# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 08:40:34 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-(5,6-dimethoxy-1-benzothiophen-2-yl)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2sc(cc2cc1OC)C(=O)CCC(O)=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
 QAD  QAD  '4-(5,6-dimethoxy-1-benzothiophen-2-yl)-4-oxobutanoic acid'  ligand  34  20  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QAD
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
 QAD  O1   O  O     0  -0.448  51.4410   7.3281  -21.2091
 QAD  C11  C  C     0   0.552  50.5172   7.9110  -20.6981
 QAD  O2   O  OH1   0  -0.595  50.3295   9.2207  -20.8168
 QAD  C10  C  CH2   0  -0.582  49.4208   7.2495  -19.9101
 QAD  C9   C  CH2   0  -0.589  49.8452   5.9196  -19.3209
 QAD  C8   C  C     0   0.414  50.9814   6.0625  -18.3402
 QAD  O    O  O     0  -0.407  51.4587   7.1448  -18.0577
 QAD  C6   C  CR5   0  -0.286  51.4963   4.8500  -17.7117
 QAD  S    S  S2    0   0.246  52.8289   5.0131  -16.6057
 QAD  C4   C  CR56  0  -0.234  52.8272   3.3103  -16.3124
 QAD  C5   C  CR16  0  -0.416  53.6857   2.6115  -15.4599
 QAD  C    C  CR6   0   0.322  53.5304   1.2463  -15.3418
 QAD  O4   O  O2    0  -0.452  54.2830   0.4591  -14.5649
 QAD  C13  C  CH3   0  -0.443  55.3123   1.0568  -13.7997
 QAD  C7   C  CR15  0  -0.251  51.0781   3.5604  -17.8433
 QAD  C3   C  CR56  0   0.242  51.8294   2.6551  -17.0433
 QAD  C2   C  CR16  0  -0.458  51.6782   1.2611  -16.9147
 QAD  C1   C  CR6   0   0.324  52.5114   0.5628  -16.0758
 QAD  O3   O  O2    0  -0.459  52.4643  -0.7622  -15.8642
 QAD  C12  C  CH3   0  -0.441  51.4802  -1.5072  -16.5525
 QAD  H7   H  HOH1  0   0.478  51.0304   9.6054  -21.3642
 QAD  H5   H  HCH2  0   0.279  49.0490   7.9238  -19.1384
 QAD  H6   H  HCH2  0   0.304  48.5844   7.0859  -20.5969
 QAD  H3   H  HCH2  0   0.296  48.9967   5.4661  -18.8016
 QAD  H4   H  HCH2  0   0.285  50.1275   5.2109  -20.1029
 QAD  H1   H  HCR6  0   0.297  54.4530   3.1407  -14.9119
 QAD  H11  H  HCH3  0   0.266  55.7921   0.2528  -13.2480
 QAD  H12  H  HCH3  0   0.233  56.0569   1.5454  -14.4332
 QAD  H13  H  HCH3  0   0.234  54.9163   1.7873  -13.0898
 QAD  H2   H  HCR5  0   0.277  50.2573   3.2565  -18.4792
 QAD  H    H  HCR6  0   0.287  50.9019   0.7649  -17.4815
 QAD  H10  H  HCH3  0   0.264  51.6082  -2.5430  -16.2490
 QAD  H8   H  HCH3  0   0.230  50.4688  -1.1844  -16.2917
 QAD  H9   H  HCH3  0   0.230  51.6025  -1.4394  -17.6367

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
 QAD  O2   C11  single    1.328  0.020  1.328
 QAD  O1   C11  double    1.206  0.020  1.206
 QAD  C11  C10  single    1.504  0.020  1.504
 QAD  C10  C9   single    1.515  0.020  1.515
 QAD  C9   C8   single    1.508  0.020  1.508
 QAD  C8   O    double    1.216  0.020  1.216
 QAD  C8   C6   single    1.460  0.020  1.460
 QAD  C7   C6   aromatic  1.362  0.020  1.362
 QAD  C7   C3   aromatic  1.423  0.020  1.423
