# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 02:27:50 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: ~{N}-[2-(2,4-dimethylphenyl)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]-3,4-dimethyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(n2nc3CSCc3c2NC(=O)c4ccc(C)c(C)c4)c(C)c1
#
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
 DYU  DYU  ~{N}-[2-(2,4-dimethylphenyl)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]-3,4-dimethyl-benzamide  ligand  50  27  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DYU
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
 DYU  C10  C  CR5   0   0.599  -1.2204   0.9349  -0.1474
 DYU  C15  C  CR6   0   0.191  -2.0985  -1.3683  -0.4417
 DYU  C17  C  CR16  0  -0.329  -2.3262  -3.2877  -1.8671
 DYU  C20  C  CR6   0   0.126  -1.6405  -2.1661   0.6088
 DYU  C21  C  CH3   0  -0.741  -1.2915  -1.6024   1.9541
 DYU  C01  C  CR16  0  -0.317   3.5634   1.1008   0.7078
 DYU  C02  C  CR6   0   0.089   4.8199   0.5136   0.6685
 DYU  C03  C  CR6   0   0.071   4.9222  -0.8642   0.4170
 DYU  C04  C  CR16  0  -0.282   3.7608  -1.6019   0.2145
 DYU  C05  C  CR16  0  -0.293   2.5109  -1.0041   0.2403
 DYU  C06  C  CR6   0  -0.032   2.4041   0.3613   0.4819
 DYU  C07  C  C     0   0.511   1.0926   1.0562   0.5681
 DYU  C11  C  CR55  0  -0.108  -1.8128   2.1715  -0.0634
 DYU  C12  C  CR55  0   0.267  -3.1799   1.8963  -0.1650
 DYU  C16  C  CR16  0  -0.227  -2.4435  -1.9234  -1.6664
 DYU  C18  C  CR6   0   0.125  -1.8499  -4.1125  -0.8509
 DYU  C19  C  CR16  0  -0.354  -1.5192  -3.5327   0.3703
 DYU  C23  C  CH2   0  -0.603  -4.1106   3.0587  -0.1243
 DYU  C25  C  CH2   0  -0.604  -1.4242   3.5997   0.0559
 DYU  N09  N  NH1   0  -0.764   0.0926   0.5021  -0.1751
 DYU  N13  N  N     0  -0.301  -3.4405   0.6173  -0.3030
 DYU  N14  N  NR5   0  -0.449  -2.2321   0.0326  -0.2700
 DYU  O08  O  O     0  -0.441   0.9184   2.0454   1.2537
 DYU  S24  S  S2    0  -0.046  -2.9962   4.5107  -0.2713
 DYU  H1   H  HCR6  0   0.257  -2.6051  -3.7120  -2.8236
 DYU  H2   H  HCH3  0   0.254  -1.9332  -0.7672   2.2319
 DYU  H3   H  HCH3  0   0.263  -1.3834  -2.3667   2.7240
 DYU  H4   H  HCH3  0   0.249  -0.2608  -1.2433   1.9816
 DYU  H5   H  HCH3  0   0.253  -0.6456  -5.8186  -1.3359
 DYU  H6   H  HCH3  0   0.248  -1.9148  -6.1548  -0.1696
 DYU  H7   H  HCH3  0   0.247  -2.3125  -5.9480  -1.8772
 DYU  H8   H  HCH3  0   0.249   6.8196  -1.3895   1.2928
 DYU  H9   H  HCH3  0   0.255   6.1628  -2.6043   0.1967
 DYU  H10  H  HCH3  0   0.250   6.8780  -1.1237  -0.4372
 DYU  H11  H  HCR6  0   0.254   3.4833   2.1630   0.9046
