# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:09:51 2021
#   Inital geometry file: a 143 line input string
#   Ligand name: 5-{[(2S)-1-(3-oxo-3-{4-[5-(trifluoromethyl)pyrimidin-2-yl]piperazin-1-yl}propoxy)propan-2-yl]amino}-4-(trifluoromethyl)pyridazin-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](COCCC(=O)N1CCN(CC1)c2ncc(cn2)C(F)(F)F)NC3=C(C(=O)NN=C3)C(F)(F)F
#
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
 QO4  QO4  5-{[(2S)-1-(3-oxo-3-{4-[5-(trifluoromethyl)pyrimidin-2-yl]piperazin-1-yl}propoxy)propan-2-yl]amino}-4-(trifluoromethyl)pyridazin-3(2H)-one  ligand  59  36  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QO4
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
 QO4  C5   C  CH2   0  -0.131  -29.5470  22.1855  -10.4142
 QO4  C6   C  CH2   0  -0.631  -28.6612  23.3960  -10.6021
 QO4  C7   C  C     0   0.585  -27.1981  23.0140  -10.7591
 QO4  C10  C  CH2   0  -0.327  -26.6674  25.3870  -11.3075
 QO4  N12  N  NT    0  -0.497  -24.5384  25.8837  -10.2153
 QO4  C13  C  CH2   0  -0.300  -24.2026  24.4715  -10.1724
 QO4  C15  C  CR6   0   0.670  -23.6085  26.8543  -10.1919
 QO4  C17  C  CR16  0   0.014  -21.4165  27.4411  -10.1479
 QO4  C26  C  CR6   0   0.426  -27.3288  20.5701  -13.5096
 QO4  C28  C  CR6   0   0.538  -25.3128  21.8073  -14.1718
 QO4  C1   C  CH3   0  -0.676  -29.8301  17.9569  -12.7928
 QO4  C2   C  CH1   0  -0.171  -29.4591  19.4314  -12.8217
 QO4  O4   O  O2    0  -0.481  -29.5716  21.4760  -11.6278
 QO4  O8   O  O     0  -0.482  -26.8068  21.8919  -10.4803
 QO4  N9   N  NT    0  -0.464  -26.3550  23.9746  -11.2154
 QO4  C11  C  CH2   0  -0.298  -25.9622  26.1623  -10.2007
 QO4  C14  C  CH2   0  -0.334  -24.9278  23.7300  -11.2856
 QO4  N16  N  N     0  -0.469  -22.3170  26.4855  -10.1667
 QO4  C18  C  CR6   0  -0.419  -21.7498  28.7914  -10.1546
 QO4  C19  C  CR16  0   0.013  -23.1120  29.0693  -10.1763
 QO4  N20  N  N     0  -0.470  -24.0298  28.1295  -10.1954
 QO4  F22  F  F     0  -0.310  -21.1478  30.9997  -10.6476
 QO4  F23  F  F     0  -0.315  -20.3627  30.1576   -8.8341
 QO4  F24  F  F     0  -0.311  -19.5948  29.5041  -10.7298
 QO4  N25  N  NH1   0  -0.677  -28.0187  19.5440  -13.0035
 QO4  C27  C  CR6   0  -0.469  -25.9396  20.6752  -13.5482
 QO4  O29  O  O     0  -0.502  -24.1026  21.9899  -14.2752
 QO4  N30  N  NR16  0  -0.504  -26.1818  22.7426  -14.6816
 QO4  N31  N  N     0  -0.174  -27.4963  22.6726  -14.6789
 QO4  C32  C  CR16  0  -0.139  -28.0564  21.6566  -14.1336
 QO4  C33  C  CT    0   1.077  -24.9720  19.6880  -12.9899
 QO4  F34  F  F     0  -0.316  -25.5605  18.6509  -12.3632
 QO4  F35  F  F     0  -0.305  -24.1394  20.2245  -12.0878
