# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 18:08:29 2022
#   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  33  20  .  2022-03-23  2022-03-23
;
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  -0.594  51.6258   6.4967  -20.4063
 QAD  C11  C  C      0   0.424  50.7586   7.3425  -20.7112
 QAD  O2   O  OC    -1  -0.614  50.8200   8.1873  -21.6243
 QAD  C10  C  CH2    0  -0.587  49.4746   7.3538  -19.8575
 QAD  C9   C  CH2    0  -0.562  49.4388   6.2368  -18.8303
 QAD  C8   C  C      0   0.429  50.6075   6.3006  -17.8841
 QAD  O    O  O      0  -0.425  51.0165   7.3534  -17.4286
 QAD  C6   C  CR5    0  -0.286  51.2089   5.0472  -17.4187
 QAD  S    S  S2     0   0.225  52.5312   5.1786  -16.2935
 QAD  C4   C  CR56   0  -0.234  52.6563   3.4578  -16.1911
 QAD  C5   C  CR16   0  -0.416  53.5669   2.7298  -15.4206
 QAD  C    C  CR6    0   0.317  53.5052   1.3522  -15.4491
 QAD  O4   O  O2     0  -0.454  54.3163   0.5395  -14.7583
 QAD  C13  C  CH3    0  -0.440  55.3450   1.1192  -13.9806
 QAD  C7   C  CR15   0  -0.259  50.8863   3.7540  -17.6916
 QAD  C3   C  CR56   0   0.241  51.7023   2.8200  -16.9902
 QAD  C2   C  CR16   0  -0.457  51.6472   1.4140  -17.0134
 QAD  C1   C  CR6    0   0.322  52.5283   0.6857  -16.2514
 QAD  O3   O  O2     0  -0.460  52.5673  -0.6557  -16.1849
 QAD  C12  C  CH3    0  -0.438  51.6387  -1.3861  -16.9588
 QAD  H5   H  HCH2   0   0.230  49.3828   8.3265  -19.3665
 QAD  H6   H  HCH2   0   0.237  48.6022   7.2730  -20.5118
 QAD  H3   H  HCH2   0   0.262  48.5333   6.3101  -18.2165
 QAD  H4   H  HCH2   0   0.245  49.3911   5.2678  -19.3256
 QAD  H1   H  HCR6   0   0.294  54.2980   3.2471  -14.8144
 QAD  H11  H  HCH3   0   0.263  55.8918   0.2948  -13.5299
 QAD  H12  H  HCH3   0   0.232  56.0331   1.7089  -14.5921
 QAD  H13  H  HCH3   0   0.231  54.9461   1.7547  -13.1857
 QAD  H2   H  HCR5   0   0.271  50.0921   3.4589  -18.3634
 QAD  H    H  HCR6   0   0.285  50.9047   0.9297  -17.6338
 QAD  H10  H  HCH3   0   0.261  51.8282  -2.4374  -16.7573
 QAD  H8   H  HCH3   0   0.228  50.6060  -1.1547  -16.6840
 QAD  H9   H  HCH3   0   0.229  51.7668  -1.2028  -18.0292

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  deloc     1.245  0.020  1.245
 QAD  O1   C11  deloc     1.249  0.020  1.249
 QAD  C11  C10  single    1.542  0.020  1.542
 QAD  C10  C9   single    1.518  0.020  1.518
 QAD  C9   C8   single    1.505  0.020  1.505
 QAD  C8   O    double    1.218  0.020  1.218
 QAD  C8   C6   single    1.466  0.020  1.466
 QAD  C7   C6   aromatic  1.360  0.020  1.360
 QAD  C7   C3   aromatic  1.425  0.020  1.425
 QAD  C12  O3   single    1.412  0.020  1.412
 QAD  C6   S    aromatic  1.741  0.020  1.741
 QAD  C2   C3   aromatic  1.407  0.020  1.407
 QAD  C2   C1   aromatic  1.374  0.020  1.374
