data_OGX
# 
_chem_comp.id                                    OGX 
_chem_comp.name                                  "2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}-8-oxoguanosine" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H19 N6 O7 P S" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-09-10 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        422.354 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OGX 
_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        3JR5 
_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 
OGX OP2    OP2    O 0 1 N Y N -16.137 53.340 29.650 3.354  -3.085 0.212  OP2    OGX 1  
OGX P      P      P 0 1 N N N -15.057 52.189 29.496 3.711  -1.884 -0.576 P      OGX 2  
OGX S      S      S 0 1 N N N -11.150 51.253 29.128 6.448  2.540  -0.720 S      OGX 3  
OGX N1     N1     N 0 1 N N N -21.635 53.602 25.620 -6.333 0.229  -1.192 N1     OGX 4  
OGX C2     C2     C 0 1 N N N -20.355 54.089 25.805 -5.427 1.145  -1.631 C2     OGX 5  
OGX N2     N2     N 0 1 N N N -20.219 55.223 26.518 -5.803 2.049  -2.592 N2     OGX 6  
OGX N3     N3     N 0 1 N N N -19.273 53.490 25.318 -4.201 1.187  -1.157 N3     OGX 7  
OGX C4     C4     C 0 1 N N N -19.548 52.361 24.620 -3.793 0.324  -0.219 C4     OGX 8  
OGX N4     N4     N 0 1 N N N -13.507 52.577 29.724 5.148  -1.235 0.010  N4     OGX 9  
OGX C5     C5     C 0 1 N N N -20.790 51.824 24.377 -4.678 -0.632 0.264  C5     OGX 10 
OGX C6     C6     C 0 1 N N N -21.946 52.442 24.911 -5.985 -0.667 -0.242 C6     OGX 11 
OGX O6     O6     O 0 1 N N N -23.124 52.085 24.815 -6.788 -1.494 0.160  O6     OGX 12 
OGX N7     N7     N 0 1 N N N -20.611 50.676 23.612 -3.987 -1.381 1.220  N7     OGX 13 
OGX C8     C8     C 0 1 N N N -19.336 50.513 23.379 -2.735 -0.889 1.304  C8     OGX 14 
OGX O8     O8     O 0 1 N N N -18.793 49.620 22.729 -1.863 -1.309 2.041  O8     OGX 15 
OGX N9     N9     N 0 1 N N N -18.639 51.539 23.983 -2.598 0.139  0.445  N9     OGX 16 
OGX "C1'"  "C1'"  C 0 1 N N R -17.185 51.619 23.987 -1.381 0.930  0.248  "C1'"  OGX 17 
OGX "C2'"  "C2'"  C 0 1 N N N -16.379 52.796 24.525 -1.048 1.709  1.535  "C2'"  OGX 18 
OGX "C3'"  "C3'"  C 0 1 N N S -15.151 52.059 25.054 0.371  1.223  1.916  "C3'"  OGX 19 
OGX "O3'"  "O3'"  O 0 1 N N N -14.360 51.520 23.967 1.179  2.312  2.369  "O3'"  OGX 20 
OGX "C4'"  "C4'"  C 0 1 N N R -15.848 50.962 25.848 0.897  0.667  0.569  "C4'"  OGX 21 
OGX "O4'"  "O4'"  O 0 1 N N N -17.023 50.650 25.049 -0.270 0.058  -0.023 "O4'"  OGX 22 
OGX "C5'"  "C5'"  C 0 1 N N N -16.224 51.396 27.268 1.988  -0.379 0.807  "C5'"  OGX 23 
OGX "O5'"  "O5'"  O 0 1 N N N -15.049 51.748 27.945 2.536  -0.790 -0.448 "O5'"  OGX 24 
OGX "C7'"  "C7'"  C 0 1 N N N -12.871 52.378 31.024 5.534  -0.038 -0.750 "C7'"  OGX 25 
OGX "C8'"  "C8'"  C 0 1 N N N -11.779 51.330 30.847 5.971  1.063  0.219  "C8'"  OGX 26 
OGX OP1    OP1    O 0 1 N N N -15.545 51.064 30.330 3.897  -2.292 -2.122 OP1    OGX 27 
OGX HS     HS     H 0 1 N N N -10.252 50.317 29.211 6.802  3.409  0.243  HS     OGX 28 
OGX HN1    HN1    H 0 1 N N N -22.391 54.118 26.023 -7.231 0.221  -1.559 HN1    OGX 29 
OGX HN2    HN2    H 0 1 N N N -19.310 55.608 26.677 -6.704 2.030  -2.951 HN2    OGX 30 
OGX HN2A   HN2A   H 0 0 N N N -21.027 55.681 26.888 -5.167 2.708  -2.914 HN2A   OGX 31 
OGX HN4    HN4    H 0 1 N N N -12.987 52.019 29.077 5.077  -1.030 0.996  HN4    OGX 32 
OGX HN7    HN7    H 0 1 N N N -21.341 50.072 23.292 -4.344 -2.123 1.732  HN7    OGX 33 
OGX "H1'"  "H1'"  H 0 1 N N N -16.841 51.573 22.943 -1.520 1.624  -0.581 "H1'"  OGX 34 
OGX "H2'"  "H2'"  H 0 1 N N N -16.130 53.532 23.746 -1.045 2.782  1.341  "H2'"  OGX 35 
OGX "H2'A" "H2'A" H 0 0 N N N -16.912 53.353 25.310 -1.760 1.465  2.323  "H2'A" OGX 36 
OGX "H3'"  "H3'"  H 0 1 N N N -14.437 52.667 25.628 0.324  0.436  2.670  "H3'"  OGX 37 
OGX "HO3'" "HO3'" H 0 0 N Y N -13.603 51.067 24.320 0.839  2.750  3.161  "HO3'" OGX 38 
OGX "H4'"  "H4'"  H 0 1 N N N -15.192 50.093 26.006 1.273  1.475  -0.060 "H4'"  OGX 39 
