# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 00:55:45 2022
#   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  57  34  .  2022-03-23  2022-03-23
;
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  -0.311  -83.5127  28.8477  32.9526
 QZY  C15  C  CR16   0  -0.263  -83.9472  29.5587  35.2163
 QZY  C17  C  CR16   0  -0.327  -84.1165  27.2258  34.6358
 QZY  C01  C  CR5    0  -0.491  -87.4327  26.5804  25.3432
 QZY  C02  C  CR5    0   0.441  -86.1036  26.5082  24.9850
 QZY  C04  C  CR5    0  -0.197  -85.9127  26.5703  27.3003
 QZY  C06  C  CR6    0   0.124  -85.3405  26.5734  28.6456
 QZY  C08  C  CR16   0  -0.311  -83.5619  25.9412  30.1640
 QZY  C11  C  CR16   0  -0.308  -85.9796  27.2083  29.7124
 QZY  C12  C  CR6    0   0.332  -83.7731  27.5346  33.3277
 QZY  C14  C  CR16   0  -0.246  -83.6066  29.8546  33.9023
 QZY  C16  C  CR16   0  -0.248  -84.1960  28.2421  35.5786
 QZY  C03  C  CR15   0  -0.273  -85.2337  26.5036  26.1127
 QZY  C07  C  CR16   0  -0.312  -84.1253  25.9335  28.9002
 QZY  C09  C  CR6    0   0.335  -84.2175  26.5770  31.2109
 QZY  C10  C  CR16   0  -0.306  -85.4346  27.2096  30.9857
 QZY  C18  C  C      0   0.733  -84.5230  26.3316  23.1051
 QZY  C19  C  CH2    0  -0.292  -83.1561  26.0818  21.1271
 QZY  C20  C  CH2    0  -0.438  -85.5760  26.5209  20.8483
 QZY  C21  C  CR6    0   0.139  -86.1493  25.2362  20.2938
 QZY  C22  C  CR16   0  -0.310  -86.4157  25.1315  18.9329
 QZY  C23  C  CR16   0  -0.239  -86.9574  23.9685  18.3990
 QZY  C24  C  CR16   0  -0.268  -87.2372  22.8900  19.2253
 QZY  C25  C  CR16   0  -0.238  -86.9724  22.9844  20.5866
 QZY  C26  C  CR16   0  -0.298  -86.4355  24.1481  21.1163
 QZY  C28  C  CH3    0  -0.658  -82.7822  24.6075  21.0670
 QZY  N02  N  NT     0  -0.486  -84.4496  26.3484  21.7421
 QZY  O01  O  OC    -1  -0.573  -89.7406  26.6696  25.0336
 QZY  O02  O  O      0  -0.593  -88.4240  26.5576  23.2260
 QZY  O03  O  O2     0  -0.506  -83.6438  26.4964  32.4446
 QZY  O04  O  O      0  -0.526  -83.5191  26.2064  23.7975
 QZY  S01  S  S2     0   0.209  -87.6145  26.6348  27.0508
 QZY  H1   H  HCR6   0   0.278  -83.2360  29.0862  31.9330
 QZY  H2   H  HCR6   0   0.257  -84.0155  30.3489  35.9520
 QZY  H3   H  HCR6   0   0.268  -84.3151  26.1981  34.9130
 QZY  H4   H  HCR6   0   0.270  -82.6190  25.4403  30.3431
 QZY  H5   H  HCR6   0   0.257  -86.9183  27.7254  29.5541
 QZY  H6   H  HCR6   0   0.262  -83.4050  30.8773  33.6113
 QZY  H7   H  HCR6   0   0.261  -84.4611  27.9999  36.5995
 QZY  H8   H  HCR5   0   0.273  -84.1586  26.4752  26.0494
 QZY  H9   H  HCR6   0   0.259  -83.6115  25.4116  28.1032
 QZY  H10  H  HCR6   0   0.282  -85.9615  27.7066  31.7900
 QZY  H11  H  HCH2   0   0.239  -83.1947  26.4911  20.1173
 QZY  H12  H  HCH2   0   0.244  -82.3839  26.6390  21.6567
 QZY  H13  H  HCH2   0   0.280  -85.2456  27.1454  20.0154
 QZY  H14  H  HCH2   0   0.268  -86.3610  27.1053  21.3310
 QZY  H15  H  HCR6   0   0.250  -86.1915  25.9663  18.2788
 QZY  H16  H  HCR6   0   0.253  -87.1528  23.9048  17.3362
 QZY  H17  H  HCR6   0   0.253  -87.6545  21.9803  18.8133
 QZY  H18  H  HCR6   0   0.253  -87.1858  22.1473  21.2390
 QZY  H19  H  HCR6   0   0.249  -86.2302  24.1967  22.1784
