# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:34:57 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: 3-{[benzyl(ethyl)carbamoyl]amino}-5-(4-phenoxyphenyl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(Cc1ccccc1)C(=O)Nc2cc(sc2C(O)=O)c3ccc(Oc4ccccc4)cc3
#
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
 QZY  QZY  '3-{[benzyl(ethyl)carbamoyl]amino}-5-(4-phenoxyphenyl)thiophene-2-carboxylic acid'  ligand  58  34  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QZY
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
 QZY  C13  C  CR16  0  -0.300  -83.3561  28.9824  33.1191
 QZY  C15  C  CR16  0  -0.258  -84.1422  29.3432  35.3687
 QZY  C17  C  CR16  0  -0.315  -84.0466  27.1070  34.4758
 QZY  C01  C  CR5   0  -0.469  -87.5160  26.5797  25.4963
 QZY  C02  C  CR5   0   0.491  -86.2064  26.5029  25.0397
 QZY  C04  C  CR5   0  -0.176  -85.8763  26.6169  27.3374
 QZY  C06  C  CR6   0   0.122  -85.2134  26.6641  28.6374
 QZY  C08  C  CR16  0  -0.310  -83.3171  26.1095  30.0336
 QZY  C11  C  CR16  0  -0.302  -85.7913  27.3113  29.7291
 QZY  C12  C  CR6   0   0.310  -83.5584  27.6185  33.2841
 QZY  C14  C  CR16  0  -0.251  -83.6536  29.8415  34.1669
 QZY  C16  C  CR16  0  -0.252  -84.3324  27.9769  35.5207
 QZY  C03  C  CR15  0  -0.275  -85.2739  26.5257  26.1106
 QZY  C07  C  CR16  0  -0.303  -83.9659  26.0594  28.8157
 QZY  C09  C  CR6   0   0.357  -83.9106  26.7623  31.1111
 QZY  C10  C  CR16  0  -0.320  -85.1559  27.3620  30.9588
 QZY  C18  C  C     0   0.759  -84.6890  26.3265  23.1083
 QZY  C19  C  CH2   0  -0.296  -83.3812  26.1252  21.0942
 QZY  C20  C  CH2   0  -0.460  -85.8155  26.5150  20.8814
 QZY  C21  C  CR6   0   0.152  -86.2999  25.2249  20.2631
 QZY  C22  C  CR16  0  -0.310  -86.3906  25.1110  18.8808
 QZY  C23  C  CR16  0  -0.239  -86.8329  23.9324  18.2914
 QZY  C24  C  CR16  0  -0.267  -87.1887  22.8520  19.0848
 QZY  C25  C  CR16  0  -0.240  -87.0998  22.9566  20.4683
 QZY  C26  C  CR16  0  -0.291  -86.6584  24.1339  21.0523
 QZY  C28  C  CH3   0  -0.658  -82.9614  24.6640  21.0365
 QZY  N01  N  NH1   0  -0.825  -85.9340  26.4393  23.6956
 QZY  N02  N  NT    0  -0.482  -84.6646  26.3552  21.7514
 QZY  O01  O  OH1   0  -0.600  -89.8184  26.6748  25.4080
 QZY  O02  O  O     0  -0.470  -88.7088  26.5224  23.4683
 QZY  O03  O  O2    0  -0.507  -83.2253  26.7392  32.2824
 QZY  O04  O  O     0  -0.513  -83.6718  26.2079  23.7745
 QZY  S01  S  S2    0   0.270  -87.5866  26.6653  27.2187
 QZY  H1   H  HCR6  0   0.279  -82.9681  29.3702  32.1854
 QZY  H2   H  HCR6  0   0.261  -84.3700  30.0179  36.1832
