# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:40:40 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-(4-methoxy-3-thiophen-3-yl-phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC(O)=O)cc1c2cscc2
#
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
 5V6  5V6  '2-(4-methoxy-3-thiophen-3-yl-phenyl)ethanoic acid'  ligand  29  17  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5V6
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
 5V6  C1   C  CH2   0  -0.693   3.2411   0.5646   0.8911
 5V6  C2   C  CR6   0   0.143   1.9979  -0.2259   0.6197
 5V6  C3   C  CR16  0  -0.349   0.7623   0.4029   0.5223
 5V6  O1   O  O     0  -0.435   3.4138   1.0130  -1.4739
 5V6  C11  C  CR16  0  -0.371   0.8912  -2.3251   0.1718
 5V6  C12  C  CR16  0  -0.295   2.0436  -1.5997   0.4414
 5V6  C    C  C     0   0.556   3.8711   1.1155  -0.3649
 5V6  O    O  OH1   0  -0.594   5.0108   1.7445  -0.0989
 5V6  C4   C  CR6   0  -0.005  -0.4149  -0.2892   0.2536
 5V6  C9   C  CR6   0   0.335  -0.3395  -1.6829   0.0738
 5V6  C10  C  CH3   0  -0.438  -1.4771  -3.7337  -0.3095
 5V6  C5   C  CR5   0   0.170  -1.6860   0.4517   0.1929
 5V6  C6   C  CR15  0  -0.540  -2.7133   0.2280  -0.6832
 5V6  S    S  S2    0   0.220  -3.9968   1.3384  -0.4729
 5V6  C7   C  CR15  0  -0.468  -3.1824   2.1288   0.8100
 5V6  C8   C  CR15  0  -0.218  -1.9735   1.5592   1.0540
 5V6  H1   H  HCH2  0   0.304   3.0329   1.4063   1.5588
 5V6  H2   H  HCH2  0   0.302   3.9862  -0.0441   1.4102
 5V6  H3   H  HCR6  0   0.251   0.7099   1.4779   0.6531
 5V6  H4   H  HCR6  0   0.281   0.9705  -3.3961   0.0459
 5V6  H5   H  HCR6  0   0.256   2.9871  -2.1275   0.5135
 5V6  H6   H  HOH1  0   0.481   5.3978   2.0911  -0.9170
 5V6  H7   H  HCH3  0   0.229  -1.1118  -4.2308   0.5931
 5V6  H8   H  HCH3  0   0.260  -2.5068  -4.0360  -0.4829
 5V6  H9   H  HCH3  0   0.230  -0.8700  -4.0550  -1.1597
 5V6  H10  H  HCR5  0   0.289  -2.7776  -0.5170  -1.4594
 5V6  H11  H  HCR5  0   0.296  -3.6402   2.9590   1.3246
 5V6  H12  H  HCR5  0   0.265  -1.3108   1.9017   1.8367
 5V6  O2   O  O2    0  -0.464  -1.4936  -2.3275  -0.1698

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
 5V6  S    C7   aromatic  1.713  0.020  1.713
 5V6  S    C6   aromatic  1.710  0.020  1.710
 5V6  C7   C8   aromatic  1.358  0.020  1.358
 5V6  C6   C5   aromatic  1.369  0.020  1.369
 5V6  C8   C5   aromatic  1.432  0.020  1.432
 5V6  C5   C4   single    1.473  0.020  1.473
 5V6  C4   C3   aromatic  1.392  0.020  1.392
 5V6  C4   C9   aromatic  1.407  0.020  1.407
 5V6  O2   C9   single    1.344  0.020  1.344
 5V6  O2   C10  single    1.413  0.020  1.413
 5V6  C3   C2   aromatic  1.390  0.020  1.390
 5V6  C9   C11  aromatic  1.392  0.020  1.392
 5V6  C2   C1   single    1.498  0.020  1.498
 5V6  C2   C12  aromatic  1.386  0.020  1.386
 5V6  C11  C12  aromatic  1.388  0.020  1.388
 5V6  C1   C    single    1.509  0.020  1.509
 5V6  O1   C    double    1.204  0.020  1.204
 5V6  C    O    single    1.329  0.020  1.329
 5V6  C1   H1   single    0.970  0.020  1.090
 5V6  C1   H2   single    0.970  0.020  1.090
 5V6  C3   H3   single    0.930  0.020  1.080
 5V6  C11  H4   single    0.930  0.020  1.080
 5V6  C12  H5   single    0.930  0.020  1.080
 5V6  O    H6   single    0.850  0.020  0.980
 5V6  C10  H7   single    0.970  0.020  1.090
 5V6  C10  H8   single    0.970  0.020  1.090
 5V6  C10  H9   single    0.970  0.020  1.090
 5V6  C6   H10  single    0.930  0.020  1.080
 5V6  C7   H11  single    0.930  0.020  1.080
 5V6  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
 5V6  H2   C1   H1   105.56  3.000
 5V6  H2   C1   C    108.30  3.000
 5V6  H1   C1   C    107.84  3.000
 5V6  H2   C1   C2   110.97  3.000
 5V6  H1   C1   C2   111.01  3.000
 5V6  C    C1   C2   112.84  3.000