 DYU  H12  H  HCR6  0   0.257   3.8336  -2.6682   0.0396
 DYU  H13  H  HCR6  0   0.244   1.6348  -1.6259   0.0993
 DYU  H14  H  HCR6  0   0.269  -2.8061  -1.2839  -2.4610
 DYU  H15  H  HCR6  0   0.249  -1.1691  -4.1674   1.1773
 DYU  H16  H  HCH2  0   0.290  -4.8165   3.0652  -0.9542
 DYU  H17  H  HCH2  0   0.287  -4.6762   3.1007   0.8074
 DYU  H18  H  HCH2  0   0.281  -1.0467   3.8508   1.0457
 DYU  H19  H  HCH2  0   0.279  -0.6860   3.9134  -0.6814
 DYU  H20  H  HCH3  0   0.248   6.5930   1.0042   1.7862
 DYU  H21  H  HCH3  0   0.247   6.7447   1.2651   0.0595
 DYU  H22  H  HCH3  0   0.254   5.8045   2.3898   1.0370
 DYU  H23  H  HNH1  0   0.425   0.3166  -0.2465  -0.8146
 DYU  C22  C  CH3   0  -0.723  -1.6785  -5.5866  -1.0688
 DYU  C27  C  CH3   0  -0.736   6.0511   1.3385   0.8989
 DYU  C26  C  CH3   0  -0.736   6.2614  -1.5334   0.3657

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
 DYU  C04  C05  aromatic  1.386  0.020  1.386
 DYU  C04  C03  aromatic  1.391  0.020  1.391
 DYU  C26  C03  single    1.498  0.020  1.498
 DYU  C05  C06  aromatic  1.391  0.020  1.391
 DYU  C03  C02  aromatic  1.404  0.020  1.404
 DYU  O08  C07  double    1.216  0.020  1.216
 DYU  C06  C07  single    1.487  0.020  1.487
 DYU  C06  C01  aromatic  1.394  0.020  1.394
 DYU  C02  C01  aromatic  1.387  0.020  1.387
 DYU  C02  C27  single    1.500  0.020  1.500
 DYU  C07  N09  single    1.364  0.020  1.364
 DYU  C25  S24  single    1.846  0.020  1.846
 DYU  C25  C11  single    1.485  0.020  1.485
 DYU  S24  C23  single    1.836  0.020  1.836
 DYU  N09  C10  single    1.383  0.020  1.383
 DYU  C11  C10  aromatic  1.374  0.020  1.374
 DYU  C11  C12  aromatic  1.398  0.020  1.398
 DYU  C10  N14  aromatic  1.361  0.020  1.361
 DYU  C21  C20  single    1.500  0.020  1.500
 DYU  C23  C12  single    1.490  0.020  1.490
 DYU  C12  N13  aromatic  1.313  0.020  1.313
 DYU  N14  N13  aromatic  1.343  0.020  1.343
 DYU  N14  C15  single    1.418  0.020  1.418
 DYU  C20  C15  aromatic  1.396  0.020  1.396
 DYU  C20  C19  aromatic  1.393  0.020  1.393
 DYU  C15  C16  aromatic  1.388  0.020  1.388
 DYU  C19  C18  aromatic  1.392  0.020  1.392
 DYU  C16  C17  aromatic  1.384  0.020  1.384
 DYU  C18  C17  aromatic  1.393  0.020  1.393
 DYU  C18  C22  single    1.500  0.020  1.500
 DYU  C17  H1   single    0.930  0.020  1.080
 DYU  C21  H2   single    0.970  0.020  1.090
 DYU  C21  H3   single    0.970  0.020  1.090
 DYU  C21  H4   single    0.970  0.020  1.090
 DYU  C22  H5   single    0.970  0.020  1.090
 DYU  C22  H6   single    0.970  0.020  1.090
