# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:18:10 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {[5-(3-chloro-1-benzothiophen-2-yl)-4-phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1nnc(n1c2ccccc2)c3sc4ccccc4c3Cl
#
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
 1EK  1EK  '{[5-(3-chloro-1-benzothiophen-2-yl)-4-phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid'  ligand  38  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1EK
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
 1EK  C01  C   CR16  0  -0.261  -6.2108   0.5475   0.3444
 1EK  C02  C   CR16  0  -0.276  -4.9956   1.1762   0.5296
 1EK  C03  C   CR56  0  -0.233  -3.8371   0.4260   0.3458
 1EK  C04  C   CR56  0   0.330  -3.8860  -0.9251  -0.0207
 1EK  C05  C   CR16  0  -0.302  -5.1270  -1.5437  -0.2068
 1EK  C06  C   CR16  0  -0.251  -6.2753  -0.8039  -0.0230
 1EK  S07  S   S2    0   0.266  -2.2123   0.9929   0.5105
 1EK  C08  C   CR5   0  -0.243  -1.5708  -0.5796   0.1000
 1EK  C09  C   CR5   0  -0.047  -2.5702  -1.4706  -0.1516
 1EK  C10  C   CR5   0   0.448  -0.1478  -0.8409   0.0985
 1EK  N11  N   NR5   0  -0.587   0.8295   0.1154   0.0144
 1EK  C12  C   CR5   0   0.281   1.9923  -0.5813   0.0524
 1EK  N13  N   N     0  -0.322   1.7521  -1.8578   0.1483
 1EK  N14  N   N     0  -0.300   0.4095  -2.0179   0.1791
 1EK  S15  S   S2    0   0.100   3.5258   0.2292  -0.0378
 1EK  C16  C   CH2   0  -0.678   4.5855  -1.2364   0.0333
 1EK  C17  C   C     0   0.571   6.0096  -0.7517  -0.0167
 1EK  O18  O   OH1   0  -0.580   6.8597  -1.7606   0.0105
 1EK  O19  O   O     0  -0.428   6.3198   0.4097  -0.0780
 1EK  C20  C   CR6   0   0.172   0.7147   1.5295  -0.0752
 1EK  C21  C   CR16  0  -0.222   0.8504   2.2941   1.0751
 1EK  C22  C   CR16  0  -0.257   0.7219   3.6718   0.9854
 1EK  C23  C   CR16  0  -0.232   0.4628   4.2680  -0.2419
 1EK  C24  C   CR16  0  -0.256   0.3391   3.4916  -1.3872
 1EK  C25  C   CR16  0  -0.221   0.4696   2.1140  -1.3094
 1EK  CL2  CL  CL    0  -0.092  -2.3506  -3.1018  -0.6142
 1EK  H1   H   HCR6  0   0.270  -7.1259   1.1070   0.4844
 1EK  H2   H   HCR6  0   0.277  -4.9459   2.2195   0.8116
 1EK  H3   H   HCR6  0   0.261  -5.1826  -2.5865  -0.4904
 1EK  H4   H   HCR6  0   0.267  -7.2404  -1.2714  -0.1645
 1EK  H5   H   HCH2  0   0.334   4.4101  -1.7932   0.9553
 1EK  H6   H   HCH2  0   0.334   4.3824  -1.9052  -0.8044
 1EK  H7   H   HOH1  0   0.492   7.7729  -1.4360  -0.0206
 1EK  H8   H   HCR6  0   0.284   1.0400   1.8154   2.0269
 1EK  H9   H   HCR6  0   0.273   0.8191   4.2786   1.8749
 1EK  H10  H   HCR6  0   0.271   0.3580   5.3428  -0.3052
 1EK  H11  H   HCR6  0   0.273   0.1389   3.9588  -2.3418
 1EK  H12  H   HCR6  0   0.282   0.3732   1.4958  -2.1925

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
