data_A12
#

_chem_comp.id                                   A12
_chem_comp.name                                 "PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H17 N5 O9 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2000-12-15
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       425.228
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    A12
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1HPU
_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
A12  PB      PB    P  0  1  N  N  N  -2.904  -0.420  -1.838  -6.106   1.026  -0.312  PB      A12   1  
A12  O1B     O1B   O  0  1  N  N  N  -1.601  -0.830  -2.460  -6.748  -0.266   0.019  O1B     A12   2  
A12  O2B     O2B   O  0  1  N  N  N  -2.880  -0.654  -0.363  -5.912   1.889   1.033  O2B     A12   3  
A12  O3B     O3B   O  0  1  N  N  N  -3.172   1.022  -2.074  -7.039   1.840  -1.341  O3B     A12   4  
A12  PA      PA    P  0  1  N  N  S  -5.850  -0.876  -1.948  -3.425  -0.203   0.087  PA      A12   5  
A12  O1A     O1A   O  0  1  N  N  N  -5.873  -0.862  -0.461  -4.066  -1.495   0.418  O1A     A12   6  
A12  O2A     O2A   O  0  1  N  N  N  -6.860  -1.819  -2.490  -3.230   0.659   1.433  O2A     A12   7  
A12  C3A     C3A   C  0  1  N  N  N  -4.236  -1.356  -2.511  -4.481   0.719  -1.078  C3A     A12   8  
A12  "O5'"   O5*   O  0  1  N  N  N  -6.160   0.599  -2.462  -1.989  -0.474  -0.589  "O5'"   A12   9  
A12  "C5'"   C5*   C  0  1  N  N  N  -6.136   0.837  -3.854  -1.253  -1.297   0.319  "C5'"   A12  10  
A12  "C4'"   C4*   C  0  1  N  N  R  -7.018   2.009  -4.197   0.129  -1.593  -0.267  "C4'"   A12  11  
A12  "O4'"   O4*   O  0  1  N  N  N  -6.428   3.242  -3.692   0.912  -0.383  -0.344  "O4'"   A12  12  
A12  "C3'"   C3*   C  0  1  N  N  S  -7.147   2.222  -5.693   0.927  -2.521   0.676  "C3'"   A12  13  
A12  "O3'"   O3*   O  0  1  N  N  N  -8.203   1.386  -6.173   0.844  -3.877   0.233  "O3'"   A12  14  
A12  "C2'"   C2*   C  0  1  N  N  R  -7.457   3.712  -5.783   2.381  -2.004   0.570  "C2'"   A12  15  
A12  "O2'"   O2*   O  0  1  N  N  N  -8.798   3.978  -5.471   3.240  -3.026   0.061  "O2'"   A12  16  
A12  "C1'"   C1*   C  0  1  N  N  R  -6.582   4.277  -4.653   2.286  -0.823  -0.421  "C1'"   A12  17  
A12  N9      N9    N  0  1  Y  N  N  -5.252   4.698  -5.096   3.191   0.256  -0.018  N9      A12  18  
A12  C8      C8    C  0  1  Y  N  N  -4.069   4.025  -4.919   2.870   1.330   0.758  C8      A12  19  
A12  N7      N7    N  0  1  Y  N  N  -3.024   4.642  -5.428   3.913   2.091   0.918  N7      A12  20  
A12  C5      C5    C  0  1  Y  N  N  -3.557   5.801  -5.970   4.969   1.552   0.262  C5      A12  21  
A12  C6      C6    C  0  1  Y  N  N  -2.965   6.882  -6.634   6.312   1.923   0.077  C6      A12  22  
A12  N6      N6    N  0  1  N  N  N  -1.655   6.979  -6.857   6.813   3.078   0.651  N6      A12  23  
A12  N1      N1    N  0  1  Y  N  N  -3.771   7.877  -7.062   7.091   1.135  -0.658  N1      A12  24  
A12  C2      C2    C  0  1  Y  N  N  -5.082   7.790  -6.807   6.621   0.031  -1.210  C2      A12  25  
A12  N3      N3    N  0  1  Y  N  N  -5.760   6.828  -6.174   5.370  -0.352  -1.069  N3      A12  26  
A12  C4      C4    C  0  1  Y  N  N  -4.928   5.849  -5.778   4.516   0.371  -0.351  C4      A12  27  
A12  HOB2    2HOB  H  0  0  N  N  N  -2.875  -1.588  -0.190  -5.492   2.720   0.774  HOB2    A12  28  
A12  HXT     HXT   H  0  1  N  N  N  -3.229   1.474  -1.241  -7.887   1.982  -0.898  HXT     A12  29  
A12  HOA2    2HOA  H  0  0  N  N  N  -7.499  -2.020  -1.817  -2.810   1.491   1.173  HOA2    A12  30  
A12  H3A1    1H3A  H  0  0  N  N  N  -4.086  -2.393  -2.177  -4.008   1.670  -1.322  H3A1    A12  31  
A12  H3A2    2H3A  H  0  0  N  N  N  -4.213  -1.232  -3.604  -4.613   0.135  -1.989  H3A2    A12  32  
A12  "H5'1"  1H5*  H  0  0  N  N  N  -6.506  -0.057  -4.378  -1.789  -2.232   0.477  "H5'1"  A12  33  
A12  "H5'2"  2H5*  H  0  0  N  N  N  -5.104   1.057  -4.166  -1.141  -0.777   1.270  "H5'2"  A12  34  
A12  "H4'"   H4*   H  0  1  N  N  N  -7.998   1.783  -3.751   0.032  -2.047  -1.253  "H4'"   A12  35  
