# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 02:09:11 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-(2-ethylphenyl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2sc(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
 ZJD  ZJD  "5-(2-ethylphenyl)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_ZJD
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
 ZJD  C10  C  C1     0  -0.290   2.7298  51.9300  10.1814
 ZJD  C13  C  CH3    0  -0.660   5.7475  52.7969  10.8449
 ZJD  C01  C  CR15   0  -0.208   5.7734  49.9414  14.8546
 ZJD  C02  C  CR5    0  -0.325   5.0340  48.8136  15.0620
 ZJD  S03  S  S2     0   0.209   3.6508  48.7987  14.0428
 ZJD  C04  C  CR5    0  -0.253   4.0580  50.3189  13.3286
 ZJD  C05  C  CR15   0  -0.217   5.2214  50.7980  13.8695
 ZJD  C06  C  C      0   0.063   3.1748  50.9087  12.3131
 ZJD  C07  C  C1     0  -0.298   1.7979  50.9370  12.5691
 ZJD  C08  C  C1     0  -0.256   0.9007  51.4551  11.6523
 ZJD  C09  C  C1     0  -0.248   1.3712  51.9590  10.4470
 ZJD  C11  C  C      0   0.099   3.6523  51.4113  11.0911
 ZJD  C12  C  CH2    0  -0.532   5.1056  51.4177  10.6982
 ZJD  O15  O  OC    -1  -0.578   6.2832  47.7097  16.7051
 ZJD  O16  O  O      0  -0.594   4.3937  46.7635  15.9538
 ZJD  H1   H  H      0   0.248   3.0939  52.3083   9.2326
 ZJD  H2   H  HCH3   0   0.232   6.7952  52.7694  10.5444
 ZJD  H3   H  HCH3   0   0.228   5.2417  53.5335  10.2194
 ZJD  H4   H  HCH3   0   0.229   5.7028  53.1559  11.8734
 ZJD  H5   H  HCR5   0   0.250   6.6852  50.1560  15.3944
 ZJD  H6   H  HCR5   0   0.260   5.6608  51.7454  13.5901
 ZJD  H7   H  H      0   0.250   1.4286  50.5578  13.5144
 ZJD  H8   H  H      0   0.254  -0.1576  51.4663  11.8784
 ZJD  H9   H  H      0   0.252   0.6831  52.3646   9.7165
 ZJD  H10  H  HCH2   0   0.247   5.1847  51.1063   9.6536
 ZJD  H11  H  HCH2   0   0.247   5.6659  50.6860  11.2804
 ZJD  C14  C  C      0   0.390   5.2633  47.6551  15.9968

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
 ZJD  C10  C09  aromatic  1.385  0.020  1.385
 ZJD  C10  C11  aromatic  1.396  0.020  1.396
 ZJD  C09  C08  aromatic  1.389  0.020  1.389
 ZJD  C12  C13  single    1.528  0.020  1.528
 ZJD  C12  C11  single    1.505  0.020  1.505
 ZJD  C11  C06  aromatic  1.405  0.020  1.405
 ZJD  C08  C07  aromatic  1.383  0.020  1.383
 ZJD  C06  C07  aromatic  1.401  0.020  1.401
 ZJD  C06  C04  single    1.469  0.020  1.469
 ZJD  C04  C05  aromatic  1.369  0.020  1.369
 ZJD  C04  S03  aromatic  1.728  0.020  1.728
 ZJD  C05  C01  aromatic  1.417  0.020  1.417
 ZJD  S03  C02  aromatic  1.718  0.020  1.718
 ZJD  C01  C02  aromatic  1.364  0.020  1.364
 ZJD  C02  C14  single    1.506  0.020  1.506
 ZJD  C14  O16  deloc     1.246  0.020  1.246
