# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 00:14:15 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 4-(thiophen-3-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)c2cscc2
#
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
 EJD  EJD  '4-(thiophen-3-yl)benzoic acid'  ligand  22  14  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EJD
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
 EJD  C10  C  CR5   0   0.160  -1.8035  -0.1188   0.0409
 EJD  C13  C  CR15  0  -0.464  -3.9088  -1.0786  -0.1819
 EJD  C04  C  CR6   0  -0.099   2.4669   0.0482  -0.0177
 EJD  C05  C  CR16  0  -0.237   1.7107   1.1976  -0.2417
 EJD  C06  C  CR16  0  -0.305   0.3303   1.1433  -0.2298
 EJD  C07  C  CR6   0   0.112  -0.3378  -0.0598   0.0140
 EJD  C08  C  CR16  0  -0.307   0.4264  -1.2072   0.2361
 EJD  C09  C  CR16  0  -0.239   1.8093  -1.1574   0.2206
 EJD  C11  C  CR15  0  -0.550  -2.6102   0.9318   0.3875
 EJD  C14  C  CR15  0  -0.218  -2.5698  -1.2815  -0.2849
 EJD  O01  O  O     0  -0.440   4.5399   1.1914  -0.2281
 EJD  O03  O  OH1   0  -0.594   4.5536  -1.0052   0.1513
 EJD  S12  S  S2    0   0.239  -4.2656   0.5205   0.3208
 EJD  H1   H  HCR5  0   0.300  -4.7034  -1.7793  -0.3856
 EJD  H2   H  HCR6  0   0.267   2.2031   2.1403  -0.4395
 EJD  H3   H  HCR6  0   0.260  -0.2341   2.0441  -0.4334
 EJD  H4   H  HCR6  0   0.261  -0.0598  -2.1516   0.4435
 EJD  H5   H  HCR6  0   0.269   2.3652  -2.0663   0.4045
 EJD  H6   H  HCR5  0   0.298  -2.3115   1.9189   0.7060
 EJD  H7   H  HCR5  0   0.269  -2.1400  -2.2194  -0.6063
 EJD  H8   H  HOH1  0   0.488   5.5139  -0.8818   0.1258
 EJD  C02  C  C     0   0.531   3.9440   0.1560  -0.0452

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
 EJD  O01  C02  double    1.209  0.020  1.209
 EJD  C02  O03  single    1.326  0.020  1.326
 EJD  C02  C04  single    1.481  0.020  1.481
 EJD  C09  C04  aromatic  1.394  0.020  1.394
 EJD  C09  C08  aromatic  1.384  0.020  1.384
 EJD  C04  C05  aromatic  1.394  0.020  1.394
 EJD  C08  C07  aromatic  1.396  0.020  1.396
 EJD  C05  C06  aromatic  1.382  0.020  1.382
 EJD  C07  C06  aromatic  1.398  0.020  1.398
 EJD  C07  C10  single    1.467  0.020  1.467
 EJD  C11  C10  aromatic  1.369  0.020  1.369
 EJD  C11  S12  aromatic  1.707  0.020  1.707
 EJD  C10  C14  aromatic  1.430  0.020  1.430
 EJD  S12  C13  aromatic  1.714  0.020  1.714
 EJD  C14  C13  aromatic  1.358  0.020  1.358
 EJD  C13  H1   single    0.930  0.020  1.080
 EJD  C05  H2   single    0.930  0.020  1.080
 EJD  C06  H3   single    0.930  0.020  1.080
 EJD  C08  H4   single    0.930  0.020  1.080
 EJD  C09  H5   single    0.930  0.020  1.080
 EJD  C11  H6   single    0.930  0.020  1.080
 EJD  C14  H7   single    0.930  0.020  1.080
 EJD  O03  H8   single    0.850  0.020  0.980

