# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 03:00:04 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-(2,6-dimethylphenyl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C)c1c2sc(cc2)C(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
 ZJ4  ZJ4  "5-(2,6-dimethylphenyl)thiophene-2-carboxylic acid"  ligand  27  16  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZJ4
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
 ZJ4  C10  C  C      0   0.388  -5.8881  24.7310  3.9489
 ZJ4  C15  C  CH3    0  -0.734  -8.6001  19.8001  2.1559
 ZJ4  C01  C  CR16   0  -0.230  -6.0678  17.1942  1.0837
 ZJ4  C02  C  CR16   0  -0.322  -4.9124  17.9513  0.9689
 ZJ4  C03  C  CR6    0   0.092  -4.9283  19.3182  1.2327
 ZJ4  C04  C  CH3    0  -0.735  -3.6692  20.1262  1.1075
 ZJ4  C05  C  CR6    0   0.015  -6.1358  19.9194  1.6126
 ZJ4  C06  C  CR5    0  -0.263  -6.1775  21.3687  1.8859
 ZJ4  C07  C  CR15   0  -0.190  -6.5156  22.3811  1.0343
 ZJ4  C08  C  CR15   0  -0.214  -6.4564  23.6623  1.6436
 ZJ4  C09  C  CR5    0  -0.320  -6.0743  23.6173  2.9519
 ZJ4  O11  O  OC    -1  -0.594  -5.5152  24.3703  5.0822
 ZJ4  O12  O  O      0  -0.580  -6.1231  25.8819  3.5414
 ZJ4  S13  S  S2     0   0.206  -5.7848  21.9935  3.4444
 ZJ4  C14  C  CR6    0   0.092  -7.3079  19.1610  1.7364
 ZJ4  C16  C  CR16   0  -0.322  -7.2563  17.7963  1.4659
 ZJ4  H1   H  HCH3   0   0.242  -8.5034  20.3055  3.1182
 ZJ4  H2   H  HCH3   0   0.247  -8.9281  20.5530  1.4379
 ZJ4  H3   H  HCH3   0   0.247  -9.3918  19.0575  2.2458
 ZJ4  H4   H  HCR6   0   0.250  -6.0421  16.1319  0.8763
 ZJ4  H5   H  HCR6   0   0.245  -3.9846  17.4778  0.6708
 ZJ4  H6   H  HCH3   0   0.246  -3.7909  20.9501  0.4033
 ZJ4  H7   H  HCH3   0   0.243  -3.3804  20.5685  2.0623
 ZJ4  H8   H  HCH3   0   0.247  -2.8412  19.5084  0.7633
 ZJ4  H9   H  HCR5   0   0.250  -6.7977  22.2109  0.0038
 ZJ4  H10  H  HCR5   0   0.248  -6.6881  24.5851  1.1303
 ZJ4  H12  H  HCR6   0   0.245  -8.1573  17.2016  1.5566

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
 ZJ4  C02  C01  aromatic  1.386  0.020  1.386
 ZJ4  C02  C03  aromatic  1.392  0.020  1.392
 ZJ4  C01  C16  aromatic  1.386  0.020  1.386
 ZJ4  C07  C08  aromatic  1.420  0.020  1.420
 ZJ4  C07  C06  aromatic  1.365  0.020  1.365
 ZJ4  C04  C03  single    1.501  0.020  1.501
 ZJ4  C03  C05  aromatic  1.401  0.020  1.401
 ZJ4  C16  C14  aromatic  1.392  0.020  1.392
 ZJ4  C05  C14  aromatic  1.401  0.020  1.401
 ZJ4  C05  C06  single    1.475  0.020  1.475
 ZJ4  C14  C15  single    1.501  0.020  1.501
 ZJ4  C08  C09  aromatic  1.364  0.020  1.364
 ZJ4  C06  S13  aromatic  1.724  0.020  1.724
 ZJ4  C09  S13  aromatic  1.721  0.020  1.721
 ZJ4  C09  C10  single    1.506  0.020  1.506
 ZJ4  O12  C10  deloc     1.243  0.020  1.243
