data_V7E
#

_chem_comp.id                                   V7E
_chem_comp.name                                 "3',3'-c-di-araAMP"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H24 N10 O12 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(1S,6R,8R,9S,10S,15R,17R,18S)-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-04-22
_chem_comp.pdbx_modified_date                   2022-04-29
_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                       658.412
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    V7E
_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       7OB3
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
V7E  P       P1   P  0  1  N  N  N  73.101  58.549  31.802    0.716   2.275   0.685  P       V7E   1  
V7E  O1P     O1   O  0  1  N  N  N  73.749  57.429  31.023    0.921   2.508  -0.762  O1P     V7E   2  
V7E  O2P     O2   O  0  1  N  N  N  71.634  58.667  31.461    0.450   3.682   1.423  O2P     V7E   3  
V7E  "O5'"   O3   O  0  1  N  N  N  73.259  58.248  33.373   -0.554   1.309   0.899  "O5'"   V7E   4  
V7E  "C5'"   C1   C  0  1  N  N  N  72.585  59.076  34.313   -1.901   1.735   0.684  "C5'"   V7E   5  
V7E  "C4'"   C2   C  0  1  N  N  R  73.187  58.903  35.696   -2.860   0.736   1.334  "C4'"   V7E   6  
V7E  "O4'"   O4   O  0  1  N  N  N  73.274  57.524  36.085   -4.205   1.214   1.235  "O4'"   V7E   7  
V7E  "C3'"   C3   C  0  1  N  N  S  74.612  59.436  35.802   -2.793  -0.609   0.592  "C3'"   V7E   8  
V7E  "O3'"   O5   O  0  1  N  N  N  74.705  60.832  36.005   -2.033  -1.556   1.346  "O3'"   V7E   9  
V7E  "C2'"   C4   C  0  1  N  N  S  75.175  58.648  36.977   -4.260  -1.067   0.472  "C2'"   V7E  10  
V7E  "O2'"   O6   O  0  1  N  N  N  76.589  58.519  36.901   -4.581  -1.351  -0.891  "O2'"   V7E  11  
V7E  "C1'"   C5   C  0  1  N  N  R  74.455  57.308  36.871   -5.090   0.121   0.980  "C1'"   V7E  12  
V7E  N9      N1   N  0  1  Y  N  N  75.367  56.339  36.216   -6.073   0.507  -0.035  N9      V7E  13  
V7E  C8      C6   C  0  1  Y  N  N  75.440  56.089  34.895   -5.924   1.489  -0.969  C8      V7E  14  
V7E  N7      N2   N  0  1  Y  N  N  76.389  55.152  34.638   -6.991   1.562  -1.710  N7      V7E  15  
V7E  C5      C7   C  0  1  Y  N  N  76.944  54.797  35.810   -7.890   0.635  -1.300  C5      V7E  16  
V7E  C6      C8   C  0  1  Y  N  N  78.002  53.860  36.257   -9.180   0.260  -1.711  C6      V7E  17  
V7E  N6      N3   N  0  1  N  N  N  78.678  53.091  35.371   -9.801   0.901  -2.769  N6      V7E  18  
V7E  N1      N4   N  0  1  Y  N  N  78.269  53.799  37.580   -9.791  -0.725  -1.060  N1      V7E  19  
V7E  C2      C9   C  0  1  Y  N  N  77.611  54.555  38.480   -9.206  -1.342  -0.050  C2      V7E  20  
V7E  N3      N5   N  0  1  Y  N  N  76.641  55.421  38.139   -7.999  -1.025   0.369  N3      V7E  21  
V7E  C4      C10  C  0  1  Y  N  N  76.269  55.585  36.848   -7.309  -0.056  -0.223  C4      V7E  22  
