# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 02:44:08 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 5-(2,4,6-trimethylphenyl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(c(C)c1)c2sc(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
 ZJ7  ZJ7  "5-(2,4,6-trimethylphenyl)thiophene-2-carboxylic acid"  ligand  30  17  .  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_ZJ7
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
 ZJ7  C10  C  CR16   0  -0.377  -4.9724  20.3502  -33.8491
 ZJ7  C13  C  CR15   0  -0.192  -4.0858  24.7788  -35.2244
 ZJ7  C15  C  CR5    0  -0.321  -1.8687  25.2517  -35.7350
 ZJ7  C17  C  C      0   0.388  -0.6028  25.8769  -36.2595
 ZJ7  S01  S  S2     0   0.204  -1.7710  23.7873  -34.8364
 ZJ7  O02  O  OC    -1  -0.595   0.4460  25.2610  -35.9868
 ZJ7  O03  O  O      0  -0.580  -0.7364  26.9301  -36.9064
 ZJ7  C04  C  CR6    0  -0.006  -4.1095  22.5956  -33.8927
 ZJ7  C05  C  CR6    0   0.114  -4.4537  22.7508  -32.5437
 ZJ7  C06  C  CR6    0   0.114  -4.3674  21.3873  -34.5519
 ZJ7  C07  C  CR5    0  -0.264  -3.4811  23.7106  -34.6252
 ZJ7  C08  C  CR6    0   0.133  -5.3209  20.4811  -32.5098
 ZJ7  C09  C  CR16   0  -0.375  -5.0555  21.6900  -31.8753
 ZJ7  C11  C  CH3    0  -0.735  -4.1852  24.0400  -31.8222
 ZJ7  C12  C  CH3    0  -0.738  -4.0034  21.2029  -35.9973
 ZJ7  C14  C  CH3    0  -0.723  -5.9430  19.3399  -31.7592
 ZJ7  C16  C  CR15   0  -0.215  -3.1656  25.6559  -35.8568
 ZJ7  H1   H  HCR6   0   0.237  -5.1795  19.4177  -34.3629
 ZJ7  H2   H  HCR5   0   0.249  -5.1575  24.9271  -35.2140
 ZJ7  H4   H  HCR6   0   0.236  -5.3242  21.8119  -30.8313
 ZJ7  H5   H  HCH3   0   0.246  -4.7809  24.8588  -32.2285
 ZJ7  H6   H  HCH3   0   0.246  -4.4215  23.9508  -30.7627
 ZJ7  H7   H  HCH3   0   0.240  -3.1395  24.3389  -31.9103
 ZJ7  H8   H  HCH3   0   0.244  -2.9223  21.2322  -36.1436
 ZJ7  H9   H  HCH3   0   0.247  -4.3628  20.2461  -36.3735
 ZJ7  H10  H  HCH3   0   0.244  -4.4253  21.9918  -36.6213
 ZJ7  H11  H  HCH3   0   0.246  -5.1840  18.7634  -31.2261
 ZJ7  H12  H  HCH3   0   0.242  -6.6590  19.6921  -31.0168
 ZJ7  H13  H  HCH3   0   0.242  -6.4596  18.6535  -32.4293
 ZJ7  H14  H  HCR5   0   0.248  -3.4550  26.5530  -36.3862

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
 ZJ7  O03  C17  deloc     1.243  0.020  1.243
 ZJ7  O02  C17  deloc     1.246  0.020  1.246
 ZJ7  C17  C15  single    1.506  0.020  1.506
 ZJ7  C12  C06  single    1.502  0.020  1.502
 ZJ7  C16  C15  aromatic  1.364  0.020  1.364
 ZJ7  C16  C13  aromatic  1.420  0.020  1.420
 ZJ7  C15  S01  aromatic  1.721  0.020  1.721
 ZJ7  C13  C07  aromatic  1.366  0.020  1.366
 ZJ7  S01  C07  aromatic  1.725  0.020  1.725
 ZJ7  C07  C04  single    1.475  0.020  1.475
 ZJ7  C06  C04  aromatic  1.400  0.020  1.400
 ZJ7  C06  C10  aromatic  1.391  0.020  1.391
 ZJ7  C04  C05  aromatic  1.401  0.020  1.401
 ZJ7  C10  C08  aromatic  1.390  0.020  1.390
 ZJ7  C05  C11  single    1.502  0.020  1.502
 ZJ7  C05  C09  aromatic  1.391  0.020  1.391
 ZJ7  C08  C09  aromatic  1.391  0.020  1.391