 ZJD  C14  O15  deloc     1.243  0.020  1.243
 ZJD  C10  H1   single    0.930  0.020  1.080
 ZJD  C13  H2   single    0.970  0.020  1.090
 ZJD  C13  H3   single    0.970  0.020  1.090
 ZJD  C13  H4   single    0.970  0.020  1.090
 ZJD  C01  H5   single    0.930  0.020  1.080
 ZJD  C05  H6   single    0.930  0.020  1.080
 ZJD  C07  H7   single    0.930  0.020  1.080
 ZJD  C08  H8   single    0.930  0.020  1.080
 ZJD  C09  H9   single    0.930  0.020  1.080
 ZJD  C12  H10  single    0.970  0.020  1.090
 ZJD  C12  H11  single    0.970  0.020  1.090

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
 ZJD  H1   C10  C11  118.56  3.000
 ZJD  H1   C10  C09  119.34  3.000
 ZJD  C11  C10  C09  122.10  3.000
 ZJD  H4   C13  H3   107.43  3.000
 ZJD  H4   C13  H2   107.92  3.000
 ZJD  H3   C13  H2   107.73  3.000
 ZJD  H4   C13  C12  111.74  3.000
 ZJD  H3   C13  C12  111.08  3.000
 ZJD  H2   C13  C12  110.76  3.000
 ZJD  H5   C01  C05  123.75  3.000
 ZJD  H5   C01  C02  123.03  3.000
 ZJD  C05  C01  C02  113.22  3.000
 ZJD  C14  C02  S03  118.95  3.000
 ZJD  C14  C02  C01  130.37  3.000
 ZJD  S03  C02  C01  110.69  3.000
 ZJD  C04  S03  C02   92.74  3.000
 ZJD  C06  C04  C05  130.03  3.000
 ZJD  C05  C04  S03  110.16  3.000
 ZJD  C06  C04  S03  119.80  3.000
 ZJD  H6   C05  C04  123.34  3.000
 ZJD  H6   C05  C01  123.44  3.000
 ZJD  C04  C05  C01  113.20  3.000
 ZJD  C11  C06  C07  119.07  3.000
 ZJD  C07  C06  C04  118.21  3.000
 ZJD  C11  C06  C04  122.71  3.000
 ZJD  H7   C07  C08  119.23  3.000
 ZJD  H7   C07  C06  119.17  3.000
 ZJD  C08  C07  C06  121.59  3.000
 ZJD  H8   C08  C09  120.59  3.000
 ZJD  H8   C08  C07  119.97  3.000
 ZJD  C09  C08  C07  119.43  3.000
 ZJD  H9   C09  C08  120.43  3.000
 ZJD  H9   C09  C10  120.14  3.000
 ZJD  C08  C09  C10  119.43  3.000
 ZJD  C12  C11  C06  123.82  3.000
 ZJD  C06  C11  C10  118.37  3.000
 ZJD  C12  C11  C10  117.80  3.000
 ZJD  H11  C12  H10  106.38  3.000
 ZJD  H11  C12  C11  110.73  3.000
 ZJD  H10  C12  C11  108.55  3.000
 ZJD  H11  C12  C13  109.79  3.000
 ZJD  H10  C12  C13  108.57  3.000
 ZJD  C11  C12  C13  112.60  3.000
 ZJD  O16  C14  O15  128.59  3.000
 ZJD  O15  C14  C02  116.41  3.000
 ZJD  O16  C14  C02  115.00  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
 ZJD  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 ZJD  CONST_02  C07  C06  C11  C10     0.00   0.0  0
 ZJD  CONST_03  C04  C06  C11  C10   180.00   0.0  0
 ZJD  CONST_04  C06  C04  C05  C01   180.00   0.0  0
 ZJD  CONST_05  S03  C04  C05  C01     0.00   0.0  0
 ZJD  CONST_06  C04  S03  C02  C01     0.00   0.0  0
 ZJD  CONST_07  C06  C04  S03  C02   180.00   0.0  0
 ZJD  CONST_08  C05  C04  S03  C02     0.00   0.0  0
