data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
  Cd  C  'Cytidine                            '  DNA  30  19  .  2000-01-01  2016-08-23  
;
Added neutron distances
;

data_comp_Cd
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
  Cd  P     P  P      0.714
  Cd  O1P   O  OP    -0.340
  Cd  O2P   O  OP    -0.340
  Cd  O5*   O  OC2   -0.267
  Cd  C5*   C  CH2    0.066
  Cd  H5*1  H  HCH2   0.005
  Cd  H5*2  H  HCH2   0.005
  Cd  C4*   C  CH1    0.084
  Cd  H4*   H  HCH1   0.010
  Cd  O4*   O  O2    -0.193
  Cd  C1*   C  CH1    0.245
  Cd  H1*   H  HCH1   0.005
  Cd  N1    N  NR6   -0.286
  Cd  C2    C  CR6    0.469
  Cd  O2    O  O     -0.259
  Cd  N3    N  NRD6  -0.395
  Cd  C4    C  CR6    0.315
  Cd  N4    N  NH2   -0.371
  Cd  H41   H  HNH2   0.168
  Cd  H42   H  HNH2   0.168
  Cd  C5    C  CR16  -0.135
  Cd  H5    H  HCR6   0.020
  Cd  C6    C  CR16   0.168
  Cd  H6    H  HCR6   0.020
  Cd  C2*   C  CH2   -0.043
  Cd  H2*1  H  HCH2   0.010
  Cd  H2*2  H  HCH2   0.010
  Cd  C3*   C  CH1    0.081
  Cd  H3*   H  HCH1   0.005
  Cd  O3*   O  OC2   -0.267

loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
  Cd  P     n/a  O5*   START
  Cd  O1P   P    .     .
  Cd  O2P   P    .     .
  Cd  O5*   P    C5*   .
  Cd  C5*   O5*  C4*   .
  Cd  H5*1  C5*  .     .
  Cd  H5*2  C5*  .     .
  Cd  C4*   C5*  C3*   .
  Cd  H4*   C4*  .     .
  Cd  O4*   C4*  C1*   .
  Cd  C1*   O4*  C2*   .
  Cd  H1*   C1*  .     .
  Cd  N1    C1*  C2    .
  Cd  C2    N1   N3    .
  Cd  O2    C2   .     .
  Cd  N3    C2   C4    .
  Cd  C4    N3   C5    .
  Cd  N4    C4   H42   .
  Cd  H41   N4   .     .
  Cd  H42   N4   .     .
  Cd  C5    C4   C6    .
  Cd  H5    C5   .     .
  Cd  C6    C5   H6    .
  Cd  H6    C6   .     .
  Cd  C2*   C1*  H2*2  .
  Cd  H2*1  C2*  .     .
  Cd  H2*2  C2*  .     .
  Cd  C3*   C4*  O3*   .
  Cd  H3*   C3*  .     .
  Cd  O3*   C3*  .     END
  Cd  C2*   C3*  .     ADD
  Cd  C6    N1   .     ADD

