data_B9H
#

_chem_comp.id                                   B9H
_chem_comp.name                                 "2'-methyl, 3-propyl, cytidine-5'-monophosphate"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C13 H24 N3 O8 P"
_chem_comp.mon_nstd_parent_comp_id              C
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-09-26
_chem_comp.pdbx_modified_date                   2019-05-06
_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                       381.319
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    B9H
_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       6EK0
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
B9H  C2     C1   C  0  1  N  N  N  212.115  258.149  295.824  -2.761   0.120  -0.291  C2      B9H   1  
B9H  C4     C2   C  0  1  N  N  R  210.174  257.513  297.120  -3.549  -1.238   1.554  C4      B9H   2  
B9H  C5     C3   C  0  1  N  N  N  210.005  256.437  296.284  -2.164  -1.123   2.155  C5      B9H   3  
B9H  C6     C4   C  0  1  N  N  N  210.875  256.243  295.233  -1.256  -0.426   1.497  C6      B9H   4  
B9H  C32    C5   C  0  1  N  N  N  211.199  260.899  297.209  -5.145  -1.827  -1.316  C32     B9H   5  
B9H  "C1'"  C6   C  0  1  N  N  R  212.885  256.851  293.895  -0.499   0.944  -0.385  "C1'"   B9H   6  
B9H  "C2'"  C7   C  0  1  N  N  R  214.114  256.042  294.309  -0.085   2.175   0.460  "C2'"   B9H   7  
B9H  "C3'"  C8   C  0  1  N  N  R  213.668  254.654  293.928   1.359   2.437  -0.033  "C3'"   B9H   8  
B9H  C31    C9   C  0  1  N  N  N  211.415  259.524  297.812  -5.093  -0.615  -0.384  C31     B9H   9  
B9H  C33    C10  C  0  1  N  N  N  210.971  261.966  298.251  -6.513  -1.888  -1.998  C33     B9H  10  
B9H  "C4'"  C11  C  0  1  N  N  R  213.132  254.978  292.557   1.797   1.093  -0.648  "C4'"   B9H  11  
B9H  "C5'"  C12  C  0  1  N  N  N  212.307  253.847  292.005   3.050   0.579   0.064  "C5'"   B9H  12  
B9H  N1     N1   N  0  1  N  N  N  211.920  257.047  294.994  -1.555   0.186   0.290  N1      B9H  13  
B9H  N3     N2   N  0  1  N  N  N  211.237  258.396  296.894  -3.783  -0.558   0.269  N3      B9H  14  
B9H  N4     N3   N  0  1  N  N  N  209.315  257.710  298.141  -3.845  -2.665   1.370  N4      B9H  15  
B9H  O2     O1   O  0  1  N  N  N  213.081  258.891  295.585  -2.940   0.692  -1.349  O2      B9H  16  
B9H  "O2'"  O2   O  0  1  N  N  N  215.180  256.403  293.452  -0.930   3.293   0.180  "O2'"   B9H  17  
B9H  "O3'"  O3   O  0  1  N  N  N  214.441  253.438  294.115   1.371   3.467  -1.023  "O3'"   B9H  18  
B9H  "O4'"  O4   O  0  1  N  N  N  212.326  256.123  292.806   0.715   0.166  -0.463  "O4'"   B9H  19  
B9H  "O5'"  O5   O  0  1  N  N  N  211.466  253.422  293.048   3.506  -0.614  -0.576  "O5'"   B9H  20  
B9H  OP1    O6   O  0  1  N  N  N  209.463  252.161  293.816   4.667  -1.770   1.344  OP1     B9H  21  
B9H  OP2    O7   O  0  1  N  N  N  210.722  251.435  291.790   4.947  -2.781  -0.951  OP2     B9H  22  