 QAD  C12  O3   single    1.413  0.020  1.413
 QAD  C6   S    aromatic  1.739  0.020  1.739
 QAD  C2   C3   aromatic  1.408  0.020  1.408
 QAD  C2   C1   aromatic  1.373  0.020  1.373
 QAD  C3   C4   aromatic  1.400  0.020  1.400
 QAD  O3   C1   single    1.343  0.020  1.343
 QAD  C1   C    aromatic  1.430  0.020  1.430
 QAD  S    C4   aromatic  1.728  0.020  1.728
 QAD  C4   C5   aromatic  1.397  0.020  1.397
 QAD  C    C5   aromatic  1.379  0.020  1.379
 QAD  C    O4   single    1.338  0.020  1.338
 QAD  O4   C13  single    1.415  0.020  1.415
 QAD  O2   H7   single    0.850  0.020  0.980
 QAD  C10  H5   single    0.970  0.020  1.090
 QAD  C10  H6   single    0.970  0.020  1.090
 QAD  C9   H3   single    0.970  0.020  1.090
 QAD  C9   H4   single    0.970  0.020  1.090
 QAD  C5   H1   single    0.930  0.020  1.080
 QAD  C13  H11  single    0.970  0.020  1.090
 QAD  C13  H12  single    0.970  0.020  1.090
 QAD  C13  H13  single    0.970  0.020  1.090
 QAD  C7   H2   single    0.930  0.020  1.080
 QAD  C2   H    single    0.930  0.020  1.080
 QAD  C12  H10  single    0.970  0.020  1.090
 QAD  C12  H8   single    0.970  0.020  1.090
 QAD  C12  H9   single    0.970  0.020  1.090

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
 QAD  C10  C11  O2   112.18  3.000
 QAD  C10  C11  O1   124.61  3.000
 QAD  O2   C11  O1   123.16  3.000
 QAD  H7   O2   C11  109.85  3.000
 QAD  H6   C10  H5   106.02  3.000
 QAD  H6   C10  C9   109.08  3.000
 QAD  H5   C10  C9   111.29  3.000
 QAD  H6   C10  C11  107.11  3.000
 QAD  H5   C10  C11  110.34  3.000
 QAD  C9   C10  C11  112.69  3.000
 QAD  H4   C9   H3   105.75  3.000
 QAD  H4   C9   C8   109.41  3.000
 QAD  H3   C9   C8   108.37  3.000
 QAD  H4   C9   C10  111.31  3.000
 QAD  H3   C9   C10  109.35  3.000
 QAD  C8   C9   C10  112.39  3.000
 QAD  C6   C8   O    120.06  3.000
 QAD  C6   C8   C9   117.86  3.000
 QAD  O    C8   C9   122.08  3.000
 QAD  C7   C6   S    112.67  3.000
 QAD  S    C6   C8   117.79  3.000
 QAD  C7   C6   C8   129.54  3.000
 QAD  C4   S    C6    90.85  3.000
 QAD  C3   C4   C5   121.50  3.000
 QAD  C5   C4   S    126.57  3.000
 QAD  C3   C4   S    111.93  3.000
 QAD  H1   C5   C    121.40  3.000
 QAD  H1   C5   C4   120.04  3.000
 QAD  C    C5   C4   118.56  3.000
 QAD  C1   C    O4   114.69  3.000
 QAD  O4   C    C5   124.68  3.000
 QAD  C1   C    C5   120.63  3.000
 QAD  C13  O4   C    118.34  3.000
 QAD  H13  C13  H12  108.94  3.000
 QAD  H13  C13  H11  108.95  3.000
 QAD  H12  C13  H11  108.91  3.000
 QAD  H13  C13  O4   111.73  3.000
 QAD  H12  C13  O4   111.78  3.000
 QAD  H11  C13  O4   106.45  3.000
 QAD  H2   C7   C3   123.53  3.000
 QAD  H2   C7   C6   123.76  3.000
 QAD  C3   C7   C6   112.70  3.000
 QAD  C2   C3   C7   128.66  3.000
 QAD  C2   C3   C4   119.49  3.000
 QAD  C7   C3   C4   111.85  3.000
 QAD  H    C2   C1   121.48  3.000
 QAD  H    C2   C3   118.91  3.000