 QO4  F36  F  F     0  -0.314  -24.1965  19.1423  -13.9403
 QO4  H1   H  HCH2  0   0.218  -30.5558  22.5118  -10.1322
 QO4  H2   H  HCH2  0   0.208  -29.1695  21.5601   -9.5984
 QO4  H3   H  HCH2  0   0.269  -29.0143  23.9694  -11.4620
 QO4  H4   H  HCH2  0   0.277  -28.7658  24.0541   -9.7339
 QO4  H5   H  HCH2  0   0.257  -26.3379  25.7585  -12.2823
 QO4  H6   H  HCH2  0   0.281  -27.7364  25.5653  -11.2381
 QO4  H7   H  HCH2  0   0.247  -24.4980  24.0592   -9.2011
 QO4  H8   H  HCH2  0   0.281  -23.1296  24.3474  -10.2784
 QO4  H9   H  HCR6  0   0.284  -20.3808  27.1175  -10.1287
 QO4  H10  H  HCH3  0   0.251  -30.9049  17.8400  -12.6626
 QO4  H11  H  HCH3  0   0.255  -29.5460  17.4669  -13.7229
 QO4  H12  H  HCH3  0   0.234  -29.3365  17.4398  -11.9670
 QO4  H13  H  HCH1  0   0.266  -29.9701  19.8896  -13.6699
 QO4  H14  H  HCH2  0   0.209  -30.9753  19.9680  -11.3918
 QO4  H15  H  HCH2  0   0.199  -29.3841  19.6480  -10.6856
 QO4  H16  H  HCH2  0   0.282  -26.1287  27.2269  -10.3313
 QO4  H17  H  HCH2  0   0.246  -26.3783  25.8697   -9.2298
 QO4  H18  H  HCH2  0   0.275  -24.7295  22.6654  -11.2185
 QO4  H19  H  HCH2  0   0.249  -24.5590  24.0793  -12.2543
 QO4  H20  H  HCR6  0   0.284  -23.4781  30.0906  -10.1802
 QO4  H21  H  HNH1  0   0.401  -27.4939  18.8219  -12.5414
 QO4  H22  H  HNR6  0   0.421  -25.7921  23.5614  -15.1269
 QO4  H23  H  HCR6  0   0.289  -29.1332  21.6579  -14.1640
 QO4  C21  C  CT    0   1.075  -20.7209  29.8572  -10.0943
 QO4  C3   C  CH2   0  -0.093  -29.8963  20.1208  -11.5355

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
 QO4  O29  C28  double    1.228  0.020  1.228
 QO4  F36  C33  single    1.343  0.020  1.343
 QO4  N30  C28  single    1.375  0.020  1.375
 QO4  N30  N31  single    1.316  0.020  1.316
 QO4  C28  C27  single    1.436  0.020  1.436
 QO4  N31  C32  double    1.282  0.020  1.282
 QO4  C27  C33  single    1.491  0.020  1.491
 QO4  C27  C26  double    1.394  0.020  1.394
 QO4  C33  F35  single    1.340  0.020  1.340
 QO4  C33  F34  single    1.347  0.020  1.347
 QO4  C32  C26  single    1.449  0.020  1.449
 QO4  C26  N25  single    1.336  0.020  1.336
 QO4  N25  C2   single    1.456  0.020  1.456
 QO4  C1   C2   single    1.521  0.020  1.521
 QO4  C2   C3   single    1.523  0.020  1.523
 QO4  C3   O4   single    1.397  0.020  1.397
 QO4  O4   C5   single    1.406  0.020  1.406
 QO4  F22  C21  single    1.339  0.020  1.339
 QO4  C19  N20  aromatic  1.314  0.020  1.314
 QO4  C19  C18  aromatic  1.390  0.020  1.390
 QO4  N20  C15  aromatic  1.343  0.020  1.343
 QO4  C10  N9   single    1.450  0.020  1.450
 QO4  C10  C11  single    1.524  0.020  1.524
 QO4  C6   C5   single    1.512  0.020  1.512
 QO4  C6   C7   single    1.520  0.020  1.520