 ZJ7  C08  C14  single    1.501  0.020  1.501
 ZJ7  C10  H1   single    0.930  0.020  1.080
 ZJ7  C13  H2   single    0.930  0.020  1.080
 ZJ7  C09  H4   single    0.930  0.020  1.080
 ZJ7  C11  H5   single    0.970  0.020  1.090
 ZJ7  C11  H6   single    0.970  0.020  1.090
 ZJ7  C11  H7   single    0.970  0.020  1.090
 ZJ7  C12  H8   single    0.970  0.020  1.090
 ZJ7  C12  H9   single    0.970  0.020  1.090
 ZJ7  C12  H10  single    0.970  0.020  1.090
 ZJ7  C14  H11  single    0.970  0.020  1.090
 ZJ7  C14  H12  single    0.970  0.020  1.090
 ZJ7  C14  H13  single    0.970  0.020  1.090
 ZJ7  C16  H14  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
 ZJ7  H1   C10  C08  119.31  3.000
 ZJ7  H1   C10  C06  118.99  3.000
 ZJ7  C08  C10  C06  121.71  3.000
 ZJ7  H2   C13  C16  124.16  3.000
 ZJ7  H2   C13  C07  122.79  3.000
 ZJ7  C16  C13  C07  113.05  3.000
 ZJ7  C16  C15  S01  110.66  3.000
 ZJ7  S01  C15  C17  119.17  3.000
 ZJ7  C16  C15  C17  130.18  3.000
 ZJ7  O03  C17  O02  128.52  3.000
 ZJ7  O02  C17  C15  115.21  3.000
 ZJ7  O03  C17  C15  116.27  3.000
 ZJ7  C07  S01  C15   92.61  3.000
 ZJ7  C07  C04  C06  119.80  3.000
 ZJ7  C06  C04  C05  120.24  3.000
 ZJ7  C07  C04  C05  119.95  3.000
 ZJ7  C11  C05  C09  120.09  3.000
 ZJ7  C09  C05  C04  118.99  3.000
 ZJ7  C11  C05  C04  120.92  3.000
 ZJ7  C12  C06  C04  120.95  3.000
 ZJ7  C04  C06  C10  119.05  3.000
 ZJ7  C12  C06  C10  120.00  3.000
 ZJ7  C04  C07  S01  121.13  3.000
 ZJ7  C04  C07  C13  128.35  3.000
 ZJ7  S01  C07  C13  110.52  3.000
 ZJ7  C14  C08  C09  120.79  3.000
 ZJ7  C14  C08  C10  120.94  3.000
 ZJ7  C09  C08  C10  118.26  3.000
 ZJ7  H4   C09  C08  119.30  3.000
 ZJ7  H4   C09  C05  118.95  3.000
 ZJ7  C08  C09  C05  121.76  3.000
 ZJ7  H7   C11  H6   108.00  3.000
 ZJ7  H7   C11  H5   106.72  3.000
 ZJ7  H6   C11  H5   107.78  3.000
 ZJ7  H7   C11  C05  111.58  3.000
 ZJ7  H6   C11  C05  111.00  3.000
 ZJ7  H5   C11  C05  111.57  3.000
 ZJ7  H10  C12  H9   108.07  3.000
 ZJ7  H10  C12  H8   106.69  3.000
 ZJ7  H9   C12  H8   107.70  3.000
 ZJ7  H10  C12  C06  111.59  3.000
 ZJ7  H9   C12  C06  111.12  3.000
 ZJ7  H8   C12  C06  111.46  3.000
 ZJ7  H13  C14  H12  108.13  3.000
 ZJ7  H13  C14  H11  107.28  3.000
 ZJ7  H12  C14  H11  107.13  3.000
 ZJ7  H13  C14  C08  111.59  3.000
 ZJ7  H12  C14  C08  111.55  3.000
 ZJ7  H11  C14  C08  110.94  3.000
 ZJ7  H14  C16  C15  122.97  3.000
 ZJ7  H14  C16  C13  123.86  3.000
 ZJ7  C15  C16  C13  113.17  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
 ZJ7  CONST_01  C07  C04  C06  C10   180.00   0.0  0
 ZJ7  CONST_02  C05  C04  C06  C10     0.00   0.0  0
 ZJ7  CONST_03  C05  C09  C08  C10     0.00   0.0  0
 ZJ7  CONST_04  S01  C15  C16  C13     0.00   0.0  0
 ZJ7  CONST_05  C15  S01  C07  C13     0.00   0.0  0
 ZJ7  CONST_08  C07  C13  C16  C15     0.00   0.0  0
 ZJ7  CONST_09  C04  C07  S01  C15   180.00   0.0  0
 ZJ7  CONST_10  C16  C13  C07  S01     0.00   0.0  0
 ZJ7  CONST_13  C16  C13  C07  C04   180.00   0.0  0
 ZJ7  CONST_14  C08  C10  C06  C04     0.00   0.0  0
 ZJ7  CONST_15  C08  C09  C05  C04     0.00   0.0  0
