# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 20:00:27 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-pyrazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1nnc2ccccc12)N(Cc3cscc3)c4ccc(cc4)c5c[nH]nc5
#
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
 Y6A  Y6A  2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-pyrazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide  ligand  48  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y6A
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
 Y6A  C10  C  CR56  0   0.124  -19.6843  16.8094   1.4807
 Y6A  N11  N  N     0  -0.318  -19.4332  16.0743   2.6047
 Y6A  C15  C  CR5   0   0.188  -25.7837  17.6096   5.5768
 Y6A  O01  O  O     0  -0.457  -22.9347  17.8419   3.5901
 Y6A  C02  C  C     0   0.530  -23.5755  16.8632   3.2591
 Y6A  C03  C  CH2   0  -0.448  -22.8956  15.6833   2.5625
 Y6A  N04  N  NR5   0  -0.380  -21.5357  16.0050   2.2465
 Y6A  C05  C  CR56  0   0.394  -21.0594  16.7797   1.2436
 Y6A  C06  C  CR16  0  -0.290  -21.6522  17.4394   0.1651
 Y6A  C07  C  CR16  0  -0.260  -20.7957  18.1292  -0.6634
 Y6A  C08  C  CR16  0  -0.268  -19.4023  18.1660  -0.4383
 Y6A  C09  C  CR16  0  -0.289  -18.8273  17.5127   0.6275
 Y6A  N12  N  N     0  -0.058  -20.5416  15.6181   3.0412
 Y6A  N13  N  NT    0  -0.528  -24.9082  16.7419   3.4436
 Y6A  C14  C  CH2   0  -0.427  -25.6523  17.8186   4.0972
 Y6A  C16  C  CR15  0  -0.519  -24.8888  18.0679   6.4993
 Y6A  S17  S  S2    0   0.215  -25.3263  17.6181   8.0917
 Y6A  C18  C  CR15  0  -0.465  -26.7292  16.8034   7.5394
 Y6A  C19  C  CR15  0  -0.203  -26.8463  16.8790   6.1864
 Y6A  C20  C  CR6   0   0.216  -25.6091  15.5370   3.1647
 Y6A  C21  C  CR16  0  -0.223  -26.4177  15.4484   2.0377
 Y6A  C22  C  CR16  0  -0.346  -27.1219  14.2873   1.7742
 Y6A  C23  C  CR6   0   0.127  -27.0396  13.1820   2.6267
 Y6A  C24  C  CR5   0  -0.101  -27.7800  11.9548   2.3475
 Y6A  C25  C  CR15  0  -0.005  -28.6947  11.7213   1.3359
 Y6A  N26  N  NR15  0  -0.426  -29.1089  10.4567   1.4794
 Y6A  N27  N  N     0  -0.256  -28.5427   9.8312   2.5042
 Y6A  C28  C  CR15  0  -0.114  -27.7358  10.7239   3.0407
 Y6A  C29  C  CR16  0  -0.352  -26.2274  13.2892   3.7575
 Y6A  C30  C  CR16  0  -0.219  -25.5257  14.4525   4.0281
 Y6A  H1   H  HCH2  0   0.312  -23.4239  15.4034   1.6495
 Y6A  H2   H  HCH2  0   0.329  -22.8885  14.8046   3.2076
 Y6A  H3   H  HCR6  0   0.281  -22.7191  17.4147  -0.0132
 Y6A  H4   H  HCR6  0   0.267  -21.1999  18.6608  -1.5146
 Y6A  H5   H  HCR6  0   0.264  -18.7784  18.7238  -1.1237
 Y6A  H6   H  HCR6  0   0.271  -17.7599  17.5395   0.8010
 Y6A  H7   H  HCH2  0   0.279  -25.1558  18.7622   3.8810
 Y6A  H8   H  HCH2  0   0.283  -26.6392  17.8628   3.6350
