# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 20:24:26 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1nnc2ccccc12)N(Cc3cscc3)c4ccc(NC(=O)c5sccc5)cc4
#
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
 4F4  4F4  N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}thiophene-2-carboxamide  ligand  52  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4F4
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
 4F4  C10  C  CR6   0   0.308  -0.2213   0.4275  -0.6123
 4F4  O01  O  O     0  -0.448   1.8277  -0.6395   0.8179
 4F4  C02  C  C     0   0.532   2.0819   0.2171  -0.0037
 4F4  N03  N  NT    0  -0.574   1.1314   0.8508  -0.7368
 4F4  C04  C  CH2   0  -0.407   1.4352   1.9314  -1.6732
 4F4  C05  C  CR5   0   0.125   2.0281   3.1528  -1.0315
 4F4  C06  C  CR15  0  -0.517   3.0000   3.9067  -1.6191
 4F4  S07  S  S2    0   0.224   3.4447   5.2452  -0.6493
 4F4  C08  C  CR15  0  -0.453   2.3314   4.8006   0.5731
 4F4  C09  C  CR15  0  -0.204   1.6455   3.6741   0.2401
 4F4  C11  C  CR16  0  -0.254  -0.5836  -0.8822  -0.9089
 4F4  C12  C  CR16  0  -0.360  -1.9017  -1.2796  -0.8067
 4F4  C13  C  CR6   0   0.388  -2.8990  -0.3797  -0.4197
 4F4  N14  N  NH1   0  -0.773  -4.1988  -0.8852  -0.3345
 4F4  C15  C  C     0   0.556  -5.3612  -0.2128  -0.1249
 4F4  C16  C  CR5   0  -0.332  -6.5743  -1.0504  -0.0414
 4F4  C17  C  CR15  0  -0.179  -7.8518  -0.5670  -0.1217
 4F4  C18  C  CR15  0  -0.174  -8.8314  -1.5809  -0.0079
 4F4  C19  C  CR15  0  -0.445  -8.2839  -2.8177   0.1659
 4F4  S20  S  S2    0   0.240  -6.5790  -2.7599   0.1944
 4F4  O21  O  O     0  -0.454  -5.4389   0.9983  -0.0158
 4F4  C22  C  CR16  0  -0.313  -2.5388   0.9370  -0.1367
 4F4  C23  C  CR16  0  -0.268  -1.2083   1.3212  -0.2273
 4F4  C24  C  CH2   0  -0.447   3.5312   0.6245  -0.2670
 4F4  N25  N  NR5   0  -0.379   4.4236  -0.2683   0.4082
 4F4  C26  C  CR56  0   0.401   4.7699  -1.5327   0.0707
 4F4  C27  C  CR16  0  -0.293   4.4997  -2.3482  -1.0296
 4F4  C28  C  CR16  0  -0.261   5.0679  -3.6025  -1.0028
 4F4  C29  C  CR16  0  -0.269   5.8750  -4.0371   0.0709
 4F4  C30  C  CR16  0  -0.289   6.1352  -3.2258   1.1515
 4F4  C31  C  CR56  0   0.123   5.5632  -1.9491   1.1405
 4F4  N32  N  N     0  -0.319   5.6242  -0.9257   2.0443
 4F4  N33  N  N     0  -0.057   4.9368   0.0491   1.5939
 4F4  H1   H  HCH2  0   0.291   2.0866   1.5719  -2.4740
 4F4  H2   H  HCH2  0   0.305   0.4954   2.1934  -2.1591
 4F4  H3   H  HCR5  0   0.299   3.4821   3.7332  -2.5699
 4F4  H4   H  HCR5  0   0.300   2.2403   5.3897   1.4724
 4F4  H5   H  HCR5  0   0.267   0.9053   3.2268   0.8888
 4F4  H6   H  HCR6  0   0.268   0.1601  -1.5988  -1.2306
 4F4  H7   H  HCR6  0   0.277  -2.1610  -2.3050  -1.0419
 4F4  H8   H  HNH1  0   0.420  -4.2659  -1.8734  -0.5280
 4F4  H9   H  HCR5  0   0.278  -8.0781   0.4794  -0.2664
 4F4  H10  H  HCR5  0   0.278  -9.8957  -1.4023  -0.0485
