data_5HM
#

_chem_comp.id                                   5HM
_chem_comp.name                                 "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)"
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H16 N3 O9 P"
_chem_comp.mon_nstd_parent_comp_id              C
_chem_comp.pdbx_synonyms                        "5-hydroxymethylcytidine 5'-monophosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-01-22
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       353.223
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5HM
_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       4OHB
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
5HM  OP3     OP3     O  0  1  N  Y  N   3.773   -7.235   -3.234  -4.862   2.213  -1.412  OP3    5HM   1  
5HM  P       P       P  0  1  N  N  N   2.904   -6.901   -4.454  -4.584   1.141  -0.243  P      5HM   2  
5HM  OP1     OP1     O  0  1  N  N  N   3.120   -7.865   -5.629  -4.436   1.848   1.049  OP1    5HM   3  
5HM  OP2     OP2     O  0  1  N  N  N   2.791   -5.438   -4.819  -5.820   0.113  -0.153  OP2    5HM   4  
5HM  "O5'"   "O5'"   O  0  1  N  N  N   1.413   -7.204   -3.967  -3.233   0.329  -0.568  "O5'"  5HM   5  
5HM  "C5'"   "C5'"   C  0  1  N  N  N   1.126   -8.577   -3.730  -2.660  -0.622   0.331  "C5'"  5HM   6  
5HM  "C4'"   "C4'"   C  0  1  N  N  R  -0.371   -8.722   -3.582  -1.387  -1.205  -0.285  "C4'"  5HM   7  
5HM  "O4'"   "O4'"   O  0  1  N  N  N  -1.043   -8.225   -4.754  -0.346  -0.205  -0.331  "O4'"  5HM   8  
5HM  "C3'"   "C3'"   C  0  1  N  N  S  -0.720  -10.182   -3.369  -0.819  -2.326   0.613  "C3'"  5HM   9  
5HM  "O3'"   "O3'"   O  0  1  N  N  N  -1.304  -10.430   -2.073  -1.212  -3.609   0.123  "O3'"  5HM  10  
5HM  "C2'"   "C2'"   C  0  1  N  N  R  -1.674  -10.496   -4.502   0.713  -2.151   0.508  "C2'"  5HM  11  
5HM  "O2'"   "O2'"   O  0  1  N  N  N  -2.961  -10.787   -3.971   1.313  -3.321  -0.051  "O2'"  5HM  12  
5HM  "C1'"   "C1'"   C  0  1  N  N  R  -1.699   -9.304   -5.447   0.889  -0.946  -0.442  "C1'"  5HM  13  
5HM  N1      N1      N  0  1  N  N  N  -0.982   -9.669   -6.701   2.020  -0.119  -0.013  N1     5HM  14  
5HM  C2      C2      C  0  1  N  N  N  -1.560  -10.511   -7.562   1.996   0.473   1.195  C2     5HM  15  
5HM  O2      O2      O  0  1  N  N  N  -2.784  -11.010   -7.269   1.029   0.315   1.921  O2     5HM  16  
5HM  C6      C6      C  0  1  N  N  N   0.242   -9.138   -6.953   3.093   0.041  -0.838  C6     5HM  17  
5HM  C5      C5      C  0  1  N  N  N   0.945   -9.462   -8.088   4.132   0.807  -0.430  C5     5HM  18  
5HM  CM5     CM5     C  0  1  N  N  N   2.286   -8.817   -8.298   5.333   1.004  -1.319  CM5    5HM  19  
5HM  OM5     OM5     O  0  1  N  N  N   2.116   -7.403   -8.093   5.144   0.285  -2.540  OM5    5HM  20  
5HM  C4      C4      C  0  1  N  N  N   0.284  -10.413   -9.033   4.074   1.419   0.839  C4     5HM  21  
5HM  N3      N3      N  0  1  N  N  N  -0.944  -10.893   -8.700   3.011   1.229   1.610  N3     5HM  22  
5HM  N4      N4      N  0  1  N  N  N   0.837  -10.802  -10.214   5.116   2.201   1.279  N4     5HM  23  
5HM  H1      H1      H  0  1  N  N  N   4.306   -7.998   -3.424  -5.662   2.739  -1.281  H1     5HM  24  
5HM  H2      H2      H  0  1  N  N  N   2.875   -5.339   -5.760  -5.976  -0.386  -0.966  H2     5HM  25  
5HM  H3      H3      H  0  1  N  N  N   1.478   -9.184   -4.577  -2.415  -0.129   1.273  H3     5HM  26  
5HM  H4      H4      H  0  1  N  N  N   1.626   -8.909   -2.808  -3.375  -1.423   0.516  H4     5HM  27  
5HM  H5      H5      H  0  1  N  N  N  -0.695   -8.151   -2.699  -1.592  -1.588  -1.285  H5     5HM  28  
5HM  H6      H6      H  0  1  N  N  N   0.190  -10.787   -3.491  -1.150  -2.194   1.643  H6     5HM  29  
5HM  "HO3'"  "HO3'"  H  0  0  N  Y  N  -0.672  -10.220   -1.395  -0.882  -4.349   0.650  H7     5HM  30  
5HM  H8      H8      H  0  1  N  N  N  -1.291  -11.369   -5.051   1.141  -1.934   1.487  H8     5HM  31  