 Y6A  H9   H  HCR5  0   0.292  -23.9961  18.6470   6.3177
 Y6A  H10  H  HCR5  0   0.293  -27.3928  16.3179   8.2381
 Y6A  H11  H  HCR5  0   0.265  -27.6641  16.4372   5.6334
 Y6A  H12  H  HCR6  0   0.268  -26.4905  16.2903   1.3605
 Y6A  H13  H  HCR6  0   0.254  -27.7358  14.2457   0.8835
 Y6A  H14  H  HCR5  0   0.292  -29.0725  12.3499   0.5459
 Y6A  H15  H  HNR5  0   0.423  -29.7800   9.9728   0.9034
 Y6A  H16  H  HCR5  0   0.260  -27.1426  10.4614   3.9038
 Y6A  H17  H  HCR6  0   0.255  -26.1411  12.4612   4.4490
 Y6A  H18  H  HCR6  0   0.272  -24.9110  14.5154   4.9177

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
 Y6A  C08  C07  aromatic  1.412  0.020  1.412
 Y6A  C08  C09  aromatic  1.376  0.020  1.376
 Y6A  C07  C06  aromatic  1.377  0.020  1.377
 Y6A  C09  C10  aromatic  1.399  0.020  1.399
 Y6A  C06  C05  aromatic  1.396  0.020  1.396
 Y6A  C25  N26  aromatic  1.338  0.020  1.338
 Y6A  C25  C24  aromatic  1.384  0.020  1.384
 Y6A  C10  C05  aromatic  1.396  0.020  1.396
 Y6A  C10  N11  aromatic  1.366  0.020  1.366
 Y6A  N26  N27  aromatic  1.327  0.020  1.327
 Y6A  C05  N04  aromatic  1.354  0.020  1.354
 Y6A  C22  C21  aromatic  1.383  0.020  1.383
 Y6A  C22  C23  aromatic  1.398  0.020  1.398
 Y6A  N11  N12  aromatic  1.276  0.020  1.276
 Y6A  C24  C23  single    1.460  0.020  1.460
 Y6A  C24  C28  aromatic  1.413  0.020  1.413
 Y6A  N04  C03  single    1.433  0.020  1.433
 Y6A  N04  N12  aromatic  1.330  0.020  1.330
 Y6A  C21  C20  aromatic  1.390  0.020  1.390
 Y6A  N27  C28  aromatic  1.317  0.020  1.317
 Y6A  C23  C29  aromatic  1.396  0.020  1.396
 Y6A  C03  C02  single    1.530  0.020  1.530
 Y6A  C20  N13  single    1.422  0.020  1.422
 Y6A  C20  C30  aromatic  1.389  0.020  1.389
 Y6A  C02  N13  single    1.351  0.020  1.351
 Y6A  C02  O01  double    1.216  0.020  1.216
 Y6A  C29  C30  aromatic  1.385  0.020  1.385
 Y6A  N13  C14  single    1.463  0.020  1.463
 Y6A  C14  C15  single    1.500  0.020  1.500
 Y6A  C15  C19  aromatic  1.426  0.020  1.426
 Y6A  C15  C16  aromatic  1.364  0.020  1.364
 Y6A  C19  C18  aromatic  1.360  0.020  1.360
 Y6A  C16  S17  aromatic  1.712  0.020  1.712
 Y6A  C18  S17  aromatic  1.714  0.020  1.714
 Y6A  C03  H1   single    0.970  0.020  1.090
 Y6A  C03  H2   single    0.970  0.020  1.090
 Y6A  C06  H3   single    0.930  0.020  1.080
 Y6A  C07  H4   single    0.930  0.020  1.080
 Y6A  C08  H5   single    0.930  0.020  1.080
 Y6A  C09  H6   single    0.930  0.020  1.080
 Y6A  C14  H7   single    0.970  0.020  1.090
 Y6A  C14  H8   single    0.970  0.020  1.090
 Y6A  C16  H9   single    0.930  0.020  1.080
 Y6A  C18  H10  single    0.930  0.020  1.080
 Y6A  C19  H11  single    0.930  0.020  1.080
 Y6A  C21  H12  single    0.930  0.020  1.080