V7E  P1      P2   P  0  1  N  N  N  76.101  61.566  35.675   -0.700  -2.259   0.779  P1      V7E  23  
V7E  O1P1    O7   O  0  0  N  N  N  75.987  63.032  36.017   -0.529  -3.581   1.420  O1P1    V7E  24  
V7E  O2P1    O8   O  0  0  N  N  N  77.214  60.912  36.460   -0.829  -2.448  -0.815  O2P1    V7E  25  
V7E  "O5'1"  O9   O  0  0  N  N  N  76.408  61.409  34.106    0.575  -1.333   1.108  "O5'1"  V7E  26  
V7E  "C5'1"  C11  C  0  0  N  N  N  75.571  62.070  33.164    1.920  -1.732   0.835  "C5'1"  V7E  27  
V7E  "C4'1"  C12  C  0  0  N  N  R  75.753  61.468  31.783    2.883  -0.697   1.418  "C4'1"  V7E  28  
V7E  "O4'1"  O10  O  0  0  N  N  N  77.136  61.389  31.406    4.230  -1.173   1.327  "O4'1"  V7E  29  
V7E  "C3'1"  C13  C  0  0  N  N  S  75.232  60.040  31.670    2.800   0.607   0.607  "C3'1"  V7E  30  
V7E  "O3'1"  O11  O  0  0  N  N  N  73.838  59.943  31.461    2.030   1.582   1.309  "O3'1"  V7E  31  
V7E  "C2'1"  C14  C  0  0  N  N  S  76.023  59.497  30.488    4.263   1.074   0.463  "C2'1"  V7E  32  
V7E  "O2'1"  O12  O  0  0  N  N  N  76.160  58.083  30.549    4.576   1.310  -0.912  "O2'1"  V7E  33  
V7E  "C1'1"  C15  C  0  0  N  N  R  77.363  60.219  30.605    5.105  -0.088   1.011  "C1'1"  V7E  34  
V7E  N91     N6   N  0  1  Y  N  N  78.334  59.307  31.256    6.075  -0.515  -0.001  N91     V7E  35  
V7E  C81     C16  C  0  1  Y  N  N  78.601  59.248  32.574    5.918  -1.538  -0.887  C81     V7E  36  
V7E  N71     N7   N  0  1  Y  N  N  79.535  58.296  32.832    6.974  -1.640  -1.640  N71     V7E  37  
V7E  C51     C17  C  0  1  Y  N  N  79.873  57.726  31.661    7.874  -0.691  -1.286  C51     V7E  38  
V7E  C61     C18  C  0  1  Y  N  N  80.797  56.657  31.214    9.156  -0.329  -1.732  C61     V7E  39  
V7E  N61     N8   N  0  1  N  N  N  81.573  55.985  32.097    9.764  -1.014  -2.769  N61     V7E  40  
V7E  N11     N9   N  0  1  Y  N  N  80.841  56.375  29.893    9.771   0.688  -1.136  N11     V7E  41  
V7E  C21     C19  C  0  1  Y  N  N  80.080  57.029  28.995    9.198   1.347  -0.146  C21     V7E  42  
V7E  N31     N10  N  0  1  Y  N  N  79.222  58.007  29.336    7.999   1.043   0.305  N31     V7E  43  
V7E  C41     C20  C  0  1  Y  N  N  79.076  58.394  30.625    7.305   0.045  -0.233  C41     V7E  44  
V7E  H1      H1   H  0  1  N  N  N  71.404  58.007  30.817   -0.327   4.156   1.097  H1      V7E  45  
V7E  "H5'A"  H2   H  0  0  N  N  N  72.681  60.127  34.005   -2.046   2.719   1.129  "H5'A"  V7E  46  
V7E  "H5'"   H3   H  0  1  N  N  N  71.521  58.799  34.343   -2.100   1.786  -0.386  "H5'"   V7E  47  
V7E  "H4'"   H4   H  0  1  N  N  N  72.560  59.448  36.417   -2.597   0.595   2.382  "H4'"   V7E  48  
V7E  "H3'"   H5   H  0  1  N  N  N  75.161  59.150  34.893   -2.359  -0.474  -0.398  "H3'"   V7E  49  
V7E  "H2'"   H6   H  0  1  N  N  N  74.882  59.141  37.916   -4.435  -1.946   1.093  "H2'"   V7E  50  