 5V6  C12  C2   C3   117.96  3.000
 5V6  C12  C2   C1   121.26  3.000
 5V6  C3   C2   C1   120.78  3.000
 5V6  H3   C3   C4   118.39  3.000
 5V6  H3   C3   C2   118.89  3.000
 5V6  C4   C3   C2   122.72  3.000
 5V6  H4   C11  C9   120.91  3.000
 5V6  H4   C11  C12  118.64  3.000
 5V6  C9   C11  C12  120.45  3.000
 5V6  H5   C12  C11  118.77  3.000
 5V6  H5   C12  C2   120.20  3.000
 5V6  C11  C12  C2   121.03  3.000
 5V6  O    C    O1   123.40  3.000
 5V6  O    C    C1   111.36  3.000
 5V6  O1   C    C1   125.24  3.000
 5V6  H6   O    C    110.05  3.000
 5V6  C5   C4   C9   122.63  3.000
 5V6  C9   C4   C3   118.16  3.000
 5V6  C5   C4   C3   119.20  3.000
 5V6  C4   C9   C11  119.69  3.000
 5V6  C11  C9   O2   123.42  3.000
 5V6  C4   C9   O2   116.88  3.000
 5V6  H9   C10  H8   108.68  3.000
 5V6  H9   C10  H7   108.85  3.000
 5V6  H8   C10  H7   108.77  3.000
 5V6  H9   C10  O2   112.08  3.000
 5V6  H8   C10  O2   106.34  3.000
 5V6  H7   C10  O2   112.01  3.000
 5V6  C8   C5   C6   111.14  3.000
 5V6  C8   C5   C4   122.52  3.000
 5V6  C6   C5   C4   126.30  3.000
 5V6  H10  C6   S    119.51  3.000
 5V6  H10  C6   C5   128.23  3.000
 5V6  S    C6   C5   112.24  3.000
 5V6  C7   S    C6    92.00  3.000
 5V6  H11  C7   C8   127.93  3.000
 5V6  H11  C7   S    120.71  3.000
 5V6  C8   C7   S    111.35  3.000
 5V6  H12  C8   C7   122.86  3.000
 5V6  H12  C8   C5   123.86  3.000
 5V6  C7   C8   C5   113.26  3.000
 5V6  C10  O2   C9   119.01  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
 5V6  CONST_01  C5   C4   C3   C2   180.00   0.0  0
 5V6  CONST_02  C9   C4   C3   C2     0.00   0.0  0
 5V6  CONST_03  C9   C11  C12  C2     0.00   0.0  0
 5V6  CONST_06  C11  C9   C4   C3     0.00   0.0  0
 5V6  CONST_07  C11  C12  C2   C3     0.00   0.0  0
 5V6  CONST_08  C5   C4   C9   C11  180.00   0.0  0
 5V6  CONST_09  C4   C3   C2   C12    0.00   0.0  0
 5V6  CONST_10  C4   C9   C11  C12    0.00   0.0  0
 5V6  CONST_11  S    C6   C5   C4   180.00   0.0  0
 5V6  CONST_12  C7   C8   C5   C4   180.00   0.0  0
 5V6  CONST_15  C7   S    C6   C5     0.00   0.0  0
 5V6  CONST_16  S    C7   C8   C5     0.00   0.0  0
 5V6  CONST_17  C8   C7   S    C6     0.00   0.0  0
 5V6  CONST_18  C7   C8   C5   C6     0.00   0.0  0
 5V6  CONST_19  C8   C5   C6   S      0.00   0.0  0
 5V6  CONST_20  C4   C3   C2   C1   180.00   0.0  0
 5V6  CONST_21  C11  C12  C2   C1   180.00   0.0  0
 5V6  CONST_22  O2   C9   C4   C3   180.00   0.0  0
 5V6  CONST_23  C5   C4   C9   O2     0.00   0.0  0
 5V6  CONST_24  C12  C11  C9   O2   180.00   0.0  0
 5V6  CONST_25  H4   C11  C12  C2   180.00   0.0  0
 5V6  CONST_26  H5   C12  C2   C3   180.00   0.0  0
 5V6  CONST_27  H3   C3   C2   C12  180.00   0.0  0
 5V6  CONST_28  H10  C6   C5   C4     0.00   0.0  0
 5V6  CONST_29  H12  C8   C5   C4     0.00   0.0  0
 5V6  CONST_30  H11  C7   C8   C5   180.00   0.0  0
 5V6  CONST_31  H6   O    C    C1   180.00   0.0  0
 5V6  Var_01    C    C1   C2   C3   -86.30  30.0  2
 5V6  Var_02    O1   C    C1   C2     3.84  30.0  3
 5V6  Var_03    H7   C10  O2   C9    60.42  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
 5V6  plan-1  C4   0.020
 5V6  plan-1  C5   0.020
 5V6  plan-1  C6   0.020
 5V6  plan-1  S    0.020
 5V6  plan-1  C7   0.020
 5V6  plan-1  C8   0.020
 5V6  plan-1  H10  0.020
 5V6  plan-1  H11  0.020
 5V6  plan-1  H12  0.020
 5V6  plan-2  C1   0.020
 5V6  plan-2  C2   0.020
 5V6  plan-2  C3   0.020
 5V6  plan-2  C11  0.020
 5V6  plan-2  C12  0.020
 5V6  plan-2  C4   0.020
 5V6  plan-2  C9   0.020
 5V6  plan-2  C5   0.020
 5V6  plan-2  H3   0.020
 5V6  plan-2  H4   0.020
 5V6  plan-2  H5   0.020
 5V6  plan-2  O2   0.020
 5V6  plan-3  C1   0.020
 5V6  plan-3  O1   0.020
 5V6  plan-3  C    0.020
 5V6  plan-3  O    0.020
 5V6  plan-3  H6   0.020