 QAD  C3   C4   aromatic  1.398  0.020  1.398
 QAD  O3   C1   single    1.344  0.020  1.344
 QAD  C1   C    aromatic  1.429  0.020  1.429
 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    1.340  0.020  1.340
 QAD  O4   C13  single    1.414  0.020  1.414
 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   116.23  3.000
 QAD  C10  C11  O1   116.61  3.000
 QAD  O2   C11  O1   127.16  3.000
 QAD  H6   C10  H5   105.51  3.000
 QAD  H6   C10  C9   109.37  3.000
 QAD  H5   C10  C9   110.41  3.000
 QAD  H6   C10  C11  109.42  3.000
 QAD  H5   C10  C11  108.96  3.000
 QAD  C9   C10  C11  112.89  3.000
 QAD  H4   C9   H3   106.13  3.000
 QAD  H4   C9   C8   110.95  3.000
 QAD  H3   C9   C8   106.65  3.000
 QAD  H4   C9   C10  110.36  3.000
 QAD  H3   C9   C10  110.44  3.000
 QAD  C8   C9   C10  112.08  3.000
 QAD  C6   C8   O    118.86  3.000
 QAD  C6   C8   C9   118.81  3.000
 QAD  O    C8   C9   122.18  3.000
 QAD  C7   C6   S    112.43  3.000
 QAD  S    C6   C8   116.88  3.000
 QAD  C7   C6   C8   130.67  3.000
 QAD  C4   S    C6    91.04  3.000
 QAD  C3   C4   C5   121.47  3.000
 QAD  C5   C4   S    126.76  3.000
 QAD  C3   C4   S    111.76  3.000
 QAD  H1   C5   C    121.30  3.000
 QAD  H1   C5   C4   120.03  3.000
 QAD  C    C5   C4   118.67  3.000
 QAD  C1   C    O4   114.86  3.000
 QAD  O4   C    C5   124.61  3.000
 QAD  C1   C    C5   120.53  3.000
 QAD  C13  O4   C    118.38  3.000
 QAD  H13  C13  H12  108.84  3.000
 QAD  H13  C13  H11  108.84  3.000
 QAD  H12  C13  H11  108.93  3.000
 QAD  H13  C13  O4   111.89  3.000
 QAD  H12  C13  O4   111.80  3.000
 QAD  H11  C13  O4   106.45  3.000
 QAD  H2   C7   C3   123.20  3.000
 QAD  H2   C7   C6   123.94  3.000
 QAD  C3   C7   C6   112.86  3.000
 QAD  C2   C3   C7   128.64  3.000
 QAD  C2   C3   C4   119.46  3.000
 QAD  C7   C3   C4   111.91  3.000
 QAD  H    C2   C1   121.39  3.000
 QAD  H    C2   C3   118.92  3.000
 QAD  C1   C2   C3   119.69  3.000
 QAD  O3   C1   C2   125.12  3.000
 QAD  O3   C1   C    114.71  3.000
 QAD  C2   C1   C    120.17  3.000
 QAD  C12  O3   C1   118.04  3.000
 QAD  H9   C12  H8   108.73  3.000
 QAD  H9   C12  H10  108.85  3.000
 QAD  H8   C12  H10  108.82  3.000
 QAD  H9   C12  O3   111.89  3.000
 QAD  H8   C12  O3   111.95  3.000
 QAD  H10  C12  O3   106.50  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  Var_01    C7   C6   C8   C9     -0.41  30.0  2
 QAD  Var_02    C1   C    O4   C13   177.54  30.0  1
 QAD  Var_03    C6   C8   C9   C10  -143.55  30.0  3
 QAD  Var_04    H11  C13  O4   C    -178.63  30.0  3
 QAD  Var_05    H10  C12  O3   C1   -179.42  30.0  3
 QAD  Var_06    C9   C10  C11  O1     -4.40  30.0  3
 QAD  Var_07    C8   C9   C10  C11    58.63  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