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
 EJD  C14  C10  C11  111.46  3.000
 EJD  C14  C10  C07  124.32  3.000
 EJD  C11  C10  C07  124.22  3.000
 EJD  H1   C13  S12  120.54  3.000
 EJD  H1   C13  C14  127.94  3.000
 EJD  S12  C13  C14  111.52  3.000
 EJD  C09  C04  C05  119.00  3.000
 EJD  C05  C04  C02  118.55  3.000
 EJD  C09  C04  C02  122.45  3.000
 EJD  H2   C05  C06  119.38  3.000
 EJD  H2   C05  C04  120.07  3.000
 EJD  C06  C05  C04  120.54  3.000
 EJD  H3   C06  C07  120.00  3.000
 EJD  H3   C06  C05  119.12  3.000
 EJD  C07  C06  C05  120.87  3.000
 EJD  C08  C07  C06  118.26  3.000
 EJD  C06  C07  C10  121.02  3.000
 EJD  C08  C07  C10  120.71  3.000
 EJD  H4   C08  C09  118.85  3.000
 EJD  H4   C08  C07  120.11  3.000
 EJD  C09  C08  C07  121.03  3.000
 EJD  H5   C09  C08  118.80  3.000
 EJD  H5   C09  C04  120.90  3.000
 EJD  C08  C09  C04  120.30  3.000
 EJD  H6   C11  S12  120.02  3.000
 EJD  H6   C11  C10  127.83  3.000
 EJD  S12  C11  C10  112.12  3.000
 EJD  H7   C14  C13  122.97  3.000
 EJD  H7   C14  C10  124.08  3.000
 EJD  C13  C14  C10  112.93  3.000
 EJD  H8   O03  C02  109.90  3.000
 EJD  C11  S12  C13   91.97  3.000
 EJD  O03  C02  O01  123.09  3.000
 EJD  O03  C02  C04  113.08  3.000
 EJD  O01  C02  C04  123.83  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
 EJD  CONST_01  C09  C08  C07  C10  180.00   0.0  0
 EJD  CONST_02  C05  C06  C07  C10  180.00   0.0  0
 EJD  CONST_03  C13  S12  C11  C10    0.00   0.0  0
 EJD  CONST_04  S12  C13  C14  C10    0.00   0.0  0
 EJD  CONST_05  C07  C10  C14  C13  180.00   0.0  0
 EJD  CONST_06  C11  C10  C14  C13    0.00   0.0  0
 EJD  CONST_07  C07  C08  C09  C04    0.00   0.0  0
 EJD  CONST_08  C07  C06  C05  C04    0.00   0.0  0
 EJD  CONST_09  C08  C09  C04  C05    0.00   0.0  0
 EJD  CONST_10  C08  C07  C06  C05    0.00   0.0  0
 EJD  CONST_11  C09  C04  C05  C06    0.00   0.0  0
 EJD  CONST_12  C09  C08  C07  C06    0.00   0.0  0
 EJD  CONST_15  S12  C11  C10  C07  180.00   0.0  0
 EJD  CONST_18  C14  C13  S12  C11    0.00   0.0  0
 EJD  CONST_19  S12  C11  C10  C14    0.00   0.0  0
 EJD  CONST_20  C08  C09  C04  C02  180.00   0.0  0
 EJD  CONST_21  C06  C05  C04  C02  180.00   0.0  0
 EJD  CONST_22  H4   C08  C07  C10    0.00   0.0  0
 EJD  CONST_23  H3   C06  C07  C10    0.00   0.0  0
 EJD  CONST_24  H1   C13  C14  C10  180.00   0.0  0
 EJD  CONST_25  H6   C11  S12  C13  180.00   0.0  0
 EJD  CONST_26  H5   C09  C04  C05  180.00   0.0  0
 EJD  CONST_27  H2   C05  C06  C07  180.00   0.0  0
 EJD  CONST_28  H7   C14  C10  C07    0.00   0.0  0
 EJD  CONST_29  H8   O03  C02  C04  180.00   0.0  0
 EJD  Var_01    O01  C02  C04  C05    1.36  30.0  2

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
 EJD  plan-1  C10  0.020
 EJD  plan-1  C13  0.020
 EJD  plan-1  C07  0.020
 EJD  plan-1  C11  0.020
 EJD  plan-1  C14  0.020
 EJD  plan-1  S12  0.020
 EJD  plan-1  H1   0.020
 EJD  plan-1  H6   0.020
 EJD  plan-1  H7   0.020
 EJD  plan-2  C10  0.020
 EJD  plan-2  C04  0.020
 EJD  plan-2  C05  0.020
 EJD  plan-2  C06  0.020
 EJD  plan-2  C07  0.020
 EJD  plan-2  C08  0.020
 EJD  plan-2  C09  0.020
 EJD  plan-2  H2   0.020
 EJD  plan-2  H3   0.020
 EJD  plan-2  H4   0.020
 EJD  plan-2  H5   0.020
 EJD  plan-2  C02  0.020
 EJD  plan-3  C04  0.020
 EJD  plan-3  O01  0.020
 EJD  plan-3  O03  0.020
 EJD  plan-3  H8   0.020
 EJD  plan-3  C02  0.020

