data_XM7
#

_chem_comp.id                                   XM7
_chem_comp.name                                 "5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H16 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-18
_chem_comp.pdbx_modified_date                   2020-12-25
_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                       361.248
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XM7
_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       7L3Q
_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
XM7  C2      C1   C  0  1  Y  N  N   4.580   1.923  -20.779   5.480  -0.455  -0.861  C2      XM7   1  
XM7  N1      N1   N  0  1  Y  N  N   4.072   2.914  -20.042   5.990   0.680  -0.421  N1      XM7   2  
XM7  C6      C2   C  0  1  Y  N  N   4.214   2.890  -18.714   5.217   1.623   0.108  C6      XM7   3  
XM7  "C4'"   C3   C  0  1  N  N  R   8.286  -2.584  -17.479  -1.210  -1.441  -0.337  "C4'"   XM7   4  
XM7  "C3'"   C4   C  0  1  N  N  S   8.972  -1.449  -18.201  -0.463  -2.514   0.479  "C3'"   XM7   5  
XM7  "C2'"   C5   C  0  1  N  N  R   8.021  -1.168  -19.362   0.947  -1.912   0.698  "C2'"   XM7   6  
XM7  "C1'"   C6   C  0  1  N  N  R   6.667  -1.319  -18.631   1.030  -0.860  -0.438  "C1'"   XM7   7  
XM7  C8      C7   C  0  1  Y  N  N   5.874   0.375  -16.922   1.686   1.395   0.486  C8      XM7   8  
XM7  C5      C8   C  0  1  Y  N  N   4.896   1.815  -18.151   3.834   1.387   0.190  C5      XM7   9  
XM7  C4      C9   C  0  1  Y  N  N   5.382   0.844  -19.007   3.340   0.163  -0.292  C4      XM7  10  
XM7  "C5'"   C10  C  0  1  N  N  N   8.828  -2.805  -16.078  -2.460  -0.989   0.420  "C5'"   XM7  11  
XM7  C22     C11  C  0  1  N  N  N   6.272  -1.568  -12.742  -6.194   2.532  -0.817  C22     XM7  12  
XM7  N9      N2   N  0  1  Y  N  N   6.008  -0.076  -18.221   1.984   0.197  -0.093  N9      XM7  13  
XM7  N7      N3   N  0  1  Y  N  N   5.215   1.494  -16.838   2.773   2.092   0.651  N7      XM7  14  
XM7  N3      N4   N  0  1  Y  N  N   5.241   0.863  -20.340   4.192  -0.720  -0.805  N3      XM7  15  
XM7  N6      N5   N  0  1  N  N  N   3.691   3.883  -17.983   5.761   2.810   0.567  N6      XM7  16  
XM7  "O3'"   O1   O  0  1  N  N  N  10.181  -1.957  -18.790  -0.379  -3.735  -0.259  "O3'"   XM7  17  
XM7  "O4'"   O2   O  0  1  N  N  N   6.906  -2.070  -17.447  -0.312  -0.331  -0.506  "O4'"   XM7  18  
XM7  "O2'"   O3   O  0  1  N  N  N   8.151  -2.148  -20.395   1.957  -2.910   0.543  "O2'"   XM7  19  
XM7  "O5'"   O4   O  0  1  N  N  N   7.762  -3.025  -15.157  -3.198  -0.069  -0.387  "O5'"   XM7  20  
XM7  OP3     O5   O  0  1  N  N  N   7.645  -1.912  -13.002  -5.058   1.684  -1.002  OP3     XM7  21  
XM7  OP2     O6   O  0  1  N  N  N   6.838  -4.449  -13.114  -5.703  -0.524   0.270  OP2     XM7  22  
XM7  OP1     O7   O  0  1  N  N  N   9.460  -3.782  -13.310  -4.360   1.295   1.392  OP1     XM7  23  
XM7  P       P1   P  0  1  N  N  N   7.950  -3.464  -13.549  -4.575   0.612   0.097  P       XM7  24  
XM7  "H4'"   H1   H  0  1  N  N  N   4.436   1.994  -21.847   6.143  -1.193  -1.288  "H4'"   XM7  25  
XM7  H1      H2   H  0  1  N  N  N   8.350  -3.511  -18.067  -1.491  -1.842  -1.311  H1      XM7  26  
XM7  "H3'"   H3   H  0  1  N  N  N   9.124  -0.568  -17.560  -0.959  -2.681   1.435  "H3'"   XM7  27  
XM7  "H2'"   H4   H  0  1  N  N  N   8.149  -0.142  -19.737   1.019  -1.436   1.675  "H2'"   XM7  28  
XM7  "H1'"   H5   H  0  1  N  N  N   5.989  -1.880  -19.290   1.307  -1.333  -1.380  "H1'"   XM7  29  
XM7  "H5''"  H6   H  0  0  N  N  N   6.274  -0.147  -16.065   0.694   1.719   0.766  "H5''"  XM7  30  
XM7  "H5'"   H7   H  0  1  N  N  N   9.490  -3.683  -16.081  -3.082  -1.855   0.645  "H5'"   XM7  31  