5HM  H9      H9      H  0  1  N  N  N  -2.902  -11.535   -3.388   1.180  -4.121   0.476  H9     5HM  32  
5HM  H10     H10     H  0  1  N  N  N  -2.742   -9.040   -5.676   1.035  -1.288  -1.467  H10    5HM  33  
5HM  H11     H11     H  0  1  N  N  N   0.673   -8.445   -6.245   3.114  -0.438  -1.806  H11    5HM  34  
5HM  H12     H12     H  0  1  N  N  N   2.640   -9.009   -9.321   5.453   2.065  -1.538  H12    5HM  35  
5HM  H13     H13     H  0  1  N  N  N   3.014   -9.217   -7.577   6.224   0.634  -0.813  H13    5HM  36  
5HM  H14     H14     H  0  1  N  N  N   2.404   -7.173   -7.217   5.880   0.367  -3.162  H14    5HM  37  
5HM  H15     H15     H  0  1  N  N  N   0.341  -11.428  -10.816   5.075   2.616   2.155  H15    5HM  38  
5HM  H16     H16     H  0  1  N  N  N   1.739  -10.462  -10.480   5.892   2.338   0.713  H16    5HM  39  
#   #
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
5HM  N4     C4      SING  N  N   1  
5HM  C4     N3      DOUB  N  N   2  
5HM  C4     C5      SING  N  N   3  
5HM  N3     C2      SING  N  N   4  
5HM  CM5    OM5     SING  N  N   5  
5HM  CM5    C5      SING  N  N   6  
5HM  C5     C6      DOUB  N  N   7  
5HM  C2     O2      DOUB  N  N   8  
5HM  C2     N1      SING  N  N   9  
5HM  C6     N1      SING  N  N  10  
5HM  N1     "C1'"   SING  N  N  11  
5HM  OP1    P       DOUB  N  N  12  
5HM  "C1'"  "O4'"   SING  N  N  13  
5HM  "C1'"  "C2'"   SING  N  N  14  
5HM  OP2    P       SING  N  N  15  
5HM  "O4'"  "C4'"   SING  N  N  16  
5HM  "C2'"  "O2'"   SING  N  N  17  
5HM  "C2'"  "C3'"   SING  N  N  18  
5HM  P      "O5'"   SING  N  N  19  
5HM  P      OP3     SING  N  N  20  
5HM  "O5'"  "C5'"   SING  N  N  21  
5HM  "C5'"  "C4'"   SING  N  N  22  
5HM  "C4'"  "C3'"   SING  N  N  23  
5HM  "C3'"  "O3'"   SING  N  N  24  
5HM  OP3    H1      SING  N  N  25  
5HM  OP2    H2      SING  N  N  26  
5HM  "C5'"  H3      SING  N  N  27  
5HM  "C5'"  H4      SING  N  N  28  
5HM  "C4'"  H5      SING  N  N  29  
5HM  "C3'"  H6      SING  N  N  30  
5HM  "O3'"  "HO3'"  SING  N  N  31  
5HM  "C2'"  H8      SING  N  N  32  
5HM  "O2'"  H9      SING  N  N  33  
5HM  "C1'"  H10     SING  N  N  34  
5HM  C6     H11     SING  N  N  35  
5HM  CM5    H12     SING  N  N  36  
5HM  CM5    H13     SING  N  N  37  
5HM  OM5    H14     SING  N  N  38  
5HM  N4     H15     SING  N  N  39  
5HM  N4     H16     SING  N  N  40  
#   #
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
5HM  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)CO)C(O)C2O"  
5HM  InChI             InChI                 1.03   "InChI=1S/C10H16N3O9P/c11-8-4(2-14)1-13(10(17)12-8)9-7(16)6(15)5(22-9)3-21-23(18,19)20/h1,5-7,9,14-16H,2-3H2,(H2,11,12,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1"  
5HM  InChIKey          InChI                 1.03   KPUOHXMVCZBWQC-JXOAFFINSA-N  
5HM  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1CO)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"  
5HM  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1CO)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O"  
5HM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)CO"  
5HM  SMILES            "OpenEye OEToolkits"  1.7.6  "C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)CO"  
#   #
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
5HM  "SYSTEMATIC NAME"  ACDLabs               12.01  "5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)"  
5HM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,4R,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(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
5HM  "Create component"  2014-01-22  PDBJ  
5HM  "Initial release"   2014-06-25  RCSB  
5HM  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5HM
_pdbx_chem_comp_synonyms.name        "5-hydroxymethylcytidine 5'-monophosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