 QAD  C1   C2   C3   119.61  3.000
 QAD  O3   C1   C2   125.23  3.000
 QAD  O3   C1   C    114.57  3.000
 QAD  C2   C1   C    120.20  3.000
 QAD  C12  O3   C1   117.90  3.000
 QAD  H9   C12  H8   108.78  3.000
 QAD  H9   C12  H10  108.84  3.000
 QAD  H8   C12  H10  108.89  3.000
 QAD  H9   C12  O3   111.86  3.000
 QAD  H8   C12  O3   111.86  3.000
 QAD  H10  C12  O3   106.52  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
 QAD  CONST_01  C2   C3   C7   C6    180.00   0.0  0
 QAD  CONST_02  C4   C3   C7   C6      0.00   0.0  0
 QAD  CONST_03  C3   C4   S    C6      0.00   0.0  0
 QAD  CONST_04  C5   C4   S    C6    180.00   0.0  0
 QAD  CONST_05  C3   C7   C6   S       0.00   0.0  0
 QAD  CONST_06  C7   C3   C4   S       0.00   0.0  0
 QAD  CONST_07  C2   C3   C4   S     180.00   0.0  0
 QAD  CONST_08  C    C5   C4   S     180.00   0.0  0
 QAD  CONST_09  C1   C2   C3   C4      0.00   0.0  0
 QAD  CONST_10  C7   C6   S    C4      0.00   0.0  0
 QAD  CONST_11  C1   C    C5   C4      0.00   0.0  0
 QAD  CONST_12  C7   C3   C4   C5    180.00   0.0  0
 QAD  CONST_13  C2   C3   C4   C5      0.00   0.0  0
 QAD  CONST_14  C2   C1   C    C5      0.00   0.0  0
 QAD  CONST_15  C3   C2   C1   C       0.00   0.0  0
 QAD  CONST_16  C3   C4   C5   C       0.00   0.0  0
 QAD  CONST_17  C1   C2   C3   C7    180.00   0.0  0
 QAD  CONST_18  C3   C7   C6   C8    180.00   0.0  0
 QAD  CONST_19  C4   S    C6   C8    180.00   0.0  0
 QAD  CONST_20  O4   C    C5   C4    180.00   0.0  0
 QAD  CONST_21  O3   C1   C    C5    180.00   0.0  0
 QAD  CONST_22  C2   C1   C    O4    180.00   0.0  0
 QAD  CONST_23  O3   C1   C2   C3    180.00   0.0  0
 QAD  CONST_24  H2   C7   C6   S     180.00   0.0  0
 QAD  CONST_25  H1   C5   C4   S       0.00   0.0  0
 QAD  CONST_26  H    C2   C3   C4    180.00   0.0  0
 QAD  CONST_27  H7   O2   C11  O1      0.00   0.0  0
 QAD  Var_01    C7   C6   C8   C9     -2.09  30.0  2
 QAD  Var_02    C1   C    O4   C13  -179.76  30.0  1
 QAD  Var_03    C6   C8   C9   C10  -179.28  30.0  3
 QAD  Var_04    H11  C13  O4   C     179.89  30.0  3
 QAD  Var_05    H10  C12  O3   C1    179.96  30.0  3
 QAD  Var_06    C9   C10  C11  O1     24.11  30.0  3
 QAD  Var_07    C8   C9   C10  C11    62.25  30.0  3

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
 QAD  plan-1  C8   0.020
 QAD  plan-1  C6   0.020
 QAD  plan-1  S    0.020
 QAD  plan-1  C4   0.020
 QAD  plan-1  C5   0.020
 QAD  plan-1  C    0.020
 QAD  plan-1  O4   0.020
 QAD  plan-1  C7   0.020
 QAD  plan-1  C3   0.020
 QAD  plan-1  C2   0.020
 QAD  plan-1  C1   0.020
 QAD  plan-1  O3   0.020
 QAD  plan-1  H1   0.020
 QAD  plan-1  H2   0.020
 QAD  plan-1  H    0.020
 QAD  plan-2  C9   0.020
 QAD  plan-2  C8   0.020
 QAD  plan-2  O    0.020
 QAD  plan-2  C6   0.020
 QAD  plan-3  O1   0.020
 QAD  plan-3  C11  0.020
 QAD  plan-3  O2   0.020
 QAD  plan-3  C10  0.020
 QAD  plan-3  H7   0.020