 4F4  H11  H  HCR5  0   0.310  -8.7937  -3.7607   0.2914
 4F4  H12  H  HCR6  0   0.286  -3.2720   1.6668   0.1622
 4F4  H13  H  HCR6  0   0.266  -0.9551   2.3469   0.0080
 4F4  H14  H  HCH2  0   0.308   3.7648   0.6278  -1.3333
 4F4  H15  H  HCH2  0   0.332   3.7264   1.6319   0.1005
 4F4  H16  H  HCR6  0   0.279   3.8833  -2.0252  -1.8580
 4F4  H17  H  HCR6  0   0.270   4.8906  -4.2799  -1.8273
 4F4  H18  H  HCR6  0   0.266   6.2950  -5.0333   0.0362
 4F4  H19  H  HCR6  0   0.274   6.7521  -3.5581   1.9756

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
 4F4  C18  C19  aromatic  1.364  0.020  1.364
 4F4  C18  C17  aromatic  1.414  0.020  1.414
 4F4  C19  S20  aromatic  1.706  0.020  1.706
 4F4  C17  C16  aromatic  1.368  0.020  1.368
 4F4  S20  C16  aromatic  1.726  0.020  1.726
 4F4  C16  C15  single    1.477  0.020  1.477
 4F4  C15  N14  single    1.359  0.020  1.359
 4F4  C15  O21  double    1.218  0.020  1.218
 4F4  N14  C13  single    1.397  0.020  1.397
 4F4  C22  C13  aromatic  1.394  0.020  1.394
 4F4  C22  C23  aromatic  1.388  0.020  1.388
 4F4  C13  C12  aromatic  1.398  0.020  1.398
 4F4  C23  C10  aromatic  1.386  0.020  1.386
 4F4  C12  C11  aromatic  1.380  0.020  1.380
 4F4  S07  C08  aromatic  1.712  0.020  1.712
 4F4  S07  C06  aromatic  1.712  0.020  1.712
 4F4  C08  C09  aromatic  1.360  0.020  1.360
 4F4  C10  C11  aromatic  1.391  0.020  1.391
 4F4  C10  N03  single    1.423  0.020  1.423
 4F4  C24  N25  single    1.432  0.020  1.432
 4F4  C24  C02  single    1.528  0.020  1.528
 4F4  C09  C05  aromatic  1.427  0.020  1.427
 4F4  C06  C05  aromatic  1.363  0.020  1.363
 4F4  N33  N25  aromatic  1.330  0.020  1.330
 4F4  N33  N32  aromatic  1.275  0.020  1.275
 4F4  N25  C26  aromatic  1.354  0.020  1.354
 4F4  C05  C04  single    1.502  0.020  1.502
 4F4  N03  C02  single    1.357  0.020  1.357
 4F4  N03  C04  single    1.462  0.020  1.462
 4F4  C02  O01  double    1.214  0.020  1.214
 4F4  N32  C31  aromatic  1.367  0.020  1.367
 4F4  C26  C31  aromatic  1.395  0.020  1.395
 4F4  C26  C27  aromatic  1.396  0.020  1.396
 4F4  C31  C30  aromatic  1.399  0.020  1.399
 4F4  C27  C28  aromatic  1.377  0.020  1.377
 4F4  C30  C29  aromatic  1.376  0.020  1.376
 4F4  C28  C29  aromatic  1.412  0.020  1.412
 4F4  C04  H1   single    0.970  0.020  1.090
 4F4  C04  H2   single    0.970  0.020  1.090
 4F4  C06  H3   single    0.930  0.020  1.080
 4F4  C08  H4   single    0.930  0.020  1.080
 4F4  C09  H5   single    0.930  0.020  1.080
 4F4  C11  H6   single    0.930  0.020  1.080
 4F4  C12  H7   single    0.930  0.020  1.080
 4F4  N14  H8   single    0.860  0.020  1.020
 4F4  C17  H9   single    0.930  0.020  1.080
 4F4  C18  H10  single    0.930  0.020  1.080
 4F4  C19  H11  single    0.930  0.020  1.080
 4F4  C22  H12  single    0.930  0.020  1.080
 4F4  C23  H13  single    0.930  0.020  1.080
 4F4  C24  H14  single    0.970  0.020  1.090
 4F4  C24  H15  single    0.970  0.020  1.090
