# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 13:55:52 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-[6-bromo-2-fluoro-3-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-chlorobenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1c(Cc2n[nH]c3nnccc23)ccc(Br)c1Oc4cc(Cl)cc(c4)C#N
#
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
 PZL  PZL  3-[6-bromo-2-fluoro-3-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-chlorobenzonitrile  ligand  38  28  .  2022-07-22  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_PZL
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
 PZL  N19   N   NS    0  -0.237  -3.6571  -4.6220   2.0730
 PZL  C16   C   CSP   0   0.069  -3.0462  -3.8265   1.5078
 PZL  C13   C   CR6   0   0.009  -2.2843  -2.8397   0.8087
 PZL  C12   C   CR16  0  -0.221  -1.3258  -3.2538  -0.1138
 PZL  C11   C   CR6   0  -0.017  -0.6011  -2.2780  -0.7723
 PZL  CL15  CL  CL    0  -0.086   0.6067  -2.7440  -1.9113
 PZL  C10   C   CR16  0  -0.265  -0.8112  -0.9285  -0.5390
 PZL  C14   C   CR16  0  -0.311  -2.5073  -1.4948   1.0831
 PZL  C9    C   CR6   0   0.389  -1.7557  -0.5489   0.4054
 PZL  O8    O   O2    0  -0.484  -2.0100   0.7580   0.7022
 PZL  C3    C   CR6   0   0.245  -1.0317   1.6745   0.4814
 PZL  C4    C   CR6   0  -0.227  -1.2668   2.7896  -0.3114
 PZL  BR17  BR  BR    0   0.006  -2.9550   3.0117  -1.0961
 PZL  C2    C   CR6   0   0.537   0.2220   1.5297   1.0599
 PZL  F5    F   F     0  -0.293   0.4185   0.4659   1.8470
 PZL  C6    C   CR6   0  -0.068   1.2678   2.3973   0.8167
 PZL  C7    C   CR16  0  -0.307   0.9967   3.5090   0.0259
 PZL  C1    C   CR16  0  -0.237  -0.2595   3.7215  -0.5195
 PZL  C18   C   CH2   0  -0.613   2.6579   2.0785   1.3034
 PZL  C26   C   CR5   0   0.252   3.2840   1.0740   0.3857
 PZL  N27   N   N     0  -0.217   3.8843   1.4502  -0.7154
 PZL  N28   N   NR15  0  -0.497   4.2726   0.3604  -1.3755
 PZL  C24   C   CR56  0   0.479   3.9307  -0.7649  -0.7152
 PZL  N20   N   N     0  -0.270   4.1743  -2.0152  -1.0806
 PZL  C25   C   CR56  0  -0.029   3.2742  -0.3509   0.4590
 PZL  C23   C   CR16  0  -0.333   2.8583  -1.3666   1.3035
 PZL  C22   C   CR16  0  -0.106   3.1329  -2.6523   0.8687
 PZL  N21   N   N     0  -0.255   3.7620  -2.9500  -0.2751
 PZL  H12   H   HCR6  0   0.306  -1.1538  -4.3037  -0.3027
 PZL  H10   H   HCR6  0   0.318  -0.2355  -0.1967  -1.0905
 PZL  H14   H   HCR6  0   0.305  -3.2435  -1.1911   1.8149
 PZL  H7    H   HCR6  0   0.280   1.7869   4.2199  -0.1772
 PZL  H1    H   HCR6  0   0.292  -0.4414   4.5958  -1.1289
 PZL  H18   H   HCH2  0   0.299   3.2579   2.9882   1.3037
 PZL  H18A  H   HCH2  0   0.294   2.6458   1.7042   2.3275
 PZL  HN28  H   HNR5  0   0.429   4.7611   0.4429  -2.2536
 PZL  H23   H   HCR6  0   0.280   2.3630  -1.1977   2.2483
 PZL  H22   H   HCR6  0   0.285   2.8426  -3.5083   1.4623

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
 PZL  N19  C16   triple    1.151  0.020  1.151
 PZL  C16  C13   single    1.429  0.020  1.429
 PZL  C13  C12   aromatic  1.393  0.020  1.393
 PZL  C13  C14   aromatic  1.391  0.020  1.391
 PZL  C12  C11   aromatic  1.382  0.020  1.382
 PZL  C11  CL15  single    1.724  0.020  1.724
 PZL  C11  C10   aromatic  1.385  0.020  1.385
