# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 08:31:40 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: ~{N}-[4-[2-(benzotriazol-1-yl)ethanoyl-(thiophen-3-ylmethyl)amino]phenyl]cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1nnc2ccccc12)N(Cc3cscc3)c4ccc(NC(=O)C5CC5)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
 Y6J  Y6J  ~{N}-[4-[2-(benzotriazol-1-yl)ethanoyl-(thiophen-3-ylmethyl)amino]phenyl]cyclopropanecarboxamide  ligand  52  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y6J
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
 Y6J  C10  C  CR56  0   0.126  22.1822   1.0097  18.5459
 Y6J  N11  N  N     0  -0.318  21.2450   0.4136  17.7503
 Y6J  N13  N  NT    0  -0.545  25.3555   0.0268  14.0428
 Y6J  C15  C  CR5   0   0.170  24.9443   0.6799  11.6848
 Y6J  C20  C  CR6   0   0.217  26.1486  -1.1404  14.2304
 Y6J  C23  C  CR6   0   0.387  27.7407  -3.4073  14.6336
 Y6J  C19  C  CR15  0  -0.205  25.2966   1.3174  10.4568
 Y6J  C18  C  CR15  0  -0.458  24.4683   0.9867   9.4309
 Y6J  C16  C  CR15  0  -0.535  23.8517  -0.1204  11.5436
 Y6J  C02  C  C     0   0.530  24.3536   0.3593  14.8896
 Y6J  C03  C  CH2   0  -0.452  24.0751  -0.6422  16.0102
 Y6J  C05  C  CR56  0   0.390  23.4431   0.6971  18.0360
 Y6J  C06  C  CR16  0  -0.289  24.6270   1.1472  18.6233
 Y6J  C07  C  CR16  0  -0.260  24.4818   1.9267  19.7490
 Y6J  C08  C  CR16  0  -0.267  23.2132   2.2521  20.2767
 Y6J  C09  C  CR16  0  -0.289  22.0520   1.8026  19.6912
 Y6J  C14  C  CH2   0  -0.369  25.7057   0.9253  12.9556
 Y6J  C21  C  CR16  0  -0.240  25.7281  -2.3803  13.7682
 Y6J  C22  C  CR16  0  -0.354  26.5123  -3.5004  13.9740
 Y6J  C25  C  C     0   0.590  29.6001  -4.8150  15.5046
 Y6J  C26  C  CH1   0  -0.434  30.0521  -6.2302  15.4774
 Y6J  C27  C  CH2   0  -0.461  30.7040  -6.7846  16.7186
 Y6J  C28  C  CH2   0  -0.462  31.5345  -6.4974  15.5239
 Y6J  C30  C  CR16  0  -0.321  28.1704  -2.1554  15.0825
 Y6J  C31  C  CR16  0  -0.229  27.3721  -1.0421  14.8786
 Y6J  N04  N  NR5   0  -0.379  23.1653  -0.0861  16.9670
 Y6J  N12  N  N     0  -0.057  21.8504  -0.2191  16.8223
 Y6J  N24  N  NH1   0  -0.760  28.4611  -4.5899  14.7918
 Y6J  O01  O  O     0  -0.452  23.6945   1.3734  14.7797
 Y6J  O29  O  O     0  -0.467  30.2010  -3.9466  16.1129
 Y6J  S17  S  S2    0   0.212  23.2511  -0.1066   9.9373
 Y6J  H1   H  HCR5  0   0.263  26.1353   1.9922  10.3505
 Y6J  H2   H  HCR5  0   0.293  24.5148   1.3225   8.4064
 Y6J  H3   H  HCR5  0   0.289  23.3596  -0.7191  12.2948
 Y6J  H4   H  HCH2  0   0.330  23.6297  -1.5495  15.5991
 Y6J  H5   H  HCH2  0   0.313  24.9874  -0.9431  16.5258
 Y6J  H6   H  HCR6  0   0.281  25.6017   0.9013  18.2227
 Y6J  H7   H  HCR6  0   0.267  25.3654   2.3039  20.2465
 Y6J  H8   H  HCR6  0   0.263  23.1607   2.8689  21.1639
 Y6J  H9   H  HCR6  0   0.271  21.0796   2.0485  20.0963