 ZJ4  C10  O11  deloc     1.246  0.020  1.246
 ZJ4  C15  H1   single    0.970  0.020  1.090
 ZJ4  C15  H2   single    0.970  0.020  1.090
 ZJ4  C15  H3   single    0.970  0.020  1.090
 ZJ4  C01  H4   single    0.930  0.020  1.080
 ZJ4  C02  H5   single    0.930  0.020  1.080
 ZJ4  C04  H6   single    0.970  0.020  1.090
 ZJ4  C04  H7   single    0.970  0.020  1.090
 ZJ4  C04  H8   single    0.970  0.020  1.090
 ZJ4  C07  H9   single    0.930  0.020  1.080
 ZJ4  C08  H10  single    0.930  0.020  1.080
 ZJ4  C16  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
 ZJ4  O12  C10  O11  128.49  3.000
 ZJ4  O11  C10  C09  115.14  3.000
 ZJ4  O12  C10  C09  116.37  3.000
 ZJ4  H3   C15  H2   107.84  3.000
 ZJ4  H3   C15  H1   107.90  3.000
 ZJ4  H2   C15  H1   106.70  3.000
 ZJ4  H3   C15  C14  111.00  3.000
 ZJ4  H2   C15  C14  111.63  3.000
 ZJ4  H1   C15  C14  111.54  3.000
 ZJ4  H4   C01  C16  119.96  3.000
 ZJ4  H4   C01  C02  120.02  3.000
 ZJ4  C16  C01  C02  120.02  3.000
 ZJ4  H5   C02  C03  119.41  3.000
 ZJ4  H5   C02  C01  119.86  3.000
 ZJ4  C03  C02  C01  120.73  3.000
 ZJ4  C05  C03  C04  120.95  3.000
 ZJ4  C05  C03  C02  118.84  3.000
 ZJ4  C04  C03  C02  120.20  3.000
 ZJ4  H8   C04  H7   107.77  3.000
 ZJ4  H8   C04  H6   108.01  3.000
 ZJ4  H7   C04  H6   106.76  3.000
 ZJ4  H8   C04  C03  111.02  3.000
 ZJ4  H7   C04  C03  111.55  3.000
 ZJ4  H6   C04  C03  111.52  3.000
 ZJ4  C14  C05  C06  119.44  3.000
 ZJ4  C06  C05  C03  119.73  3.000
 ZJ4  C14  C05  C03  120.82  3.000
 ZJ4  S13  C06  C07  110.57  3.000
 ZJ4  S13  C06  C05  121.12  3.000
 ZJ4  C07  C06  C05  128.30  3.000
 ZJ4  H9   C07  C08  124.16  3.000
 ZJ4  H9   C07  C06  122.82  3.000
 ZJ4  C08  C07  C06  113.02  3.000
 ZJ4  H10  C08  C09  122.94  3.000
 ZJ4  H10  C08  C07  123.88  3.000
 ZJ4  C09  C08  C07  113.18  3.000
 ZJ4  S13  C09  C08  110.65  3.000
 ZJ4  S13  C09  C10  119.17  3.000
 ZJ4  C08  C09  C10  130.18  3.000
 ZJ4  C09  S13  C06   92.58  3.000
 ZJ4  C16  C14  C05  118.84  3.000
 ZJ4  C05  C14  C15  120.94  3.000
 ZJ4  C16  C14  C15  120.22  3.000
 ZJ4  H12  C16  C14  119.41  3.000
 ZJ4  H12  C16  C01  119.85  3.000
 ZJ4  C14  C16  C01  120.74  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
 ZJ4  CONST_01  C05  C03  C02  C01     0.00   0.0  0
 ZJ4  CONST_02  C05  C14  C16  C01     0.00   0.0  0
 ZJ4  CONST_03  C14  C16  C01  C02     0.00   0.0  0
 ZJ4  CONST_04  C14  C05  C03  C02     0.00   0.0  0
 ZJ4  CONST_05  C06  C05  C03  C02   180.00   0.0  0
 ZJ4  CONST_06  C16  C01  C02  C03     0.00   0.0  0
 ZJ4  CONST_07  C16  C14  C05  C03     0.00   0.0  0
 ZJ4  CONST_10  C08  C07  C06  C05   180.00   0.0  0
 ZJ4  CONST_11  C09  S13  C06  C05   180.00   0.0  0
 ZJ4  CONST_12  C09  C08  C07  C06     0.00   0.0  0