 Y6A  C22  H13  single    0.930  0.020  1.080
 Y6A  C25  H14  single    0.930  0.020  1.080
 Y6A  N26  H15  single    0.860  0.020  1.020
 Y6A  C28  H16  single    0.930  0.020  1.080
 Y6A  C29  H17  single    0.930  0.020  1.080
 Y6A  C30  H18  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
 Y6A  C09  C10  C05  120.71  3.000
 Y6A  C05  C10  N11  108.03  3.000
 Y6A  C09  C10  N11  131.27  3.000
 Y6A  N12  N11  C10  108.31  3.000
 Y6A  C19  C15  C16  111.82  3.000
 Y6A  C16  C15  C14  124.24  3.000
 Y6A  C19  C15  C14  123.93  3.000
 Y6A  N13  C02  C03  115.56  3.000
 Y6A  N13  C02  O01  123.71  3.000
 Y6A  C03  C02  O01  120.71  3.000
 Y6A  H2   C03  H1   106.95  3.000
 Y6A  H2   C03  N04  107.78  3.000
 Y6A  H1   C03  N04  109.43  3.000
 Y6A  H2   C03  C02  110.80  3.000
 Y6A  H1   C03  C02  111.32  3.000
 Y6A  N04  C03  C02  110.44  3.000
 Y6A  N12  N04  C05  110.25  3.000
 Y6A  N12  N04  C03  120.82  3.000
 Y6A  C05  N04  C03  128.74  3.000
 Y6A  C06  C05  N04  133.88  3.000
 Y6A  N04  C05  C10  103.47  3.000
 Y6A  C06  C05  C10  122.65  3.000
 Y6A  H3   C06  C07  121.71  3.000
 Y6A  H3   C06  C05  122.36  3.000
 Y6A  C07  C06  C05  115.93  3.000
 Y6A  H4   C07  C08  118.77  3.000
 Y6A  H4   C07  C06  119.16  3.000
 Y6A  C08  C07  C06  122.08  3.000
 Y6A  H5   C08  C09  119.64  3.000
 Y6A  H5   C08  C07  118.79  3.000
 Y6A  C09  C08  C07  121.57  3.000
 Y6A  H6   C09  C08  121.66  3.000
 Y6A  H6   C09  C10  121.27  3.000
 Y6A  C08  C09  C10  117.07  3.000
 Y6A  N04  N12  N11  109.93  3.000
 Y6A  C20  N13  C14  117.43  3.000
 Y6A  C14  N13  C02  119.78  3.000
 Y6A  C20  N13  C02  122.39  3.000
 Y6A  H8   C14  H7   107.07  3.000
 Y6A  H8   C14  N13  107.50  3.000
 Y6A  H7   C14  N13  108.51  3.000
 Y6A  H8   C14  C15  110.14  3.000
 Y6A  H7   C14  C15  110.91  3.000
 Y6A  N13  C14  C15  112.50  3.000
 Y6A  H9   C16  S17  120.59  3.000
 Y6A  H9   C16  C15  127.50  3.000
 Y6A  S17  C16  C15  111.91  3.000
 Y6A  C18  S17  C16   91.97  3.000
 Y6A  H10  C18  C19  128.04  3.000
 Y6A  H10  C18  S17  120.58  3.000
 Y6A  C19  C18  S17  111.38  3.000
 Y6A  H11  C19  C18  123.43  3.000
 Y6A  H11  C19  C15  123.65  3.000
 Y6A  C18  C19  C15  112.92  3.000
 Y6A  C30  C20  C21  119.29  3.000
 Y6A  C30  C20  N13  120.68  3.000
 Y6A  C21  C20  N13  120.00  3.000
 Y6A  H12  C21  C22  119.95  3.000
 Y6A  H12  C21  C20  119.78  3.000
 Y6A  C22  C21  C20  120.27  3.000
 Y6A  H13  C22  C23  120.31  3.000
 Y6A  H13  C22  C21  118.53  3.000
 Y6A  C23  C22  C21  121.16  3.000
 Y6A  C29  C23  C24  120.95  3.000
 Y6A  C29  C23  C22  117.85  3.000
 Y6A  C24  C23  C22  121.19  3.000
 Y6A  C28  C24  C25  103.43  3.000
 Y6A  C28  C24  C23  128.49  3.000
 Y6A  C25  C24  C23  128.09  3.000
 Y6A  H14  C25  N26  121.40  3.000