 ZJ7  CONST_16  C09  C05  C04  C06     0.00   0.0  0
 ZJ7  CONST_17  C09  C08  C10  C06     0.00   0.0  0
 ZJ7  CONST_18  C16  C15  S01  C07     0.00   0.0  0
 ZJ7  CONST_19  C09  C05  C04  C07   180.00   0.0  0
 ZJ7  CONST_20  C17  C15  C16  C13   180.00   0.0  0
 ZJ7  CONST_21  C07  S01  C15  C17   180.00   0.0  0
 ZJ7  CONST_22  C12  C06  C04  C05   180.00   0.0  0
 ZJ7  CONST_23  C14  C08  C09  C05   180.00   0.0  0
 ZJ7  CONST_24  C11  C05  C04  C06   180.00   0.0  0
 ZJ7  CONST_25  C14  C08  C10  C06   180.00   0.0  0
 ZJ7  CONST_26  C12  C06  C04  C07     0.00   0.0  0
 ZJ7  CONST_27  C11  C05  C04  C07     0.00   0.0  0
 ZJ7  CONST_28  C12  C06  C10  C08   180.00   0.0  0
 ZJ7  CONST_29  C11  C05  C09  C08   180.00   0.0  0
 ZJ7  CONST_30  H4   C09  C08  C10   180.00   0.0  0
 ZJ7  CONST_31  H2   C13  C16  C15   180.00   0.0  0
 ZJ7  CONST_32  H14  C16  C15  S01   180.00   0.0  0
 ZJ7  CONST_33  H2   C13  C07  S01   180.00   0.0  0
 ZJ7  CONST_34  H2   C13  C07  C04     0.00   0.0  0
 ZJ7  CONST_35  H1   C10  C06  C04   180.00   0.0  0
 ZJ7  CONST_36  H4   C09  C05  C04   180.00   0.0  0
 ZJ7  CONST_37  H14  C16  C13  C07   180.00   0.0  0
 ZJ7  CONST_38  H1   C10  C08  C09   180.00   0.0  0
 ZJ7  Var_01    O03  C17  C15  S01   179.68  30.0  3
 ZJ7  Var_02    O02  C17  C15  S01    -0.14  30.0  3
 ZJ7  Var_03    C16  C15  C17  O02  -179.66  30.0  2
 ZJ7  Var_04    C16  C15  C17  O03     0.16  30.0  2
 ZJ7  Var_05    H8   C12  C06  C10  -114.60  30.0  2
 ZJ7  Var_06    H9   C12  C06  C10     5.54  30.0  2
 ZJ7  Var_07    H10  C12  C06  C10   126.23  30.0  2
 ZJ7  Var_08    H11  C14  C08  C10    94.48  30.0  2
 ZJ7  Var_09    H12  C14  C08  C10  -146.16  30.0  2
 ZJ7  Var_10    H13  C14  C08  C10   -25.09  30.0  2
 ZJ7  Var_11    H8   C12  C06  C04    65.53  30.0  2
 ZJ7  Var_12    H9   C12  C06  C04  -174.33  30.0  2
 ZJ7  Var_13    H10  C12  C06  C04   -53.64  30.0  2
 ZJ7  Var_14    H5   C11  C05  C04    65.54  30.0  2
 ZJ7  Var_15    H6   C11  C05  C04  -174.24  30.0  2
 ZJ7  Var_16    H7   C11  C05  C04   -53.73  30.0  2
 ZJ7  Var_17    H5   C11  C05  C09  -114.28  30.0  2
 ZJ7  Var_18    H6   C11  C05  C09     5.95  30.0  2
 ZJ7  Var_19    H7   C11  C05  C09   126.45  30.0  2
 ZJ7  Var_20    H11  C14  C08  C09   -84.32  30.0  2
 ZJ7  Var_21    H12  C14  C08  C09    35.04  30.0  2
 ZJ7  Var_22    H13  C14  C08  C09   156.10  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
 ZJ7  plan-1  C13  0.020
 ZJ7  plan-1  C15  0.020
 ZJ7  plan-1  C17  0.020
 ZJ7  plan-1  S01  0.020
 ZJ7  plan-1  C04  0.020
 ZJ7  plan-1  C07  0.020
 ZJ7  plan-1  C16  0.020
 ZJ7  plan-1  H2   0.020
 ZJ7  plan-1  H14  0.020
 ZJ7  plan-2  C10  0.020
 ZJ7  plan-2  C04  0.020
 ZJ7  plan-2  C05  0.020
 ZJ7  plan-2  C06  0.020
 ZJ7  plan-2  C07  0.020
 ZJ7  plan-2  C08  0.020
 ZJ7  plan-2  C09  0.020
 ZJ7  plan-2  C11  0.020
 ZJ7  plan-2  C12  0.020
 ZJ7  plan-2  C14  0.020
 ZJ7  plan-2  H1   0.020
 ZJ7  plan-2  H4   0.020
 ZJ7  plan-3  C15  0.020
 ZJ7  plan-3  C17  0.020
 ZJ7  plan-3  O02  0.020
 ZJ7  plan-3  O03  0.020

