data_GMX
#

_chem_comp.id                                   GMX
_chem_comp.name                                 "2-amino-9-(6-deoxy-5-O-phosphono-beta-D-allofuranosyl)-3,9-dihydro-6H-purin-6-one"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H16 N5 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-01-06
_chem_comp.pdbx_modified_date                   2020-11-13
_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                       377.247
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GMX
_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       6VEM
_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
GMX  OP2    O1   O  0  1  N  N  N  17.465  -10.915  -16.989  -6.262  -0.798   0.229  OP2     GMX   1  
GMX  P      P1   P  0  1  N  N  N  16.700   -9.981  -17.996  -4.981   0.148   0.466  P       GMX   2  
GMX  OP1    O2   O  0  1  N  N  N  16.851  -10.194  -19.576  -4.205  -0.323   1.796  OP1     GMX   3  
GMX  "O5'"  O3   O  0  1  N  N  N  17.080   -8.456  -17.714  -3.992   0.038  -0.800  "O5'"   GMX   4  
GMX  "C5'"  C1   C  0  1  N  N  R  16.395   -7.360  -18.301  -2.815   0.836  -0.940  "C5'"   GMX   5  
GMX  "C6'"  C2   C  0  1  N  N  N  16.747   -7.194  -19.780  -2.917   1.675  -2.215  "C5''"  GMX   6  
GMX  "C4'"  C3   C  0  1  N  N  S  16.708   -6.109  -17.528  -1.588  -0.074  -1.024  "C4'"   GMX   7  
GMX  "O4'"  O4   O  0  1  N  N  N  16.128   -6.169  -16.213  -0.378   0.715  -1.057  "O4'"   GMX   8  
GMX  "C1'"  C4   C  0  1  N  N  R  17.012   -5.490  -15.306   0.673  -0.184  -0.641  "C1'"   GMX   9  
GMX  "C2'"  C5   C  0  1  N  N  R  18.132   -4.886  -16.144   0.056  -1.005   0.513  "C2'"   GMX  10  
GMX  "O2'"  O5   O  0  1  N  N  N  17.658   -3.632  -16.668   0.510  -2.359   0.462  "O2'"   GMX  11  
GMX  "C3'"  C6   C  0  1  N  N  S  18.202   -5.880  -17.296  -1.465  -0.932   0.255  "C3'"   GMX  12  
GMX  "O3'"  O6   O  0  1  N  N  N  18.867   -5.356  -18.489  -2.000  -2.238   0.035  "O3'"   GMX  13  
GMX  N9     N1   N  0  1  Y  N  N  17.573   -6.499  -14.351   1.832   0.574  -0.164  N9      GMX  14  
GMX  C8     C7   C  0  1  Y  N  N  17.491   -7.857  -14.417   1.818   1.848   0.323  C8      GMX  15  
GMX  N7     N2   N  0  1  Y  N  N  18.091   -8.408  -13.340   3.027   2.202   0.652  N7      GMX  16  
GMX  C5     C8   C  0  1  Y  N  N  18.553   -7.345  -12.568   3.875   1.179   0.395  C5      GMX  17  
GMX  C6     C9   C  0  1  N  N  N  19.223   -7.231  -11.345   5.319   0.978   0.549  C6      GMX  18  
GMX  O6     O7   O  0  1  N  N  N  19.542   -8.235  -10.684   6.027   1.863   1.003  O6      GMX  19  
GMX  N1     N3   N  0  1  N  N  N  19.581   -6.009  -10.863   5.846  -0.200   0.181  N1      GMX  20  
GMX  C2     C10  C  0  1  N  N  N  19.271   -4.884  -11.551   5.095  -1.163  -0.309  C2      GMX  21  
GMX  N2     N4   N  0  1  N  N  N  19.615   -3.665  -11.053   5.689  -2.344  -0.668  N2      GMX  22  
GMX  N3     N5   N  0  1  N  N  N  18.608   -4.948  -12.739   3.753  -1.031  -0.473  N3      GMX  23  
GMX  C4     C11  C  0  1  Y  N  N  18.233   -6.160  -13.228   3.119   0.133  -0.121  C4      GMX  24  
GMX  H1     H1   H  0  1  N  N  N  16.843  -11.318  -16.395  -6.903  -0.781   0.953  H1      GMX  25  
GMX  H2     H2   H  0  1  N  N  N  15.992  -10.313  -19.963  -3.885  -1.234   1.763  H2      GMX  26  
GMX  H3     H3   H  0  1  N  N  N  15.311   -7.537  -18.234  -2.719   1.496  -0.078  H3      GMX  27  
GMX  H4     H4   H  0  1  N  N  N  16.196   -6.337  -20.194  -3.791   2.323  -2.155  H4      GMX  28  
GMX  H5     H5   H  0  1  N  N  N  17.828   -7.019  -19.882  -2.019   2.284  -2.322  H5      GMX  29  
GMX  H6     H6   H  0  1  N  N  N  16.470   -8.107  -20.327  -3.012   1.015  -3.077  H6      GMX  30  
GMX  H7     H7   H  0  1  N  N  N  16.303   -5.244  -18.073  -1.650  -0.713  -1.905  H7      GMX  31  
GMX  H8     H8   H  0  1  N  N  N  16.485   -4.696  -14.756   0.961  -0.839  -1.464  H8      GMX  32  