 Y6A  H14  C25  C24  132.00  3.000
 Y6A  N26  C25  C24  106.60  3.000
 Y6A  H15  N26  N27  119.92  3.000
 Y6A  H15  N26  C25  126.75  3.000
 Y6A  N27  N26  C25  113.33  3.000
 Y6A  C28  N27  N26  104.85  3.000
 Y6A  H16  C28  N27  119.82  3.000
 Y6A  H16  C28  C24  128.38  3.000
 Y6A  N27  C28  C24  111.80  3.000
 Y6A  H17  C29  C30  118.51  3.000
 Y6A  H17  C29  C23  120.34  3.000
 Y6A  C30  C29  C23  121.15  3.000
 Y6A  H18  C30  C29  119.78  3.000
 Y6A  H18  C30  C20  119.96  3.000
 Y6A  C29  C30  C20  120.26  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
 Y6A  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 Y6A  CONST_02  C07  C06  C05  C10    0.00   0.0  0
 Y6A  CONST_03  N12  N04  C05  C10    0.00   0.0  0
 Y6A  CONST_04  N04  N12  N11  C10    0.00   0.0  0
 Y6A  CONST_05  C08  C09  C10  N11  180.00   0.0  0
 Y6A  CONST_06  C06  C05  C10  N11  180.00   0.0  0
 Y6A  CONST_07  N04  C05  C10  N11    0.00   0.0  0
 Y6A  CONST_08  C05  N04  N12  N11    0.00   0.0  0
 Y6A  CONST_09  S17  C18  C19  C15    0.00   0.0  0
 Y6A  CONST_10  C18  S17  C16  C15    0.00   0.0  0
 Y6A  CONST_11  C07  C06  C05  N04  180.00   0.0  0
 Y6A  CONST_12  C09  C10  C05  N04  180.00   0.0  0
 Y6A  CONST_13  C08  C07  C06  C05    0.00   0.0  0
 Y6A  CONST_14  C08  C09  C10  C05    0.00   0.0  0
 Y6A  CONST_15  N12  N11  C10  C05    0.00   0.0  0
 Y6A  CONST_16  C09  C08  C07  C06    0.00   0.0  0
 Y6A  CONST_17  C09  C10  C05  C06    0.00   0.0  0
 Y6A  CONST_18  N12  N04  C05  C06  180.00   0.0  0
 Y6A  CONST_19  N12  N11  C10  C09  180.00   0.0  0
 Y6A  CONST_20  C18  C19  C15  C16    0.00   0.0  0
 Y6A  CONST_21  C19  C18  S17  C16    0.00   0.0  0
 Y6A  CONST_22  C19  C15  C16  S17    0.00   0.0  0
 Y6A  CONST_23  C23  C22  C21  C20    0.00   0.0  0
 Y6A  CONST_24  C23  C29  C30  C20    0.00   0.0  0
 Y6A  CONST_25  C24  C23  C22  C21  180.00   0.0  0
 Y6A  CONST_26  C29  C23  C22  C21    0.00   0.0  0
 Y6A  CONST_27  C29  C30  C20  C21    0.00   0.0  0
 Y6A  CONST_28  C30  C20  C21  C22    0.00   0.0  0
 Y6A  CONST_29  C25  C24  C23  C22    0.00   0.0  0
 Y6A  CONST_30  C28  C24  C23  C22  180.00   0.0  0
 Y6A  CONST_31  C30  C29  C23  C22    0.00   0.0  0
 Y6A  CONST_32  N26  C25  C24  C23  180.00   0.0  0
 Y6A  CONST_33  N27  C28  C24  C23  180.00   0.0  0
 Y6A  CONST_34  N27  N26  C25  C24    0.00   0.0  0
 Y6A  CONST_35  C30  C29  C23  C24  180.00   0.0  0
 Y6A  CONST_36  N26  N27  C28  C24    0.00   0.0  0
 Y6A  CONST_37  C28  N27  N26  C25    0.00   0.0  0
 Y6A  CONST_38  C29  C23  C24  C25  180.00   0.0  0
 Y6A  CONST_39  N27  C28  C24  C25    0.00   0.0  0
 Y6A  CONST_40  C28  C24  C25  N26    0.00   0.0  0
 Y6A  CONST_41  C29  C23  C24  C28    0.00   0.0  0
 Y6A  CONST_42  C03  N04  C05  C10  180.00   0.0  0
