# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 06:13:35 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-(1,3-benzodioxol-5-yl)-2-{[5-(4-methylphenyl)[1,3]thiazolo[2,3-c][1,2,4]triazol-3-yl]sulfanyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2csc3nnc(SCC(=O)Nc4ccc5OCOc5c4)n23
#
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
 PKJ  PKJ  N-(1,3-benzodioxol-5-yl)-2-{[5-(4-methylphenyl)[1,3]thiazolo[2,3-c][1,2,4]triazol-3-yl]sulfanyl}acetamide  ligand  45  29  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PKJ
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
 PKJ  C24  C  CR16  0  -0.242  -4.3111   2.2395   0.8656
 PKJ  C28  C  CR16  0  -0.238  -3.1286   1.7877  -1.1754
 PKJ  C25  C  CR16  0  -0.264  -3.9052   3.5622   0.8026
 PKJ  C27  C  CR16  0  -0.265  -2.7235   3.1116  -1.2267
 PKJ  C5   C  CR16  0  -0.298   4.4922   0.5251   1.0507
 PKJ  C6   C  CR16  0  -0.323   5.8168   0.9785   1.0937
 PKJ  C12  C  CR16  0  -0.408   5.1596  -1.4399  -0.2141
 PKJ  C23  C  CR6   0   0.016  -3.9234   1.3380  -0.1229
 PKJ  C26  C  CR6   0   0.105  -3.1003   4.0198  -0.2397
 PKJ  C4   C  CR6   0   0.371   4.1653  -0.6600   0.4034
 PKJ  C7   C  CR56  0   0.297   6.7748   0.2083   0.4881
 PKJ  C11  C  CR56  0   0.318   6.4478  -0.9794  -0.1461
 PKJ  C18  C  CR55  0   0.230  -4.1219  -2.3618  -0.0936
 PKJ  C15  C  CR5   0   0.279  -2.1856  -1.4235  -0.0422
 PKJ  C20  C  CR15  0  -0.590  -5.6669  -0.4757  -0.0571
 PKJ  C21  C  CR5   0   0.502  -4.3930  -0.0497  -0.0788
 PKJ  C2   C  C     0   0.576   1.7017  -0.4609   0.3286
 PKJ  C9   C  CH2   0   0.090   8.5994  -0.5779  -0.4935
 PKJ  C29  C  CH3   0  -0.696  -2.6402   5.4464  -0.2823
 PKJ  C13  C  CH2   0  -0.681   0.4692  -1.3339   0.2120
 PKJ  N17  N  N     0  -0.330  -3.2512  -3.3218  -0.0656
 PKJ  N16  N  N     0  -0.324  -2.0287  -2.7200  -0.0377
 PKJ  N22  N  N     0  -0.573  -3.5190  -1.1381  -0.0937
 PKJ  N3   N  NH1   0  -0.736   2.8536  -1.1634   0.3452
 PKJ  O1   O  O     0  -0.464   1.6182   0.7506   0.4032
 PKJ  O8   O  O     0  -0.478   8.1159   0.4024   0.4130
 PKJ  O10  O  O     0  -0.477   7.5711  -1.5515  -0.6373
 PKJ  S19  S  S2    0   0.259  -5.8415  -2.2132  -0.0673
 PKJ  H1   H  HCR6  0   0.239  -4.9268   1.9031   1.6903
 PKJ  H2   H  HCR6  0   0.251  -2.8407   1.1112  -1.9703
 PKJ  H3   H  HCR6  0   0.234  -4.2180   4.2489   1.5798
 PKJ  H4   H  HCR6  0   0.234  -2.1138   3.4448  -2.0578
 PKJ  H6   H  HCR6  0   0.260   6.0638   1.9013   1.6006
