data_GD1
#

_chem_comp.id                                   GD1
_chem_comp.name                                 "2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C7 H7 N5 O"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "7-cyano-7-deazaguanine, bound form"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2012-05-25
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       177.163
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GD1
_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       4F8B
_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
GD1  O6   O6   O  0  1  N  N  N   4.022  19.055  14.065  -0.474  -2.188  -0.002  O6   GD1   1  
GD1  C6   C6   C  0  1  N  N  N   3.000  19.784  14.616   0.216  -1.184  -0.003  C6   GD1   2  
GD1  C5   C5   C  0  1  Y  N  N   1.673  19.938  14.089  -0.371   0.097  -0.001  C5   GD1   3  
GD1  C7   C7   C  0  1  Y  N  N   0.825  19.550  13.003  -1.754   0.600   0.001  C7   GD1   4  
GD1  C77  C77  C  0  1  N  N  N   1.061  18.705  11.818  -2.985  -0.205   0.002  C77  GD1   5  
GD1  N77  N77  N  0  1  N  N  N   2.191  18.331  11.523  -2.913  -1.499   0.002  N77  GD1   6  
GD1  N1   N1   N  0  1  N  N  N   3.298  20.404  15.796   1.566  -1.269   0.000  N1   GD1   7  
GD1  C2   C2   C  0  1  N  N  N   2.387  21.178  16.482   2.323  -0.135   0.000  C2   GD1   8  
GD1  N2   N2   N  0  1  N  N  N   2.745  21.792  17.623   3.690  -0.250   0.004  N2   GD1   9  
GD1  N3   N3   N  0  1  N  N  N   1.125  21.350  16.025   1.785   1.063  -0.003  N3   GD1  10  
GD1  C4   C4   C  0  1  Y  N  N   0.795  20.744  14.852   0.454   1.227  -0.002  C4   GD1  11  
GD1  N9   N9   N  0  1  Y  N  N  -0.431  20.855  14.290  -0.355   2.329  -0.000  N9   GD1  12  
GD1  C8   C8   C  0  1  Y  N  N  -0.443  20.112  13.141  -1.666   1.959   0.001  C8   GD1  13  
GD1  H1   H1   H  0  1  N  N  N   0.226  18.411  11.200  -3.948   0.283   0.004  H1   GD1  14  
GD1  H2   H2   H  0  1  N  N  N   2.195  17.767  10.697  -3.725  -2.030   0.003  H2   GD1  15  
GD1  H3   H3   H  0  1  N  N  N   4.215  20.292  16.178   1.996  -2.138   0.003  H3   GD1  16  
GD1  H4   H4   H  0  1  N  N  N   2.084  22.360  18.114   4.104  -1.127   0.006  H4   GD1  17  
GD1  H5   H5   H  0  1  N  N  N   3.672  21.680  17.981   4.244   0.547   0.004  H5   GD1  18  
GD1  H6   H6   H  0  1  N  N  N  -1.196  21.388  14.652  -0.040   3.246   0.000  H6   GD1  19  
GD1  H7   H7   H  0  1  N  N  N  -1.278  19.985  12.468  -2.505   2.639   0.002  H7   GD1  20  
#   #
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
GD1  N77  C77  DOUB  N  N   1  
GD1  C77  C7   SING  N  N   2  
GD1  C7   C8   DOUB  Y  N   3  
GD1  C7   C5   SING  Y  N   4  
GD1  C8   N9   SING  Y  N   5  
GD1  O6   C6   DOUB  N  N   6  
GD1  C5   C6   SING  N  N   7  
GD1  C5   C4   DOUB  Y  N   8  
GD1  N9   C4   SING  Y  N   9  
GD1  C6   N1   SING  N  N  10  
GD1  C4   N3   SING  N  N  11  
GD1  N1   C2   SING  N  N  12  
GD1  N3   C2   DOUB  N  N  13  
GD1  C2   N2   SING  N  N  14  
GD1  C77  H1   SING  N  N  15  
GD1  N77  H2   SING  N  N  16  
GD1  N1   H3   SING  N  N  17  
GD1  N2   H4   SING  N  N  18  
GD1  N2   H5   SING  N  N  19  
GD1  N9   H6   SING  N  N  20  
GD1  C8   H7   SING  N  N  21  
#   #
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
GD1  SMILES            ACDLabs               12.01  "O=C1c2c(cnc2N=C(N)N1)C=[N@H]"  
GD1  InChI             InChI                 1.03   "InChI=1S/C7H7N5O/c8-1-3-2-10-5-4(3)6(13)12-7(9)11-5/h1-2,8H,(H4,9,10,11,12,13)/b8-1-"  
GD1  InChIKey          InChI                 1.03   BETPBINTBSWYLZ-QPIMQUGISA-N  
GD1  SMILES_CANONICAL  CACTVS                3.370  "NC1=Nc2[nH]cc(C=N)c2C(=O)N1"  
GD1  SMILES            CACTVS                3.370  "NC1=Nc2[nH]cc(C=N)c2C(=O)N1"  
GD1  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "[H]/N=C\c1c[nH]c2c1C(=O)NC(=N2)N"  
GD1  SMILES            "OpenEye OEToolkits"  1.7.6  "c1c(c2c([nH]1)N=C(NC2=O)N)C=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
GD1  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one"  
GD1  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "2-azanyl-5-(iminomethyl)-3,7-dihydropyrrolo[2,3-d]pyrimidin-4-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GD1  "Create component"  2012-05-25  RCSB  
GD1  "Modify synonyms"   2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     GD1
_pdbx_chem_comp_synonyms.name        "7-cyano-7-deazaguanine, bound form"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
