# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 02:20:41 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-[6-(4-methylsulfanylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccc(cc1)c2sc3c(SCC(O)=O)ncnc3c2
#
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
 OD2  OD2  '2-[6-(4-methylsulfanylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid'  ligand  34  22  .  2021-08-17  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OD2
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
 OD2  C    C  C     0   0.570   6.0256  -1.6271  -0.2197
 OD2  O    O  O     0  -0.428   5.5368  -2.7182  -0.3586
 OD2  O1   O  OH1   0  -0.581   7.3221  -1.3778  -0.2090
 OD2  C1   C  CH2   0  -0.677   5.2307  -0.3624  -0.0323
 OD2  S    S  S2    0   0.097   3.4802  -0.8034  -0.1085
 OD2  C2   C  CR6   0   0.110   2.7422   0.7676   0.0651
 OD2  N1   N  N     0  -0.431   3.4739   1.8566   0.2040
 OD2  C14  C  CR16  0   0.037   2.8390   3.0256   0.3347
 OD2  N    N  N     0  -0.437   1.5425   3.2324   0.3423
 OD2  C4   C  CR56  0   0.351   0.7842   2.1363   0.1984
 OD2  C5   C  CR15  0  -0.270  -0.6391   2.0913   0.1796
 OD2  C6   C  CR5   0  -0.185  -1.1212   0.8276   0.0221
 OD2  S1   S  S2    0   0.251   0.1531  -0.3588  -0.1143
 OD2  C3   C  CR56  0  -0.238   1.3510   0.8645   0.0550
 OD2  C7   C  CR6   0   0.133  -2.5154   0.4061  -0.0482
 OD2  C12  C  CR16  0  -0.302  -3.5105   1.3288  -0.3893
 OD2  C11  C  CR16  0  -0.242  -4.8364   0.9555  -0.4464
 OD2  C10  C  CR6   0  -0.120  -5.2181  -0.3612  -0.1674
 OD2  S2   S  S2    0   0.061  -6.9302  -0.7229  -0.2666
 OD2  C13  C  CH3   0  -0.798  -7.0270  -2.4776   0.1283
 OD2  C9   C  CR16  0  -0.239  -4.2345  -1.2886   0.1662
 OD2  C8   C  CR16  0  -0.296  -2.9044  -0.9046   0.2244
 OD2  H1   H  HOH1  0   0.491   7.8261  -2.1971  -0.3314
 OD2  H2   H  HCH2  0   0.333   5.4714   0.0922   0.9297
 OD2  H3   H  HCH2  0   0.332   5.4781   0.3601  -0.8106
 OD2  H4   H  HCR6  0   0.266   3.4766   3.8948   0.4482
 OD2  H5   H  HCR5  0   0.280  -1.2602   2.9671   0.2998
 OD2  H6   H  HCR6  0   0.266  -3.2477   2.3499  -0.6322
 OD2  H7   H  HCR6  0   0.272  -5.5824   1.6929  -0.7172
 OD2  H8   H  HCH3  0   0.278  -6.4957  -3.0855  -0.6016
 OD2  H9   H  HCH3  0   0.278  -6.6573  -2.6864   1.1302
 OD2  H10  H  HCH3  0   0.298  -8.0844  -2.7314   0.0881
 OD2  H11  H  HCR6  0   0.274  -4.4862  -2.3144   0.3940
 OD2  H12  H  HCR6  0   0.263  -2.1716  -1.6512   0.5071

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
 OD2  N    C14  aromatic  1.313  0.020  1.313
 OD2  N    C4   aromatic  1.341  0.020  1.341
 OD2  C14  N1   aromatic  1.337  0.020  1.337
 OD2  C12  C11  aromatic  1.379  0.020  1.379
 OD2  C12  C7   aromatic  1.399  0.020  1.399
 OD2  C11  C10  aromatic  1.399  0.020  1.399
 OD2  C5   C4   aromatic  1.424  0.020  1.424
 OD2  C5   C6   aromatic  1.362  0.020  1.362
 OD2  C4   C3   aromatic  1.400  0.020  1.400
 OD2  C6   C7   single    1.458  0.020  1.458
 OD2  C6   S1   aromatic  1.746  0.020  1.746
 OD2  C7   C8   aromatic  1.394  0.020  1.394
 OD2  N1   C2   aromatic  1.319  0.020  1.319