 PKJ  H7   H  HCR6  0   0.253   4.9144  -2.3645  -0.7209
 PKJ  H8   H  HCR5  0   0.297  -6.5446   0.1510  -0.0695
 PKJ  H9   H  HCH2  0   0.219   8.8106  -0.1179  -1.4650
 PKJ  H10  H  HCH2  0   0.232   9.4958  -1.0464  -0.0891
 PKJ  H11  H  HCH3  0   0.246  -1.7907   5.5988   0.3865
 PKJ  H12  H  HCH3  0   0.235  -2.3248   5.7364  -1.2835
 PKJ  H13  H  HCH3  0   0.236  -3.4274   6.1286   0.0382
 PKJ  H14  H  HCH2  0   0.301   0.5337  -1.9939  -0.6543
 PKJ  H15  H  HCH2  0   0.316   0.3617  -1.9601   1.0999
 PKJ  H16  H  HNH1  0   0.391   2.7761  -2.1596   0.2021
 PKJ  S14  S  S2    0   0.135  -0.9406  -0.2101   0.0515
 PKJ  H5   H  HCR6  0   0.263   3.7329   1.1132   1.5405

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
 PKJ  S19  C20  aromatic  1.746  0.020  1.746
 PKJ  S19  C18  aromatic  1.726  0.020  1.726
 PKJ  C20  C21  aromatic  1.343  0.020  1.343
 PKJ  C21  C23  single    1.466  0.020  1.466
 PKJ  C21  N22  aromatic  1.396  0.020  1.396
 PKJ  C18  N22  aromatic  1.364  0.020  1.364
 PKJ  C18  N17  aromatic  1.296  0.020  1.296
 PKJ  C24  C23  aromatic  1.393  0.020  1.393
 PKJ  C24  C25  aromatic  1.385  0.020  1.385
 PKJ  C23  C28  aromatic  1.393  0.020  1.393
 PKJ  C25  C26  aromatic  1.394  0.020  1.394
 PKJ  N22  C15  aromatic  1.365  0.020  1.365
 PKJ  C28  C27  aromatic  1.385  0.020  1.385
 PKJ  N17  N16  aromatic  1.363  0.020  1.363
 PKJ  C26  C27  aromatic  1.393  0.020  1.393
 PKJ  C26  C29  single    1.500  0.020  1.500
 PKJ  C15  N16  aromatic  1.306  0.020  1.306
 PKJ  C15  S14  single    1.741  0.020  1.741
 PKJ  S14  C13  single    1.810  0.020  1.810
 PKJ  O1   C2   double    1.217  0.020  1.217
 PKJ  C13  C2   single    1.515  0.020  1.515
 PKJ  C2   N3   single    1.349  0.020  1.349
 PKJ  N3   C4   single    1.406  0.020  1.406
 PKJ  C5   C4   aromatic  1.389  0.020  1.389
 PKJ  C5   C6   aromatic  1.401  0.020  1.401
 PKJ  C4   C12  aromatic  1.406  0.020  1.406
 PKJ  C6   C7   aromatic  1.370  0.020  1.370
 PKJ  C12  C11  aromatic  1.370  0.020  1.370
 PKJ  C7   C11  aromatic  1.386  0.020  1.386
 PKJ  C7   O8   single    1.357  0.020  1.357
 PKJ  C11  O10  single    1.353  0.020  1.353
 PKJ  O8   C9   single    1.420  0.020  1.420
 PKJ  O10  C9   single    1.423  0.020  1.423
 PKJ  C24  H1   single    0.930  0.020  1.080
 PKJ  C28  H2   single    0.930  0.020  1.080
 PKJ  C25  H3   single    0.930  0.020  1.080
 PKJ  C27  H4   single    0.930  0.020  1.080
 PKJ  C5   H5   single    0.930  0.020  1.080