 Y6A  CONST_43  C03  N04  N12  N11  180.00   0.0  0
 Y6A  CONST_44  C06  C05  N04  C03    0.00   0.0  0
 Y6A  CONST_45  C22  C21  C20  N13  180.00   0.0  0
 Y6A  CONST_46  C29  C30  C20  N13  180.00   0.0  0
 Y6A  CONST_47  C18  C19  C15  C14  180.00   0.0  0
 Y6A  CONST_48  S17  C16  C15  C14  180.00   0.0  0
 Y6A  CONST_49  H5   C08  C09  C10  180.00   0.0  0
 Y6A  CONST_50  H3   C06  C05  C10  180.00   0.0  0
 Y6A  CONST_51  H6   C09  C10  N11    0.00   0.0  0
 Y6A  CONST_52  H10  C18  C19  C15  180.00   0.0  0
 Y6A  CONST_53  H4   C07  C06  C05  180.00   0.0  0
 Y6A  CONST_54  H11  C19  C15  C16  180.00   0.0  0
 Y6A  CONST_55  H9   C16  S17  C18  180.00   0.0  0
 Y6A  CONST_56  H13  C22  C21  C20  180.00   0.0  0
 Y6A  CONST_57  H17  C29  C30  C20  180.00   0.0  0
 Y6A  CONST_58  H18  C30  C20  C21  180.00   0.0  0
 Y6A  CONST_59  H12  C21  C22  C23  180.00   0.0  0
 Y6A  CONST_60  H14  C25  C24  C23    0.00   0.0  0
 Y6A  CONST_61  H16  C28  C24  C23    0.00   0.0  0
 Y6A  CONST_62  H15  N26  C25  C24  180.00   0.0  0
 Y6A  CONST_67  C20  N13  C02  O01  180.00   0.0  0
 Y6A  CONST_68  C20  N13  C02  C03    0.00   0.0  0
 Y6A  CONST_69  C14  N13  C02  O01    0.00   0.0  0
 Y6A  CONST_70  C14  N13  C02  C03  180.00   0.0  0
 Y6A  Var_01    C20  N13  C14  C15   79.88  30.0  2
 Y6A  Var_02    C05  N04  C03  C02  -76.86  30.0  3
 Y6A  Var_03    C19  C15  C14  N13  -88.45  30.0  2
 Y6A  Var_04    N04  C03  C02  O01   -7.20  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
 Y6A  plan-1  C15  0.020
 Y6A  plan-1  C14  0.020
 Y6A  plan-1  C16  0.020
 Y6A  plan-1  S17  0.020
 Y6A  plan-1  C18  0.020
 Y6A  plan-1  C19  0.020
 Y6A  plan-1  H9   0.020
 Y6A  plan-1  H10  0.020
 Y6A  plan-1  H11  0.020
 Y6A  plan-2  C23  0.020
 Y6A  plan-2  C24  0.020
 Y6A  plan-2  C25  0.020
 Y6A  plan-2  N26  0.020
 Y6A  plan-2  N27  0.020
 Y6A  plan-2  C28  0.020
 Y6A  plan-2  H14  0.020
 Y6A  plan-2  H15  0.020
 Y6A  plan-2  H16  0.020
 Y6A  plan-3  N13  0.020
 Y6A  plan-3  C20  0.020
 Y6A  plan-3  C21  0.020
 Y6A  plan-3  C22  0.020
 Y6A  plan-3  C23  0.020
 Y6A  plan-3  C24  0.020
 Y6A  plan-3  C29  0.020
 Y6A  plan-3  C30  0.020
 Y6A  plan-3  H12  0.020
 Y6A  plan-3  H13  0.020
 Y6A  plan-3  H17  0.020
 Y6A  plan-3  H18  0.020
 Y6A  plan-4  C10  0.020
 Y6A  plan-4  N11  0.020
 Y6A  plan-4  C03  0.020
 Y6A  plan-4  N04  0.020
 Y6A  plan-4  C05  0.020
 Y6A  plan-4  C06  0.020
 Y6A  plan-4  C07  0.020
 Y6A  plan-4  C08  0.020
 Y6A  plan-4  C09  0.020
 Y6A  plan-4  N12  0.020
 Y6A  plan-4  H3   0.020
 Y6A  plan-4  H4   0.020
 Y6A  plan-4  H5   0.020
 Y6A  plan-4  H6   0.020
 Y6A  plan-5  O01  0.020
 Y6A  plan-5  C02  0.020
 Y6A  plan-5  C03  0.020
 Y6A  plan-5  N13  0.020
 Y6A  plan-5  C14  0.020
 Y6A  plan-5  C20  0.020

