# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 02:49:26 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 5-(2-methylphenyl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1c2sc(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
 ZJA  ZJA  "5-(2-methylphenyl)thiophene-2-carboxylic acid"  ligand  24  15  .  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_ZJA
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
 ZJA  C12  C  C      0   0.390  1.4615   2.9084  15.2666
 ZJA  C01  C  CR16   0  -0.250  5.3559  -0.6929   9.2071
 ZJA  C02  C  CR16   0  -0.289  6.0268   0.4488   9.6182
 ZJA  C03  C  CR6    0   0.065  5.4814   1.3308  10.5497
 ZJA  C04  C  CR6    0   0.089  4.2097   1.0434  11.0758
 ZJA  C05  C  CR16   0  -0.300  3.5456  -0.1156  10.6618
 ZJA  C06  C  CR16   0  -0.255  4.1063  -0.9801   9.7368
 ZJA  C07  C  CR5    0  -0.249  3.5549   1.9214  12.0537
 ZJA  C08  C  CR15   0  -0.212  3.4012   3.2823  12.0265
 ZJA  C09  C  CR15   0  -0.206  2.6606   3.7809  13.1263
 ZJA  C10  C  CR5    0  -0.326  2.2559   2.8048  13.9903
 ZJA  S11  S  S2     0   0.209  2.7870   1.2607  13.4537
 ZJA  O13  O  OC    -1  -0.593  1.2595   1.8297  15.8565
 ZJA  O14  O  O      0  -0.578  1.0933   4.0497  15.5937
 ZJA  H1   H  HCH3   0   0.249  5.9482   3.4372  10.4468
 ZJA  H2   H  HCH3   0   0.246  6.1955   2.7320  12.0324
 ZJA  H3   H  HCH3   0   0.250  7.3318   2.3955  10.7247
 ZJA  H4   H  HCR6   0   0.253  5.8103  -1.3552   8.4815
 ZJA  H5   H  HCR6   0   0.248  7.0093   0.6613   9.2132
 ZJA  H6   H  HCR6   0   0.249  2.5618  -0.3314  11.0607
 ZJA  H7   H  HCR6   0   0.254  3.5677  -1.8667   9.4287
 ZJA  H8   H  HCR5   0   0.255  3.7834   3.9049  11.2296
 ZJA  H9   H  HCR5   0   0.250  2.4302   4.8271  13.2699
 ZJA  C15  C  CH3    0  -0.747  6.2782   2.5345  10.9639

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
 ZJA  C01  C02  aromatic  1.387  0.020  1.387
 ZJA  C01  C06  aromatic  1.387  0.020  1.387
 ZJA  C02  C03  aromatic  1.394  0.020  1.394
 ZJA  C06  C05  aromatic  1.385  0.020  1.385
 ZJA  C03  C15  single    1.502  0.020  1.502
 ZJA  C03  C04  aromatic  1.406  0.020  1.406
 ZJA  C05  C04  aromatic  1.398  0.020  1.398
 ZJA  C04  C07  single    1.468  0.020  1.468
 ZJA  C08  C07  aromatic  1.370  0.020  1.370
 ZJA  C08  C09  aromatic  1.417  0.020  1.417
 ZJA  C07  S11  aromatic  1.728  0.020  1.728
 ZJA  C09  C10  aromatic  1.365  0.020  1.365
 ZJA  S11  C10  aromatic  1.719  0.020  1.719
 ZJA  C12  O14  deloc     1.243  0.020  1.243
 ZJA  C12  O13  deloc     1.246  0.020  1.246
 ZJA  C10  C12  single    1.507  0.020  1.507
 ZJA  C15  H1   single    0.970  0.020  1.090
 ZJA  C15  H2   single    0.970  0.020  1.090
 ZJA  C15  H3   single    0.970  0.020  1.090
 ZJA  C01  H4   single    0.930  0.020  1.080
 ZJA  C02  H5   single    0.930  0.020  1.080
 ZJA  C05  H6   single    0.930  0.020  1.080
 ZJA  C06  H7   single    0.930  0.020  1.080
 ZJA  C08  H8   single    0.930  0.020  1.080
 ZJA  C09  H9   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
 ZJA  O14  C12  O13  128.49  3.000
 ZJA  O13  C12  C10  115.27  3.000
 ZJA  O14  C12  C10  116.24  3.000
 ZJA  H4   C01  C06  120.50  3.000
 ZJA  H4   C01  C02  119.96  3.000
 ZJA  C06  C01  C02  119.54  3.000
 ZJA  H5   C02  C03  118.71  3.000
 ZJA  H5   C02  C01  119.30  3.000
 ZJA  C03  C02  C01  121.99  3.000
 ZJA  C04  C03  C02  118.34  3.000
 ZJA  C04  C03  C15  122.72  3.000
 ZJA  C02  C03  C15  118.94  3.000
 ZJA  C07  C04  C05  118.75  3.000
 ZJA  C07  C04  C03  122.03  3.000
 ZJA  C05  C04  C03  119.22  3.000
 ZJA  H6   C05  C06  119.30  3.000
 ZJA  H6   C05  C04  119.17  3.000
 ZJA  C06  C05  C04  121.53  3.000
 ZJA  H7   C06  C05  120.01  3.000
 ZJA  H7   C06  C01  120.61  3.000
 ZJA  C05  C06  C01  119.38  3.000