 QZY  H3   H  HCR6  0   0.272  -84.1958  26.0406  34.5877
 QZY  H4   H  HCR6  0   0.277  -82.3533  25.6329  30.1577
 QZY  H5   H  HCR6  0   0.264  -86.7492  27.8069  29.6274
 QZY  H6   H  HCR6  0   0.265  -83.4975  30.9049  34.0427
 QZY  H7   H  HCR6  0   0.265  -84.7109  27.5811  36.4537
 QZY  H8   H  HCR5  0   0.289  -84.2056  26.5047  25.9848
 QZY  H9   H  HCR6  0   0.264  -83.4976  25.5287  27.9970
 QZY  H10  H  HCR6  0   0.287  -85.6389  27.8737  31.7801
 QZY  H11  H  HCH2  0   0.244  -83.4694  26.5226  20.0828
 QZY  H12  H  HCH2  0   0.251  -82.6123  26.7152  21.5923
 QZY  H13  H  HCH2  0   0.289  -85.5381  27.2088  20.0855
 QZY  H14  H  HCH2  0   0.271  -86.6292  27.0204  21.4024
 QZY  H15  H  HCR6  0   0.254  -86.1082  25.9506  18.2562
 QZY  H16  H  HCR6  0   0.257  -86.8938  23.8597  17.2133
 QZY  H17  H  HCR6  0   0.257  -87.5324  21.9319  18.6306
 QZY  H18  H  HCR6  0   0.257  -87.3762  22.1175  21.0937
 QZY  H19  H  HCR6  0   0.242  -86.5882  24.1894  22.1321
 QZY  H20  H  HCH3  0   0.231  -81.9998  24.5808  20.5287
 QZY  H21  H  HCH3  0   0.231  -82.8480  24.2434  22.0349
 QZY  H22  H  HCH3  0   0.231  -83.6832  24.0600  20.4882
 QZY  H23  H  HNH1  0   0.437  -86.7664  26.4724  23.1230
 QZY  H24  H  HOH1  0   0.492  -90.5972  26.6744  24.8320
 QZY  C05  C  C     0   0.562  -88.7092  26.5883  24.6858

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
 QZY  C23  C22  aromatic  1.390  0.020  1.390
 QZY  C23  C24  aromatic  1.387  0.020  1.387
 QZY  C22  C21  aromatic  1.390  0.020  1.390
 QZY  C24  C25  aromatic  1.390  0.020  1.390
 QZY  C21  C20  single    1.510  0.020  1.510
 QZY  C21  C26  aromatic  1.394  0.020  1.394
 QZY  C20  N02  single    1.452  0.020  1.452
 QZY  C19  N02  single    1.460  0.020  1.460
 QZY  C19  C28  single    1.521  0.020  1.521
 QZY  C25  C26  aromatic  1.386  0.020  1.386
 QZY  N02  C18  single    1.357  0.020  1.357
 QZY  C18  N01  single    1.381  0.020  1.381
 QZY  C18  O04  double    1.222  0.020  1.222
 QZY  O02  C05  double    1.219  0.020  1.219
 QZY  N01  C02  single    1.373  0.020  1.373
 QZY  C05  O01  single    1.326  0.020  1.326
 QZY  C05  C01  single    1.443  0.020  1.443
 QZY  C02  C01  aromatic  1.389  0.020  1.389
 QZY  C02  C03  aromatic  1.420  0.020  1.420
 QZY  C01  S01  aromatic  1.726  0.020  1.726
 QZY  C03  C04  aromatic  1.370  0.020  1.370
 QZY  S01  C04  aromatic  1.715  0.020  1.715
 QZY  C04  C06  single    1.460  0.020  1.460
 QZY  C06  C07  aromatic  1.398  0.020  1.398
 QZY  C06  C11  aromatic  1.394  0.020  1.394
 QZY  C07  C08  aromatic  1.381  0.020  1.381