 PZL  C10  C9    aromatic  1.389  0.020  1.389
 PZL  C14  C9    aromatic  1.385  0.020  1.385
 PZL  C9   O8    single    1.364  0.020  1.364
 PZL  O8   C3    single    1.359  0.020  1.359
 PZL  C3   C4    aromatic  1.388  0.020  1.388
 PZL  C3   C2    aromatic  1.388  0.020  1.388
 PZL  C4   BR17  single    1.875  0.020  1.875
 PZL  C4   C1    aromatic  1.388  0.020  1.388
 PZL  C2   F5    single    1.338  0.020  1.338
 PZL  C2   C6    aromatic  1.380  0.020  1.380
 PZL  C6   C7    aromatic  1.391  0.020  1.391
 PZL  C6   C18   single    1.507  0.020  1.507
 PZL  C7   C1    aromatic  1.386  0.020  1.386
 PZL  C18  C26   single    1.498  0.020  1.498
 PZL  C26  N27   aromatic  1.309  0.020  1.309
 PZL  C26  C25   aromatic  1.427  0.020  1.427
 PZL  N27  N28   aromatic  1.332  0.020  1.332
 PZL  N28  C24   aromatic  1.349  0.020  1.349
 PZL  C24  N20   aromatic  1.325  0.020  1.325
 PZL  C24  C25   aromatic  1.407  0.020  1.407
 PZL  N20  N21   aromatic  1.301  0.020  1.301
 PZL  C25  C23   aromatic  1.385  0.020  1.385
 PZL  C23  C22   aromatic  1.385  0.020  1.385
 PZL  C22  N21   aromatic  1.339  0.020  1.339
 PZL  C12  H12   single    0.930  0.020  1.080
 PZL  C10  H10   single    0.930  0.020  1.080
 PZL  C14  H14   single    0.930  0.020  1.080
 PZL  C7   H7    single    0.930  0.020  1.080
 PZL  C1   H1    single    0.930  0.020  1.080
 PZL  C18  H18   single    0.970  0.020  1.090
 PZL  C18  H18A  single    0.970  0.020  1.090
 PZL  N28  HN28  single    0.860  0.020  1.020
 PZL  C23  H23   single    0.930  0.020  1.080
 PZL  C22  H22   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
 PZL  C13   C16  N19   180.00  3.000
 PZL  C14   C13  C12   121.90  3.000
 PZL  C14   C13  C16   119.06  3.000
 PZL  C12   C13  C16   119.03  3.000
 PZL  H12   C12  C11   121.27  3.000
 PZL  H12   C12  C13   120.94  3.000
 PZL  C11   C12  C13   117.79  3.000
 PZL  C10   C11  CL15  118.73  3.000
 PZL  C10   C11  C12   121.86  3.000
 PZL  CL15  C11  C12   119.41  3.000
 PZL  H10   C10  C9    121.57  3.000
 PZL  H10   C10  C11   119.48  3.000
 PZL  C9    C10  C11   118.94  3.000
 PZL  H14   C14  C9    120.57  3.000
 PZL  H14   C14  C13   120.95  3.000
 PZL  C9    C14  C13   118.48  3.000
 PZL  O8    C9   C14   116.53  3.000
 PZL  O8    C9   C10   122.46  3.000
 PZL  C14   C9   C10   121.01  3.000
 PZL  C3    O8   C9    118.48  3.000
 PZL  C2    C3   C4    118.34  3.000
 PZL  C2    C3   O8    120.81  3.000
 PZL  C4    C3   O8    120.84  3.000
 PZL  C1    C4   BR17  120.75  3.000
 PZL  C1    C4   C3    120.13  3.000
 PZL  BR17  C4   C3    119.12  3.000
 PZL  C6    C2   F5    119.49  3.000
 PZL  C6    C2   C3    123.03  3.000
 PZL  F5    C2   C3    117.43  3.000
 PZL  C18   C6   C7    122.18  3.000
 PZL  C18   C6   C2    120.59  3.000
 PZL  C7    C6   C2    117.05  3.000
 PZL  H7    C7   C1    119.17  3.000
 PZL  H7    C7   C6    119.30  3.000
 PZL  C1    C7   C6    121.53  3.000
 PZL  H1    C1   C7    119.88  3.000
 PZL  H1    C1   C4    120.36  3.000
 PZL  C7    C1   C4    119.73  3.000
 PZL  H18A  C18  H18   107.00  3.000
 PZL  H18A  C18  C26   110.48  3.000
 PZL  H18   C18  C26   109.26  3.000
 PZL  H18A  C18  C6    111.45  3.000
 PZL  H18   C18  C6    109.35  3.000
 PZL  C26   C18  C6    109.25  3.000