B9H  P      P1   P  0  1  N  N  N  210.216  252.586  292.597   4.807  -1.429  -0.089  P       B9H  23  
B9H  C21    C13  C  0  1  N  N  N  215.977  257.462  293.956  -1.102   4.183   1.285  "CO2'"  B9H  24  
B9H  H1     H1   H  0  1  N  N  N  210.816  256.905  297.775  -4.262  -0.842   2.277  H1      B9H  25  
B9H  H2     H2   H  0  1  N  N  N  209.193  255.745  296.450  -1.926  -1.599   3.095  H2      B9H  26  
B9H  H3     H3   H  0  1  N  N  N  210.707  255.405  294.572  -0.262  -0.331   1.907  H3      B9H  27  
B9H  H4     H4   H  0  1  N  N  N  212.088  261.168  296.620  -4.366  -1.737  -2.073  H4      B9H  28  
B9H  H5     H5   H  0  1  N  N  N  210.320  260.859  296.549  -4.987  -2.738  -0.738  H5      B9H  29  
B9H  H6     H6   H  0  1  N  N  N  213.226  257.836  293.542  -0.824   1.252  -1.379  H6      B9H  30  
B9H  H7     H7   H  0  1  N  N  N  214.340  256.139  295.381  -0.096   1.939   1.524  H7      B9H  31  
B9H  H8     H8   H  0  1  N  N  N  212.762  254.495  294.532   2.005   2.704   0.803  H8      B9H  32  
B9H  H9     H9   H  0  1  N  N  N  210.702  259.402  298.641  -5.251   0.295  -0.962  H9      B9H  33  
B9H  H10    H10  H  0  1  N  N  N  212.442  259.483  298.203  -5.872  -0.705   0.373  H10     B9H  34  
B9H  H11    H11  H  0  1  N  N  N  210.821  262.937  297.756  -6.550  -2.751  -2.663  H11     B9H  35  
B9H  H12    H12  H  0  1  N  N  N  210.079  261.715  298.843  -7.293  -1.978  -1.242  H12     B9H  36  
B9H  H13    H13  H  0  1  N  N  N  211.847  262.024  298.914  -6.672  -0.977  -2.576  H13     B9H  37  
B9H  H14    H14  H  0  1  N  N  N  213.961  255.212  291.872   1.999   1.221  -1.711  H14     B9H  38  
B9H  H15    H15  H  0  1  N  N  N  211.707  254.195  291.151   3.831   1.338   0.018  H15     B9H  39  
B9H  H16    H16  H  0  1  N  N  N  212.960  253.022  291.683   2.814   0.364   1.106  H16     B9H  40  
B9H  H17    H17  H  0  1  N  N  N  209.580  258.531  298.646  -3.759  -3.168   2.240  H17     B9H  41  
B9H  H18    H18  H  0  1  N  N  N  208.389  257.825  297.780  -4.761  -2.795   0.966  H18     B9H  42  
B9H  H20    H20  H  0  1  N  N  N  214.709  253.369  295.024   2.251   3.672  -1.367  H20     B9H  43  
B9H  H22    H22  H  0  1  N  N  N  210.468  250.620  292.207   5.711  -3.323  -0.711  H22     B9H  44  
B9H  H23    H23  H  0  1  N  N  N  216.782  257.688  293.241  -1.756   5.004   0.992  H23     B9H  45  
B9H  H24    H24  H  0  1  N  N  N  215.352  258.356  294.098  -1.549   3.643   2.120  H24     B9H  46  
B9H  H25    H25  H  0  1  N  N  N  216.416  257.164  294.920  -0.133   4.580   1.586  H25     B9H  47  
B9H  OP3    OP3  O  0  1  N  Y  N  209.406  253.594  291.656   6.119  -0.520  -0.299  OP3     B9H  48  
B9H  H19    H19  H  0  1  N  N  N  208.552  253.765  292.035   6.274  -0.258  -1.217  H19     B9H  49  
#   #
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
B9H  OP2    P      SING  N  N   1  
B9H  "C5'"  "C4'"  SING  N  N   2  
B9H  "C5'"  "O5'"  SING  N  N   3  