A12  "H3'"   H3*   H  0  1  N  N  N  -6.267   1.963  -6.300   0.562  -2.431   1.699  "H3'"   A12  36  
A12  "HO3'"  *HO3  H  0  0  N  N  N  -8.808   1.201  -5.464   1.358  -4.407   0.857  "HO3'"  A12  37  
A12  "H2'"   H2*   H  0  1  N  N  N  -7.276   4.126  -6.786   2.735  -1.657   1.541  "H2'"   A12  38  
A12  "HO2'"  *HO2  H  0  0  N  N  N  -8.898   4.038  -4.528   3.210  -3.757   0.693  "HO2'"  A12  39  
A12  "H1'"   H1*   H  0  1  N  N  N  -7.078   5.173  -4.252   2.521  -1.157  -1.432  "H1'"   A12  40  
A12  H8      H8    H  0  1  N  N  N  -4.002   3.076  -4.409   1.893   1.522   1.177  H8      A12  41  
A12  HN61    1HN6  H  0  0  N  N  N  -0.976   6.300  -6.577   7.743   3.321   0.519  HN61    A12  42  
A12  HN62    2HN6  H  0  0  N  N  N  -1.447   7.827  -7.345   6.233   3.646   1.182  HN62    A12  43  
A12  H2      H2    H  0  1  N  N  N  -5.678   8.617  -7.164   7.289  -0.579  -1.800  H2      A12  44  
#   #
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
A12  PB     O1B     DOUB  N  N   1  
A12  PB     O2B     SING  N  N   2  
A12  PB     O3B     SING  N  N   3  
A12  PB     C3A     SING  N  N   4  
A12  O2B    HOB2    SING  N  N   5  
A12  O3B    HXT     SING  N  N   6  
A12  PA     O1A     DOUB  N  N   7  
A12  PA     O2A     SING  N  N   8  
A12  PA     C3A     SING  N  N   9  
A12  PA     "O5'"   SING  N  N  10  
A12  O2A    HOA2    SING  N  N  11  
A12  C3A    H3A1    SING  N  N  12  
A12  C3A    H3A2    SING  N  N  13  
A12  "O5'"  "C5'"   SING  N  N  14  
A12  "C5'"  "C4'"   SING  N  N  15  
A12  "C5'"  "H5'1"  SING  N  N  16  
A12  "C5'"  "H5'2"  SING  N  N  17  
A12  "C4'"  "O4'"   SING  N  N  18  
A12  "C4'"  "C3'"   SING  N  N  19  
A12  "C4'"  "H4'"   SING  N  N  20  
A12  "O4'"  "C1'"   SING  N  N  21  
A12  "C3'"  "O3'"   SING  N  N  22  
A12  "C3'"  "C2'"   SING  N  N  23  
A12  "C3'"  "H3'"   SING  N  N  24  
A12  "O3'"  "HO3'"  SING  N  N  25  
A12  "C2'"  "O2'"   SING  N  N  26  
A12  "C2'"  "C1'"   SING  N  N  27  
A12  "C2'"  "H2'"   SING  N  N  28  
A12  "O2'"  "HO2'"  SING  N  N  29  
A12  "C1'"  N9      SING  N  N  30  
A12  "C1'"  "H1'"   SING  N  N  31  
A12  N9     C8      SING  Y  N  32  
A12  N9     C4      SING  Y  N  33  
A12  C8     N7      DOUB  Y  N  34  
A12  C8     H8      SING  N  N  35  
A12  N7     C5      SING  Y  N  36  
A12  C5     C6      SING  Y  N  37  
A12  C5     C4      DOUB  Y  N  38  
A12  C6     N6      SING  N  N  39  
A12  C6     N1      DOUB  Y  N  40  
A12  N6     HN61    SING  N  N  41  
A12  N6     HN62    SING  N  N  42  
A12  N1     C2      SING  Y  N  43  
A12  C2     N3      DOUB  Y  N  44  
A12  C2     H2      SING  N  N  45  
A12  N3     C4      SING  Y  N  46  
#   #
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
A12  SMILES            ACDLabs               10.04  "O=P(O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O"  
A12  SMILES_CANONICAL  CACTVS                3.341  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O"  
A12  SMILES            CACTVS                3.341  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O"  
A12  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(CP(=O)(O)O)O)O)O)N"  
A12  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)O)O)O)O)N"  
A12  InChI             InChI                 1.03   "InChI=1S/C11H17N5O9P2/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(25-11)1-24-27(22,23)4-26(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1"  
A12  InChIKey          InChI                 1.03   OLCWZBFDIYXLAA-IOSLPCCCSA-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
A12  "SYSTEMATIC NAME"  ACDLabs               10.04  "5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]adenosine"  
A12  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]methylphosphonic 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
A12  "Create component"   2000-12-15  RCSB  
A12  "Modify descriptor"  2011-06-04  RCSB  
A12  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     A12
_pdbx_chem_comp_synonyms.name        "ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