 4F4  C27  H16  single    0.930  0.020  1.080
 4F4  C28  H17  single    0.930  0.020  1.080
 4F4  C29  H18  single    0.930  0.020  1.080
 4F4  C30  H19  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
 4F4  C23  C10  C11  118.74  3.000
 4F4  C11  C10  N03  120.61  3.000
 4F4  C23  C10  N03  120.63  3.000
 4F4  C24  C02  N03  116.52  3.000
 4F4  N03  C02  O01  123.25  3.000
 4F4  C24  C02  O01  120.22  3.000
 4F4  C04  N03  C02  123.06  3.000
 4F4  C04  N03  C10  118.27  3.000
 4F4  C02  N03  C10  118.66  3.000
 4F4  H2   C04  H1   105.44  3.000
 4F4  H2   C04  C05  109.60  3.000
 4F4  H1   C04  C05  110.20  3.000
 4F4  H2   C04  N03  106.50  3.000
 4F4  H1   C04  N03  110.49  3.000
 4F4  C05  C04  N03  114.18  3.000
 4F4  C09  C05  C06  111.92  3.000
 4F4  C06  C05  C04  123.17  3.000
 4F4  C09  C05  C04  124.91  3.000
 4F4  H3   C06  S07  120.56  3.000
 4F4  H3   C06  C05  127.51  3.000
 4F4  S07  C06  C05  111.93  3.000
 4F4  C08  S07  C06   91.86  3.000
 4F4  H4   C08  C09  127.85  3.000
 4F4  H4   C08  S07  120.55  3.000
 4F4  C09  C08  S07  111.60  3.000
 4F4  H5   C09  C08  122.75  3.000
 4F4  H5   C09  C05  124.56  3.000
 4F4  C08  C09  C05  112.68  3.000
 4F4  H6   C11  C12  119.19  3.000
 4F4  H6   C11  C10  120.54  3.000
 4F4  C12  C11  C10  120.27  3.000
 4F4  H7   C12  C13  119.90  3.000
 4F4  H7   C12  C11  119.01  3.000
 4F4  C13  C12  C11  121.09  3.000
 4F4  C22  C13  N14  124.73  3.000
 4F4  C22  C13  C12  118.67  3.000
 4F4  N14  C13  C12  116.60  3.000
 4F4  H8   N14  C15  117.21  3.000
 4F4  H8   N14  C13  113.85  3.000
 4F4  C15  N14  C13  128.76  3.000
 4F4  O21  C15  C16  120.42  3.000
 4F4  O21  C15  N14  124.06  3.000
 4F4  C16  C15  N14  115.51  3.000
 4F4  S20  C16  C17  110.82  3.000
 4F4  S20  C16  C15  124.88  3.000
 4F4  C17  C16  C15  124.29  3.000
 4F4  H9   C17  C18  124.05  3.000
 4F4  H9   C17  C16  123.07  3.000
 4F4  C18  C17  C16  112.88  3.000
 4F4  H10  C18  C19  123.39  3.000
 4F4  H10  C18  C17  124.13  3.000
 4F4  C19  C18  C17  112.47  3.000
 4F4  H11  C19  S20  119.98  3.000
 4F4  H11  C19  C18  128.14  3.000
 4F4  S20  C19  C18  111.87  3.000
 4F4  C19  S20  C16   91.95  3.000
 4F4  H12  C22  C23  118.90  3.000
 4F4  H12  C22  C13  121.37  3.000
 4F4  C23  C22  C13  119.73  3.000
 4F4  H13  C23  C22  118.19  3.000
 4F4  H13  C23  C10  120.32  3.000
 4F4  C22  C23  C10  121.49  3.000
 4F4  H15  C24  H14  106.75  3.000
 4F4  H15  C24  N25  107.81  3.000
 4F4  H14  C24  N25  109.22  3.000
 4F4  H15  C24  C02  110.98  3.000
 4F4  H14  C24  C02  111.84  3.000
 4F4  N25  C24  C02  110.10  3.000
 4F4  N33  N25  C26  110.27  3.000
 4F4  C26  N25  C24  128.64  3.000
 4F4  N33  N25  C24  120.80  3.000
 4F4  C31  C26  C27  122.68  3.000
 4F4  C27  C26  N25  133.84  3.000
 4F4  C31  C26  N25  103.47  3.000
 4F4  H16  C27  C28  121.46  3.000
 4F4  H16  C27  C26  122.64  3.000
 4F4  C28  C27  C26  115.91  3.000