 Y6J  H10  H  HCH2  0   0.276  26.7750   0.8187  12.7658
 Y6J  H11  H  HCH2  0   0.275  25.5536   1.9558  13.2813
 Y6J  H12  H  HCR6  0   0.273  24.7797  -2.4784  13.2563
 Y6J  H13  H  HCR6  0   0.277  26.1644  -4.4629  13.6180
 Y6J  H14  H  HCH1  0   0.285  29.4526  -6.9222  14.8973
 Y6J  H15  H  HCH2  0   0.259  30.7895  -6.1250  17.5720
 Y6J  H16  H  HCH2  0   0.265  30.4814  -7.8149  16.9613
 Y6J  H17  H  HCH2  0   0.265  31.8964  -7.3258  14.9300
 Y6J  H18  H  HCH2  0   0.259  32.1908  -5.6377  15.5543
 Y6J  H19  H  HCR6  0   0.286  29.1122  -2.0410  15.5915
 Y6J  H20  H  HCR6  0   0.270  27.7081  -0.0777  15.2396
 Y6J  H21  H  HNH1  0   0.419  28.0480  -5.3982  14.3507

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
 Y6J  C18  S17  aromatic  1.713  0.020  1.713
 Y6J  C18  C19  aromatic  1.359  0.020  1.359
 Y6J  S17  C16  aromatic  1.715  0.020  1.715
 Y6J  C19  C15  aromatic  1.428  0.020  1.428
 Y6J  C16  C15  aromatic  1.362  0.020  1.362
 Y6J  C15  C14  single    1.502  0.020  1.502
 Y6J  C14  N13  single    1.453  0.020  1.453
 Y6J  C21  C22  aromatic  1.383  0.020  1.383
 Y6J  C21  C20  aromatic  1.388  0.020  1.388
 Y6J  C22  C23  aromatic  1.397  0.020  1.397
 Y6J  N13  C20  single    1.424  0.020  1.424
 Y6J  N13  C02  single    1.353  0.020  1.353
 Y6J  C20  C31  aromatic  1.388  0.020  1.388
 Y6J  O29  C25  double    1.219  0.020  1.219
 Y6J  C23  N24  single    1.394  0.020  1.394
 Y6J  C23  C30  aromatic  1.398  0.020  1.398
 Y6J  C25  N24  single    1.362  0.020  1.362
 Y6J  C25  C26  single    1.486  0.020  1.486
 Y6J  O01  C02  double    1.214  0.020  1.214
 Y6J  C02  C03  single    1.529  0.020  1.529
 Y6J  C26  C28  single    1.507  0.020  1.507
 Y6J  C26  C27  single    1.508  0.020  1.508
 Y6J  C31  C30  aromatic  1.385  0.020  1.385
 Y6J  C03  N04  single    1.433  0.020  1.433
 Y6J  C28  C27  single    1.483  0.020  1.483
 Y6J  N12  N04  aromatic  1.330  0.020  1.330
 Y6J  N12  N11  aromatic  1.276  0.020  1.276
 Y6J  N04  C05  aromatic  1.354  0.020  1.354
 Y6J  N11  C10  aromatic  1.366  0.020  1.366
 Y6J  C05  C10  aromatic  1.396  0.020  1.396
 Y6J  C05  C06  aromatic  1.396  0.020  1.396
 Y6J  C10  C09  aromatic  1.399  0.020  1.399
 Y6J  C06  C07  aromatic  1.377  0.020  1.377
 Y6J  C07  C08  aromatic  1.412  0.020  1.412
 Y6J  C09  C08  aromatic  1.376  0.020  1.376
 Y6J  C19  H1   single    0.930  0.020  1.080
 Y6J  C18  H2   single    0.930  0.020  1.080
 Y6J  C16  H3   single    0.930  0.020  1.080
 Y6J  C03  H4   single    0.970  0.020  1.090
 Y6J  C03  H5   single    0.970  0.020  1.090
 Y6J  C06  H6   single    0.930  0.020  1.080
 Y6J  C07  H7   single    0.930  0.020  1.080
 Y6J  C08  H8   single    0.930  0.020  1.080
 Y6J  C09  H9   single    0.930  0.020  1.080
 Y6J  C14  H10  single    0.970  0.020  1.090
 Y6J  C14  H11  single    0.970  0.020  1.090
