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
  Td  T  'Thymidine                           '  DNA  32  20  .  2000-01-01  2016-08-23  
;
Added neutron distances
;

data_comp_Td
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
  Td  P     P  P      0.714
  Td  O1P   O  OP    -0.340
  Td  O2P   O  OP    -0.340
  Td  O5*   O  OC2   -0.267
  Td  C5*   C  CH2    0.066
  Td  H5*1  H  HCH2   0.005
  Td  H5*2  H  HCH2   0.005
  Td  C4*   C  CH1    0.084
  Td  H4*   H  HCH1   0.010
  Td  O4*   O  O2    -0.193
  Td  C1*   C  CH1    0.245
  Td  H1*   H  HCH1   0.005
  Td  N1    N  NR6   -0.369
  Td  C2    C  CR6    0.556
  Td  O2    O  O     -0.264
  Td  N3    N  NR16  -0.506
  Td  H3    H  HNR6   0.185
  Td  C4    C  CR6    0.490
  Td  O4    O  O     -0.236
  Td  C5    C  CR6   -0.297
  Td  C5M   C  CH3    0.018
  Td  H5M1  H  HCH3   0.010
  Td  H5M2  H  HCH3   0.010
  Td  H5M3  H  HCH3   0.010
  Td  C6    C  CR16   0.255
  Td  H6    H  HCR6   0.020
  Td  C2*   C  CH2   -0.043
  Td  H2*1  H  HCH2   0.010
  Td  H2*2  H  HCH2   0.010
  Td  C3*   C  CH1    0.081
  Td  H3*   H  HCH1   0.005
  Td  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
  Td  P     n/a  O5*   START
  Td  O1P   P    .     .
  Td  O2P   P    .     .
  Td  O5*   P    C5*   .
  Td  C5*   O5*  C4*   .
  Td  H5*1  C5*  .     .
  Td  H5*2  C5*  .     .
  Td  C4*   C5*  C3*   .
  Td  H4*   C4*  .     .
  Td  O4*   C4*  C1*   .
  Td  C1*   O4*  C2*   .
  Td  H1*   C1*  .     .
  Td  N1    C1*  C2    .
  Td  C2    N1   N3    .
  Td  O2    C2   .     .
  Td  N3    C2   C4    .
  Td  H3    N3   .     .
  Td  C4    N3   C5    .
  Td  O4    C4   .     .
  Td  C5    C4   C6    .
  Td  C5M   C5   H5M3  .
  Td  H5M1  C5M  .     .
  Td  H5M2  C5M  .     .
  Td  H5M3  C5M  .     .
  Td  C6    C5   H6    .
  Td  H6    C6   .     .
  Td  C2*   C1*  H2*2  .
  Td  H2*1  C2*  .     .
  Td  H2*2  C2*  .     .
  Td  C3*   C4*  O3*   .
  Td  H3*   C3*  .     .
  Td  O3*   C3*  .     END
  Td  C2*   C3*  .     ADD
  Td  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
  Td  P    O5*   coval  1.600  0.020  1.600
  Td  P    O1P   coval  1.480  0.020  1.480
  Td  P    O2P   coval  1.480  0.020  1.480
  Td  C1*  C2*   coval  1.525  0.020  1.525
  Td  C2*  C3*   coval  1.525  0.020  1.525
  Td  C3*  C4*   coval  1.523  0.020  1.523
  Td  C3*  O3*   coval  1.422  0.030  1.422
  Td  C4*  C5*   coval  1.518  0.020  1.518
  Td  C4*  O4*   coval  1.450  0.020  1.450
  Td  O4*  C1*   coval  1.414  0.020  1.414
  Td  C5*  O5*   coval  1.423  0.030  1.423
  Td  C5*  H5*1  coval  0.970  0.020  1.090
  Td  C5*  H5*2  coval  0.970  0.020  1.090
  Td  C4*  H4*   coval  0.970  0.020  1.090
  Td  C1*  H1*   coval  0.970  0.020  1.090
  Td  C2*  H2*1  coval  0.970  0.020  1.090
  Td  C2*  H2*2  coval  0.970  0.020  1.090
  Td  C3*  H3*   coval  0.970  0.020  1.090
  Td  N1   C2    coval  1.379  0.020  1.379
  Td  C2   N3    coval  1.373  0.020  1.373
  Td  N3   C4    coval  1.383  0.020  1.383
  Td  C4   C5    coval  1.440  0.020  1.440
  Td  C5   C6    coval  1.338  0.020  1.338
  Td  C6   N1    coval  1.380  0.020  1.380
  Td  C2   O2    coval  1.218  0.020  1.218
  Td  C4   O4    coval  1.227  0.020  1.227
  Td  C5   C5M   coval  1.500  0.020  1.500
  Td  N1   C1*   coval  1.490  0.030  1.490
  Td  N3   H3    coval  0.860  0.020  1.020
  Td  C5M  H5M1  coval  0.970  0.020  1.090
  Td  C5M  H5M2  coval  0.970  0.020  1.090
  Td  C5M  H5M3  coval  0.970  0.020  1.090
