data_XCI
#

_chem_comp.id                                   XCI
_chem_comp.name                                 "[(2~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylselanylphosphonous acid"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H15 N2 O6 P Se"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-07-05
_chem_comp.pdbx_modified_date                   2019-11-01
_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                       369.170
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XCI
_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       6S7D
_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
XCI  SE1     SE1  SE  0  0  N  N  N  21.354  -14.005  10.530   2.745  -0.412  -0.711  SE1     XCI   1  
XCI  "C1'"   C1   C   0  1  N  N  R  20.738  -12.692  14.489  -1.695   1.035  -0.869  "C1'"   XCI   2  
XCI  C2      C2   C   0  1  N  N  N  21.484  -10.455  14.968  -2.818  -0.147   0.934  C2      XCI   3  
XCI  "C2'"   C3   C   0  1  N  N  N  19.216  -12.644  14.347  -1.633   2.398  -0.154  "C2'"   XCI   4  
XCI  "C3'"   C4   C   0  1  N  N  S  19.002  -13.330  13.007  -0.224   2.426   0.488  "C3'"   XCI   5  
XCI  C4      C5   C   0  1  N  N  N  23.145   -9.328  13.566  -4.880  -1.208   0.652  C4      XCI   6  
XCI  "C4'"   C6   C   0  1  N  N  S  20.058  -14.417  13.106   0.538   1.372  -0.355  "C4'"   XCI   7  
XCI  C5      C7   C   0  1  N  N  N  23.102  -10.443  12.660  -4.898  -0.789  -0.700  C5      XCI   8  
XCI  "C5'"   C8   C   0  1  N  N  N  20.445  -15.142  11.840   1.713   0.795   0.437  "C5'"   XCI   9  
XCI  C6      C9   C   0  1  N  N  N  22.337  -11.487  12.990  -3.862  -0.068  -1.178  C6      XCI  10  
XCI  C7      C10  C   0  1  N  N  N  23.997  -10.430  11.463  -6.055  -1.150  -1.596  C7      XCI  11  
XCI  N1      N1   N   0  1  N  N  N  21.530  -11.511  14.104  -2.819   0.251  -0.351  N1      XCI  12  
XCI  N3      N2   N   0  1  N  N  N  22.267   -9.396  14.619  -3.835  -0.873   1.435  N3      XCI  13  
XCI  O2      O1   O   0  1  N  N  N  20.779  -10.441  15.946  -1.882   0.147   1.652  O2      XCI  14  
XCI  "O3'"   O2   O   0  1  N  N  N  17.714  -13.912  12.768   0.373   3.717   0.351  "O3'"   XCI  15  
XCI  O4      O3   O   0  1  N  N  N  23.750   -8.297  13.361  -5.802  -1.863   1.105  O4      XCI  16  
XCI  "O4'"   O4   O   0  1  N  N  N  21.183  -13.784  13.727  -0.457   0.355  -0.601  "O4'"   XCI  17  
XCI  OP1     O5   O   0  1  N  N  N  23.675  -15.038   8.712   5.239  -2.081  -0.201  OP1     XCI  18  
XCI  OP2     O6   O   0  1  N  N  N  22.192  -16.765   9.671   5.319   0.217   0.787  OP2     XCI  19  
XCI  P       P1   P   0  1  N  N  N  22.906  -15.533   9.796   4.373  -1.085   0.721  P       XCI  20  
XCI  "H1'"   H1   H   0  1  N  N  N  20.951  -12.900  15.548  -1.811   1.184  -1.942  "H1'"   XCI  21  
XCI  "H2''"  H2   H   0  0  N  N  N  18.849  -11.607  14.328  -1.741   3.211  -0.872  "H2''"  XCI  22  
XCI  "H2'"   H3   H   0  1  N  N  N  18.721  -13.194  15.161  -2.405   2.463   0.613  "H2'"   XCI  23  
XCI  "H3'"   H4   H   0  1  N  N  N  19.268  -12.636  12.196  -0.268   2.128   1.536  "H3'"   XCI  24  
XCI  "H4'"   H5   H   0  1  N  N  N  19.670  -15.175  13.803   0.882   1.806  -1.293  "H4'"   XCI  25  
XCI  "H5'"   H6   H   0  1  N  N  N  19.532  -15.544  11.377   1.335   0.243   1.298  "H5'"   XCI  26  