 QZY  C11  C10  aromatic  1.385  0.020  1.385
 QZY  C08  C09  aromatic  1.393  0.020  1.393
 QZY  C10  C09  aromatic  1.391  0.020  1.391
 QZY  C09  O03  single    1.357  0.020  1.357
 QZY  C13  C14  aromatic  1.387  0.020  1.387
 QZY  C13  C12  aromatic  1.389  0.020  1.389
 QZY  C14  C15  aromatic  1.390  0.020  1.390
 QZY  O03  C12  single    1.374  0.020  1.374
 QZY  C12  C17  aromatic  1.386  0.020  1.386
 QZY  C15  C16  aromatic  1.388  0.020  1.388
 QZY  C17  C16  aromatic  1.389  0.020  1.389
 QZY  C13  H1   single    0.930  0.020  1.080
 QZY  C15  H2   single    0.930  0.020  1.080
 QZY  C17  H3   single    0.930  0.020  1.080
 QZY  C08  H4   single    0.930  0.020  1.080
 QZY  C11  H5   single    0.930  0.020  1.080
 QZY  C14  H6   single    0.930  0.020  1.080
 QZY  C16  H7   single    0.930  0.020  1.080
 QZY  C03  H8   single    0.930  0.020  1.080
 QZY  C07  H9   single    0.930  0.020  1.080
 QZY  C10  H10  single    0.930  0.020  1.080
 QZY  C19  H11  single    0.970  0.020  1.090
 QZY  C19  H12  single    0.970  0.020  1.090
 QZY  C20  H13  single    0.970  0.020  1.090
 QZY  C20  H14  single    0.970  0.020  1.090
 QZY  C22  H15  single    0.930  0.020  1.080
 QZY  C23  H16  single    0.930  0.020  1.080
 QZY  C24  H17  single    0.930  0.020  1.080
 QZY  C25  H18  single    0.930  0.020  1.080
 QZY  C26  H19  single    0.930  0.020  1.080
 QZY  C28  H20  single    0.970  0.020  1.090
 QZY  C28  H21  single    0.970  0.020  1.090
 QZY  C28  H22  single    0.970  0.020  1.090
 QZY  N01  H23  single    0.860  0.020  1.020
 QZY  O01  H24  single    0.850  0.020  0.980

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
 QZY  H1   C13  C14  120.42  3.000
 QZY  H1   C13  C12  120.43  3.000
 QZY  C14  C13  C12  119.16  3.000
 QZY  H2   C15  C16  120.17  3.000
 QZY  H2   C15  C14  120.10  3.000
 QZY  C16  C15  C14  119.72  3.000
 QZY  H3   C17  C16  120.71  3.000
 QZY  H3   C17  C12  120.07  3.000
 QZY  C16  C17  C12  119.22  3.000
 QZY  S01  C01  C05  121.77  3.000
 QZY  S01  C01  C02  111.68  3.000
 QZY  C05  C01  C02  126.55  3.000
 QZY  N01  C02  C03  127.49  3.000
 QZY  C03  C02  C01  111.74  3.000
 QZY  N01  C02  C01  120.76  3.000
 QZY  S01  C04  C03  112.24  3.000
 QZY  S01  C04  C06  120.89  3.000
 QZY  C03  C04  C06  126.87  3.000
 QZY  C07  C06  C11  118.08  3.000
 QZY  C11  C06  C04  121.60  3.000
 QZY  C07  C06  C04  120.32  3.000
 QZY  H4   C08  C09  119.81  3.000
 QZY  H4   C08  C07  120.23  3.000
 QZY  C09  C08  C07  119.95  3.000
 QZY  H5   C11  C10  118.18  3.000
 QZY  H5   C11  C06  120.35  3.000
