data_CGY
# 
_chem_comp.id                                    CGY 
_chem_comp.name                                  "(1R)-1,4-anhydro-2-deoxy-1-[2,6-diamino-5-(dihydroxyamino)pyridin-3-yl]-5-O-phosphono-D-erythro-pentitol" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H17 N4 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-09-22 
_chem_comp.pdbx_modified_date                    2018-09-14 
_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                        352.238 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CGY 
_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        6B1S 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
CGY C1     C1  C 0 1 Y N N -18.556 9.356  181.806 1.993  0.880  0.390  C1     CGY 1  
CGY "C1'"  C2  C 0 1 N N R -17.466 9.146  180.800 0.717  1.681  0.380  "C1'"  CGY 2  
CGY C2     C3  C 0 1 Y N N -19.102 8.355  182.592 3.172  1.443  0.860  C2     CGY 3  
CGY "C2'"  C4  C 0 1 N N N -17.965 9.244  179.383 0.586  2.470  -0.941 "C2'"  CGY 4  
CGY "C3'"  C5  C 0 1 N N S -17.111 10.307 178.699 -0.923 2.413  -1.266 "C3'"  CGY 5  
CGY C4     C6  C 0 1 Y N N -20.568 9.813  183.596 4.345  -0.507 0.451  C4     CGY 6  
CGY "C4'"  C7  C 0 1 N N R -15.868 10.284 179.583 -1.526 1.596  -0.102 "C4'"  CGY 7  
CGY C5     C8  C 0 1 Y N N -20.094 10.881 182.853 3.198  -1.135 -0.035 C5     CGY 8  
CGY "C5'"  C9  C 0 1 N N N -15.014 11.522 179.484 -2.649 0.691  -0.612 "C5'"  CGY 9  
CGY C6     C10 C 0 1 Y N N -19.070 10.645 181.939 2.001  -0.430 -0.066 C6     CGY 10 
CGY N1     N1  N 0 1 N N N -18.653 7.177  182.483 3.170  2.758  1.319  N1     CGY 11 
CGY N3     N2  N 0 1 Y N N -20.090 8.559  183.483 4.298  0.745  0.877  N3     CGY 12 
CGY N4     N3  N 0 1 N N N -21.497 10.027 184.430 5.550  -1.204 0.487  N4     CGY 13 
CGY N5     N4  N 0 1 N N N -20.578 12.020 183.011 3.252  -2.463 -0.487 N5     CGY 14 
CGY "O3'"  O1  O 0 1 N N N -16.893 10.157 177.258 -1.479 3.729  -1.295 "O3'"  CGY 15 
CGY "O4'"  O2  O 0 1 N N N -16.404 10.093 180.919 -0.429 0.802  0.400  "O4'"  CGY 16 
CGY "O5'"  O3  O 0 1 N N N -15.843 12.708 179.496 -3.270 0.032  0.494  "O5'"  CGY 17 
CGY ON1    O4  O 0 1 N N N -20.034 13.052 182.419 2.058  -3.204 -0.081 ON1    CGY 18 
CGY ON2    O5  O 0 1 N N N -21.625 12.187 183.781 3.434  -2.516 -1.938 ON2    CGY 19 
CGY OP1    O6  O 0 1 N N N -14.169 14.389 178.825 -5.592 -0.345 -0.421 OP1    CGY 20 
CGY OP2    O7  O 0 1 N N N -16.352 15.173 179.879 -3.995 -2.298 -0.485 OP2    CGY 21 
CGY P      P1  P 0 1 N N N -15.258 14.163 179.800 -4.495 -1.000 0.325  P      CGY 22 
CGY "H1'1" H1  H 0 0 N N N -17.059 8.134  180.946 0.689  2.359  1.234  "H1'1" CGY 23 
CGY "H2'1" H2  H 0 0 N N N -19.024 9.542  179.372 0.909  3.502  -0.803 "H2'1" CGY 24 
CGY "H2'2" H3  H 0 0 N N N -17.851 8.277  178.872 1.167  1.992  -1.730 "H2'2" CGY 25 
CGY "H3'1" H4  H 0 0 N N N -17.607 11.275 178.865 -1.091 1.905  -2.216 "H3'1" CGY 26 
CGY "H4'1" H5  H 0 0 N N N -15.258 9.412  179.305 -1.899 2.262  0.677  "H4'1" CGY 27 
CGY "H5'2" H6  H 0 0 N N N -14.438 11.491 178.547 -3.390 1.292  -1.139 "H5'2" CGY 28 
CGY "H5'1" H7  H 0 0 N N N -14.322 11.555 180.339 -2.235 -0.054 -1.292 "H5'1" CGY 29 
CGY H61    H8  H 0 1 N N N -18.678 11.453 181.339 1.098  -0.891 -0.437 H61    CGY 30 
CGY H12    H9  H 0 1 N N N -19.141 6.574  183.115 2.349  3.275  1.309  H12    CGY 31 
CGY H11    H10 H 0 1 N N N -18.786 6.855  181.546 3.990  3.158  1.649  H11    CGY 32 
CGY H41    H11 H 0 1 N N N -21.733 9.173  184.893 5.574  -2.144 0.251  H41    CGY 33 
CGY H42    H12 H 0 1 N N N -21.191 10.698 185.105 6.366  -0.749 0.749  H42    CGY 34 