 QO4  N9   C7   single    1.357  0.020  1.357
 QO4  N9   C14  single    1.450  0.020  1.450
 QO4  C11  N12  single    1.451  0.020  1.451
 QO4  C7   O8   double    1.221  0.020  1.221
 QO4  C14  C13  single    1.521  0.020  1.521
 QO4  C18  C21  single    1.483  0.020  1.483
 QO4  C18  C17  aromatic  1.391  0.020  1.391
 QO4  C15  N12  single    1.344  0.020  1.344
 QO4  C15  N16  aromatic  1.343  0.020  1.343
 QO4  C21  F24  single    1.340  0.020  1.340
 QO4  C21  F23  single    1.344  0.020  1.344
 QO4  N12  C13  single    1.452  0.020  1.452
 QO4  N16  C17  aromatic  1.313  0.020  1.313
 QO4  C5   H1   single    0.970  0.020  1.090
 QO4  C5   H2   single    0.970  0.020  1.090
 QO4  C6   H3   single    0.970  0.020  1.090
 QO4  C6   H4   single    0.970  0.020  1.090
 QO4  C10  H5   single    0.970  0.020  1.090
 QO4  C10  H6   single    0.970  0.020  1.090
 QO4  C13  H7   single    0.970  0.020  1.090
 QO4  C13  H8   single    0.970  0.020  1.090
 QO4  C17  H9   single    0.930  0.020  1.080
 QO4  C1   H10  single    0.970  0.020  1.090
 QO4  C1   H11  single    0.970  0.020  1.090
 QO4  C1   H12  single    0.970  0.020  1.090
 QO4  C2   H13  single    0.970  0.020  1.090
 QO4  C3   H14  single    0.970  0.020  1.090
 QO4  C3   H15  single    0.970  0.020  1.090
 QO4  C11  H16  single    0.970  0.020  1.090
 QO4  C11  H17  single    0.970  0.020  1.090
 QO4  C14  H18  single    0.970  0.020  1.090
 QO4  C14  H19  single    0.970  0.020  1.090
 QO4  C19  H20  single    0.930  0.020  1.080
 QO4  N25  H21  single    0.860  0.020  1.020
 QO4  N30  H22  single    0.860  0.020  1.020
 QO4  C32  H23  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
 QO4  H2   C5   H1   107.17  3.000
 QO4  H2   C5   O4   111.16  3.000
 QO4  H1   C5   O4   110.85  3.000
 QO4  H2   C5   C6   110.36  3.000
 QO4  H1   C5   C6   109.43  3.000
 QO4  O4   C5   C6   107.88  3.000
 QO4  H4   C6   H3   106.13  3.000
 QO4  H4   C6   C7   108.97  3.000
 QO4  H3   C6   C7   111.21  3.000
 QO4  H4   C6   C5   109.08  3.000
 QO4  H3   C6   C5   109.19  3.000
 QO4  C7   C6   C5   112.06  3.000
 QO4  N9   C7   O8   121.89  3.000
 QO4  O8   C7   C6   121.05  3.000
 QO4  N9   C7   C6   117.05  3.000
 QO4  H6   C10  H5   107.31  3.000
 QO4  H6   C10  C11  109.00  3.000
 QO4  H5   C10  C11  109.57  3.000
 QO4  H6   C10  N9   111.60  3.000
 QO4  H5   C10  N9   108.82  3.000
 QO4  C11  C10  N9   110.48  3.000
 QO4  C11  N12  C15  122.69  3.000
 QO4  C15  N12  C13  122.80  3.000
 QO4  C11  N12  C13  114.41  3.000
 QO4  H8   C13  H7   108.05  3.000
 QO4  H8   C13  C14  110.12  3.000
 QO4  H7   C13  C14  109.68  3.000
 QO4  H8   C13  N12  109.69  3.000