 QZY  C10  C11  C06  121.47  3.000
 QZY  O03  C12  C17  118.44  3.000
 QZY  C17  C12  C13  121.07  3.000
 QZY  O03  C12  C13  120.43  3.000
 QZY  H6   C14  C15  120.16  3.000
 QZY  H6   C14  C13  119.41  3.000
 QZY  C15  C14  C13  120.44  3.000
 QZY  H7   C16  C17  119.44  3.000
 QZY  H7   C16  C15  120.17  3.000
 QZY  C17  C16  C15  120.39  3.000
 QZY  H8   C03  C04  122.87  3.000
 QZY  H8   C03  C02  124.30  3.000
 QZY  C04  C03  C02  112.81  3.000
 QZY  H9   C07  C08  118.79  3.000
 QZY  H9   C07  C06  120.13  3.000
 QZY  C08  C07  C06  121.07  3.000
 QZY  O03  C09  C10  123.64  3.000
 QZY  O03  C09  C08  116.40  3.000
 QZY  C10  C09  C08  119.94  3.000
 QZY  H10  C10  C09  121.39  3.000
 QZY  H10  C10  C11  119.12  3.000
 QZY  C09  C10  C11  119.48  3.000
 QZY  O04  C18  N02  122.15  3.000
 QZY  O04  C18  N01  121.77  3.000
 QZY  N02  C18  N01  116.08  3.000
 QZY  H12  C19  H11  106.48  3.000
 QZY  H12  C19  N02  109.22  3.000
 QZY  H11  C19  N02  106.80  3.000
 QZY  H12  C19  C28  110.04  3.000
 QZY  H11  C19  C28  109.71  3.000
 QZY  N02  C19  C28  114.26  3.000
 QZY  H14  C20  H13  104.08  3.000
 QZY  H14  C20  N02  110.87  3.000
 QZY  H13  C20  N02  107.78  3.000
 QZY  H14  C20  C21  110.63  3.000
 QZY  H13  C20  C21  109.02  3.000
 QZY  N02  C20  C21  113.93  3.000
 QZY  C26  C21  C22  118.84  3.000
 QZY  C26  C21  C20  121.29  3.000
 QZY  C22  C21  C20  119.87  3.000
 QZY  H15  C22  C23  119.70  3.000
 QZY  H15  C22  C21  119.51  3.000
 QZY  C23  C22  C21  120.79  3.000
 QZY  H16  C23  C24  120.20  3.000
 QZY  H16  C23  C22  119.82  3.000
 QZY  C24  C23  C22  119.98  3.000
 QZY  H17  C24  C25  120.13  3.000
 QZY  H17  C24  C23  120.25  3.000
 QZY  C25  C24  C23  119.62  3.000
 QZY  H18  C25  C26  119.75  3.000
 QZY  H18  C25  C24  120.02  3.000
 QZY  C26  C25  C24  120.23  3.000
 QZY  H19  C26  C25  118.95  3.000
 QZY  H19  C26  C21  120.50  3.000
 QZY  C25  C26  C21  120.55  3.000
 QZY  H22  C28  H21  108.44  3.000
 QZY  H22  C28  H20  107.91  3.000
 QZY  H21  C28  H20  107.79  3.000
 QZY  H22  C28  C19  111.65  3.000
 QZY  H21  C28  C19  111.40  3.000
 QZY  H20  C28  C19  109.52  3.000
 QZY  H23  N01  C18  120.27  3.000
 QZY  H23  N01  C02  112.93  3.000
 QZY  C18  N01  C02  126.80  3.000
 QZY  C20  N02  C19  116.39  3.000
 QZY  C19  N02  C18  117.54  3.000
 QZY  C20  N02  C18  125.96  3.000
 QZY  H24  O01  C05  110.40  3.000
 QZY  C09  O03  C12  119.73  3.000
 QZY  C04  S01  C01   91.54  3.000
 QZY  O02  C05  O01  123.20  3.000
 QZY  O01  C05  C01  112.72  3.000
 QZY  O02  C05  C01  124.08  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