 4F4  H17  C28  C29  118.73  3.000
 4F4  H17  C28  C27  119.20  3.000
 4F4  C29  C28  C27  122.07  3.000
 4F4  H18  C29  C30  119.66  3.000
 4F4  H18  C29  C28  118.75  3.000
 4F4  C30  C29  C28  121.59  3.000
 4F4  H19  C30  C31  121.30  3.000
 4F4  H19  C30  C29  121.67  3.000
 4F4  C31  C30  C29  117.03  3.000
 4F4  N32  C31  C30  131.29  3.000
 4F4  C30  C31  C26  120.72  3.000
 4F4  N32  C31  C26  107.99  3.000
 4F4  N33  N32  C31  108.35  3.000
 4F4  N32  N33  N25  109.90  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
 4F4  CONST_01  C13  C22  C23  C10     0.00   0.0  0
 4F4  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 4F4  CONST_03  S07  C08  C09  C05     0.00   0.0  0
 4F4  CONST_04  C08  S07  C06  C05     0.00   0.0  0
 4F4  CONST_05  C09  C08  S07  C06     0.00   0.0  0
 4F4  CONST_06  C08  C09  C05  C06     0.00   0.0  0
 4F4  CONST_07  C09  C05  C06  S07     0.00   0.0  0
 4F4  CONST_08  C22  C13  C12  C11     0.00   0.0  0
 4F4  CONST_09  C22  C23  C10  C11     0.00   0.0  0
 4F4  CONST_10  C23  C22  C13  C12     0.00   0.0  0
 4F4  CONST_11  C23  C10  C11  C12     0.00   0.0  0
 4F4  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 4F4  CONST_13  C18  C19  S20  C16     0.00   0.0  0
 4F4  CONST_14  S20  C19  C18  C17     0.00   0.0  0
 4F4  CONST_15  C19  S20  C16  C17     0.00   0.0  0
 4F4  CONST_16  S20  C16  C17  C18     0.00   0.0  0
 4F4  CONST_17  C31  N32  N33  N25     0.00   0.0  0
 4F4  CONST_18  N32  C31  C26  N25     0.00   0.0  0
 4F4  CONST_19  C30  C31  C26  N25   180.00   0.0  0
 4F4  CONST_20  C28  C27  C26  N25   180.00   0.0  0
 4F4  CONST_21  N32  N33  N25  C26     0.00   0.0  0
 4F4  CONST_22  N33  N32  C31  C26     0.00   0.0  0
 4F4  CONST_23  C29  C30  C31  C26     0.00   0.0  0
 4F4  CONST_24  C29  C28  C27  C26     0.00   0.0  0
 4F4  CONST_25  N33  N25  C26  C27   180.00   0.0  0
 4F4  CONST_26  N32  C31  C26  C27   180.00   0.0  0
 4F4  CONST_27  C30  C31  C26  C27     0.00   0.0  0
 4F4  CONST_28  C30  C29  C28  C27     0.00   0.0  0
 4F4  CONST_29  C31  C26  C27  C28     0.00   0.0  0
 4F4  CONST_30  C31  C30  C29  C28     0.00   0.0  0
 4F4  CONST_31  N32  C31  C30  C29   180.00   0.0  0
 4F4  CONST_32  N33  N32  C31  C30   180.00   0.0  0
 4F4  CONST_33  N33  N25  C26  C31     0.00   0.0  0
 4F4  CONST_34  C22  C23  C10  N03   180.00   0.0  0
 4F4  CONST_35  C12  C11  C10  N03   180.00   0.0  0
 4F4  CONST_36  C08  C09  C05  C04   180.00   0.0  0
 4F4  CONST_37  S07  C06  C05  C04   180.00   0.0  0
 4F4  CONST_38  N14  C13  C12  C11   180.00   0.0  0
 4F4  CONST_39  C23  C22  C13  N14   180.00   0.0  0
 4F4  CONST_40  C18  C17  C16  C15   180.00   0.0  0
 4F4  CONST_41  C19  S20  C16  C15   180.00   0.0  0
 4F4  CONST_42  N32  N33  N25  C24   180.00   0.0  0
 4F4  CONST_43  C31  C26  N25  C24   180.00   0.0  0
 4F4  CONST_44  C27  C26  N25  C24     0.00   0.0  0