 DYU  C22  H7   single    0.970  0.020  1.090
 DYU  C26  H8   single    0.970  0.020  1.090
 DYU  C26  H9   single    0.970  0.020  1.090
 DYU  C26  H10  single    0.970  0.020  1.090
 DYU  C01  H11  single    0.930  0.020  1.080
 DYU  C04  H12  single    0.930  0.020  1.080
 DYU  C05  H13  single    0.930  0.020  1.080
 DYU  C16  H14  single    0.930  0.020  1.080
 DYU  C19  H15  single    0.930  0.020  1.080
 DYU  C23  H16  single    0.970  0.020  1.090
 DYU  C23  H17  single    0.970  0.020  1.090
 DYU  C25  H18  single    0.970  0.020  1.090
 DYU  C25  H19  single    0.970  0.020  1.090
 DYU  C27  H20  single    0.970  0.020  1.090
 DYU  C27  H21  single    0.970  0.020  1.090
 DYU  C27  H22  single    0.970  0.020  1.090
 DYU  N09  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
 DYU  N14  C10  N09  119.77  3.000
 DYU  N14  C10  C11  106.36  3.000
 DYU  N09  C10  C11  133.82  3.000
 DYU  N14  C15  C16  118.59  3.000
 DYU  C16  C15  C20  121.12  3.000
 DYU  N14  C15  C20  120.29  3.000
 DYU  H1   C17  C18  120.03  3.000
 DYU  H1   C17  C16  119.51  3.000
 DYU  C18  C17  C16  120.46  3.000
 DYU  C19  C20  C21  120.15  3.000
 DYU  C19  C20  C15  117.41  3.000
 DYU  C21  C20  C15  122.44  3.000
 DYU  H4   C21  H3   107.03  3.000
 DYU  H4   C21  H2   107.31  3.000
 DYU  H3   C21  H2   107.95  3.000
 DYU  H4   C21  C20  111.46  3.000
 DYU  H3   C21  C20  110.54  3.000
 DYU  H2   C21  C20  112.32  3.000
 DYU  H11  C01  C06  119.22  3.000
 DYU  H11  C01  C02  119.16  3.000
 DYU  C06  C01  C02  121.61  3.000
 DYU  C27  C02  C03  120.49  3.000
 DYU  C27  C02  C01  120.41  3.000
 DYU  C03  C02  C01  119.10  3.000
 DYU  C04  C03  C02  119.05  3.000
 DYU  C02  C03  C26  120.64  3.000
 DYU  C04  C03  C26  120.31  3.000
 DYU  H12  C04  C05  119.23  3.000
 DYU  H12  C04  C03  119.31  3.000
 DYU  C05  C04  C03  121.45  3.000
 DYU  H13  C05  C06  121.59  3.000
 DYU  H13  C05  C04  118.64  3.000
 DYU  C06  C05  C04  119.74  3.000
 DYU  C07  C06  C05  122.46  3.000
 DYU  C07  C06  C01  118.45  3.000
 DYU  C05  C06  C01  119.03  3.000
 DYU  O08  C07  N09  122.20  3.000
 DYU  N09  C07  C06  115.17  3.000
 DYU  O08  C07  C06  122.63  3.000
 DYU  C25  C11  C12  116.81  3.000
 DYU  C12  C11  C10  103.89  3.000
 DYU  C25  C11  C10  139.28  3.000
 DYU  N13  C12  C23  129.73  3.000
 DYU  N13  C12  C11  113.18  3.000
 DYU  C23  C12  C11  117.09  3.000
 DYU  H14  C16  C17  120.29  3.000
 DYU  H14  C16  C15  119.65  3.000
 DYU  C17  C16  C15  120.07  3.000
 DYU  C19  C18  C22  120.64  3.000
 DYU  C22  C18  C17  121.01  3.000
 DYU  C19  C18  C17  118.35  3.000