 PKJ  C6   H6   single    0.930  0.020  1.080
 PKJ  C12  H7   single    0.930  0.020  1.080
 PKJ  C20  H8   single    0.930  0.020  1.080
 PKJ  C9   H9   single    0.970  0.020  1.090
 PKJ  C9   H10  single    0.970  0.020  1.090
 PKJ  C29  H11  single    0.970  0.020  1.090
 PKJ  C29  H12  single    0.970  0.020  1.090
 PKJ  C29  H13  single    0.970  0.020  1.090
 PKJ  C13  H14  single    0.970  0.020  1.090
 PKJ  C13  H15  single    0.970  0.020  1.090
 PKJ  N3   H16  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
 PKJ  H1   C24  C23  119.85  3.000
 PKJ  H1   C24  C25  119.87  3.000
 PKJ  C23  C24  C25  120.28  3.000
 PKJ  H2   C28  C23  120.30  3.000
 PKJ  H2   C28  C27  119.48  3.000
 PKJ  C23  C28  C27  120.21  3.000
 PKJ  H3   C25  C26  119.67  3.000
 PKJ  H3   C25  C24  119.21  3.000
 PKJ  C26  C25  C24  121.12  3.000
 PKJ  H4   C27  C26  119.69  3.000
 PKJ  H4   C27  C28  119.13  3.000
 PKJ  C26  C27  C28  121.17  3.000
 PKJ  H5   C5   C4   120.75  3.000
 PKJ  H5   C5   C6   118.39  3.000
 PKJ  C4   C5   C6   120.86  3.000
 PKJ  H6   C6   C7   121.81  3.000
 PKJ  H6   C6   C5   120.44  3.000
 PKJ  C7   C6   C5   117.75  3.000
 PKJ  H7   C12  C11  121.56  3.000
 PKJ  H7   C12  C4   121.27  3.000
 PKJ  C11  C12  C4   117.17  3.000
 PKJ  C21  C23  C28  120.73  3.000
 PKJ  C28  C23  C24  119.07  3.000
 PKJ  C21  C23  C24  120.15  3.000
 PKJ  C29  C26  C27  121.13  3.000
 PKJ  C29  C26  C25  120.71  3.000
 PKJ  C27  C26  C25  118.15  3.000
 PKJ  N3   C4   C12  116.28  3.000
 PKJ  C12  C4   C5   120.75  3.000
 PKJ  N3   C4   C5   122.96  3.000
 PKJ  O8   C7   C11  109.30  3.000
 PKJ  O8   C7   C6   129.41  3.000
 PKJ  C11  C7   C6   121.27  3.000
 PKJ  O10  C11  C7   109.43  3.000
 PKJ  O10  C11  C12  128.36  3.000
 PKJ  C7   C11  C12  122.20  3.000
 PKJ  S19  C18  N22  111.29  3.000
 PKJ  N22  C18  N17  111.56  3.000
 PKJ  S19  C18  N17  137.10  3.000
 PKJ  S14  C15  N22  123.71  3.000
 PKJ  S14  C15  N16  127.29  3.000
 PKJ  N22  C15  N16  108.97  3.000
 PKJ  H8   C20  S19  119.78  3.000
 PKJ  H8   C20  C21  125.96  3.000
 PKJ  S19  C20  C21  114.22  3.000
 PKJ  N22  C21  C20  110.28  3.000
 PKJ  N22  C21  C23  122.50  3.000
 PKJ  C20  C21  C23  127.19  3.000
 PKJ  O1   C2   N3   125.19  3.000
 PKJ  N3   C2   C13  113.29  3.000
 PKJ  O1   C2   C13  121.52  3.000
 PKJ  H10  C9   H9   110.57  3.000
 PKJ  H10  C9   O10  109.75  3.000
 PKJ  H9   C9   O10  109.69  3.000
 PKJ  H10  C9   O8   109.88  3.000
 PKJ  H9   C9   O8   109.99  3.000