 QO4  H7   C13  N12  109.25  3.000
 QO4  C14  C13  N12  110.01  3.000
 QO4  N20  C15  N16  124.21  3.000
 QO4  N16  C15  N12  117.85  3.000
 QO4  N20  C15  N12  117.94  3.000
 QO4  H9   C17  C18  121.22  3.000
 QO4  H9   C17  N16  115.96  3.000
 QO4  C18  C17  N16  122.82  3.000
 QO4  C32  C26  C27  115.60  3.000
 QO4  C32  C26  N25  118.67  3.000
 QO4  C27  C26  N25  125.67  3.000
 QO4  N30  C28  O29  119.37  3.000
 QO4  N30  C28  C27  114.92  3.000
 QO4  O29  C28  C27  125.71  3.000
 QO4  H12  C1   H11  108.35  3.000
 QO4  H12  C1   H10  107.75  3.000
 QO4  H11  C1   H10  108.13  3.000
 QO4  H12  C1   C2   111.30  3.000
 QO4  H11  C1   C2   110.88  3.000
 QO4  H10  C1   C2   110.31  3.000
 QO4  H13  C2   N25  109.50  3.000
 QO4  H13  C2   C3   109.39  3.000
 QO4  N25  C2   C3   110.75  3.000
 QO4  H13  C2   C1   107.92  3.000
 QO4  C3   C2   C1   110.66  3.000
 QO4  N25  C2   C1   108.58  3.000
 QO4  C3   O4   C5   115.89  3.000
 QO4  C14  N9   C10  111.93  3.000
 QO4  C14  N9   C7   120.56  3.000
 QO4  C10  N9   C7   125.25  3.000
 QO4  H17  C11  H16  108.07  3.000
 QO4  H17  C11  N12  109.28  3.000
 QO4  H16  C11  N12  109.73  3.000
 QO4  H17  C11  C10  109.38  3.000
 QO4  H16  C11  C10  109.91  3.000
 QO4  N12  C11  C10  110.43  3.000
 QO4  H19  C14  H18  107.85  3.000
 QO4  H19  C14  N9   108.72  3.000
 QO4  H18  C14  N9   110.02  3.000
 QO4  H19  C14  C13  109.37  3.000
 QO4  H18  C14  C13  110.23  3.000
 QO4  N9   C14  C13  110.58  3.000
 QO4  C17  N16  C15  117.38  3.000
 QO4  C19  C18  C21  122.47  3.000
 QO4  C21  C18  C17  122.10  3.000
 QO4  C19  C18  C17  115.40  3.000
 QO4  H20  C19  N20  115.95  3.000
 QO4  H20  C19  C18  121.25  3.000
 QO4  N20  C19  C18  122.80  3.000
 QO4  C19  N20  C15  117.39  3.000
 QO4  H21  N25  C2   113.80  3.000
 QO4  H21  N25  C26  117.14  3.000
 QO4  C2   N25  C26  128.13  3.000
 QO4  C33  C27  C28  113.66  3.000
 QO4  C33  C27  C26  125.92  3.000
 QO4  C28  C27  C26  120.43  3.000
 QO4  H22  N30  N31  115.42  3.000
 QO4  H22  N30  C28  118.10  3.000
 QO4  N31  N30  C28  126.46  3.000
 QO4  C32  N31  N30  118.64  3.000
 QO4  H23  C32  N31  115.08  3.000
 QO4  H23  C32  C26  121.00  3.000
 QO4  N31  C32  C26  123.93  3.000
 QO4  F36  C33  F35  106.28  3.000
 QO4  F35  C33  F34  105.46  3.000
 QO4  F36  C33  F34  105.59  3.000
 QO4  F34  C33  C27  113.61  3.000
 QO4  F35  C33  C27  112.98  3.000
 QO4  F36  C33  C27  112.27  3.000
 QO4  F24  C21  F23  106.23  3.000
 QO4  F23  C21  F22  106.36  3.000
 QO4  F24  C21  F22  107.26  3.000
 QO4  F23  C21  C18  112.56  3.000
 QO4  F24  C21  C18  111.99  3.000
 QO4  F22  C21  C18  112.04  3.000
 QO4  H15  C3   H14  107.25  3.000
 QO4  H15  C3   O4   111.11  3.000
