# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:12:04 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2'-deoxy-5'-O-sulfouridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[S](O)(=O)=O)N2C=CC(=O)NC2=O
#
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
 DUS  DUS  2'-deoxy-5'-O-sulfouridine  ligand  32  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DUS
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 DUS  O7   O  OS    0  -0.704  -4.5139   0.6667   0.8442
 DUS  S    S  S     0   1.651  -3.7178   1.1417  -0.2605
 DUS  O5   O  OS    0  -0.573  -4.3285   1.5461  -1.4945
 DUS  O6   O  OS    0  -0.709  -2.7466   2.2918   0.2529
 DUS  O4   O  OC2   0  -0.374  -2.6345   0.0742  -0.6778
 DUS  C8   C  CH2   0  -0.276  -1.8970  -0.6213   0.3497
 DUS  C7   C  CH1   0   0.023  -0.9088  -1.5271  -0.3342
 DUS  C    C  CH1   0   0.016  -0.1952  -2.4422   0.6672
 DUS  O    O  OH1   0  -0.652  -0.9281  -3.6329   0.7849
 DUS  O3   O  O2    0  -0.532   0.0913  -0.7620  -0.9765
 DUS  C2   C  CH1   0   0.246   1.3488  -1.3787  -0.8782
 DUS  C1   C  CH2   0  -0.525   1.1867  -2.5967   0.0301
 DUS  N    N  NR6   0  -0.542   2.3445  -0.3873  -0.4784
 DUS  C6   C  CR16  0   0.066   3.3001   0.0066  -1.3726
 DUS  C5   C  CR16  0  -0.499   4.2301   0.9367  -1.1084
 DUS  C4   C  CR6   0   0.528   4.2541   1.5695   0.1866
 DUS  O1   O  O     0  -0.395   5.0369   2.4241   0.5539
 DUS  N1   N  NR16  0  -0.625   3.2620   1.1064   1.0399
 DUS  C3   C  CR6   0   0.707   2.2759   0.1933   0.7731
 DUS  O2   O  O     0  -0.582   1.4227  -0.0856   1.5872
 DUS  H1   H  HCH2  0   0.197  -1.3675   0.0826   0.9951
 DUS  H2   H  HCH2  0   0.226  -2.5778  -1.2273   0.9498
 DUS  H3   H  HCH1  0   0.276  -1.4263  -2.1658  -1.0638
 DUS  H4   H  HCH1  0   0.217  -0.0976  -1.9456   1.6361
 DUS  H5   H  HOH1  0   0.465  -0.6095  -4.1085   1.5574
 DUS  H6   H  HCH1  0   0.216   1.6817  -1.6954  -1.8692
 DUS  H7   H  HCH2  0   0.271   1.9943  -2.6996   0.7531
 DUS  H8   H  HCH2  0   0.256   1.1844  -3.4921  -0.5942
 DUS  H9   H  HCR6  0   0.345   3.2586  -0.4799  -2.3369
 DUS  H10  H  HCR6  0   0.306   4.9588   1.2124  -1.8542
 DUS  H11  H  HNR6  0   0.440   3.2120   1.5363   1.9553
 DUS  H12  H  H     0   0.535  -3.1301   2.7746   1.0040

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
 DUS  O1  C4   double  1.216  0.020  1.216
 DUS  O2  C3   double  1.212  0.020  1.212
 DUS  N1  C3   single  1.370  0.020  1.370
 DUS  N1  C4   single  1.388  0.020  1.388
 DUS  C3  N    single  1.381  0.020  1.381
 DUS  C4  C5   single  1.442  0.020  1.442
 DUS  O7  S    double  1.442  0.020  1.442
 DUS  C1  C2   single  1.528  0.020  1.528
 DUS  C1  C    single  1.530  0.020  1.530
 DUS  N   C2   single  1.461  0.020  1.461
 DUS  N   C6   single  1.367  0.020  1.367
 DUS  C5  C6   double  1.342  0.020  1.342
 DUS  S   O4   single  1.577  0.020  1.577
 DUS  S   O5   double  1.435  0.020  1.435
 DUS  S   O6   single  1.590  0.020  1.590
 DUS  C2  O3   single  1.404  0.020  1.404
 DUS  C   O    single  1.403  0.020  1.403
 DUS  C   C7   single  1.533  0.020  1.533
 DUS  O4  C8   single  1.443  0.020  1.443
 DUS  O3  C7   single  1.414  0.020  1.414
 DUS  C7  C8   single  1.505  0.020  1.505
 DUS  C8  H1   single  0.970  0.020  1.090
 DUS  C8  H2   single  0.970  0.020  1.090
 DUS  C7  H3   single  0.970  0.020  1.090
 DUS  C   H4   single  0.970  0.020  1.090
 DUS  O   H5   single  0.850  0.020  0.980
 DUS  C2  H6   single  0.970  0.020  1.090
 DUS  C1  H7   single  0.970  0.020  1.090
 DUS  C1  H8   single  0.970  0.020  1.090
 DUS  C6  H9   single  0.930  0.020  1.080
 DUS  C5  H10  single  0.930  0.020  1.080
 DUS  N1  H11  single  0.860  0.020  1.020
 DUS  O6  H12  single  0.850  0.020  0.980