 PKJ  O10  C9   O8   106.90  3.000
 PKJ  H13  C29  H12  108.23  3.000
 PKJ  H13  C29  H11  107.12  3.000
 PKJ  H12  C29  H11  107.50  3.000
 PKJ  H13  C29  C26  111.44  3.000
 PKJ  H12  C29  C26  111.62  3.000
 PKJ  H11  C29  C26  110.74  3.000
 PKJ  H15  C13  H14  107.74  3.000
 PKJ  H15  C13  S14  110.58  3.000
 PKJ  H14  C13  S14  110.56  3.000
 PKJ  H15  C13  C2   110.37  3.000
 PKJ  H14  C13  C2   111.20  3.000
 PKJ  S14  C13  C2   106.42  3.000
 PKJ  N16  N17  C18  106.02  3.000
 PKJ  N17  N16  C15  109.30  3.000
 PKJ  C21  N22  C15  140.75  3.000
 PKJ  C15  N22  C18  104.14  3.000
 PKJ  C21  N22  C18  115.00  3.000
 PKJ  H16  N3   C2   116.53  3.000
 PKJ  H16  N3   C4   115.52  3.000
 PKJ  C2   N3   C4   127.62  3.000
 PKJ  C9   O8   C7   105.84  3.000
 PKJ  C9   O10  C11  105.90  3.000
 PKJ  C20  S19  C18   89.21  3.000
 PKJ  C13  S14  C15   97.41  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
 PKJ  CONST_03  C27  C28  C23  C24     0.00   0.0  0
 PKJ  CONST_04  C27  C26  C25  C24     0.00   0.0  0
 PKJ  CONST_07  C25  C24  C23  C28     0.00   0.0  0
 PKJ  CONST_08  C25  C26  C27  C28     0.00   0.0  0
 PKJ  CONST_09  C21  C23  C24  C25   180.00   0.0  0
 PKJ  CONST_10  C21  C23  C28  C27   180.00   0.0  0
 PKJ  CONST_11  C11  C12  C4   C5      0.00   0.0  0
 PKJ  CONST_12  C11  C7   C6   C5      0.00   0.0  0
 PKJ  CONST_13  C12  C4   C5   C6      0.00   0.0  0
 PKJ  CONST_14  C12  C11  C7   C6      0.00   0.0  0
 PKJ  CONST_15  S19  C20  C21  C23   180.00   0.0  0
 PKJ  CONST_16  C18  N22  C21  C23   180.00   0.0  0
 PKJ  CONST_17  C15  N22  C21  C23     0.00   0.0  0
 PKJ  CONST_18  C26  C25  C24  C23     0.00   0.0  0
 PKJ  CONST_19  C26  C27  C28  C23     0.00   0.0  0
 PKJ  CONST_20  C7   C6   C5   C4      0.00   0.0  0
 PKJ  CONST_21  C7   C11  C12  C4      0.00   0.0  0
 PKJ  CONST_22  C21  C20  S19  C18     0.00   0.0  0
 PKJ  CONST_23  C20  C21  N22  C18     0.00   0.0  0
 PKJ  CONST_24  N16  C15  N22  C18     0.00   0.0  0
 PKJ  CONST_25  C15  N16  N17  C18     0.00   0.0  0
 PKJ  CONST_26  C20  C21  N22  C15   180.00   0.0  0
 PKJ  CONST_27  S19  C18  N22  C15   180.00   0.0  0
 PKJ  CONST_28  N17  C18  N22  C15     0.00   0.0  0
 PKJ  CONST_29  N22  C18  S19  C20     0.00   0.0  0
 PKJ  CONST_30  N17  C18  S19  C20   180.00   0.0  0
 PKJ  CONST_31  S19  C18  N22  C21     0.00   0.0  0
 PKJ  CONST_32  N17  C18  N22  C21   180.00   0.0  0
 PKJ  CONST_33  N16  C15  N22  C21   180.00   0.0  0