 DYU  H15  C19  C18  119.06  3.000
 DYU  H15  C19  C20  118.35  3.000
 DYU  C18  C19  C20  122.58  3.000
 DYU  H17  C23  H16  108.33  3.000
 DYU  H17  C23  S24  110.65  3.000
 DYU  H16  C23  S24  109.12  3.000
 DYU  H17  C23  C12  112.17  3.000
 DYU  H16  C23  C12  112.87  3.000
 DYU  S24  C23  C12  103.63  3.000
 DYU  H19  C25  H18  108.29  3.000
 DYU  H19  C25  S24  108.36  3.000
 DYU  H18  C25  S24  110.03  3.000
 DYU  H19  C25  C11  113.57  3.000
 DYU  H18  C25  C11  112.68  3.000
 DYU  S24  C25  C11  103.74  3.000
 DYU  H23  N09  C07  118.93  3.000
 DYU  H23  N09  C10  117.09  3.000
 DYU  C07  N09  C10  123.93  3.000
 DYU  N14  N13  C12  104.06  3.000
 DYU  N13  N14  C15  120.80  3.000
 DYU  C15  N14  C10  126.57  3.000
 DYU  N13  N14  C10  112.49  3.000
 DYU  C25  S24  C23   96.45  3.000
 DYU  H7   C22  H6   108.25  3.000
 DYU  H7   C22  H5   107.37  3.000
 DYU  H6   C22  H5   107.23  3.000
 DYU  H7   C22  C18  111.55  3.000
 DYU  H6   C22  C18  111.59  3.000
 DYU  H5   C22  C18  110.65  3.000
 DYU  H22  C27  H21  107.85  3.000
 DYU  H22  C27  H20  107.75  3.000
 DYU  H21  C27  H20  106.80  3.000
 DYU  H22  C27  C02  111.39  3.000
 DYU  H21  C27  C02  111.50  3.000
 DYU  H20  C27  C02  111.33  3.000
 DYU  H10  C26  H9   107.83  3.000
 DYU  H10  C26  H8   106.63  3.000
 DYU  H9   C26  H8   107.93  3.000
 DYU  H10  C26  C03  111.25  3.000
 DYU  H9   C26  C03  111.33  3.000
 DYU  H8   C26  C03  111.66  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
 DYU  CONST_01  N13  C12  C11  C10    0.00   0.0  0
 DYU  CONST_02  C12  N13  N14  C10    0.00   0.0  0
 DYU  CONST_05  C11  C10  N14  C15  180.00   0.0  0
 DYU  CONST_06  C12  N13  N14  C15  180.00   0.0  0
 DYU  CONST_07  C18  C19  C20  C15    0.00   0.0  0
 DYU  CONST_08  C18  C17  C16  C15    0.00   0.0  0
 DYU  CONST_09  N14  C15  C16  C17  180.00   0.0  0
 DYU  CONST_10  C20  C15  C16  C17    0.00   0.0  0
 DYU  CONST_11  C20  C19  C18  C17    0.00   0.0  0
 DYU  CONST_13  C04  C05  C06  C01    0.00   0.0  0
 DYU  CONST_14  C04  C03  C02  C01    0.00   0.0  0
 DYU  CONST_15  C05  C04  C03  C02    0.00   0.0  0
 DYU  CONST_16  C05  C06  C01  C02    0.00   0.0  0
 DYU  CONST_17  C06  C05  C04  C03    0.00   0.0  0
 DYU  CONST_18  C06  C01  C02  C03    0.00   0.0  0
 DYU  CONST_19  N13  N14  C10  C11    0.00   0.0  0
 DYU  CONST_20  N14  N13  C12  C11    0.00   0.0  0
 DYU  CONST_21  N14  C10  C11  C12    0.00   0.0  0
 DYU  CONST_23  C19  C20  C15  C16    0.00   0.0  0
 DYU  CONST_24  C19  C18  C17  C16    0.00   0.0  0
 DYU  CONST_25  N14  C15  C20  C19  180.00   0.0  0