 ZJ4  CONST_13  C16  C14  C05  C06   180.00   0.0  0
 ZJ4  CONST_14  C08  C09  S13  C06     0.00   0.0  0
 ZJ4  CONST_15  S13  C09  C08  C07     0.00   0.0  0
 ZJ4  CONST_17  C09  S13  C06  C07     0.00   0.0  0
 ZJ4  CONST_18  S13  C06  C07  C08     0.00   0.0  0
 ZJ4  CONST_20  C07  C08  C09  C10   180.00   0.0  0
 ZJ4  CONST_21  C06  S13  C09  C10   180.00   0.0  0
 ZJ4  CONST_22  C01  C16  C14  C15   180.00   0.0  0
 ZJ4  CONST_23  C03  C05  C14  C15   180.00   0.0  0
 ZJ4  CONST_24  C06  C05  C14  C15     0.00   0.0  0
 ZJ4  CONST_25  C04  C03  C02  C01   180.00   0.0  0
 ZJ4  CONST_26  C14  C05  C03  C04   180.00   0.0  0
 ZJ4  CONST_27  C06  C05  C03  C04     0.00   0.0  0
 ZJ4  CONST_28  H12  C16  C01  C02   180.00   0.0  0
 ZJ4  CONST_29  H4   C01  C02  C03   180.00   0.0  0
 ZJ4  CONST_30  H5   C02  C03  C05   180.00   0.0  0
 ZJ4  CONST_31  H12  C16  C14  C05   180.00   0.0  0
 ZJ4  CONST_32  H9   C07  C06  C05     0.00   0.0  0
 ZJ4  CONST_33  H10  C08  C07  C06   180.00   0.0  0
 ZJ4  CONST_34  H9   C07  C08  C09   180.00   0.0  0
 ZJ4  CONST_35  H9   C07  C06  S13   180.00   0.0  0
 ZJ4  CONST_36  H10  C08  C09  S13   180.00   0.0  0
 ZJ4  CONST_37  H4   C01  C16  C14   180.00   0.0  0
 ZJ4  CONST_38  H5   C02  C01  C16   180.00   0.0  0
 ZJ4  Var_01    O12  C10  C09  C08     0.59  30.0  2
 ZJ4  Var_02    O11  C10  C09  C08  -179.39  30.0  2
 ZJ4  Var_03    S13  C09  C10  O11     0.65  30.0  2
 ZJ4  Var_04    S13  C09  C10  O12  -179.37  30.0  2
 ZJ4  Var_05    H6   C04  C03  C02   122.84  30.0  2
 ZJ4  Var_06    H7   C04  C03  C02  -117.89  30.0  2
 ZJ4  Var_07    H8   C04  C03  C02     2.33  30.0  2
 ZJ4  Var_08    H6   C04  C03  C05   -57.06  30.0  2
 ZJ4  Var_09    H7   C04  C03  C05    62.21  30.0  2
 ZJ4  Var_10    H8   C04  C03  C05  -177.57  30.0  2
 ZJ4  Var_11    H1   C15  C14  C05   -56.90  30.0  2
 ZJ4  Var_12    H2   C15  C14  C05    62.37  30.0  2
 ZJ4  Var_13    H3   C15  C14  C05  -177.27  30.0  2
 ZJ4  Var_14    H1   C15  C14  C16   122.95  30.0  2
 ZJ4  Var_15    H2   C15  C14  C16  -117.77  30.0  2
 ZJ4  Var_16    H3   C15  C14  C16     2.58  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
 ZJ4  plan-1  C10  0.020
 ZJ4  plan-1  C05  0.020
 ZJ4  plan-1  C06  0.020
 ZJ4  plan-1  C07  0.020
 ZJ4  plan-1  C08  0.020
 ZJ4  plan-1  C09  0.020
 ZJ4  plan-1  S13  0.020
 ZJ4  plan-1  H9   0.020
 ZJ4  plan-1  H10  0.020
 ZJ4  plan-2  C15  0.020
 ZJ4  plan-2  C01  0.020
 ZJ4  plan-2  C02  0.020
 ZJ4  plan-2  C03  0.020
 ZJ4  plan-2  C04  0.020
 ZJ4  plan-2  C05  0.020
 ZJ4  plan-2  C06  0.020
 ZJ4  plan-2  C14  0.020
 ZJ4  plan-2  C16  0.020
 ZJ4  plan-2  H4   0.020
 ZJ4  plan-2  H5   0.020
 ZJ4  plan-2  H12  0.020
 ZJ4  plan-3  C10  0.020
 ZJ4  plan-3  C09  0.020
 ZJ4  plan-3  O11  0.020
 ZJ4  plan-3  O12  0.020

