# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:06:16 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: 5'-thiothymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CS)O2)C(=O)NC1=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
 WUV  WUV  '5'-thiothymidine         '  ligand  31  17  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WUV
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
 WUV  C10  C  CH2   0  -0.595  4.9114   -98.8830  16.5535
 WUV  C13  C  CR6   0   0.732  4.0085   -96.5795  21.1963
 WUV  C01  C  CH3   0  -0.706  8.0269   -96.0603  19.6875
 WUV  C02  C  CR6   0  -0.185  6.6399   -96.2409  20.2120
 WUV  C03  C  CR16  0   0.054  5.7741   -97.1252  19.6841
 WUV  N04  N  NR6   0  -0.572  4.5025   -97.3181  20.1494
 WUV  C05  C  CR15  0   0.236  3.5794   -98.2620  19.5003
 WUV  C06  C  CH2   0  -0.558  2.7314   -97.6209  18.4059
 WUV  C07  C  CR15  0   0.006  2.5457   -98.7749  17.4302
 WUV  O08  O  OH1   0  -0.668  1.5730   -99.6915  17.8712
 WUV  C09  C  CR15  0   0.016  3.9040   -99.4651  17.5302
 WUV  S11  S  S2    0  -0.234  6.5691   -99.5412  16.9316
 WUV  O12  O  O     0  -0.497  4.3150   -99.2824  18.8846
 WUV  N15  N  NR16  0  -0.733  4.9041   -95.7003  21.7448
 WUV  C16  C  CR6   0   0.558  6.2037   -95.4472  21.3413
 WUV  O17  O  O     0  -0.456  6.8812   -94.6177  21.9212
 WUV  H1   H  HCH2  0   0.274  4.9338   -97.7927  16.5960
 WUV  H2   H  HCH2  0   0.299  4.6281   -99.1773  15.5433
 WUV  H3   H  HCH3  0   0.246  8.1909   -95.0410  19.3354
 WUV  H4   H  HCH3  0   0.246  8.7741   -96.2598  20.4568
 WUV  H5   H  HCH3  0   0.241  8.2156   -96.7363  18.8544
 WUV  H6   H  HCR6  0   0.318  6.0751   -97.7521  18.8556
 WUV  H7   H  HCR5  0   0.270  2.9621   -98.6849  20.2938
 WUV  H8   H  HCH2  0   0.266  3.2681   -96.7976  17.9290
 WUV  H9   H  HCH2  0   0.288  1.7920   -97.2212  18.7864
 WUV  H10  H  HCR5  0   0.253  2.3423   -98.4259  16.4111
 WUV  H11  H  HOH1  0   0.457  0.7291   -99.2324  17.9330
 WUV  H12  H  HCR5  0   0.273  3.8148  -100.5401  17.3522
 WUV  H13  H  HSH1  0   0.232  7.1932   -99.0153  15.8727
 WUV  H14  H  HNR6  0   0.425  4.5539   -95.1573  22.5246
 WUV  O14  O  O     0  -0.486  2.8693   -96.6873  21.6063

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
 WUV  C10  S11  single  1.823  0.020  1.823
 WUV  C10  C09  single  1.519  0.020  1.519
 WUV  C07  C09  single  1.527  0.020  1.527
 WUV  C07  O08  single  1.407  0.020  1.407
 WUV  C07  C06  single  1.523  0.020  1.523
 WUV  C09  O12  single  1.427  0.020  1.427
 WUV  C06  C05  single  1.526  0.020  1.526
 WUV  O12  C05  single  1.401  0.020  1.401
 WUV  C01  C02  single  1.494  0.020  1.494
 WUV  C03  C02  double  1.345  0.020  1.345
 WUV  C03  N04  single  1.368  0.020  1.368
 WUV  C05  N04  single  1.471  0.020  1.471
 WUV  C02  C16  single  1.448  0.020  1.448
 WUV  N04  C13  single  1.373  0.020  1.373
 WUV  C16  O17  double  1.218  0.020  1.218
 WUV  C16  N15  single  1.384  0.020  1.384
 WUV  C13  N15  single  1.370  0.020  1.370
 WUV  C13  O14  double  1.216  0.020  1.216
 WUV  C10  H1   single  0.970  0.020  1.090
 WUV  C10  H2   single  0.970  0.020  1.090
 WUV  C01  H3   single  0.970  0.020  1.090
 WUV  C01  H4   single  0.970  0.020  1.090
 WUV  C01  H5   single  0.970  0.020  1.090
 WUV  C03  H6   single  0.930  0.020  1.080
 WUV  C05  H7   single  0.970  0.020  1.090
 WUV  C06  H8   single  0.970  0.020  1.090