 OD2  S2   C10  single    1.753  0.020  1.753
 OD2  S2   C13  single    1.801  0.020  1.801
 OD2  C10  C9   aromatic  1.392  0.020  1.392
 OD2  C3   C2   aromatic  1.395  0.020  1.395
 OD2  C3   S1   aromatic  1.721  0.020  1.721
 OD2  C2   S    single    1.744  0.020  1.744
 OD2  C8   C9   aromatic  1.386  0.020  1.386
 OD2  S    C1   single    1.807  0.020  1.807
 OD2  C1   C    single    1.505  0.020  1.505
 OD2  C    O    double    1.204  0.020  1.204
 OD2  C    O1   single    1.320  0.020  1.320
 OD2  O1   H1   single    0.850  0.020  0.980
 OD2  C1   H2   single    0.970  0.020  1.090
 OD2  C1   H3   single    0.970  0.020  1.090
 OD2  C14  H4   single    0.930  0.020  1.080
 OD2  C5   H5   single    0.930  0.020  1.080
 OD2  C12  H6   single    0.930  0.020  1.080
 OD2  C11  H7   single    0.930  0.020  1.080
 OD2  C13  H8   single    0.970  0.020  1.090
 OD2  C13  H9   single    0.970  0.020  1.090
 OD2  C13  H10  single    0.970  0.020  1.090
 OD2  C9   H11  single    0.930  0.020  1.080
 OD2  C8   H12  single    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
 OD2  C1   C    O1   111.03  3.000
 OD2  O1   C    O    124.81  3.000
 OD2  C1   C    O    124.15  3.000
 OD2  H1   O1   C    110.47  3.000
 OD2  H3   C1   H2   107.65  3.000
 OD2  H3   C1   S    110.57  3.000
 OD2  H2   C1   S    110.65  3.000
 OD2  H3   C1   C    110.36  3.000
 OD2  H2   C1   C    110.08  3.000
 OD2  S    C1   C    107.54  3.000
 OD2  C2   S    C1   100.71  3.000
 OD2  C3   C2   N1   119.78  3.000
 OD2  C3   C2   S    118.94  3.000
 OD2  N1   C2   S    121.28  3.000
 OD2  C14  N1   C2   117.95  3.000
 OD2  H4   C14  N    117.00  3.000
 OD2  H4   C14  N1   115.60  3.000
 OD2  N    C14  N1   127.40  3.000
 OD2  C4   N    C14  115.41  3.000
 OD2  C3   C4   C5   112.01  3.000
 OD2  C3   C4   N    121.65  3.000
 OD2  C5   C4   N    126.34  3.000
 OD2  H5   C5   C6   124.17  3.000
 OD2  H5   C5   C4   123.19  3.000
 OD2  C6   C5   C4   112.62  3.000
 OD2  C7   C6   S1   119.84  3.000
 OD2  S1   C6   C5   112.40  3.000
 OD2  C7   C6   C5   127.76  3.000
 OD2  C3   S1   C6    91.00  3.000
 OD2  S1   C3   C4   111.97  3.000
 OD2  S1   C3   C2   130.23  3.000
 OD2  C4   C3   C2   117.80  3.000
 OD2  C8   C7   C12  117.98  3.000
 OD2  C8   C7   C6   121.95  3.000
 OD2  C12  C7   C6   120.08  3.000
 OD2  H6   C12  C11  118.67  3.000
 OD2  H6   C12  C7   120.28  3.000
 OD2  C11  C12  C7   121.03  3.000
 OD2  H7   C11  C10  120.18  3.000
 OD2  H7   C11  C12  119.23  3.000
 OD2  C10  C11  C12  120.59  3.000
 OD2  C9   C10  S2   124.48  3.000
 OD2  C9   C10  C11  118.81  3.000
 OD2  S2   C10  C11  116.71  3.000
 OD2  C13  S2   C10  103.95  3.000
 OD2  H10  C13  H9   108.62  3.000
 OD2  H10  C13  H8   108.62  3.000
 OD2  H9   C13  H8   110.15  3.000
 OD2  H10  C13  S2   105.74  3.000
 OD2  H9   C13  S2   111.74  3.000
 OD2  H8   C13  S2   111.77  3.000
 OD2  H11  C9   C8   118.54  3.000
 OD2  H11  C9   C10  121.22  3.000
 OD2  C8   C9   C10  120.24  3.000
 OD2  H12  C8   C9   117.98  3.000
 OD2  H12  C8   C7   120.66  3.000
 OD2  C9   C8   C7   121.35  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