 ZJD  CONST_09  C04  C05  C01  C02     0.00   0.0  0
 ZJD  CONST_12  C05  C01  C02  S03     0.00   0.0  0
 ZJD  CONST_13  C08  C07  C06  C04   180.00   0.0  0
 ZJD  CONST_16  C09  C10  C11  C06     0.00   0.0  0
 ZJD  CONST_17  C09  C08  C07  C06     0.00   0.0  0
 ZJD  CONST_18  C11  C10  C09  C08     0.00   0.0  0
 ZJD  CONST_19  C11  C06  C07  C08     0.00   0.0  0
 ZJD  CONST_20  C12  C11  C06  C04     0.00   0.0  0
 ZJD  CONST_21  C14  C02  S03  C04   180.00   0.0  0
 ZJD  CONST_22  C14  C02  C01  C05   180.00   0.0  0
 ZJD  CONST_23  C12  C11  C06  C07   180.00   0.0  0
 ZJD  CONST_24  C12  C11  C10  C09   180.00   0.0  0
 ZJD  CONST_25  H8   C08  C09  C10   180.00   0.0  0
 ZJD  CONST_26  H6   C05  C01  C02   180.00   0.0  0
 ZJD  CONST_27  H6   C05  C04  S03   180.00   0.0  0
 ZJD  CONST_28  H5   C01  C02  S03   180.00   0.0  0
 ZJD  CONST_29  H7   C07  C06  C04     0.00   0.0  0
 ZJD  CONST_30  H5   C01  C05  C04   180.00   0.0  0
 ZJD  CONST_31  H1   C10  C11  C06   180.00   0.0  0
 ZJD  CONST_32  H8   C08  C07  C06   180.00   0.0  0
 ZJD  CONST_33  H6   C05  C04  C06     0.00   0.0  0
 ZJD  CONST_34  H9   C09  C08  C07   180.00   0.0  0
 ZJD  CONST_35  H1   C10  C09  C08   180.00   0.0  0
 ZJD  CONST_36  H7   C07  C08  C09   180.00   0.0  0
 ZJD  CONST_37  H9   C09  C10  C11   180.00   0.0  0
 ZJD  CONST_38  H7   C07  C06  C11   180.00   0.0  0
 ZJD  Var_01    C13  C12  C11  C10    77.67  30.0  1
 ZJD  Var_02    C06  C11  C12  C13  -102.67  30.0  2
 ZJD  Var_03    O16  C14  C02  C01   179.96  30.0  2
 ZJD  Var_04    O15  C14  C02  C01    -0.00  30.0  2
 ZJD  Var_05    O16  C14  C02  S03    -0.56  30.0  2
 ZJD  Var_06    O15  C14  C02  S03   179.47  30.0  2
 ZJD  Var_07    H10  C12  C11  C10   -42.56  30.0  1
 ZJD  Var_08    H11  C12  C11  C10  -158.99  30.0  1
 ZJD  Var_09    H10  C12  C11  C06   137.10  30.0  1
 ZJD  Var_10    H11  C12  C11  C06    20.67  30.0  1
 ZJD  Var_11    H2   C13  C12  C11  -179.49  30.0  3
 ZJD  Var_12    H3   C13  C12  C11   -59.80  30.0  3
 ZJD  Var_13    H4   C13  C12  C11    60.16  30.0  3

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
 ZJD  plan-1  C01  0.020
 ZJD  plan-1  C02  0.020
 ZJD  plan-1  S03  0.020
 ZJD  plan-1  C04  0.020
 ZJD  plan-1  C05  0.020
 ZJD  plan-1  C06  0.020
 ZJD  plan-1  H5   0.020
 ZJD  plan-1  H6   0.020
 ZJD  plan-1  C14  0.020
 ZJD  plan-2  C10  0.020
 ZJD  plan-2  C04  0.020
 ZJD  plan-2  C06  0.020
 ZJD  plan-2  C07  0.020
 ZJD  plan-2  C08  0.020
 ZJD  plan-2  C09  0.020
 ZJD  plan-2  C11  0.020
 ZJD  plan-2  C12  0.020
 ZJD  plan-2  H1   0.020
 ZJD  plan-2  H7   0.020
 ZJD  plan-2  H8   0.020
 ZJD  plan-2  H9   0.020
 ZJD  plan-3  C02  0.020
 ZJD  plan-3  O15  0.020
 ZJD  plan-3  O16  0.020
 ZJD  plan-3  C14  0.020