  Td  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
  Td  C6    N1   C2    121.300  1.500
  Td  C1*   N1   C2    119.350  1.500
  Td  C1*   N1   C6    119.350  1.500
  Td  N1    C2   N3    114.800  1.500
  Td  C2    N3   C4    127.000  1.500
  Td  N3    C4   C5    114.800  1.500
  Td  N3    C4   O4    122.600  1.500
  Td  C5    C4   O4    122.600  1.500
  Td  C4    C5   C6    119.200  1.500
  Td  C5    C6   N1    122.800  1.500
  Td  N1    C2   O2    123.200  1.500
  Td  N3    C2   O2    122.000  1.500
  Td  C4    C5   C5M   122.400  1.500
  Td  C6    C5   C5M   124.000  1.500
  Td  N1    C1*  O4*   108.400  1.500
  Td  N1    C1*  C2*   113.500  1.500
  Td  C2    N3   H3    116.500  1.500
  Td  C4    N3   H3    116.500  1.500
  Td  H5M1  C5M  H5M2  109.000  1.500
  Td  H5M2  C5M  H5M3  109.000  1.500
  Td  H5M1  C5M  H5M3  109.000  1.500
  Td  C5    C5M  H5M1  109.000  1.500
  Td  C5    C5M  H5M2  109.000  1.500
  Td  C5    C5M  H5M3  109.000  1.500
  Td  N1    C6   H6    118.600  1.500
  Td  C5    C6   H6    118.600  1.500
  Td  O4*   C1*  C2*   106.400  1.500
  Td  C1*   C2*  C3*   101.600  1.500
  Td  C2*   C3*  C4*   102.400  1.500
  Td  C2*   C3*  O3*   111.500  1.500
  Td  O3*   C3*  C4*   110.000  1.500
  Td  C3*   C4*  C5*   114.900  1.500
  Td  C3*   C4*  O4*   105.400  1.500
  Td  O4*   C4*  C5*   109.400  1.500
  Td  C4*   O4*  C1*   109.700  1.500
  Td  C4*   C5*  O5*   110.800  1.500
  Td  C5*   O5*  P     120.000  1.500
  Td  O5*   P    O1P   109.000  3.000
  Td  O5*   P    O2P   108.000  3.000
  Td  O1P   P    O2P   120.000  3.000
  Td  O5*   C5*  H5*1  109.000  1.500
  Td  O5*   C5*  H5*2  109.000  1.500
  Td  C4*   C5*  H5*1  109.000  1.500
  Td  C4*   C5*  H5*2  109.000  1.500
  Td  H5*1  C5*  H5*2  109.000  1.500
  Td  C5*   C4*  H4*   109.000  1.500
  Td  O4*   C4*  H4*   109.000  1.500
  Td  C3*   C4*  H4*   109.000  1.500
  Td  O4*   C1*  H1*   109.000  1.500
  Td  C2*   C1*  H1*   109.000  1.500
  Td  N1    C1*  H1*   109.000  1.500
  Td  C1*   C2*  H2*1  109.000  1.500
  Td  C1*   C2*  H2*2  109.000  1.500
  Td  H2*1  C2*  H2*2  109.000  1.500
  Td  C4*   C3*  H3*   109.000  1.500
  Td  C3*   C2*  H2*1  109.000  1.500
  Td  C3*   C2*  H2*2  109.000  1.500
  Td  C2*   C3*  H3*   109.000  1.500
  Td  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
  Td  beta      P    O5*  C5*  C4*   170.000  25.000  3
  Td  gamma     O5*  C5*  C4*  C3*    55.000  20.000  3
  Td  delta     C5*  C4*  C3*  O3*    88.000  30.000  3
  Td  nu0       C4*  O4*  C1*  C2*    13.000  40.000  3
  Td  nu1       O4*  C1*  C2*  C3*   -33.000  40.000  3
  Td  nu4       C5*  C4*  O4*  C1*   137.000  40.000  3
  Td  chi       O4*  C1*  N1   C2     30.000  40.000  2
  Td  CONST_01  C1*  N1   C2   N3    180.000   0.000  0
  Td  CONST_02  N1   C2   N3   C4      0.000   0.000  0
  Td  CONST_03  C2   N3   C4   C5      0.000   0.000  0
  Td  CONST_04  N3   C4   C5   C6      0.000   0.000  0
  Td  hh1       C4   C5   C5M  H5M3    0.000  40.000  3
  Td  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
  Td  chir_01  C3*  C2*  O3*  C4*  positiv
  Td  chir_02  C4*  C3*  O4*  C5*  positiv
  Td  chir_03  C1*  N1   O4*  C2*  positiv
  Td  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
  Td  plan  N1   0.020
  Td  plan  C2   0.020
  Td  plan  O2   0.020
  Td  plan  N3   0.020
  Td  plan  C4   0.020
  Td  plan  O4   0.020
  Td  plan  C5   0.020
  Td  plan  C6   0.020
  Td  plan  C1*  0.020
  Td  plan  C5M  0.020
  Td  plan  H3   0.020
  Td  plan  H6   0.020