 1EK  O19  C17  double    1.204  0.020  1.204
 1EK  O18  C17  single    1.320  0.020  1.320
 1EK  C17  C16  single    1.505  0.020  1.505
 1EK  C23  C24  aromatic  1.389  0.020  1.389
 1EK  C23  C22  aromatic  1.389  0.020  1.389
 1EK  C24  C25  aromatic  1.386  0.020  1.386
 1EK  C22  C21  aromatic  1.387  0.020  1.387
 1EK  S15  C16  single    1.810  0.020  1.810
 1EK  S15  C12  single    1.737  0.020  1.737
 1EK  C25  C20  aromatic  1.387  0.020  1.387
 1EK  C21  C20  aromatic  1.388  0.020  1.388
 1EK  C20  N11  single    1.422  0.020  1.422
 1EK  C12  N11  aromatic  1.356  0.020  1.356
 1EK  C12  N13  aromatic  1.302  0.020  1.302
 1EK  N11  C10  aromatic  1.370  0.020  1.370
 1EK  N13  N14  aromatic  1.352  0.020  1.352
 1EK  C10  N14  aromatic  1.305  0.020  1.305
 1EK  C10  C08  single    1.447  0.020  1.447
 1EK  C08  C09  aromatic  1.362  0.020  1.362
 1EK  C08  S07  aromatic  1.747  0.020  1.747
 1EK  CL2  C09  single    1.710  0.020  1.710
 1EK  C09  C04  aromatic  1.430  0.020  1.430
 1EK  S07  C03  aromatic  1.729  0.020  1.729
 1EK  C04  C03  aromatic  1.401  0.020  1.401
 1EK  C04  C05  aromatic  1.399  0.020  1.399
 1EK  C03  C02  aromatic  1.392  0.020  1.392
 1EK  C05  C06  aromatic  1.378  0.020  1.378
 1EK  C02  C01  aromatic  1.381  0.020  1.381
 1EK  C06  C01  aromatic  1.402  0.020  1.402
 1EK  C01  H1   single    0.930  0.020  1.080
 1EK  C02  H2   single    0.930  0.020  1.080
 1EK  C05  H3   single    0.930  0.020  1.080
 1EK  C06  H4   single    0.930  0.020  1.080
 1EK  C16  H5   single    0.970  0.020  1.090
 1EK  C16  H6   single    0.970  0.020  1.090
 1EK  O18  H7   single    0.850  0.020  0.980
 1EK  C21  H8   single    0.930  0.020  1.080
 1EK  C22  H9   single    0.930  0.020  1.080
 1EK  C23  H10  single    0.930  0.020  1.080
 1EK  C24  H11  single    0.930  0.020  1.080
 1EK  C25  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
 1EK  H1   C01  C06  119.57  3.000
 1EK  H1   C01  C02  119.46  3.000
 1EK  C06  C01  C02  120.97  3.000
 1EK  H2   C02  C03  121.04  3.000
 1EK  H2   C02  C01  120.96  3.000
 1EK  C03  C02  C01  117.99  3.000
 1EK  S07  C03  C04  111.97  3.000
 1EK  C04  C03  C02  121.68  3.000
 1EK  S07  C03  C02  126.36  3.000
 1EK  C09  C04  C05  129.43  3.000
 1EK  C05  C04  C03  119.49  3.000
 1EK  C09  C04  C03  111.08  3.000
 1EK  H3   C05  C06  120.62  3.000
 1EK  H3   C05  C04  120.43  3.000
 1EK  C06  C05  C04  118.94  3.000
 1EK  H4   C06  C05  119.60  3.000
 1EK  H4   C06  C01  119.48  3.000
 1EK  C05  C06  C01  120.93  3.000
 1EK  C08  S07  C03   91.58  3.000
 1EK  C10  C08  C09  127.10  3.000
 1EK  C09  C08  S07  111.27  3.000
 1EK  C10  C08  S07  121.59  3.000
 1EK  CL2  C09  C08  125.43  3.000
 1EK  CL2  C09  C04  120.45  3.000