 Y6J  C21  H12  single    0.930  0.020  1.080
 Y6J  C22  H13  single    0.930  0.020  1.080
 Y6J  C26  H14  single    0.970  0.020  1.090
 Y6J  C27  H15  single    0.970  0.020  1.090
 Y6J  C27  H16  single    0.970  0.020  1.090
 Y6J  C28  H17  single    0.970  0.020  1.090
 Y6J  C28  H18  single    0.970  0.020  1.090
 Y6J  C30  H19  single    0.930  0.020  1.080
 Y6J  C31  H20  single    0.930  0.020  1.080
 Y6J  N24  H21  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
 Y6J  C09  C10  C05  120.67  3.000
 Y6J  C09  C10  N11  131.31  3.000
 Y6J  C05  C10  N11  108.02  3.000
 Y6J  N12  N11  C10  108.32  3.000
 Y6J  C14  N13  C02  119.64  3.000
 Y6J  C02  N13  C20  122.10  3.000
 Y6J  C14  N13  C20  118.12  3.000
 Y6J  C14  C15  C16  126.21  3.000
 Y6J  C14  C15  C19  121.99  3.000
 Y6J  C16  C15  C19  111.79  3.000
 Y6J  C31  C20  C21  119.06  3.000
 Y6J  C31  C20  N13  119.63  3.000
 Y6J  C21  C20  N13  121.30  3.000
 Y6J  N24  C23  C30  124.38  3.000
 Y6J  C30  C23  C22  118.79  3.000
 Y6J  N24  C23  C22  116.83  3.000
 Y6J  H1   C19  C18  123.37  3.000
 Y6J  H1   C19  C15  123.67  3.000
 Y6J  C18  C19  C15  112.96  3.000
 Y6J  H2   C18  S17  120.66  3.000
 Y6J  H2   C18  C19  127.91  3.000
 Y6J  S17  C18  C19  111.42  3.000
 Y6J  H3   C16  S17  119.78  3.000
 Y6J  H3   C16  C15  128.29  3.000
 Y6J  S17  C16  C15  111.93  3.000
 Y6J  O01  C02  C03  120.97  3.000
 Y6J  C03  C02  N13  115.64  3.000
 Y6J  O01  C02  N13  123.39  3.000
 Y6J  H5   C03  H4   106.88  3.000
 Y6J  H5   C03  N04  108.82  3.000
 Y6J  H4   C03  N04  108.37  3.000
 Y6J  H5   C03  C02  112.03  3.000
 Y6J  H4   C03  C02  110.06  3.000
 Y6J  N04  C03  C02  110.55  3.000
 Y6J  N04  C05  C06  133.83  3.000
 Y6J  C06  C05  C10  122.70  3.000
 Y6J  N04  C05  C10  103.46  3.000
 Y6J  H6   C06  C07  121.76  3.000
 Y6J  H6   C06  C05  122.33  3.000
 Y6J  C07  C06  C05  115.91  3.000
 Y6J  H7   C07  C08  118.78  3.000
 Y6J  H7   C07  C06  119.16  3.000
 Y6J  C08  C07  C06  122.06  3.000
 Y6J  H8   C08  C09  119.62  3.000
 Y6J  H8   C08  C07  118.79  3.000
 Y6J  C09  C08  C07  121.59  3.000
 Y6J  H9   C09  C08  121.67  3.000
 Y6J  H9   C09  C10  121.27  3.000
 Y6J  C08  C09  C10  117.06  3.000
 Y6J  H11  C14  H10  106.30  3.000
 Y6J  H11  C14  C15  109.65  3.000
 Y6J  H10  C14  C15  109.50  3.000
 Y6J  H11  C14  N13  109.08  3.000
 Y6J  H10  C14  N13  107.80  3.000
 Y6J  C15  C14  N13  114.20  3.000
 Y6J  H12  C21  C22  119.60  3.000
 Y6J  H12  C21  C20  120.26  3.000
 Y6J  C22  C21  C20  120.14  3.000
 Y6J  H13  C22  C21  119.26  3.000
 Y6J  H13  C22  C23  119.76  3.000
 Y6J  C21  C22  C23  120.98  3.000
 Y6J  O29  C25  N24  123.75  3.000
 Y6J  N24  C25  C26  113.71  3.000
 Y6J  O29  C25  C26  122.54  3.000
 Y6J  H14  C26  C28  116.58  3.000
 Y6J  H14  C26  C27  116.42  3.000
 Y6J  C28  C26  C27   58.94  3.000
 Y6J  H14  C26  C25  116.72  3.000