 OD2  CONST_01  N    C14  N1   C2     0.00   0.0  0
 OD2  CONST_02  N    C4   C3   C2     0.00   0.0  0
 OD2  CONST_03  C5   C4   C3   C2   180.00   0.0  0
 OD2  CONST_04  C6   S1   C3   C2   180.00   0.0  0
 OD2  CONST_05  C4   N    C14  N1     0.00   0.0  0
 OD2  CONST_06  C4   C3   C2   N1     0.00   0.0  0
 OD2  CONST_07  S1   C3   C2   N1   180.00   0.0  0
 OD2  CONST_08  C5   C4   N    C14  180.00   0.0  0
 OD2  CONST_09  C3   C4   N    C14    0.00   0.0  0
 OD2  CONST_10  C3   C2   N1   C14    0.00   0.0  0
 OD2  CONST_11  C6   C5   C4   N    180.00   0.0  0
 OD2  CONST_12  S1   C3   C4   N    180.00   0.0  0
 OD2  CONST_13  C7   C6   C5   C4   180.00   0.0  0
 OD2  CONST_14  S1   C6   C5   C4     0.00   0.0  0
 OD2  CONST_15  C6   S1   C3   C4     0.00   0.0  0
 OD2  CONST_16  S1   C3   C4   C5     0.00   0.0  0
 OD2  CONST_19  C3   S1   C6   C5     0.00   0.0  0
 OD2  CONST_20  C3   C4   C5   C6     0.00   0.0  0
 OD2  CONST_21  C11  C12  C7   C6   180.00   0.0  0
 OD2  CONST_22  C9   C8   C7   C6   180.00   0.0  0
 OD2  CONST_25  C7   C6   S1   C3   180.00   0.0  0
 OD2  CONST_26  C10  C11  C12  C7     0.00   0.0  0
 OD2  CONST_27  C10  C9   C8   C7     0.00   0.0  0
 OD2  CONST_28  C9   C10  C11  C12    0.00   0.0  0
 OD2  CONST_29  C9   C8   C7   C12    0.00   0.0  0
 OD2  CONST_30  C8   C7   C12  C11    0.00   0.0  0
 OD2  CONST_31  C8   C9   C10  C11    0.00   0.0  0
 OD2  CONST_32  C14  N1   C2   S    180.00   0.0  0
 OD2  CONST_33  C4   C3   C2   S    180.00   0.0  0
 OD2  CONST_34  S1   C3   C2   S      0.00   0.0  0
 OD2  CONST_35  S2   C10  C11  C12  180.00   0.0  0
 OD2  CONST_36  C8   C9   C10  S2   180.00   0.0  0
 OD2  CONST_37  H4   C14  N1   C2   180.00   0.0  0
 OD2  CONST_38  H5   C5   C4   N      0.00   0.0  0
 OD2  CONST_39  H6   C12  C7   C6     0.00   0.0  0
 OD2  CONST_40  H12  C8   C7   C6     0.00   0.0  0
 OD2  CONST_41  H7   C11  C12  C7   180.00   0.0  0
 OD2  CONST_42  H11  C9   C8   C7   180.00   0.0  0
 OD2  CONST_43  H1   O1   C    O      0.00   0.0  0
 OD2  Var_01    N1   C2   S    C1    -0.05  30.0  2
 OD2  Var_02    C9   C10  S2   C13   -0.70  30.0  2
 OD2  Var_03    H2   C1   S    C2    61.74  30.0  3
 OD2  Var_04    H8   C13  S2   C10  -62.73  30.0  3
 OD2  Var_05    S    C1   C    O     -1.65  30.0  1

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
 OD2  plan-1  C6   0.020
 OD2  plan-1  C7   0.020
 OD2  plan-1  C12  0.020
 OD2  plan-1  C11  0.020
 OD2  plan-1  C10  0.020
 OD2  plan-1  S2   0.020
 OD2  plan-1  C9   0.020
 OD2  plan-1  C8   0.020
 OD2  plan-1  H6   0.020
 OD2  plan-1  H7   0.020
 OD2  plan-1  H11  0.020
 OD2  plan-1  H12  0.020
 OD2  plan-2  S    0.020
 OD2  plan-2  C2   0.020
 OD2  plan-2  N1   0.020
 OD2  plan-2  C14  0.020
 OD2  plan-2  N    0.020
 OD2  plan-2  C4   0.020
 OD2  plan-2  C5   0.020
 OD2  plan-2  C6   0.020
 OD2  plan-2  S1   0.020
 OD2  plan-2  C3   0.020
 OD2  plan-2  C7   0.020
 OD2  plan-2  H4   0.020
 OD2  plan-2  H5   0.020
 OD2  plan-3  C    0.020
 OD2  plan-3  O    0.020
 OD2  plan-3  O1   0.020
 OD2  plan-3  C1   0.020
 OD2  plan-3  H1   0.020