XM7  H2      H8   H  0  1  N  N  N   9.398  -1.917  -15.766  -2.166  -0.502   1.350  H2      XM7  32  
XM7  H9      H9   H  0  1  N  N  N   6.214  -0.527  -12.391  -6.319   3.168  -1.692  H9      XM7  33  
XM7  H10     H10  H  0  1  N  N  N   5.686  -1.676  -13.666  -7.085   1.920  -0.681  H10     XM7  34  
XM7  H11     H11  H  0  1  N  N  N   5.866  -2.238  -11.970  -6.042   3.154   0.066  H11     XM7  35  
XM7  H61     H12  H  0  1  N  N  N   3.240   4.540  -18.587   6.717   2.961   0.505  H61     XM7  36  
XM7  H62     H13  H  0  1  N  N  N   3.023   3.508  -17.341   5.186   3.490   0.951  H62     XM7  37  
XM7  "HO3'"  H14  H  0  0  N  N  N  10.811  -2.149  -18.105   0.082  -4.446   0.208  "HO3'"  XM7  38  
XM7  "HO2'"  H15  H  0  0  N  N  N   8.988  -2.039  -20.832   1.946  -3.591   1.229  "HO2'"  XM7  39  
XM7  HOP2    H16  H  0  0  N  N  N   7.232  -5.213  -12.710  -5.896  -1.014  -0.542  HOP2    XM7  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
XM7  C2     N3      DOUB  Y  N   1  
XM7  C2     N1      SING  Y  N   2  
XM7  "O2'"  "C2'"   SING  N  N   3  
XM7  N3     C4      SING  Y  N   4  
XM7  N1     C6      DOUB  Y  N   5  
XM7  "C2'"  "C1'"   SING  N  N   6  
XM7  "C2'"  "C3'"   SING  N  N   7  
XM7  C4     N9      SING  Y  N   8  
XM7  C4     C5      DOUB  Y  N   9  
XM7  "O3'"  "C3'"   SING  N  N  10  
XM7  C6     C5      SING  Y  N  11  
XM7  C6     N6      SING  N  N  12  
XM7  "C1'"  N9      SING  N  N  13  
XM7  "C1'"  "O4'"   SING  N  N  14  
XM7  N9     C8      SING  Y  N  15  
XM7  "C3'"  "C4'"   SING  N  N  16  
XM7  C5     N7      SING  Y  N  17  
XM7  "C4'"  "O4'"   SING  N  N  18  
XM7  "C4'"  "C5'"   SING  N  N  19  
XM7  C8     N7      DOUB  Y  N  20  
XM7  "C5'"  "O5'"   SING  N  N  21  
XM7  "O5'"  P       SING  N  N  22  
XM7  P      OP1     DOUB  N  N  23  
XM7  P      OP2     SING  N  N  24  
XM7  P      OP3     SING  N  N  25  
XM7  OP3    C22     SING  N  N  26  
XM7  C2     "H4'"   SING  N  N  27  
XM7  "C4'"  H1      SING  N  N  28  
XM7  "C3'"  "H3'"   SING  N  N  29  
XM7  "C2'"  "H2'"   SING  N  N  30  
XM7  "C1'"  "H1'"   SING  N  N  31  
XM7  C8     "H5''"  SING  N  N  32  
XM7  "C5'"  "H5'"   SING  N  N  33  
XM7  "C5'"  H2      SING  N  N  34  
XM7  C22    H9      SING  N  N  35  
XM7  C22    H10     SING  N  N  36  
XM7  C22    H11     SING  N  N  37  
XM7  N6     H61     SING  N  N  38  
XM7  N6     H62     SING  N  N  39  
XM7  "O3'"  "HO3'"  SING  N  N  40  
XM7  "O2'"  "HO2'"  SING  N  N  41  
XM7  OP2    HOP2    SING  N  N  42  
#   #
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
XM7  SMILES            ACDLabs               12.01  "c1nc3c(c(n1)N)ncn3C2C(C(C(O2)COP(OC)(O)=O)O)O"  
XM7  InChI             InChI                 1.03   "InChI=1S/C11H16N5O7P/c1-21-24(19,20)22-2-5-7(17)8(18)11(23-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H2,12,13,14)/t5-,7-,8-,11-/m1/s1"  
XM7  InChIKey          InChI                 1.03   OYQVPLDFZZKUTQ-IOSLPCCCSA-N  
XM7  SMILES_CANONICAL  CACTVS                3.385  "CO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"  
XM7  SMILES            CACTVS                3.385  "CO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"  
XM7  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "COP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O"  
XM7  SMILES            "OpenEye OEToolkits"  2.0.7  "COP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)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
XM7  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine"  
XM7  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl methyl hydrogen 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
XM7  "Create component"  2020-12-18  RCSB  
XM7  "Initial release"   2020-12-30  RCSB  
##