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
 DUS  O4   S   O6   98.94  3.000
 DUS  O6   S   O5  109.50  3.000
 DUS  O4   S   O5  104.81  3.000
 DUS  O6   S   O7  109.14  3.000
 DUS  O5   S   O7  121.10  3.000
 DUS  O4   S   O7  111.03  3.000
 DUS  H12  O6  S   111.58  3.000
 DUS  C8   O4  S   119.26  3.000
 DUS  H2   C8  H1  109.60  3.000
 DUS  H2   C8  C7  108.98  3.000
 DUS  H1   C8  C7  109.77  3.000
 DUS  H2   C8  O4  109.89  3.000
 DUS  H1   C8  O4  110.97  3.000
 DUS  C7   C8  O4  107.58  3.000
 DUS  H3   C7  O3  110.24  3.000
 DUS  H3   C7  C   107.82  3.000
 DUS  O3   C7  C   106.89  3.000
 DUS  H3   C7  C8  110.02  3.000
 DUS  O3   C7  C8  110.20  3.000
 DUS  C    C7  C8  111.61  3.000
 DUS  H4   C   C1  109.54  3.000
 DUS  H4   C   O   110.96  3.000
 DUS  C1   C   O   114.91  3.000
 DUS  H4   C   C7  110.45  3.000
 DUS  O    C   C7  108.56  3.000
 DUS  C1   C   C7  102.06  3.000
 DUS  H5   O   C   108.31  3.000
 DUS  C2   O3  C7  111.35  3.000
 DUS  H6   C2  N   103.73  3.000
 DUS  H6   C2  C1  109.91  3.000
 DUS  N    C2  C1  116.78  3.000
 DUS  H6   C2  O3  109.68  3.000
 DUS  N    C2  O3  109.36  3.000
 DUS  C1   C2  O3  107.26  3.000
 DUS  H8   C1  H7  107.69  3.000
 DUS  H8   C1  C2  108.31  3.000
 DUS  H7   C1  C2  113.05  3.000
 DUS  H8   C1  C   108.61  3.000
 DUS  H7   C1  C   113.77  3.000
 DUS  C2   C1  C   105.24  3.000
 DUS  C3   N   C6  120.42  3.000
 DUS  C6   N   C2  119.54  3.000
 DUS  C3   N   C2  119.96  3.000
 DUS  H9   C6  C5  120.95  3.000
 DUS  H9   C6  N   115.29  3.000
 DUS  C5   C6  N   123.76  3.000
 DUS  H10  C5  C4  119.85  3.000
 DUS  H10  C5  C6  120.63  3.000
 DUS  C4   C5  C6  119.52  3.000
 DUS  N1   C4  O1  120.60  3.000
 DUS  N1   C4  C5  113.20  3.000
 DUS  O1   C4  C5  126.20  3.000
 DUS  H11  N1  C3  115.05  3.000
 DUS  H11  N1  C4  116.70  3.000
 DUS  C3   N1  C4  128.10  3.000
 DUS  O2   C3  N1  121.95  3.000
 DUS  N1   C3  N   114.89  3.000
 DUS  O2   C3  N   123.16  3.000

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
 DUS  CONST_01  N1   C3  N   C2   180.00   0.0  0
 DUS  CONST_02  C4   N1  C3  N      0.00   0.0  0
 DUS  CONST_03  N1   C3  N   C6     0.00   0.0  0
 DUS  CONST_04  C3   N1  C4  C5     0.00   0.0  0
 DUS  CONST_05  O2   C3  N   C2     0.00   0.0  0
 DUS  CONST_06  O2   C3  N   C6   180.00   0.0  0
 DUS  CONST_07  O2   C3  N1  C4   180.00   0.0  0
 DUS  CONST_08  C3   N1  C4  O1   180.00   0.0  0
 DUS  CONST_09  H11  N1  C3  N    180.00   0.0  0
 DUS  Var_01    C7   C8  O4  S   -177.85  30.0  3

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
 DUS  chir_01  C7  C   O3  C8  positiv
 DUS  chir_02  C   O   C1  C7  negativ
 DUS  chir_03  C2  O3  N   C1  negativ

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
 DUS  plan-1  C2   0.020
 DUS  plan-1  N    0.020
 DUS  plan-1  C6   0.020
 DUS  plan-1  C5   0.020
 DUS  plan-1  C4   0.020
 DUS  plan-1  O1   0.020
 DUS  plan-1  N1   0.020
 DUS  plan-1  C3   0.020
 DUS  plan-1  O2   0.020
 DUS  plan-1  H9   0.020
 DUS  plan-1  H10  0.020
 DUS  plan-1  H11  0.020