 QZY  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 QZY  CONST_02  C16  C17  C12  C13     0.00   0.0  0
 QZY  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 QZY  CONST_04  C12  C17  C16  C15     0.00   0.0  0
 QZY  CONST_05  C14  C13  C12  C17     0.00   0.0  0
 QZY  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 QZY  CONST_07  C04  C03  C02  C01     0.00   0.0  0
 QZY  CONST_08  C03  C04  S01  C01     0.00   0.0  0
 QZY  CONST_09  C06  C04  S01  C01   180.00   0.0  0
 QZY  CONST_10  C04  S01  C01  C02     0.00   0.0  0
 QZY  CONST_11  S01  C04  C03  C02     0.00   0.0  0
 QZY  CONST_12  C06  C04  C03  C02   180.00   0.0  0
 QZY  CONST_13  C08  C07  C06  C04   180.00   0.0  0
 QZY  CONST_14  C10  C11  C06  C04   180.00   0.0  0
 QZY  CONST_15  C09  C08  C07  C06     0.00   0.0  0
 QZY  CONST_16  C09  C10  C11  C06     0.00   0.0  0
 QZY  CONST_17  C11  C06  C07  C08     0.00   0.0  0
 QZY  CONST_18  C11  C10  C09  C08     0.00   0.0  0
 QZY  CONST_21  S01  C01  C02  C03     0.00   0.0  0
 QZY  CONST_24  C10  C11  C06  C07     0.00   0.0  0
 QZY  CONST_25  C10  C09  C08  C07     0.00   0.0  0
 QZY  CONST_26  C24  C23  C22  C21     0.00   0.0  0
 QZY  CONST_27  C24  C25  C26  C21     0.00   0.0  0
 QZY  CONST_28  C25  C24  C23  C22     0.00   0.0  0
 QZY  CONST_29  C25  C26  C21  C22     0.00   0.0  0
 QZY  CONST_30  C26  C21  C22  C23     0.00   0.0  0
 QZY  CONST_31  C26  C25  C24  C23     0.00   0.0  0
 QZY  CONST_32  N01  C02  C03  C04   180.00   0.0  0
 QZY  CONST_33  C05  C01  S01  C04   180.00   0.0  0
 QZY  CONST_34  C03  C02  C01  C05   180.00   0.0  0
 QZY  CONST_35  O03  C09  C10  C11   180.00   0.0  0
 QZY  CONST_36  O03  C12  C13  C14   180.00   0.0  0
 QZY  CONST_37  O03  C12  C17  C16   180.00   0.0  0
 QZY  CONST_38  O03  C09  C08  C07   180.00   0.0  0
 QZY  CONST_39  C23  C22  C21  C20   180.00   0.0  0
 QZY  CONST_40  C25  C26  C21  C20   180.00   0.0  0
 QZY  CONST_41  S01  C01  C02  N01   180.00   0.0  0
 QZY  CONST_42  H2   C15  C14  C13   180.00   0.0  0
 QZY  CONST_43  H3   C17  C12  C13   180.00   0.0  0
 QZY  CONST_44  H1   C13  C14  C15   180.00   0.0  0
 QZY  CONST_45  H8   C03  C02  C01   180.00   0.0  0
 QZY  CONST_46  H9   C07  C06  C04     0.00   0.0  0
 QZY  CONST_47  H5   C11  C06  C04     0.00   0.0  0
 QZY  CONST_48  H4   C08  C07  C06   180.00   0.0  0
 QZY  CONST_49  H10  C10  C11  C06   180.00   0.0  0
 QZY  CONST_50  H6   C14  C13  C12   180.00   0.0  0
 QZY  CONST_51  H7   C16  C17  C12   180.00   0.0  0
 QZY  CONST_52  H16  C23  C22  C21   180.00   0.0  0