 1EK  C08  C09  C04  114.11  3.000
 1EK  N14  C10  N11  109.20  3.000
 1EK  N14  C10  C08  125.66  3.000
 1EK  N11  C10  C08  125.15  3.000
 1EK  C20  N11  C12  125.60  3.000
 1EK  C12  N11  C10  104.56  3.000
 1EK  C20  N11  C10  129.84  3.000
 1EK  S15  C12  N13  128.61  3.000
 1EK  N13  C12  N11  110.33  3.000
 1EK  S15  C12  N11  121.06  3.000
 1EK  N14  N13  C12  107.50  3.000
 1EK  N13  N14  C10  108.41  3.000
 1EK  C16  S15  C12   97.88  3.000
 1EK  H6   C16  H5   107.82  3.000
 1EK  H6   C16  C17  110.36  3.000
 1EK  H5   C16  C17  110.15  3.000
 1EK  H6   C16  S15  110.93  3.000
 1EK  H5   C16  S15  110.63  3.000
 1EK  C17  C16  S15  106.97  3.000
 1EK  O19  C17  O18  124.94  3.000
 1EK  O18  C17  C16  111.26  3.000
 1EK  O19  C17  C16  123.80  3.000
 1EK  H7   O18  C17  110.49  3.000
 1EK  C25  C20  C21  121.50  3.000
 1EK  C21  C20  N11  119.20  3.000
 1EK  C25  C20  N11  119.30  3.000
 1EK  H8   C21  C22  120.84  3.000
 1EK  H8   C21  C20  120.16  3.000
 1EK  C22  C21  C20  118.99  3.000
 1EK  H9   C22  C23  120.19  3.000
 1EK  H9   C22  C21  119.74  3.000
 1EK  C23  C22  C21  120.06  3.000
 1EK  H10  C23  C24  119.89  3.000
 1EK  H10  C23  C22  119.76  3.000
 1EK  C24  C23  C22  120.35  3.000
 1EK  H11  C24  C25  119.76  3.000
 1EK  H11  C24  C23  120.19  3.000
 1EK  C25  C24  C23  120.06  3.000
 1EK  H12  C25  C24  120.90  3.000
 1EK  H12  C25  C20  120.07  3.000
 1EK  C24  C25  C20  119.03  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
 1EK  CONST_01  S07  C03  C02  C01   180.00   0.0  0
 1EK  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 1EK  CONST_03  C04  C05  C06  C01     0.00   0.0  0
 1EK  CONST_04  C08  S07  C03  C02   180.00   0.0  0
 1EK  CONST_05  C09  C04  C03  C02   180.00   0.0  0
 1EK  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 1EK  CONST_07  C05  C06  C01  C02     0.00   0.0  0
 1EK  CONST_08  C10  C08  S07  C03   180.00   0.0  0
 1EK  CONST_09  C09  C08  S07  C03     0.00   0.0  0
 1EK  CONST_10  C08  C09  C04  C03     0.00   0.0  0
 1EK  CONST_11  C06  C05  C04  C03     0.00   0.0  0
 1EK  CONST_12  C06  C01  C02  C03     0.00   0.0  0
 1EK  CONST_13  C10  C08  C09  C04   180.00   0.0  0
 1EK  CONST_14  S07  C08  C09  C04     0.00   0.0  0
 1EK  CONST_15  C08  S07  C03  C04     0.00   0.0  0
 1EK  CONST_16  C08  C09  C04  C05   180.00   0.0  0
 1EK  CONST_17  S07  C03  C04  C05   180.00   0.0  0
 1EK  CONST_18  C09  C04  C05  C06   180.00   0.0  0
 1EK  CONST_21  C09  C04  C03  S07     0.00   0.0  0
 1EK  CONST_22  C20  N11  C10  C08     0.00   0.0  0
 1EK  CONST_23  C12  N11  C10  C08   180.00   0.0  0
 1EK  CONST_24  N13  N14  C10  C08   180.00   0.0  0
 1EK  CONST_29  N13  C12  N11  C10     0.00   0.0  0
 1EK  CONST_30  C12  N13  N14  C10     0.00   0.0  0