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
  Cd  P    O5*   coval  1.600  0.020  1.600
  Cd  P    O1P   coval  1.480  0.020  1.480
  Cd  P    O2P   coval  1.480  0.020  1.480
  Cd  C1*  C2*   coval  1.525  0.020  1.525
  Cd  C2*  C3*   coval  1.525  0.020  1.525
  Cd  C3*  C4*   coval  1.523  0.020  1.523
  Cd  C3*  O3*   coval  1.422  0.030  1.422
  Cd  C4*  C5*   coval  1.518  0.020  1.518
  Cd  C4*  O4*   coval  1.450  0.020  1.450
  Cd  O4*  C1*   coval  1.414  0.020  1.414
  Cd  C5*  O5*   coval  1.423  0.030  1.423
  Cd  C5*  H5*1  coval  0.970  0.020  1.090
  Cd  C5*  H5*2  coval  0.970  0.020  1.090
  Cd  C4*  H4*   coval  0.970  0.020  1.090
  Cd  C1*  H1*   coval  0.970  0.020  1.090
  Cd  C2*  H2*1  coval  0.970  0.020  1.090
  Cd  C2*  H2*2  coval  0.970  0.020  1.090
  Cd  C3*  H3*   coval  0.970  0.020  1.090
  Cd  N1   C2    coval  1.399  0.020  1.399
  Cd  C2   N3    coval  1.356  0.020  1.356
  Cd  N3   C4    coval  1.334  0.020  1.334
  Cd  C4   C5    coval  1.426  0.020  1.426
  Cd  C5   C6    coval  1.337  0.020  1.337
  Cd  C6   N1    coval  1.364  0.020  1.364
  Cd  C2   O2    coval  1.237  0.020  1.237
  Cd  C4   N4    coval  1.337  0.020  1.337
  Cd  N1   C1*   coval  1.490  0.030  1.490
  Cd  N4   H41   coval  0.860  0.020  1.020
  Cd  N4   H42   coval  0.860  0.020  1.020
  Cd  C5   H5    coval  0.930  0.020  1.080
  Cd  C6   H6    coval  0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
  Cd  C6    N1   C2    120.600  1.500
  Cd  C1*   N1   C2    119.700  1.500
  Cd  C1*   N1   C6    119.700  1.500
  Cd  N1    C2   N3    118.900  1.500
  Cd  C2    N3   C4    120.000  1.500
  Cd  N3    C4   C5    121.800  1.500
  Cd  C4    C5   C6    117.600  1.500
  Cd  C5    C6   N1    121.000  1.500
  Cd  N1    C2   O2    119.200  1.500
  Cd  N3    C2   O2    121.900  1.500
  Cd  N3    C4   N4    117.900  1.500
  Cd  C5    C4   N4    120.300  1.500
  Cd  N1    C1*  O4*   108.400  1.500
  Cd  N1    C1*  C2*   113.500  1.500
  Cd  C4    N4   H41   120.000  1.500
  Cd  C4    N4   H42   120.000  1.500
  Cd  H41   N4   H42   120.000  1.500
  Cd  C4    C5   H5    121.200  1.500
  Cd  C6    C5   H5    121.200  1.500
  Cd  C5    C6   H6    119.500  1.500
  Cd  N1    C6   H6    119.500  1.500
  Cd  O4*   C1*  C2*   106.400  1.500
  Cd  C1*   C2*  C3*   101.600  1.500
  Cd  C2*   C3*  C4*   102.400  1.500
  Cd  C2*   C3*  O3*   111.500  1.500
  Cd  O3*   C3*  C4*   110.000  1.500
  Cd  C3*   C4*  C5*   114.900  1.500
  Cd  C3*   C4*  O4*   105.400  1.500
  Cd  O4*   C4*  C5*   109.400  1.500
  Cd  C4*   O4*  C1*   109.700  1.500
  Cd  C4*   C5*  O5*   110.800  1.500
  Cd  C5*   O5*  P     120.000  1.500
  Cd  O5*   P    O1P   109.000  3.000
  Cd  O5*   P    O2P   108.000  3.000
  Cd  O1P   P    O2P   120.000  3.000
  Cd  O5*   C5*  H5*1  109.000  1.500
  Cd  O5*   C5*  H5*2  109.000  1.500
  Cd  C4*   C5*  H5*1  109.000  1.500
  Cd  C4*   C5*  H5*2  109.000  1.500
  Cd  H5*1  C5*  H5*2  109.000  1.500
  Cd  C5*   C4*  H4*   109.000  1.500
  Cd  O4*   C4*  H4*   109.000  1.500
  Cd  C3*   C4*  H4*   109.000  1.500
  Cd  O4*   C1*  H1*   109.000  1.500
  Cd  C2*   C1*  H1*   109.000  1.500
  Cd  N1    C1*  H1*   109.000  1.500
  Cd  C1*   C2*  H2*1  109.000  1.500
  Cd  C1*   C2*  H2*2  109.000  1.500
  Cd  H2*1  C2*  H2*2  109.000  1.500
  Cd  C4*   C3*  H3*   109.000  1.500
  Cd  C3*   C2*  H2*1  109.000  1.500
  Cd  C3*   C2*  H2*2  109.000  1.500
  Cd  C2*   C3*  H3*   109.000  1.500
  Cd  O3*   C3*  H3*   109.000  1.500

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
  Cd  beta      P    O5*  C5*  C4*  170.000  25.000  3
  Cd  gamma     O5*  C5*  C4*  C3*   55.000  20.000  3
  Cd  delta     C5*  C4*  C3*  O3*   88.000  30.000  3
  Cd  nu0       C4*  O4*  C1*  C2*   13.000  40.000  3
  Cd  nu1       O4*  C1*  C2*  C3*  -33.000  40.000  3
  Cd  nu4       C5*  C4*  O4*  C1*  137.000  40.000  3
  Cd  chi       O4*  C1*  N1   C2    30.000  40.000  2
  Cd  CONST_01  C1*  N1   C2   N3   180.000   0.000  0
  Cd  CONST_02  N1   C2   N3   C4     0.000   0.000  0
  Cd  CONST_03  C2   N3   C4   C5     0.000   0.000  0
  Cd  hh1       N3   C4   N4   H42    0.000  40.000  2
  Cd  CONST_04  N3   C4   C5   C6     0.000   0.000  0
  Cd  CONST_05  C4   C5   C6   N1     0.000   0.000  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
  Cd  chir_01  C3*  C2*  O3*  C4*  positiv
  Cd  chir_02  C4*  C3*  O4*  C5*  positiv
  Cd  chir_03  C1*  N1   O4*  C2*  positiv
  Cd  chir_04  P    O5*  O1P  O2P  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
  Cd  plan   N1   0.020
  Cd  plan   C2   0.020
  Cd  plan   O2   0.020
  Cd  plan   N3   0.020
  Cd  plan   C4   0.020
  Cd  plan   N4   0.020
  Cd  plan   C5   0.020
  Cd  plan   C6   0.020
  Cd  plan   C1*  0.020
  Cd  plan   H6   0.020
  Cd  plan   H5   0.020
  Cd  plan2  C4   0.020
  Cd  plan2  N4   0.020
  Cd  plan2  H41  0.020
  Cd  plan2  H42  0.020