V7E  "HO2'"  H7   H  0  0  N  N  N  76.903  58.023  37.648   -5.493  -1.644  -1.027  "HO2'"  V7E  51  
V7E  "H1'"   H8   H  0  1  N  N  N  74.192  56.954  37.879   -5.604  -0.157   1.900  "H1'"   V7E  52  
V7E  H8      H9   H  0  1  N  N  N  74.829  56.567  34.144   -5.050   2.114  -1.078  H8      V7E  53  
V7E  H3      H10  H  0  1  N  N  N  79.346  52.529  35.859   -9.345   1.619  -3.236  H3      V7E  54  
V7E  HN6     H11  H  0  1  N  N  N  78.035  52.499  34.885  -10.692   0.633  -3.043  HN6     V7E  55  
V7E  H2      H12  H  0  1  N  N  N  77.875  54.461  39.523   -9.738  -2.138   0.451  H2      V7E  56  
V7E  H4      H13  H  0  1  N  N  N  77.628  61.557  37.021   -0.060  -2.866  -1.225  H4      V7E  57  
V7E  "HC5'"  H14  H  0  0  N  N  N  74.521  61.960  33.472    2.111  -2.704   1.291  "HC5'"  V7E  58  
V7E  HC5A    H15  H  0  0  N  N  N  75.834  63.138  33.132    2.068  -1.800  -0.243  HC5A    V7E  59  
V7E  "HC4'"  H16  H  0  0  N  N  N  75.210  62.092  31.058    2.633  -0.500   2.460  "HC4'"  V7E  60  
V7E  "HC3'"  H17  H  0  0  N  N  N  75.522  59.485  32.575    2.370   0.414  -0.376  "HC3'"  V7E  61  
V7E  "HC2'"  H18  H  0  0  N  N  N  75.530  59.799  29.552    4.432   1.977   1.050  "HC2'"  V7E  62  
V7E  HO2A    H19  H  0  0  N  N  N  75.313  57.690  30.725    5.484   1.607  -1.063  HO2A    V7E  63  
V7E  "HC1'"  H20  H  0  0  N  N  N  77.719  60.496  29.602    5.632   0.232   1.910  "HC1'"  V7E  64  
V7E  HC8     H21  H  0  1  N  N  N  78.136  59.872  33.323    5.045  -2.171  -0.955  HC8     V7E  65  
V7E  H5      H22  H  0  1  N  N  N  82.125  55.309  31.609    9.306  -1.754  -3.197  H5      V7E  66  
V7E  H1N6    H23  H  0  0  N  N  N  82.175  56.629  32.569   10.650  -0.754  -3.069  H1N6    V7E  67  
V7E  HC2     H24  H  0  1  N  N  N  80.162  56.756  27.953    9.733   2.167   0.311  HC2     V7E  68  
#   #
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
V7E  P       O1P     DOUB  N  N   1  
V7E  P       O2P     SING  N  N   2  
V7E  P       "O5'"   SING  N  N   3  
V7E  P       "O3'1"  SING  N  N   4  
V7E  "O5'"   "C5'"   SING  N  N   5  
V7E  "C5'"   "C4'"   SING  N  N   6  
V7E  "C4'"   "O4'"   SING  N  N   7  
V7E  "C4'"   "C3'"   SING  N  N   8  
V7E  "O4'"   "C1'"   SING  N  N   9  
V7E  "C3'"   "O3'"   SING  N  N  10  
V7E  "C3'"   "C2'"   SING  N  N  11  
V7E  "O3'"   P1      SING  N  N  12  
V7E  "C2'"   "O2'"   SING  N  N  13  
V7E  "C2'"   "C1'"   SING  N  N  14  
V7E  "C1'"   N9      SING  N  N  15  
V7E  N9      C8      SING  Y  N  16  
V7E  N9      C4      SING  Y  N  17  
V7E  C8      N7      DOUB  Y  N  18  
V7E  N7      C5      SING  Y  N  19  
V7E  C5      C6      DOUB  Y  N  20  
V7E  C5      C4      SING  Y  N  21  
V7E  C6      N6      SING  N  N  22  
V7E  C6      N1      SING  Y  N  23  
V7E  N1      C2      DOUB  Y  N  24  
V7E  C2      N3      SING  Y  N  25  
V7E  N3      C4      DOUB  Y  N  26  