XCI  "H5''"  H7   H   0  0  N  N  N  21.117  -15.971  12.106   2.354   1.607   0.780  "H5''"  XCI  27  
XCI  H6      H8   H   0  1  N  N  N  22.353  -12.357  12.350  -3.858   0.261  -2.207  H6      XCI  28  
XCI  H72     H9   H   0  1  N  N  N  24.520   -9.464  11.406  -5.854  -2.105  -2.082  H72     XCI  29  
XCI  H73     H10  H   0  1  N  N  N  24.734  -11.242  11.548  -6.964  -1.230  -1.001  H73     XCI  30  
XCI  H71     H11  H   0  1  N  N  N  23.395  -10.575  10.554  -6.183  -0.377  -2.353  H71     XCI  31  
XCI  H3      H12  H   0  1  N  N  N  22.194   -8.580  15.192  -3.816  -1.156   2.362  H3      XCI  32  
XCI  H1      H13  H   0  1  N  N  N  17.061  -13.224  12.708  -0.068   4.410   0.860  H1      XCI  33  
XCI  H2      H14  H   0  1  N  N  N  24.081  -14.216   8.961   5.997  -2.476   0.251  H2      XCI  34  
XCI  H4      H15  H   0  1  N  N  N  21.733  -16.949  10.482   4.954   0.942   1.312  H4      XCI  35  
#   #
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
XCI  OP1    P       SING  N  N   1  
XCI  OP2    P       SING  N  N   2  
XCI  P      SE1     SING  N  N   3  
XCI  SE1    "C5'"   SING  N  N   4  
XCI  C7     C5      SING  N  N   5  
XCI  "C5'"  "C4'"   SING  N  N   6  
XCI  C5     C6      DOUB  N  N   7  
XCI  C5     C4      SING  N  N   8  
XCI  "O3'"  "C3'"   SING  N  N   9  
XCI  C6     N1      SING  N  N  10  
XCI  "C3'"  "C4'"   SING  N  N  11  
XCI  "C3'"  "C2'"   SING  N  N  12  
XCI  "C4'"  "O4'"   SING  N  N  13  
XCI  O4     C4      DOUB  N  N  14  
XCI  C4     N3      SING  N  N  15  
XCI  "O4'"  "C1'"   SING  N  N  16  
XCI  N1     "C1'"   SING  N  N  17  
XCI  N1     C2      SING  N  N  18  
XCI  "C2'"  "C1'"   SING  N  N  19  
XCI  N3     C2      SING  N  N  20  
XCI  C2     O2      DOUB  N  N  21  
XCI  "C1'"  "H1'"   SING  N  N  22  
XCI  "C2'"  "H2''"  SING  N  N  23  
XCI  "C2'"  "H2'"   SING  N  N  24  
XCI  "C3'"  "H3'"   SING  N  N  25  
XCI  "C4'"  "H4'"   SING  N  N  26  
XCI  "C5'"  "H5'"   SING  N  N  27  
XCI  "C5'"  "H5''"  SING  N  N  28  
XCI  C6     H6      SING  N  N  29  
XCI  C7     H72     SING  N  N  30  
XCI  C7     H73     SING  N  N  31  
XCI  C7     H71     SING  N  N  32  
XCI  N3     H3      SING  N  N  33  
XCI  "O3'"  H1      SING  N  N  34  
XCI  OP1    H2      SING  N  N  35  
XCI  OP2    H4      SING  N  N  36  
#   #
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
XCI  InChI             InChI                 1.03   "InChI=1S/C10H15N2O6PSe/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(18-8)4-20-19(16)17/h3,6-8,13,16-17H,2,4H2,1H3,(H,11,14,15)/t6-,7+,8+/m0/s1"  
XCI  InChIKey          InChI                 1.03   HCHHJSSYSFJUHX-XLPZGREQSA-N  
XCI  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@H](O)[C@@H](C[Se]P(O)O)O2)C(=O)NC1=O"  
XCI  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](O)[CH](C[Se]P(O)O)O2)C(=O)NC1=O"  
XCI  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)C[Se]P(O)O)O"  
XCI  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)C[Se]P(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          XCI
_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       "[(2~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylselanylphosphonous 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
XCI  "Create component"  2019-07-05  EBI   
XCI  "Initial release"   2019-11-06  RCSB  
##