OGX "H5'"  "H5'"  H 0 1 N N N -16.905 52.259 27.227 2.777  0.052  1.424  "H5'"  OGX 40 
OGX "H5'A" "H5'A" H 0 0 N N N -16.724 50.568 27.792 1.559  -1.242 1.315  "H5'A" OGX 41 
OGX "H7'"  "H7'"  H 0 1 N N N -12.434 53.323 31.380 6.360  -0.283 -1.418 "H7'"  OGX 42 
OGX "H7'A" "H7'A" H 0 0 N N N -13.613 52.031 31.759 4.684  0.310  -1.336 "H7'A" OGX 43 
OGX "H8'"  "H8'"  H 0 1 N N N -12.195 50.346 31.110 6.821  0.715  0.805  "H8'"  OGX 44 
OGX "H8'A" "H8'A" H 0 0 N N N -10.941 51.584 31.513 5.145  1.307  0.887  "H8'A" OGX 45 
OGX HOP1   HOP1   H 0 0 N N N -16.366 51.307 30.741 4.132  -1.553 -2.699 HOP1   OGX 46 
# 
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 
OGX P     OP2    DOUB N N 1  
OGX "O5'" P      SING N N 2  
OGX P     N4     SING N N 3  
OGX P     OP1    SING N N 4  
OGX S     "C8'"  SING N N 5  
OGX S     HS     SING N N 6  
OGX C6    N1     SING N N 7  
OGX N1    C2     SING N N 8  
OGX N1    HN1    SING N N 9  
OGX N3    C2     DOUB N N 10 
OGX C2    N2     SING N N 11 
OGX N2    HN2    SING N N 12 
OGX N2    HN2A   SING N N 13 
OGX C4    N3     SING N N 14 
OGX N9    C4     SING N N 15 
OGX C5    C4     DOUB N N 16 
OGX N4    "C7'"  SING N N 17 
OGX N4    HN4    SING N N 18 
OGX N7    C5     SING N N 19 
OGX C5    C6     SING N N 20 
OGX O6    C6     DOUB N N 21 
OGX C8    N7     SING N N 22 
OGX N7    HN7    SING N N 23 
OGX O8    C8     DOUB N N 24 
OGX C8    N9     SING N N 25 
OGX N9    "C1'"  SING N N 26 
OGX "C1'" "C2'"  SING N N 27 
OGX "C1'" "O4'"  SING N N 28 
OGX "C1'" "H1'"  SING N N 29 
OGX "C2'" "C3'"  SING N N 30 
OGX "C2'" "H2'"  SING N N 31 
OGX "C2'" "H2'A" SING N N 32 
OGX "O3'" "C3'"  SING N N 33 
OGX "C3'" "C4'"  SING N N 34 
OGX "C3'" "H3'"  SING N N 35 
OGX "O3'" "HO3'" SING N N 36 
OGX "O4'" "C4'"  SING N N 37 
OGX "C4'" "C5'"  SING N N 38 
OGX "C4'" "H4'"  SING N N 39 
OGX "C5'" "O5'"  SING N N 40 
OGX "C5'" "H5'"  SING N N 41 
OGX "C5'" "H5'A" SING N N 42 
OGX "C8'" "C7'"  SING N N 43 
OGX "C7'" "H7'"  SING N N 44 
OGX "C7'" "H7'A" SING N N 45 
OGX "C8'" "H8'"  SING N N 46 
OGX "C8'" "H8'A" SING N N 47 
OGX OP1   HOP1   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 
OGX SMILES           ACDLabs              11.02 "O=P(O)(OCC3OC(N2C(=O)NC1=C2N=C(N)NC1=O)CC3O)NCCS"                                                                                                                               
OGX SMILES_CANONICAL CACTVS               3.352 "NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)O3)C(=O)N1"                                                                                                            
OGX SMILES           CACTVS               3.352 "NC1=NC2=C(NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)NCCS)O3)C(=O)N1"                                                                                                                
OGX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO[P@](=O)(NCCS)O)O"                                                                                                           
OGX SMILES           "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(NCCS)O)O"                                                                                                                           
OGX InChI            InChI                1.03  "InChI=1S/C12H19N6O7PS/c13-11-16-9-8(10(20)17-11)15-12(21)18(9)7-3-5(19)6(25-7)4-24-26(22,23)14-1-2-27/h5-7,19,27H,1-4H2,(H,15,21)(H2,14,22,23)(H3,13,16,17,20)/t5-,6+,7+/m0/s1" 
OGX InChIKey         InChI                1.03  QTNBODRGZGXUEH-RRKCRQDMSA-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 
OGX "SYSTEMATIC NAME" ACDLabs              11.02 "2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}-8-oxoguanosine"                                                  
OGX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(2-azanyl-6,8-dioxo-1,7-dihydropurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic 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 
OGX "Create component"  2009-09-10 RCSB 
OGX "Modify descriptor" 2011-06-04 RCSB 
# 