 WUV  C06  H9   single  0.970  0.020  1.090
 WUV  C07  H10  single  0.970  0.020  1.090
 WUV  O08  H11  single  0.850  0.020  0.980
 WUV  C09  H12  single  0.970  0.020  1.090
 WUV  S11  H13  single  1.200  0.020  1.300
 WUV  N15  H14  single  0.860  0.020  1.020

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
 WUV  H2   C10  H1   108.13  3.000
 WUV  H2   C10  S11  109.34  3.000
 WUV  H1   C10  S11  109.51  3.000
 WUV  H2   C10  C09  108.67  3.000
 WUV  H1   C10  C09  111.80  3.000
 WUV  S11  C10  C09  109.35  3.000
 WUV  N15  C13  O14  122.33  3.000
 WUV  O14  C13  N04  123.13  3.000
 WUV  N15  C13  N04  114.54  3.000
 WUV  H5   C01  H4   107.89  3.000
 WUV  H5   C01  H3   107.88  3.000
 WUV  H4   C01  H3   107.19  3.000
 WUV  H5   C01  C02  110.75  3.000
 WUV  H4   C01  C02  111.49  3.000
 WUV  H3   C01  C02  111.46  3.000
 WUV  C16  C02  C03  118.20  3.000
 WUV  C16  C02  C01  119.17  3.000
 WUV  C03  C02  C01  122.63  3.000
 WUV  H6   C03  N04  115.95  3.000
 WUV  H6   C03  C02  120.16  3.000
 WUV  N04  C03  C02  123.88  3.000
 WUV  C05  N04  C03  121.58  3.000
 WUV  C05  N04  C13  117.11  3.000
 WUV  C03  N04  C13  121.20  3.000
 WUV  H7   C05  O12  109.55  3.000
 WUV  H7   C05  C06  111.73  3.000
 WUV  O12  C05  C06  106.42  3.000
 WUV  H7   C05  N04  106.44  3.000
 WUV  O12  C05  N04  109.38  3.000
 WUV  C06  C05  N04  113.30  3.000
 WUV  H9   C06  H8   107.44  3.000
 WUV  H9   C06  C07  113.37  3.000
 WUV  H8   C06  C07  110.57  3.000
 WUV  H9   C06  C05  112.51  3.000
 WUV  H8   C06  C05  110.90  3.000
 WUV  C07  C06  C05  102.06  3.000
 WUV  H10  C07  C09  111.70  3.000
 WUV  H10  C07  O08  111.74  3.000
 WUV  C09  C07  O08  107.45  3.000
 WUV  H10  C07  C06  112.15  3.000
 WUV  O08  C07  C06  112.16  3.000
 WUV  C09  C07  C06  101.08  3.000
 WUV  H11  O08  C07  108.38  3.000
 WUV  H12  C09  O12  107.69  3.000
 WUV  H12  C09  C07  111.18  3.000
 WUV  O12  C09  C07  105.10  3.000
 WUV  H12  C09  C10  109.04  3.000
 WUV  O12  C09  C10  111.72  3.000
 WUV  C07  C09  C10  112.00  3.000
 WUV  H13  S11  C10   96.79  3.000
 WUV  C09  O12  C05  111.05  3.000
 WUV  H14  N15  C16  116.81  3.000
 WUV  H14  N15  C13  115.24  3.000
 WUV  C16  N15  C13  127.92  3.000
 WUV  O17  C16  N15  120.54  3.000
 WUV  N15  C16  C02  114.21  3.000
 WUV  O17  C16  C02  125.25  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
 WUV  CONST_01  C02  C16  N15  C13    0.00   0.0  0
 WUV  CONST_02  N15  C13  N04  C03    0.00   0.0  0
 WUV  CONST_03  C16  N15  C13  N04    0.00   0.0  0
 WUV  CONST_04  N15  C13  N04  C05  180.00   0.0  0
 WUV  CONST_05  O17  C16  N15  C13  180.00   0.0  0
 WUV  CONST_06  O14  C13  N04  C03  180.00   0.0  0
 WUV  CONST_07  O14  C13  N04  C05    0.00   0.0  0
 WUV  CONST_08  C16  N15  C13  O14  180.00   0.0  0
 WUV  CONST_09  H14  N15  C16  C02  180.00   0.0  0
 WUV  Var_01    H3   C01  C02  C03  119.59  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
 WUV  chir_01  C05  C06  O12  N04  negativ
 WUV  chir_02  C07  O08  C09  C06  positiv
 WUV  chir_03  C09  O12  C07  C10  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
 WUV  plan-1  C13  0.020
 WUV  plan-1  C01  0.020
 WUV  plan-1  C02  0.020
 WUV  plan-1  C03  0.020
 WUV  plan-1  N04  0.020
 WUV  plan-1  C05  0.020
 WUV  plan-1  N15  0.020
 WUV  plan-1  C16  0.020
 WUV  plan-1  O17  0.020
 WUV  plan-1  H6   0.020
 WUV  plan-1  H14  0.020
 WUV  plan-1  O14  0.020