 QZY  H20  H  HCH3   0   0.228  -81.8026  24.4933  20.6010
 QZY  H21  H  HCH3   0   0.227  -82.7290  24.1708  22.0635
 QZY  H22  H  HCH3   0   0.228  -83.5003  24.0351  20.4806
 QZY  H23  H  HNH1   0   0.438  -86.6283  26.4833  23.0779
 QZY  C05  C  C      0   0.456  -88.6392  26.6056  24.4661
 QZY  N01  N  NH1    0  -0.828  -85.7723  26.4668  23.6416

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  1.391  0.020  1.391
 QZY  C24  C25  aromatic  1.390  0.020  1.390
 QZY  C21  C20  single    1.512  0.020  1.512
 QZY  C21  C26  aromatic  1.394  0.020  1.394
 QZY  C20  N02  single    1.448  0.020  1.448
 QZY  C19  N02  single    1.457  0.020  1.457
 QZY  C19  C28  single    1.522  0.020  1.522
 QZY  C25  C26  aromatic  1.387  0.020  1.387
 QZY  N02  C18  single    1.365  0.020  1.365
 QZY  C18  N01  single    1.366  0.020  1.366
 QZY  C18  O04  double    1.226  0.020  1.226
 QZY  O02  C05  deloc     1.260  0.020  1.260
 QZY  N01  C02  single    1.384  0.020  1.384
 QZY  C05  O01  deloc     1.241  0.020  1.241
 QZY  C05  C01  single    1.492  0.020  1.492
 QZY  C02  C01  aromatic  1.378  0.020  1.378
 QZY  C02  C03  aromatic  1.424  0.020  1.424
 QZY  C01  S01  aromatic  1.718  0.020  1.718
 QZY  C03  C04  aromatic  1.370  0.020  1.370
 QZY  S01  C04  aromatic  1.721  0.020  1.721
 QZY  C04  C06  single    1.462  0.020  1.462
 QZY  C06  C07  aromatic  1.397  0.020  1.397
 QZY  C06  C11  aromatic  1.396  0.020  1.396
 QZY  C07  C08  aromatic  1.384  0.020  1.384
 QZY  C11  C10  aromatic  1.385  0.020  1.385
 QZY  C08  C09  aromatic  1.389  0.020  1.389
 QZY  C10  C09  aromatic  1.390  0.020  1.390
 QZY  C09  O03  single    1.363  0.020  1.363
 QZY  C13  C14  aromatic  1.387  0.020  1.387
 QZY  C13  C12  aromatic  1.390  0.020  1.390
 QZY  C14  C15  aromatic  1.389  0.020  1.389
 QZY  O03  C12  single    1.369  0.020  1.369
 QZY  C12  C17  aromatic  1.387  0.020  1.387
 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

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  120.13  3.000
 QZY  H1   C13  C12  120.65  3.000
 QZY  C14  C13  C12  119.22  3.000
 QZY  H2   C15  C16  120.27  3.000
 QZY  H2   C15  C14  120.20  3.000
 QZY  C16  C15  C14  119.53  3.000
 QZY  H3   C17  C16  120.69  3.000
 QZY  H3   C17  C12  119.87  3.000
 QZY  C16  C17  C12  119.44  3.000
 QZY  S01  C01  C05  119.88  3.000
 QZY  S01  C01  C02  111.22  3.000
 QZY  C05  C01  C02  128.90  3.000
 QZY  N01  C02  C03  128.47  3.000
 QZY  C03  C02  C01  112.54  3.000
 QZY  N01  C02  C01  118.98  3.000
 QZY  S01  C04  C03  111.49  3.000
 QZY  S01  C04  C06  121.35  3.000
 QZY  C03  C04  C06  127.15  3.000
 QZY  C07  C06  C11  117.86  3.000
 QZY  C11  C06  C04  121.66  3.000
 QZY  C07  C06  C04  120.49  3.000
 QZY  H4   C08  C09  119.87  3.000
 QZY  H4   C08  C07  120.21  3.000
 QZY  C09  C08  C07  119.92  3.000
 QZY  H5   C11  C10  118.35  3.000
 QZY  H5   C11  C06  120.14  3.000
 QZY  C10  C11  C06  121.51  3.000
 QZY  O03  C12  C17  117.57  3.000
 QZY  C17  C12  C13  120.73  3.000
 QZY  O03  C12  C13  121.63  3.000
 QZY  H6   C14  C15  120.09  3.000
 QZY  H6   C14  C13  119.29  3.000
 QZY  C15  C14  C13  120.63  3.000