B9H  "C4'"  "O4'"  SING  N  N   4  
B9H  "C4'"  "C3'"  SING  N  N   5  
B9H  P      "O5'"  SING  N  N   6  
B9H  P      OP1    DOUB  N  N   7  
B9H  "O4'"  "C1'"  SING  N  N   8  
B9H  "O2'"  C21    SING  N  N   9  
B9H  "O2'"  "C2'"  SING  N  N  10  
B9H  "C1'"  "C2'"  SING  N  N  11  
B9H  "C1'"  N1     SING  N  N  12  
B9H  "C3'"  "O3'"  SING  N  N  13  
B9H  "C3'"  "C2'"  SING  N  N  14  
B9H  N1     C6     SING  N  N  15  
B9H  N1     C2     SING  N  N  16  
B9H  C6     C5     DOUB  N  N  17  
B9H  O2     C2     DOUB  N  N  18  
B9H  C2     N3     SING  N  N  19  
B9H  C5     C4     SING  N  N  20  
B9H  N3     C4     SING  N  N  21  
B9H  N3     C31    SING  N  N  22  
B9H  C4     N4     SING  N  N  23  
B9H  C32    C31    SING  N  N  24  
B9H  C32    C33    SING  N  N  25  
B9H  C4     H1     SING  N  N  26  
B9H  C5     H2     SING  N  N  27  
B9H  C6     H3     SING  N  N  28  
B9H  C32    H4     SING  N  N  29  
B9H  C32    H5     SING  N  N  30  
B9H  "C1'"  H6     SING  N  N  31  
B9H  "C2'"  H7     SING  N  N  32  
B9H  "C3'"  H8     SING  N  N  33  
B9H  C31    H9     SING  N  N  34  
B9H  C31    H10    SING  N  N  35  
B9H  C33    H11    SING  N  N  36  
B9H  C33    H12    SING  N  N  37  
B9H  C33    H13    SING  N  N  38  
B9H  "C4'"  H14    SING  N  N  39  
B9H  "C5'"  H15    SING  N  N  40  
B9H  "C5'"  H16    SING  N  N  41  
B9H  N4     H17    SING  N  N  42  
B9H  N4     H18    SING  N  N  43  
B9H  "O3'"  H20    SING  N  N  44  
B9H  OP2    H22    SING  N  N  45  
B9H  C21    H23    SING  N  N  46  
B9H  C21    H24    SING  N  N  47  
B9H  C21    H25    SING  N  N  48  
B9H  P      OP3    SING  N  N  49  
B9H  OP3    H19    SING  N  N  50  
#   #
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
B9H  InChI             InChI                 1.03   "InChI=1S/C13H24N3O8P/c1-3-5-15-9(14)4-6-16(13(15)18)12-11(22-2)10(17)8(24-12)7-23-25(19,20)21/h4,6,8-12,17H,3,5,7,14H2,1-2H3,(H2,19,20,21)/t8-,9-,10-,11-,12-/m1/s1"  
B9H  InChIKey          InChI                 1.03   GQHNKIBEOWBMPQ-LZQZFOIKSA-N  
B9H  SMILES_CANONICAL  CACTVS                3.385  "CCCN1[C@@H](N)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2OC)C1=O"  
B9H  SMILES            CACTVS                3.385  "CCCN1[CH](N)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2OC)C1=O"  
B9H  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CCCN1C(C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC)N"  
B9H  SMILES            "OpenEye OEToolkits"  2.0.6  "CCCN1C(C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC)N"  
#
_pdbx_chem_comp_identifier.comp_id          B9H
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-3-propyl-4~{H}-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl 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
B9H  "Create component"        2017-09-26  EBI   
B9H  "Initial release"         2018-01-24  RCSB  
B9H  "Modify one letter code"  2019-05-06  EBI   
##