 DYU  CONST_26  N09  C10  N14  C15    0.00   0.0  0
 DYU  CONST_27  C22  C18  C19  C20  180.00   0.0  0
 DYU  CONST_28  N14  C15  C20  C21    0.00   0.0  0
 DYU  CONST_29  C16  C15  C20  C21  180.00   0.0  0
 DYU  CONST_30  C18  C19  C20  C21  180.00   0.0  0
 DYU  CONST_31  C16  C17  C18  C22  180.00   0.0  0
 DYU  CONST_32  C05  C04  C03  C26  180.00   0.0  0
 DYU  CONST_33  C01  C02  C03  C26  180.00   0.0  0
 DYU  CONST_34  C07  C06  C01  C02  180.00   0.0  0
 DYU  CONST_35  C07  C06  C05  C04  180.00   0.0  0
 DYU  CONST_36  C27  C02  C03  C04  180.00   0.0  0
 DYU  CONST_37  C27  C02  C01  C06  180.00   0.0  0
 DYU  CONST_38  N09  C10  C11  C12  180.00   0.0  0
 DYU  CONST_39  N09  C10  C11  C25    0.00   0.0  0
 DYU  CONST_40  N13  N14  C10  N09  180.00   0.0  0
 DYU  CONST_41  H15  C19  C20  C15  180.00   0.0  0
 DYU  CONST_42  H1   C17  C16  C15  180.00   0.0  0
 DYU  CONST_43  H14  C16  C15  C20  180.00   0.0  0
 DYU  CONST_44  H13  C05  C06  C01  180.00   0.0  0
 DYU  CONST_45  H12  C04  C03  C02  180.00   0.0  0
 DYU  CONST_46  H11  C01  C02  C03  180.00   0.0  0
 DYU  CONST_47  C06  C07  N09  C10  180.00   0.0  0
 DYU  CONST_51  O08  C07  N09  C10    0.00   0.0  0
 DYU  Var_01    S24  C25  C11  C10  168.29  30.0  1
 DYU  Var_02    S24  C23  C12  C11   10.59  30.0  1
 DYU  Var_03    O08  C07  C06  C01  -26.82  30.0  2
 DYU  Var_04    H2   C21  C20  C15   34.52  30.0  2
 DYU  Var_05    H5   C22  C18  C17   96.39  30.0  2
 DYU  Var_06    H20  C27  C02  C01  117.56  30.0  2
 DYU  Var_07    H8   C26  C03  C02   57.28  30.0  2

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
 DYU  plan-1  C15  0.020
 DYU  plan-1  C17  0.020
 DYU  plan-1  C20  0.020
 DYU  plan-1  C21  0.020
 DYU  plan-1  C16  0.020
 DYU  plan-1  C18  0.020
 DYU  plan-1  C19  0.020
 DYU  plan-1  N14  0.020
 DYU  plan-1  H1   0.020
 DYU  plan-1  H14  0.020
 DYU  plan-1  H15  0.020
 DYU  plan-1  C22  0.020
 DYU  plan-2  C01  0.020
 DYU  plan-2  C02  0.020
 DYU  plan-2  C03  0.020
 DYU  plan-2  C04  0.020
 DYU  plan-2  C05  0.020
 DYU  plan-2  C06  0.020
 DYU  plan-2  C07  0.020
 DYU  plan-2  H11  0.020
 DYU  plan-2  H12  0.020
 DYU  plan-2  H13  0.020
 DYU  plan-2  C27  0.020
 DYU  plan-2  C26  0.020
 DYU  plan-3  C10  0.020
 DYU  plan-3  C06  0.020
 DYU  plan-3  C07  0.020
 DYU  plan-3  N09  0.020
 DYU  plan-3  O08  0.020
 DYU  plan-3  H23  0.020
 DYU  plan-4  C10  0.020
 DYU  plan-4  C15  0.020
 DYU  plan-4  C11  0.020
 DYU  plan-4  C12  0.020
 DYU  plan-4  C23  0.020
 DYU  plan-4  C25  0.020
 DYU  plan-4  N09  0.020
 DYU  plan-4  N13  0.020
 DYU  plan-4  N14  0.020