 QZY  H7   C16  C17  119.39  3.000
 QZY  H7   C16  C15  120.16  3.000
 QZY  C17  C16  C15  120.45  3.000
 QZY  H8   C03  C04  123.16  3.000
 QZY  H8   C03  C02  124.27  3.000
 QZY  C04  C03  C02  112.56  3.000
 QZY  H9   C07  C08  118.82  3.000
 QZY  H9   C07  C06  119.97  3.000
 QZY  C08  C07  C06  121.21  3.000
 QZY  O03  C09  C10  122.83  3.000
 QZY  O03  C09  C08  117.16  3.000
 QZY  C10  C09  C08  119.96  3.000
 QZY  H10  C10  C09  120.98  3.000
 QZY  H10  C10  C11  119.47  3.000
 QZY  C09  C10  C11  119.54  3.000
 QZY  O04  C18  N02  121.41  3.000
 QZY  O04  C18  N01  122.48  3.000
 QZY  N02  C18  N01  116.11  3.000
 QZY  H12  C19  H11  106.45  3.000
 QZY  H12  C19  N02  109.30  3.000
 QZY  H11  C19  N02  106.91  3.000
 QZY  H12  C19  C28  109.91  3.000
 QZY  H11  C19  C28  109.62  3.000
 QZY  N02  C19  C28  114.33  3.000
 QZY  H14  C20  H13  104.41  3.000
 QZY  H14  C20  N02  110.50  3.000
 QZY  H13  C20  N02  107.67  3.000
 QZY  H14  C20  C21  110.14  3.000
 QZY  H13  C20  C21  108.71  3.000
 QZY  N02  C20  C21  114.84  3.000
 QZY  C26  C21  C22  118.64  3.000
 QZY  C26  C21  C20  121.65  3.000
 QZY  C22  C21  C20  119.70  3.000
 QZY  H15  C22  C23  119.56  3.000
 QZY  H15  C22  C21  119.53  3.000
 QZY  C23  C22  C21  120.91  3.000
 QZY  H16  C23  C24  120.18  3.000
 QZY  H16  C23  C22  119.79  3.000
 QZY  C24  C23  C22  120.03  3.000
 QZY  H17  C24  C25  120.22  3.000
 QZY  H17  C24  C23  120.30  3.000
 QZY  C25  C24  C23  119.48  3.000
 QZY  H18  C25  C26  119.67  3.000
 QZY  H18  C25  C24  120.01  3.000
 QZY  C26  C25  C24  120.32  3.000
 QZY  H19  C26  C25  119.06  3.000
 QZY  H19  C26  C21  120.32  3.000
 QZY  C25  C26  C21  120.62  3.000
 QZY  H22  C28  H21  108.29  3.000
 QZY  H22  C28  H20  107.87  3.000
 QZY  H21  C28  H20  107.76  3.000
 QZY  H22  C28  C19  111.61  3.000
 QZY  H21  C28  C19  111.36  3.000
 QZY  H20  C28  C19  109.81  3.000
 QZY  C20  N02  C19  116.86  3.000
 QZY  C19  N02  C18  117.84  3.000
 QZY  C20  N02  C18  125.16  3.000
 QZY  C09  O03  C12  119.95  3.000
 QZY  C04  S01  C01   92.20  3.000
 QZY  O02  C05  O01  127.15  3.000
 QZY  O01  C05  C01  116.74  3.000
 QZY  O02  C05  C01  116.11  3.000
 QZY  H23  N01  C18  123.31  3.000
 QZY  H23  N01  C02  109.47  3.000
 QZY  C18  N01  C02  127.08  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  O04  C18  N02  C19     0.00   0.0  0
 QZY  CONST_63  O04  C18  N02  C20   180.00   0.0  0
 QZY  CONST_64  N01  C18  N02  C19   180.00   0.0  0
 QZY  CONST_65  N01  C18  N02  C20     0.00   0.0  0
 QZY  Var_01    C10  C09  O03  C12   -35.34  30.0  2
 QZY  Var_02    O02  C05  C01  C02    -0.18  30.0  2
 QZY  Var_03    N02  C20  C21  C22  -132.82  30.0  2
 QZY  Var_04    C21  C20  N02  C18   -97.23  30.0  2
 QZY  Var_05    C28  C19  N02  C18    79.15  30.0  2
 QZY  Var_06    H20  C28  C19  N02  -179.64  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  S01  0.020
 QZY  plan-1  H8   0.020
 QZY  plan-1  C05  0.020
 QZY  plan-1  N01  0.020
 QZY  plan-2  C01  0.020
 QZY  plan-2  O01  0.020
 QZY  plan-2  O02  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  N02  0.020
 QZY  plan-6  O04  0.020
 QZY  plan-6  H23  0.020
 QZY  plan-6  N01  0.020