 4F4  CONST_45  H12  C22  C23  C10   180.00   0.0  0
 4F4  CONST_46  H7   C12  C11  C10   180.00   0.0  0
 4F4  CONST_47  H4   C08  C09  C05   180.00   0.0  0
 4F4  CONST_48  H5   C09  C05  C06   180.00   0.0  0
 4F4  CONST_49  H3   C06  S07  C08   180.00   0.0  0
 4F4  CONST_50  H13  C23  C10  C11   180.00   0.0  0
 4F4  CONST_51  H6   C11  C12  C13   180.00   0.0  0
 4F4  CONST_52  H10  C18  C17  C16   180.00   0.0  0
 4F4  CONST_53  H11  C19  S20  C16   180.00   0.0  0
 4F4  CONST_54  H9   C17  C18  C19   180.00   0.0  0
 4F4  CONST_55  H16  C27  C26  N25     0.00   0.0  0
 4F4  CONST_56  H19  C30  C31  C26   180.00   0.0  0
 4F4  CONST_57  H17  C28  C27  C26   180.00   0.0  0
 4F4  CONST_58  H18  C29  C28  C27   180.00   0.0  0
 4F4  CONST_59  C16  C15  N14  C13   180.00   0.0  0
 4F4  CONST_64  C15  N14  C13  C12   180.00   0.0  0
 4F4  CONST_65  C22  C13  N14  C15     0.00   0.0  0
 4F4  CONST_66  H8   N14  C13  C12     0.00   0.0  0
 4F4  CONST_67  C24  C02  N03  C10   180.00   0.0  0
 4F4  CONST_68  O01  C02  N03  C10     0.00   0.0  0
 4F4  CONST_69  O21  C15  N14  C13     0.00   0.0  0
 4F4  CONST_70  C04  N03  C02  O01   180.00   0.0  0
 4F4  CONST_71  C24  C02  N03  C04     0.00   0.0  0
 4F4  Var_01    C05  C04  N03  C10   118.71  30.0  3
 4F4  Var_02    N33  N25  C24  C02   -97.12  30.0  2
 4F4  Var_03    C09  C05  C04  N03   -37.83  30.0  2
 4F4  Var_04    C17  C16  C15  N14  -165.42  30.0  2
 4F4  Var_05    N25  C24  C02  O01     8.88  30.0  1

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
 4F4  plan-1  C04  0.020
 4F4  plan-1  C05  0.020
 4F4  plan-1  C06  0.020
 4F4  plan-1  S07  0.020
 4F4  plan-1  C08  0.020
 4F4  plan-1  C09  0.020
 4F4  plan-1  H3   0.020
 4F4  plan-1  H4   0.020
 4F4  plan-1  H5   0.020
 4F4  plan-2  C15  0.020
 4F4  plan-2  C16  0.020
 4F4  plan-2  C17  0.020
 4F4  plan-2  C18  0.020
 4F4  plan-2  C19  0.020
 4F4  plan-2  S20  0.020
 4F4  plan-2  H9   0.020
 4F4  plan-2  H10  0.020
 4F4  plan-2  H11  0.020
 4F4  plan-3  C10  0.020
 4F4  plan-3  N03  0.020
 4F4  plan-3  C11  0.020
 4F4  plan-3  C12  0.020
 4F4  plan-3  C13  0.020
 4F4  plan-3  N14  0.020
 4F4  plan-3  C22  0.020
 4F4  plan-3  C23  0.020
 4F4  plan-3  H6   0.020
 4F4  plan-3  H7   0.020
 4F4  plan-3  H12  0.020
 4F4  plan-3  H13  0.020
 4F4  plan-4  C24  0.020
 4F4  plan-4  N25  0.020
 4F4  plan-4  C26  0.020
 4F4  plan-4  C27  0.020
 4F4  plan-4  C28  0.020
 4F4  plan-4  C29  0.020
 4F4  plan-4  C30  0.020
 4F4  plan-4  C31  0.020
 4F4  plan-4  N32  0.020
 4F4  plan-4  N33  0.020
 4F4  plan-4  H16  0.020
 4F4  plan-4  H17  0.020
 4F4  plan-4  H18  0.020
 4F4  plan-4  H19  0.020
 4F4  plan-5  C10  0.020
 4F4  plan-5  O01  0.020
 4F4  plan-5  C02  0.020
 4F4  plan-5  N03  0.020
 4F4  plan-5  C04  0.020
 4F4  plan-5  C24  0.020
 4F4  plan-6  C13  0.020
 4F4  plan-6  N14  0.020
 4F4  plan-6  C15  0.020
 4F4  plan-6  C16  0.020
 4F4  plan-6  O21  0.020
 4F4  plan-6  H8   0.020