 ZJA  S11  C07  C08  110.25  3.000
 ZJA  S11  C07  C04  120.60  3.000
 ZJA  C08  C07  C04  129.12  3.000
 ZJA  H8   C08  C09  123.68  3.000
 ZJA  H8   C08  C07  123.17  3.000
 ZJA  C09  C08  C07  113.13  3.000
 ZJA  H9   C09  C10  123.02  3.000
 ZJA  H9   C09  C08  123.72  3.000
 ZJA  C10  C09  C08  113.25  3.000
 ZJA  S11  C10  C09  110.68  3.000
 ZJA  S11  C10  C12  119.28  3.000
 ZJA  C09  C10  C12  130.03  3.000
 ZJA  C10  S11  C07   92.68  3.000
 ZJA  H3   C15  H2   108.18  3.000
 ZJA  H3   C15  H1   107.10  3.000
 ZJA  H2   C15  H1   106.96  3.000
 ZJA  H3   C15  C03  110.51  3.000
 ZJA  H2   C15  C03  112.05  3.000
 ZJA  H1   C15  C03  111.82  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
 ZJA  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 ZJA  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 ZJA  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 ZJA  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 ZJA  CONST_05  C07  C04  C03  C02   180.00   0.0  0
 ZJA  CONST_06  C06  C01  C02  C03     0.00   0.0  0
 ZJA  CONST_07  C06  C05  C04  C03     0.00   0.0  0
 ZJA  CONST_10  C09  C08  C07  C04   180.00   0.0  0
 ZJA  CONST_11  C10  S11  C07  C04   180.00   0.0  0
 ZJA  CONST_14  C07  C04  C05  C06   180.00   0.0  0
 ZJA  CONST_15  C10  C09  C08  C07     0.00   0.0  0
 ZJA  CONST_16  C09  C10  S11  C07     0.00   0.0  0
 ZJA  CONST_17  C10  S11  C07  C08     0.00   0.0  0
 ZJA  CONST_18  S11  C10  C09  C08     0.00   0.0  0
 ZJA  CONST_19  S11  C07  C08  C09     0.00   0.0  0
 ZJA  CONST_20  C08  C09  C10  C12   180.00   0.0  0
 ZJA  CONST_21  C07  S11  C10  C12   180.00   0.0  0
 ZJA  CONST_22  C01  C02  C03  C15   180.00   0.0  0
 ZJA  CONST_23  C05  C04  C03  C15   180.00   0.0  0
 ZJA  CONST_24  C07  C04  C03  C15     0.00   0.0  0
 ZJA  CONST_25  H6   C05  C06  C01   180.00   0.0  0
 ZJA  CONST_26  H7   C06  C01  C02   180.00   0.0  0
 ZJA  CONST_27  H4   C01  C02  C03   180.00   0.0  0
 ZJA  CONST_28  H6   C05  C04  C03   180.00   0.0  0
 ZJA  CONST_29  H5   C02  C03  C04   180.00   0.0  0
 ZJA  CONST_30  H7   C06  C05  C04   180.00   0.0  0
 ZJA  CONST_31  H8   C08  C07  C04     0.00   0.0  0
 ZJA  CONST_32  H4   C01  C06  C05   180.00   0.0  0
 ZJA  CONST_33  H5   C02  C01  C06   180.00   0.0  0
 ZJA  CONST_34  H6   C05  C04  C07     0.00   0.0  0
 ZJA  CONST_35  H9   C09  C08  C07   180.00   0.0  0
 ZJA  CONST_36  H8   C08  C09  C10   180.00   0.0  0
 ZJA  CONST_37  H8   C08  C07  S11   180.00   0.0  0
 ZJA  CONST_38  H9   C09  C10  S11   180.00   0.0  0
 ZJA  Var_01    O14  C12  C10  C09     0.98  30.0  2
 ZJA  Var_02    O13  C12  C10  C09  -179.06  30.0  2
 ZJA  Var_03    O14  C12  C10  S11  -179.21  30.0  2
 ZJA  Var_04    O13  C12  C10  S11     0.75  30.0  2
 ZJA  Var_05    H1   C15  C03  C02   100.30  30.0  2
 ZJA  Var_06    H2   C15  C03  C02  -139.62  30.0  2
 ZJA  Var_07    H3   C15  C03  C02   -18.91  30.0  2
 ZJA  Var_08    H1   C15  C03  C04   -80.56  30.0  2
 ZJA  Var_09    H2   C15  C03  C04    39.52  30.0  2
 ZJA  Var_10    H3   C15  C03  C04   160.24  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
 ZJA  plan-1  C12  0.020
 ZJA  plan-1  C04  0.020
 ZJA  plan-1  C07  0.020
 ZJA  plan-1  C08  0.020
 ZJA  plan-1  C09  0.020
 ZJA  plan-1  C10  0.020
 ZJA  plan-1  S11  0.020
 ZJA  plan-1  H8   0.020
 ZJA  plan-1  H9   0.020
 ZJA  plan-2  C01  0.020
 ZJA  plan-2  C02  0.020
 ZJA  plan-2  C03  0.020
 ZJA  plan-2  C04  0.020
 ZJA  plan-2  C05  0.020
 ZJA  plan-2  C06  0.020
 ZJA  plan-2  C07  0.020
 ZJA  plan-2  H4   0.020
 ZJA  plan-2  H5   0.020
 ZJA  plan-2  H6   0.020
 ZJA  plan-2  H7   0.020
 ZJA  plan-2  C15  0.020
 ZJA  plan-3  C12  0.020
 ZJA  plan-3  C10  0.020
 ZJA  plan-3  O13  0.020
 ZJA  plan-3  O14  0.020