 QO4  H14  C3   O4   111.83  3.000
 QO4  H15  C3   C2   108.93  3.000
 QO4  H14  C3   C2   109.22  3.000
 QO4  O4   C3   C2   108.46  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
 QO4  CONST_01  C18  C19  N20  C15     0.00   0.0  0
 QO4  CONST_02  C18  C17  N16  C15     0.00   0.0  0
 QO4  CONST_03  N20  C19  C18  C17     0.00   0.0  0
 QO4  CONST_04  N20  C15  N16  C17     0.00   0.0  0
 QO4  CONST_05  C19  N20  C15  N16     0.00   0.0  0
 QO4  CONST_06  C19  C18  C17  N16     0.00   0.0  0
 QO4  CONST_07  C19  N20  C15  N12   180.00   0.0  0
 QO4  CONST_08  C17  N16  C15  N12   180.00   0.0  0
 QO4  CONST_09  N31  N30  C28  C27     0.00   0.0  0
 QO4  CONST_10  N20  C19  C18  C21   180.00   0.0  0
 QO4  CONST_11  N16  C17  C18  C21   180.00   0.0  0
 QO4  CONST_12  N31  N30  C28  O29   180.00   0.0  0
 QO4  CONST_13  H20  C19  N20  C15   180.00   0.0  0
 QO4  CONST_14  H9   C17  N16  C15   180.00   0.0  0
 QO4  CONST_15  H22  N30  C28  C27   180.00   0.0  0
 QO4  CONST_16  C10  N9   C7   C6      0.00   0.0  0
 QO4  CONST_17  C14  N9   C7   C6    180.00   0.0  0
 QO4  CONST_18  O8   C7   N9   C10   180.00   0.0  0
 QO4  CONST_19  C14  N9   C7   O8      0.00   0.0  0
 QO4  Var_01    C13  C14  N9   C10    58.25  30.0  1
 QO4  Var_02    C15  N12  C11  C10   130.42  30.0  1
 QO4  Var_03    N9   C10  C11  N12    53.67  30.0  1
 QO4  Var_04    N9   C14  C13  N12   -54.53  30.0  1
 QO4  Var_05    N20  C15  N12  C13  -178.05  30.0  2
 QO4  Var_06    C14  C13  N12  C15  -130.12  30.0  1
 QO4  Var_07    C14  N9   C10  C11   -57.64  30.0  1
 QO4  Var_08    F22  C21  C18  C17   154.24  30.0  2
 QO4  Var_09    F36  C33  C27  C26   117.18  30.0  3
 QO4  Var_10    C27  C26  N25  C2    173.72  30.0  3
 QO4  Var_11    N9   C7   C6   C5    166.26  30.0  3
 QO4  Var_12    C2   C3   O4   C5   -162.50  30.0  1
 QO4  Var_13    O4   C5   C6   C7    -69.11  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
 QO4  chir_01  C2  N25  C1  C3  negativ

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
 QO4  plan-1  N12  0.020
 QO4  plan-1  C15  0.020
 QO4  plan-1  C17  0.020
 QO4  plan-1  N16  0.020
 QO4  plan-1  C18  0.020
 QO4  plan-1  C19  0.020
 QO4  plan-1  N20  0.020
 QO4  plan-1  H9   0.020
 QO4  plan-1  H20  0.020
 QO4  plan-1  C21  0.020
 QO4  plan-2  C26  0.020
 QO4  plan-2  C28  0.020
 QO4  plan-2  N25  0.020
 QO4  plan-2  C27  0.020
 QO4  plan-2  O29  0.020
 QO4  plan-2  N30  0.020
 QO4  plan-2  N31  0.020
 QO4  plan-2  C32  0.020
 QO4  plan-2  C33  0.020
 QO4  plan-2  H22  0.020
 QO4  plan-2  H23  0.020
 QO4  plan-3  C6   0.020
 QO4  plan-3  C7   0.020
 QO4  plan-3  C10  0.020
 QO4  plan-3  O8   0.020
 QO4  plan-3  N9   0.020
 QO4  plan-3  C14  0.020