 Y6J  C27  C26  C25  117.82  3.000
 Y6J  C28  C26  C25  117.87  3.000
 Y6J  H16  C27  H15  114.84  3.000
 Y6J  H16  C27  C28  118.72  3.000
 Y6J  H15  C27  C28  118.23  3.000
 Y6J  H16  C27  C26  116.48  3.000
 Y6J  H15  C27  C26  117.34  3.000
 Y6J  C28  C27  C26   60.51  3.000
 Y6J  H18  C28  H17  114.90  3.000
 Y6J  H18  C28  C27  118.10  3.000
 Y6J  H17  C28  C27  118.77  3.000
 Y6J  H18  C28  C26  117.17  3.000
 Y6J  H17  C28  C26  116.61  3.000
 Y6J  C27  C28  C26   60.55  3.000
 Y6J  H19  C30  C31  119.23  3.000
 Y6J  H19  C30  C23  121.06  3.000
 Y6J  C31  C30  C23  119.71  3.000
 Y6J  H20  C31  C30  119.19  3.000
 Y6J  H20  C31  C20  119.49  3.000
 Y6J  C30  C31  C20  121.32  3.000
 Y6J  N12  N04  C05  110.28  3.000
 Y6J  C05  N04  C03  128.43  3.000
 Y6J  N12  N04  C03  121.10  3.000
 Y6J  N04  N12  N11  109.91  3.000
 Y6J  H21  N24  C25  116.01  3.000
 Y6J  H21  N24  C23  114.73  3.000
 Y6J  C25  N24  C23  129.18  3.000
 Y6J  C16  S17  C18   91.90  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
 Y6J  CONST_01  N04  N12  N11  C10     0.00   0.0  0
 Y6J  CONST_02  N12  N04  C05  C10     0.00   0.0  0
 Y6J  CONST_03  C07  C06  C05  C10     0.00   0.0  0
 Y6J  CONST_04  C07  C08  C09  C10     0.00   0.0  0
 Y6J  CONST_05  C05  N04  N12  N11     0.00   0.0  0
 Y6J  CONST_06  N04  C05  C10  N11     0.00   0.0  0
 Y6J  CONST_07  C06  C05  C10  N11   180.00   0.0  0
 Y6J  CONST_08  C08  C09  C10  N11   180.00   0.0  0
 Y6J  CONST_09  S17  C18  C19  C15     0.00   0.0  0
 Y6J  CONST_10  C18  S17  C16  C15     0.00   0.0  0
 Y6J  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 Y6J  CONST_12  C23  C30  C31  C20     0.00   0.0  0
 Y6J  CONST_13  C16  S17  C18  C19     0.00   0.0  0
 Y6J  CONST_14  S17  C16  C15  C19     0.00   0.0  0
 Y6J  CONST_15  C16  C15  C19  C18     0.00   0.0  0
 Y6J  CONST_16  N12  N11  C10  C05     0.00   0.0  0
 Y6J  CONST_17  C08  C09  C10  C05     0.00   0.0  0
 Y6J  CONST_18  C08  C07  C06  C05     0.00   0.0  0
 Y6J  CONST_19  N12  N04  C05  C06   180.00   0.0  0
 Y6J  CONST_20  C09  C10  C05  C06     0.00   0.0  0
 Y6J  CONST_21  C09  C08  C07  C06     0.00   0.0  0
 Y6J  CONST_22  N04  C05  C06  C07   180.00   0.0  0
 Y6J  CONST_23  N12  N11  C10  C09   180.00   0.0  0
 Y6J  CONST_24  N04  C05  C10  C09   180.00   0.0  0
 Y6J  CONST_25  C30  C23  C22  C21     0.00   0.0  0
 Y6J  CONST_26  C30  C31  C20  C21     0.00   0.0  0
 Y6J  CONST_27  C31  C20  C21  C22     0.00   0.0  0
 Y6J  CONST_28  C31  C30  C23  C22     0.00   0.0  0
 Y6J  CONST_29  C03  N04  C05  C10   180.00   0.0  0
 Y6J  CONST_30  C03  N04  N12  N11   180.00   0.0  0
 Y6J  CONST_31  C22  C21  C20  N13   180.00   0.0  0
 Y6J  CONST_32  C30  C31  C20  N13   180.00   0.0  0
 Y6J  CONST_33  C14  C15  C19  C18   180.00   0.0  0
 Y6J  CONST_34  C06  C05  N04  C03     0.00   0.0  0
 Y6J  CONST_35  S17  C16  C15  C14   180.00   0.0  0
