30.566 -30.199 10.163 -3.114 -1.227 H1H1   AG9 52 
AG9 H2H1   H2H1   H 0 0 N N N -113.525 31.173 -31.549 9.337  -2.275 -2.401 H2H1   AG9 53 
AG9 H1H2   H1H2   H 0 0 N N N -116.628 30.167 -30.456 9.301  -1.452 1.040  H1H2   AG9 54 
AG9 H2H2   H2H2   H 0 0 N N N -116.082 31.697 -30.283 7.960  -2.352 1.435  H2H2   AG9 55 
AG9 HOP2   HOP2   H 0 0 N N N -124.103 30.876 -22.279 -6.774 -2.423 -3.127 HOP2   AG9 56 
AG9 HOP3   HOP3   H 0 0 N N N -123.749 27.196 -22.342 -6.233 0.460  -1.960 HOP3   AG9 57 
AG9 HZ     HZ     H 0 1 N N N -114.610 29.815 -31.272 7.802  -3.227 -0.775 HZ     AG9 58 
AG9 H4     H4     H 0 1 N N N -117.965 28.823 -24.349 -0.078 4.007  -2.055 H4     AG9 59 
# 
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 
AG9 NH2   CZ     SING N N 1  
AG9 NH1   CZ     SING N N 2  
AG9 CZ    NE     SING N N 3  
AG9 NE    CD     SING N N 4  
AG9 CD    CG     SING N N 5  
AG9 "O2'" "C2'"  SING N N 6  
AG9 CA    CB     SING N N 7  
AG9 CA    N2     SING N N 8  
AG9 CG    CB     SING N N 9  
AG9 "O3'" "C3'"  SING N N 10 
AG9 "C2'" "C3'"  SING N N 11 
AG9 "C2'" "C1'"  SING N N 12 
AG9 N2    C2     SING N N 13 
AG9 "C3'" "C4'"  SING N N 14 
AG9 "C1'" "O4'"  SING N N 15 
AG9 "C1'" N1     SING N N 16 
AG9 "C4'" "O4'"  SING N N 17 
AG9 "C4'" "C5'"  SING N N 18 
AG9 C2    N1     SING N N 19 
AG9 C2    N3     DOUB N N 20 
AG9 N1    C6     SING N N 21 
AG9 N3    C4     SING N N 22 
AG9 "C5'" "O5'"  SING N N 23 
AG9 "O5'" P      SING N N 24 
AG9 C6    C5     DOUB N N 25 
AG9 C4    C5     SING N N 26 
AG9 C4    N4     SING N N 27 
AG9 P     OP1    DOUB N N 28 
AG9 P     OP2    SING N N 29 
AG9 P     OP3    SING N N 30 
AG9 N2    HN2    SING N N 31 
AG9 N4    H1N4   SING N N 32 
AG9 N4    H2N4   SING N N 33 
AG9 C5    H5     SING N N 34 
AG9 C6    H6     SING N N 35 
AG9 CA    H1A    SING N N 36 
AG9 CA    H2A    SING N N 37 
AG9 CB    H1B    SING N N 38 
AG9 CB    H2B    SING N N 39 
AG9 CD    H1D    SING N N 40 
AG9 CD    H2D    SING N N 41 
AG9 NE    HNE    SING N N 42 
AG9 CG    H1G    SING N N 43 
AG9 CG    H2G    SING N N 44 
AG9 "C1'" "H1'"  SING N N 45 
AG9 "C2'" "H2'"  SING N N 46 
AG9 "O2'" "HO2'" SING N N 47 
AG9 "C3'" "H3'"  SING N N 48 
AG9 "O3'" "HO3'" SING N N 49 
AG9 "C4'" "H4'"  SING N N 50 
AG9 "C5'" "H15'" SING N N 51 
AG9 "C5'" "H25'" SING N N 52 
AG9 NH1   H1H1   SING N N 53 
AG9 NH1   H2H1   SING N N 54 
AG9 NH2   H1H2   SING N N 55 
AG9 NH2   H2H2   SING N N 56 
AG9 OP2   HOP2   SING N N 57 
AG9 OP3   HOP3   SING N N 58 
AG9 CZ    HZ     SING N N 59 
AG9 C4    H4     SING N N 60 
# 
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 
AG9 SMILES           ACDLabs              12.01 "[O-]P([O-])(=O)OCC2OC([n+]1c(nc(N)cc1)NCCCCNC(=[NH2+])\N)C(O)C2O"                                                                                                                               
AG9 InChI            InChI                1.03  "InChI=1S/C14H26N7O7P/c15-9-3-6-21(14(20-9)19-5-2-1-4-18-13(16)17)12-11(23)10(22)8(28-12)7-27-29(24,25)26/h3,6,8,10-12,22-23H,1-2,4-5,7H2,(H8,15,16,17,18,19,20,24,25,26)/t8-,10-,11-,12-/m1/s1" 
AG9 InChIKey         InChI                1.03  IIGUQJFGJGKMTR-HJQYOEGKSA-N                                                                                                                                                                      
AG9 SMILES_CANONICAL CACTVS               3.370 "NC(N)NCCCCNC1=N[C@@H](N)C=CN1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"                                                                                                                      
AG9 SMILES           CACTVS               3.370 "NC(N)NCCCCNC1=N[CH](N)C=CN1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O"                                                                                                                              
AG9 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=NC1N)NCCCCNC(N)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                                                         
AG9 SMILES           "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=NC1N)NCCCCNC(N)N)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                                                                           
# 
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 
AG9 "SYSTEMATIC NAME" ACDLabs              12.01 "4-amino-2-[(4-{[amino(iminio)methyl]amino}butyl)amino]-1-(5-O-phosphonato-beta-D-ribofuranosyl)pyrimidin-1-ium"                                  
AG9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-[4-azanyl-2-[4-[bis(azanyl)methylamino]butylamino]-4H-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
AG9 "Create component" 2013-02-14 EBI  
AG9 "Initial release"  2013-04-03 RCSB 
# 