 QZY  CONST_53  H18  C25  C26  C21   180.00   0.0  0
 QZY  CONST_54  H17  C24  C23  C22   180.00   0.0  0
 QZY  CONST_55  H19  C26  C21  C22   180.00   0.0  0
 QZY  CONST_56  H15  C22  C23  C24   180.00   0.0  0
 QZY  CONST_57  C18  N01  C02  C01   180.00   0.0  0
 QZY  CONST_58  C18  N01  C02  C03     0.00   0.0  0
 QZY  CONST_59  H23  N01  C02  C01     0.00   0.0  0
 QZY  CONST_60  O04  C18  N01  C02     0.00   0.0  0
 QZY  CONST_61  N02  C18  N01  C02   180.00   0.0  0
 QZY  CONST_62  H24  O01  C05  C01   180.00   0.0  0
 QZY  CONST_63  O04  C18  N02  C19     0.00   0.0  0
 QZY  CONST_64  O04  C18  N02  C20   180.00   0.0  0
 QZY  CONST_65  N01  C18  N02  C19   180.00   0.0  0
 QZY  CONST_66  N01  C18  N02  C20     0.00   0.0  0
 QZY  Var_01    C10  C09  O03  C12   -17.87  30.0  2
 QZY  Var_02    O02  C05  C01  C02     0.28  30.0  2
 QZY  Var_03    N02  C20  C21  C22  -123.44  30.0  2
 QZY  Var_04    C21  C20  N02  C18  -101.48  30.0  2
 QZY  Var_05    C28  C19  N02  C18    78.05  30.0  3
 QZY  Var_06    H20  C28  C19  N02   179.74  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
 QZY  plan-1  C01  0.020
 QZY  plan-1  C02  0.020
 QZY  plan-1  C04  0.020
 QZY  plan-1  C06  0.020
 QZY  plan-1  C03  0.020
 QZY  plan-1  N01  0.020
 QZY  plan-1  S01  0.020
 QZY  plan-1  H8   0.020
 QZY  plan-1  C05  0.020
 QZY  plan-2  C01  0.020
 QZY  plan-2  O01  0.020
 QZY  plan-2  O02  0.020
 QZY  plan-2  H24  0.020
 QZY  plan-2  C05  0.020
 QZY  plan-3  C13  0.020
 QZY  plan-3  C15  0.020
 QZY  plan-3  C17  0.020
 QZY  plan-3  C12  0.020
 QZY  plan-3  C14  0.020
 QZY  plan-3  C16  0.020
 QZY  plan-3  O03  0.020
 QZY  plan-3  H1   0.020
 QZY  plan-3  H2   0.020
 QZY  plan-3  H3   0.020
 QZY  plan-3  H6   0.020
 QZY  plan-3  H7   0.020
 QZY  plan-4  C04  0.020
 QZY  plan-4  C06  0.020
 QZY  plan-4  C08  0.020
 QZY  plan-4  C11  0.020
 QZY  plan-4  C07  0.020
 QZY  plan-4  C09  0.020
 QZY  plan-4  C10  0.020
 QZY  plan-4  O03  0.020
 QZY  plan-4  H4   0.020
 QZY  plan-4  H5   0.020
 QZY  plan-4  H9   0.020
 QZY  plan-4  H10  0.020
 QZY  plan-5  C20  0.020
 QZY  plan-5  C21  0.020
 QZY  plan-5  C22  0.020
 QZY  plan-5  C23  0.020
 QZY  plan-5  C24  0.020
 QZY  plan-5  C25  0.020
 QZY  plan-5  C26  0.020
 QZY  plan-5  H15  0.020
 QZY  plan-5  H16  0.020
 QZY  plan-5  H17  0.020
 QZY  plan-5  H18  0.020
 QZY  plan-5  H19  0.020
 QZY  plan-6  C02  0.020
 QZY  plan-6  C18  0.020
 QZY  plan-6  C19  0.020
 QZY  plan-6  C20  0.020
 QZY  plan-6  N01  0.020
 QZY  plan-6  N02  0.020
 QZY  plan-6  O04  0.020
 QZY  plan-6  H23  0.020