 Y6J  CONST_36  N24  C23  C22  C21   180.00   0.0  0
 Y6J  CONST_37  N24  C23  C30  C31   180.00   0.0  0
 Y6J  CONST_38  H6   C06  C05  C10   180.00   0.0  0
 Y6J  CONST_39  H8   C08  C09  C10   180.00   0.0  0
 Y6J  CONST_40  H9   C09  C10  N11     0.00   0.0  0
 Y6J  CONST_41  H2   C18  C19  C15   180.00   0.0  0
 Y6J  CONST_42  H13  C22  C21  C20   180.00   0.0  0
 Y6J  CONST_43  H19  C30  C31  C20   180.00   0.0  0
 Y6J  CONST_44  H12  C21  C22  C23   180.00   0.0  0
 Y6J  CONST_45  H20  C31  C30  C23   180.00   0.0  0
 Y6J  CONST_46  H3   C16  C15  C19   180.00   0.0  0
 Y6J  CONST_47  H1   C19  C15  C16   180.00   0.0  0
 Y6J  CONST_48  H7   C07  C06  C05   180.00   0.0  0
 Y6J  CONST_49  C26  C25  N24  C23   180.00   0.0  0
 Y6J  CONST_54  C25  N24  C23  C22   180.00   0.0  0
 Y6J  CONST_55  C30  C23  N24  C25     0.00   0.0  0
 Y6J  CONST_56  H21  N24  C23  C22     0.00   0.0  0
 Y6J  CONST_57  O01  C02  N13  C20   180.00   0.0  0
 Y6J  CONST_58  C03  C02  N13  C20     0.00   0.0  0
 Y6J  CONST_59  O29  C25  N24  C23     0.00   0.0  0
 Y6J  CONST_60  C14  N13  C02  C03   180.00   0.0  0
 Y6J  CONST_61  O01  C02  N13  C14     0.00   0.0  0
 Y6J  Var_01    C27  C28  C26  C25   107.32  30.0  1
 Y6J  Var_02    H15  C27  C28  C26  -107.18  30.0  1
 Y6J  Var_03    C19  C15  C14  N13  -169.98  30.0  2
 Y6J  Var_04    C20  N13  C14  C15    94.76  30.0  3
 Y6J  Var_05    N12  N04  C03  C02    88.90  30.0  2
 Y6J  Var_06    O29  C25  C26  C27    34.68  30.0  2
 Y6J  Var_07    N04  C03  C02  N13   170.07  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 Y6J  chir_01  C26  C25  C28  C27  both

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
 Y6J  plan-1  C15  0.020
 Y6J  plan-1  C19  0.020
 Y6J  plan-1  C18  0.020
 Y6J  plan-1  C16  0.020
 Y6J  plan-1  C14  0.020
 Y6J  plan-1  S17  0.020
 Y6J  plan-1  H1   0.020
 Y6J  plan-1  H2   0.020
 Y6J  plan-1  H3   0.020
 Y6J  plan-2  N13  0.020
 Y6J  plan-2  C20  0.020
 Y6J  plan-2  C23  0.020
 Y6J  plan-2  C21  0.020
 Y6J  plan-2  C22  0.020
 Y6J  plan-2  C30  0.020
 Y6J  plan-2  C31  0.020
 Y6J  plan-2  N24  0.020
 Y6J  plan-2  H12  0.020
 Y6J  plan-2  H13  0.020
 Y6J  plan-2  H19  0.020
 Y6J  plan-2  H20  0.020
 Y6J  plan-3  C10  0.020
 Y6J  plan-3  N11  0.020
 Y6J  plan-3  C03  0.020
 Y6J  plan-3  C05  0.020
 Y6J  plan-3  C06  0.020
 Y6J  plan-3  C07  0.020
 Y6J  plan-3  C08  0.020
 Y6J  plan-3  C09  0.020
 Y6J  plan-3  N04  0.020
 Y6J  plan-3  N12  0.020
 Y6J  plan-3  H6   0.020
 Y6J  plan-3  H7   0.020
 Y6J  plan-3  H8   0.020
 Y6J  plan-3  H9   0.020
 Y6J  plan-4  C23  0.020
 Y6J  plan-4  C25  0.020
 Y6J  plan-4  C26  0.020
 Y6J  plan-4  N24  0.020
 Y6J  plan-4  O29  0.020
 Y6J  plan-4  H21  0.020
 Y6J  plan-5  N13  0.020
 Y6J  plan-5  C20  0.020
 Y6J  plan-5  C02  0.020
 Y6J  plan-5  C03  0.020
 Y6J  plan-5  C14  0.020
 Y6J  plan-5  O01  0.020