CGY "H3'2" H13 H 0 0 N N N -16.351 10.871 176.943 -1.093 4.304  -1.969 "H3'2" CGY 35 
CGY HN11   H14 H 0 0 N N N -20.520 13.838 182.642 2.050  -4.127 -0.371 HN11   CGY 36 
CGY HN21   H15 H 0 0 N N N -21.897 11.347 184.133 3.477  -3.413 -2.297 HN21   CGY 37 
CGY H1     H16 H 0 1 N N N -16.188 15.867 179.252 -3.275 -2.778 -0.054 H1     CGY 38 
CGY OP3    O8  O 0 1 N Y N -14.729 14.047 181.294 -5.025 -1.445 1.778  O1     CGY 39 
CGY "HO3'" H17 H 0 0 N Y N -13.784 14.145 181.304 -5.765 -2.068 1.753  H2     CGY 40 
# 
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 
CGY "O3'" "C3'"  SING N N 1  
CGY "C3'" "C2'"  SING N N 2  
CGY "C3'" "C4'"  SING N N 3  
CGY OP1   P      DOUB N N 4  
CGY "C2'" "C1'"  SING N N 5  
CGY "C5'" "O5'"  SING N N 6  
CGY "C5'" "C4'"  SING N N 7  
CGY "O5'" P      SING N N 8  
CGY "C4'" "O4'"  SING N N 9  
CGY P     OP2    SING N N 10 
CGY "C1'" "O4'"  SING N N 11 
CGY "C1'" C1     SING N N 12 
CGY C1    C6     DOUB Y N 13 
CGY C1    C2     SING Y N 14 
CGY C6    C5     SING Y N 15 
CGY ON1   N5     SING N N 16 
CGY N1    C2     SING N N 17 
CGY C2    N3     DOUB Y N 18 
CGY C5    N5     SING N N 19 
CGY C5    C4     DOUB Y N 20 
CGY N5    ON2    SING N N 21 
CGY N3    C4     SING Y N 22 
CGY C4    N4     SING N N 23 
CGY "C1'" "H1'1" SING N N 24 
CGY "C2'" "H2'1" SING N N 25 
CGY "C2'" "H2'2" SING N N 26 
CGY "C3'" "H3'1" SING N N 27 
CGY "C4'" "H4'1" SING N N 28 
CGY "C5'" "H5'2" SING N N 29 
CGY "C5'" "H5'1" SING N N 30 
CGY C6    H61    SING N N 31 
CGY N1    H12    SING N N 32 
CGY N1    H11    SING N N 33 
CGY N4    H41    SING N N 34 
CGY N4    H42    SING N N 35 
CGY "O3'" "H3'2" SING N N 36 
CGY ON1   HN11   SING N N 37 
CGY ON2   HN21   SING N N 38 
CGY OP2   H1     SING N N 39 
CGY P     OP3    SING N N 40 
CGY OP3   "HO3'" SING N N 41 
# 
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 
CGY SMILES           ACDLabs              12.01 "c1(cc(c(N)nc1N)N(O)O)C2OC(C(C2)O)COP(=O)(O)O"                                                                                                         
CGY InChI            InChI                1.03  "InChI=1S/C10H17N4O8P/c11-9-4(1-5(14(16)17)10(12)13-9)7-2-6(15)8(22-7)3-21-23(18,19)20/h1,6-8,15-17H,2-3H2,(H4,11,12,13)(H2,18,19,20)/t6-,7+,8+/m0/s1" 
CGY InChIKey         InChI                1.03  VFFYYNDFZAMVIU-XLPZGREQSA-N                                                                                                                            
CGY SMILES_CANONICAL CACTVS               3.385 "Nc1nc(N)c(cc1[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)N(O)O"                                                                                            
CGY SMILES           CACTVS               3.385 "Nc1nc(N)c(cc1[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)N(O)O"                                                                                                
CGY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1c(c(nc(c1N(O)O)N)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                            
CGY SMILES           "OpenEye OEToolkits" 2.0.6 "c1c(c(nc(c1N(O)O)N)N)C2CC(C(O2)COP(=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 
CGY "SYSTEMATIC NAME" ACDLabs              12.01 "(1R)-1,4-anhydro-2-deoxy-1-[2,6-diamino-5-(dihydroxyamino)pyridin-3-yl]-5-O-phosphono-D-erythro-pentitol"                       
CGY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2,6-bis(azanyl)-5-[bis(oxidanyl)amino]pyridin-3-yl]-3-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 
CGY "Create component" 2017-09-22 RCSB 
CGY "Initial release"  2018-09-19 RCSB 
# 