V7E  P1      O1P1    DOUB  N  N  27  
V7E  P1      O2P1    SING  N  N  28  
V7E  P1      "O5'1"  SING  N  N  29  
V7E  "O5'1"  "C5'1"  SING  N  N  30  
V7E  "C5'1"  "C4'1"  SING  N  N  31  
V7E  "C4'1"  "O4'1"  SING  N  N  32  
V7E  "C4'1"  "C3'1"  SING  N  N  33  
V7E  "O4'1"  "C1'1"  SING  N  N  34  
V7E  "C3'1"  "O3'1"  SING  N  N  35  
V7E  "C3'1"  "C2'1"  SING  N  N  36  
V7E  "C2'1"  "O2'1"  SING  N  N  37  
V7E  "C2'1"  "C1'1"  SING  N  N  38  
V7E  "C1'1"  N91     SING  N  N  39  
V7E  N91     C81     SING  Y  N  40  
V7E  N91     C41     SING  Y  N  41  
V7E  C81     N71     DOUB  Y  N  42  
V7E  N71     C51     SING  Y  N  43  
V7E  C51     C61     DOUB  Y  N  44  
V7E  C51     C41     SING  Y  N  45  
V7E  C61     N61     SING  N  N  46  
V7E  C61     N11     SING  Y  N  47  
V7E  N11     C21     DOUB  Y  N  48  
V7E  C21     N31     SING  Y  N  49  
V7E  N31     C41     DOUB  Y  N  50  
V7E  O2P     H1      SING  N  N  51  
V7E  "C5'"   "H5'A"  SING  N  N  52  
V7E  "C5'"   "H5'"   SING  N  N  53  
V7E  "C4'"   "H4'"   SING  N  N  54  
V7E  "C3'"   "H3'"   SING  N  N  55  
V7E  "C2'"   "H2'"   SING  N  N  56  
V7E  "O2'"   "HO2'"  SING  N  N  57  
V7E  "C1'"   "H1'"   SING  N  N  58  
V7E  C8      H8      SING  N  N  59  
V7E  N6      H3      SING  N  N  60  
V7E  N6      HN6     SING  N  N  61  
V7E  C2      H2      SING  N  N  62  
V7E  O2P1    H4      SING  N  N  63  
V7E  "C5'1"  "HC5'"  SING  N  N  64  
V7E  "C5'1"  HC5A    SING  N  N  65  
V7E  "C4'1"  "HC4'"  SING  N  N  66  
V7E  "C3'1"  "HC3'"  SING  N  N  67  
V7E  "C2'1"  "HC2'"  SING  N  N  68  
V7E  "O2'1"  HO2A    SING  N  N  69  
V7E  "C1'1"  "HC1'"  SING  N  N  70  
V7E  C81     HC8     SING  N  N  71  
V7E  N61     H5      SING  N  N  72  
V7E  N61     H1N6    SING  N  N  73  
V7E  C21     HC2     SING  N  N  74  
#   #
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
V7E  InChI             InChI                 1.03   "InChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11+,12+,13-,14-,19-,20-/m1/s1"  
V7E  InChIKey          InChI                 1.03   PDXMFTWFFKBFIN-SVHUXIIHSA-N  
V7E  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@@H]3O)n6cnc7c(N)ncnc67"  
V7E  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67"  
V7E  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H](COP(=O)(O4)O)O[C@H]([C@H]5O)n6cnc7c6ncnc7N)O)O)N"  
V7E  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6ncnc7N)O)O)N"  
#
_pdbx_chem_comp_identifier.comp_id          V7E
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "(1~{S},6~{R},8~{R},9~{S},10~{S},15~{R},17~{R},18~{S})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     V7E
_pdbx_chem_comp_synonyms.name        "(1S,6R,8R,9S,10S,15R,17R,18S)-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
V7E  "Create component"  2021-04-22  PDBE  
V7E  "Initial release"   2022-05-04  RCSB  
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