 PKJ  CONST_34  N22  C15  N16  N17     0.00   0.0  0
 PKJ  CONST_35  S19  C18  N17  N16   180.00   0.0  0
 PKJ  CONST_36  N22  C18  N17  N16     0.00   0.0  0
 PKJ  CONST_37  S19  C20  C21  N22     0.00   0.0  0
 PKJ  CONST_38  C29  C26  C25  C24   180.00   0.0  0
 PKJ  CONST_39  C29  C26  C27  C28   180.00   0.0  0
 PKJ  CONST_40  N3   C4   C5   C6    180.00   0.0  0
 PKJ  CONST_41  N3   C4   C12  C11   180.00   0.0  0
 PKJ  CONST_42  S14  C15  N22  C18   180.00   0.0  0
 PKJ  CONST_43  S14  C15  N22  C21     0.00   0.0  0
 PKJ  CONST_44  S14  C15  N16  N17   180.00   0.0  0
 PKJ  CONST_45  H2   C28  C23  C24   180.00   0.0  0
 PKJ  CONST_46  H1   C24  C23  C28   180.00   0.0  0
 PKJ  CONST_47  H4   C27  C26  C25   180.00   0.0  0
 PKJ  CONST_48  H3   C25  C26  C27   180.00   0.0  0
 PKJ  CONST_49  H7   C12  C4   C5    180.00   0.0  0
 PKJ  CONST_50  H5   C5   C4   C12   180.00   0.0  0
 PKJ  CONST_51  H8   C20  C21  C23     0.00   0.0  0
 PKJ  CONST_52  H6   C6   C5   C4    180.00   0.0  0
 PKJ  CONST_56  O1   C2   N3   C4      0.00   0.0  0
 PKJ  CONST_57  C13  C2   N3   C4    180.00   0.0  0
 PKJ  Var_01    O10  C9   O8   C7    -15.84  30.0  1
 PKJ  Var_02    O8   C9   O10  C11    15.67  30.0  1
 PKJ  Var_03    N22  C15  S14  C13   175.81  30.0  1
 PKJ  Var_04    H11  C29  C26  C25    79.70  30.0  2
 PKJ  Var_05    C2   C13  S14  C15  -179.35  30.0  3
 PKJ  Var_06    S14  C13  C2   N3   -174.85  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
 PKJ  plan-1  C24  0.020
 PKJ  plan-1  C28  0.020
 PKJ  plan-1  C25  0.020
 PKJ  plan-1  C27  0.020
 PKJ  plan-1  C23  0.020
 PKJ  plan-1  C26  0.020
 PKJ  plan-1  C21  0.020
 PKJ  plan-1  C29  0.020
 PKJ  plan-1  H1   0.020
 PKJ  plan-1  H2   0.020
 PKJ  plan-1  H3   0.020
 PKJ  plan-1  H4   0.020
 PKJ  plan-2  C5   0.020
 PKJ  plan-2  C6   0.020
 PKJ  plan-2  C12  0.020
 PKJ  plan-2  C4   0.020
 PKJ  plan-2  C7   0.020
 PKJ  plan-2  C11  0.020
 PKJ  plan-2  N3   0.020
 PKJ  plan-2  O8   0.020
 PKJ  plan-2  O10  0.020
 PKJ  plan-2  H6   0.020
 PKJ  plan-2  H7   0.020
 PKJ  plan-2  H5   0.020
 PKJ  plan-3  C23  0.020
 PKJ  plan-3  C18  0.020
 PKJ  plan-3  C15  0.020
 PKJ  plan-3  C20  0.020
 PKJ  plan-3  C21  0.020
 PKJ  plan-3  N17  0.020
 PKJ  plan-3  N16  0.020
 PKJ  plan-3  N22  0.020
 PKJ  plan-3  S19  0.020
 PKJ  plan-3  H8   0.020
 PKJ  plan-3  S14  0.020
 PKJ  plan-4  C4   0.020
 PKJ  plan-4  C2   0.020
 PKJ  plan-4  C13  0.020
 PKJ  plan-4  N3   0.020
 PKJ  plan-4  O1   0.020
 PKJ  plan-4  H16  0.020