GMX  H9     H9   H  0  1  N  N  N  19.080   -4.811  -15.592   0.303  -0.557   1.475  H9      GMX  33  
GMX  H10    H10  H  0  1  N  N  N  17.606   -2.994  -15.966   0.154  -2.921   1.164  H10     GMX  34  
GMX  H11    H11  H  0  1  N  N  N  18.677   -6.813  -16.960  -1.971  -0.447   1.090  H11     GMX  35  
GMX  H12    H12  H  0  1  N  N  N  19.790   -5.227  -18.307  -1.949  -2.819   0.806  H12     GMX  36  
GMX  H13    H13  H  0  1  N  N  N  17.016   -8.411  -15.213   0.939   2.468   0.420  H13     GMX  37  
GMX  H14    H14  H  0  1  N  N  N  20.097   -3.600  -10.179   6.646  -2.458  -0.559  H14     GMX  38  
GMX  H15    H15  H  0  1  N  N  N  19.386   -2.835  -11.561   5.153  -3.066  -1.031  H15     GMX  39  
GMX  H16    H16  H  0  1  N  N  N  18.399   -4.112  -13.246   3.238  -1.767  -0.838  H16     GMX  40  
GMX  OP3    OP3  O  0  1  N  Y  N  15.161  -10.048  -17.656  -5.425   1.551   0.624  OP3     GMX  41  
#   #
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
GMX  "C6'"  "C5'"  SING  N  N   1  
GMX  OP1    P      SING  N  N   2  
GMX  "O3'"  "C3'"  SING  N  N   3  
GMX  "C5'"  "O5'"  SING  N  N   4  
GMX  "C5'"  "C4'"  SING  N  N   5  
GMX  P      "O5'"  SING  N  N   6  
GMX  P      OP2    SING  N  N   7  
GMX  "C4'"  "C3'"  SING  N  N   8  
GMX  "C4'"  "O4'"  SING  N  N   9  
GMX  "C3'"  "C2'"  SING  N  N  10  
GMX  "O2'"  "C2'"  SING  N  N  11  
GMX  "O4'"  "C1'"  SING  N  N  12  
GMX  "C2'"  "C1'"  SING  N  N  13  
GMX  "C1'"  N9     SING  N  N  14  
GMX  C8     N9     SING  Y  N  15  
GMX  C8     N7     DOUB  Y  N  16  
GMX  N9     C4     SING  Y  N  17  
GMX  N7     C5     SING  Y  N  18  
GMX  C4     N3     SING  N  N  19  
GMX  C4     C5     DOUB  Y  N  20  
GMX  N3     C2     SING  N  N  21  
GMX  C5     C6     SING  N  N  22  
GMX  C2     N2     SING  N  N  23  
GMX  C2     N1     DOUB  N  N  24  
GMX  C6     N1     SING  N  N  25  
GMX  C6     O6     DOUB  N  N  26  
GMX  OP2    H1     SING  N  N  27  
GMX  OP1    H2     SING  N  N  28  
GMX  "C5'"  H3     SING  N  N  29  
GMX  "C6'"  H4     SING  N  N  30  
GMX  "C6'"  H5     SING  N  N  31  
GMX  "C6'"  H6     SING  N  N  32  
GMX  "C4'"  H7     SING  N  N  33  
GMX  "C1'"  H8     SING  N  N  34  
GMX  "C2'"  H9     SING  N  N  35  
GMX  "O2'"  H10    SING  N  N  36  
GMX  "C3'"  H11    SING  N  N  37  
GMX  "O3'"  H12    SING  N  N  38  
GMX  C8     H13    SING  N  N  39  
GMX  N2     H14    SING  N  N  40  
GMX  N2     H15    SING  N  N  41  
GMX  N3     H16    SING  N  N  42  
GMX  P      OP3    DOUB  N  N  43  
#   #
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
GMX  SMILES            ACDLabs               12.01  "OP(OC(C1C(C(C(O1)n2c3c(nc2)C(N=C(N)N3)=O)O)O)C)(=O)O"  
GMX  InChI             InChI                 1.03   "InChI=1S/C11H16N5O8P/c1-3(24-25(20,21)22)7-5(17)6(18)10(23-7)16-2-13-4-8(16)14-11(12)15-9(4)19/h2-3,5-7,10,17-18H,1H3,(H2,20,21,22)(H3,12,14,15,19)/t3-,5+,6-,7-,10-/m1/s1"  
GMX  InChIKey          InChI                 1.03   QYBUIBIHUIWDID-KPCPHYELSA-N  
GMX  SMILES_CANONICAL  CACTVS                3.385  "C[C@@H](O[P](O)(O)=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)N=C(N)Nc23"  
GMX  SMILES            CACTVS                3.385  "C[CH](O[P](O)(O)=O)[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)N=C(N)Nc23"  
GMX  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C[C@H]([C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2NC(=NC3=O)N)O)O)OP(=O)(O)O"  
GMX  SMILES            "OpenEye OEToolkits"  2.0.7  "CC(C1C(C(C(O1)n2cnc3c2NC(=NC3=O)N)O)O)OP(=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
GMX  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-amino-9-(6-deoxy-5-O-phosphono-beta-D-allofuranosyl)-3,9-dihydro-6H-purin-6-one"  
GMX  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(1~{R})-1-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]ethyl] 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
GMX  "Create component"  2020-01-06  RCSB  
GMX  "Initial release"   2020-11-18  RCSB  
##