 1EK  CONST_31  C24  C25  C20  N11   180.00   0.0  0
 1EK  CONST_32  C22  C21  C20  N11   180.00   0.0  0
 1EK  CONST_33  N14  N13  C12  N11     0.00   0.0  0
 1EK  CONST_34  N13  N14  C10  N11     0.00   0.0  0
 1EK  CONST_37  N14  C10  N11  C12     0.00   0.0  0
 1EK  CONST_38  C20  N11  C12  N13   180.00   0.0  0
 1EK  CONST_39  C20  N11  C10  N14   180.00   0.0  0
 1EK  CONST_40  C23  C24  C25  C20     0.00   0.0  0
 1EK  CONST_41  C23  C22  C21  C20     0.00   0.0  0
 1EK  CONST_42  C24  C23  C22  C21     0.00   0.0  0
 1EK  CONST_43  C24  C25  C20  C21     0.00   0.0  0
 1EK  CONST_44  C25  C24  C23  C22     0.00   0.0  0
 1EK  CONST_45  C25  C20  C21  C22     0.00   0.0  0
 1EK  CONST_46  CL2  C09  C04  C03   180.00   0.0  0
 1EK  CONST_47  CL2  C09  C04  C05     0.00   0.0  0
 1EK  CONST_48  CL2  C09  C08  S07   180.00   0.0  0
 1EK  CONST_49  S15  C12  N11  C10   180.00   0.0  0
 1EK  CONST_50  CL2  C09  C08  C10     0.00   0.0  0
 1EK  CONST_51  S15  C12  N13  N14   180.00   0.0  0
 1EK  CONST_52  C20  N11  C12  S15     0.00   0.0  0
 1EK  CONST_53  H3   C05  C06  C01   180.00   0.0  0
 1EK  CONST_54  H4   C06  C01  C02   180.00   0.0  0
 1EK  CONST_55  H1   C01  C02  C03   180.00   0.0  0
 1EK  CONST_56  H2   C02  C03  C04   180.00   0.0  0
 1EK  CONST_57  H12  C25  C20  N11     0.00   0.0  0
 1EK  CONST_58  H8   C21  C20  N11     0.00   0.0  0
 1EK  CONST_59  H11  C24  C25  C20   180.00   0.0  0
 1EK  CONST_60  H9   C22  C21  C20   180.00   0.0  0
 1EK  CONST_61  H10  C23  C22  C21   180.00   0.0  0
 1EK  CONST_62  H7   O18  C17  C16   180.00   0.0  0
 1EK  Var_01    C17  C16  S15  C12  -179.36  30.0  3
 1EK  Var_02    O19  C17  C16  S15     0.70  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
 1EK  plan-1  C08  0.020
 1EK  plan-1  C10  0.020
 1EK  plan-1  N11  0.020
 1EK  plan-1  C12  0.020
 1EK  plan-1  N13  0.020
 1EK  plan-1  N14  0.020
 1EK  plan-1  S15  0.020
 1EK  plan-1  C20  0.020
 1EK  plan-2  N11  0.020
 1EK  plan-2  C20  0.020
 1EK  plan-2  C21  0.020
 1EK  plan-2  C22  0.020
 1EK  plan-2  C23  0.020
 1EK  plan-2  C24  0.020
 1EK  plan-2  C25  0.020
 1EK  plan-2  H8   0.020
 1EK  plan-2  H9   0.020
 1EK  plan-2  H10  0.020
 1EK  plan-2  H11  0.020
 1EK  plan-2  H12  0.020
 1EK  plan-3  C01  0.020
 1EK  plan-3  C02  0.020
 1EK  plan-3  C03  0.020
 1EK  plan-3  C04  0.020
 1EK  plan-3  C05  0.020
 1EK  plan-3  C06  0.020
 1EK  plan-3  S07  0.020
 1EK  plan-3  C08  0.020
 1EK  plan-3  C09  0.020
 1EK  plan-3  C10  0.020
 1EK  plan-3  CL2  0.020
 1EK  plan-3  H1   0.020
 1EK  plan-3  H2   0.020
 1EK  plan-3  H3   0.020
 1EK  plan-3  H4   0.020
 1EK  plan-4  C16  0.020
 1EK  plan-4  C17  0.020
 1EK  plan-4  O18  0.020
 1EK  plan-4  O19  0.020
 1EK  plan-4  H7   0.020