 PZL  C25   C26  N27   109.47  3.000
 PZL  C25   C26  C18   129.45  3.000
 PZL  N27   C26  C18   120.95  3.000
 PZL  N28   N27  C26   108.38  3.000
 PZL  HN28  N28  C24   128.13  3.000
 PZL  HN28  N28  N27   120.39  3.000
 PZL  C24   N28  N27   111.48  3.000
 PZL  C25   C24  N20   126.39  3.000
 PZL  C25   C24  N28   106.34  3.000
 PZL  N20   C24  N28   127.27  3.000
 PZL  N21   N20  C24   116.67  3.000
 PZL  C23   C25  C24   115.66  3.000
 PZL  C23   C25  C26   139.98  3.000
 PZL  C24   C25  C26   104.34  3.000
 PZL  H23   C23  C22   120.72  3.000
 PZL  H23   C23  C25   123.81  3.000
 PZL  C22   C23  C25   115.46  3.000
 PZL  H22   C22  N21   114.78  3.000
 PZL  H22   C22  C23   120.62  3.000
 PZL  N21   C22  C23   124.60  3.000
 PZL  C22   N21  N20   121.20  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
 PZL  CONST_01  C10   C11  C12  C13     0.00   0.0  0
 PZL  CONST_02  C10   C9   C14  C13     0.00   0.0  0
 PZL  CONST_03  C9    C14  C13  C12     0.00   0.0  0
 PZL  CONST_04  C9    C10  C11  C12     0.00   0.0  0
 PZL  CONST_05  C14   C13  C12  C11     0.00   0.0  0
 PZL  CONST_06  C14   C9   C10  C11     0.00   0.0  0
 PZL  CONST_07  C7    C1   C4   C3      0.00   0.0  0
 PZL  CONST_08  C7    C6   C2   C3      0.00   0.0  0
 PZL  CONST_09  C6    C2   C3   C4      0.00   0.0  0
 PZL  CONST_10  C6    C7   C1   C4      0.00   0.0  0
 PZL  CONST_11  C1    C4   C3   C2      0.00   0.0  0
 PZL  CONST_12  C1    C7   C6   C2      0.00   0.0  0
 PZL  CONST_13  C24   N28  N27  C26     0.00   0.0  0
 PZL  CONST_14  N28   C24  C25  C26     0.00   0.0  0
 PZL  CONST_15  N20   C24  C25  C26   180.00   0.0  0
 PZL  CONST_16  C22   C23  C25  C26   180.00   0.0  0
 PZL  CONST_17  C24   C25  C26  N27     0.00   0.0  0
 PZL  CONST_18  C23   C25  C26  N27   180.00   0.0  0
 PZL  CONST_19  N20   C24  N28  N27   180.00   0.0  0
 PZL  CONST_20  C25   C24  N28  N27     0.00   0.0  0
 PZL  CONST_21  C25   C26  N27  N28     0.00   0.0  0
 PZL  CONST_22  N21   N20  C24  N28   180.00   0.0  0
 PZL  CONST_23  C23   C25  C24  N28   180.00   0.0  0
 PZL  CONST_24  C22   N21  N20  C24     0.00   0.0  0
 PZL  CONST_25  C22   C23  C25  C24     0.00   0.0  0
 PZL  CONST_26  C23   C25  C24  N20     0.00   0.0  0
 PZL  CONST_27  C23   C22  N21  N20     0.00   0.0  0
 PZL  CONST_28  N21   N20  C24  C25     0.00   0.0  0
 PZL  CONST_29  N21   C22  C23  C25     0.00   0.0  0
 PZL  CONST_30  C11   C12  C13  C16   180.00   0.0  0
 PZL  CONST_31  C9    C14  C13  C16   180.00   0.0  0
 PZL  CONST_32  CL15  C11  C12  C13   180.00   0.0  0
 PZL  CONST_33  O8    C9   C14  C13   180.00   0.0  0
 PZL  CONST_34  O8    C9   C10  C11   180.00   0.0  0
 PZL  CONST_35  C9    C10  C11  CL15  180.00   0.0  0
 PZL  CONST_36  C1    C4   C3   O8    180.00   0.0  0
 PZL  CONST_37  C6    C2   C3   O8    180.00   0.0  0
 PZL  CONST_38  C18   C6   C2   C3    180.00   0.0  0
 PZL  CONST_39  F5    C2   C3   C4    180.00   0.0  0
 PZL  CONST_40  C2    C3   C4   BR17  180.00   0.0  0
 PZL  CONST_41  C7    C1   C4   BR17  180.00   0.0  0
 PZL  CONST_42  C7    C6   C2   F5    180.00   0.0  0
 PZL  CONST_43  C18   C6   C7   C1    180.00   0.0  0
 PZL  CONST_44  N28   N27  C26  C18   180.00   0.0  0
 PZL  CONST_45  C24   C25  C26  C18   180.00   0.0  0
 PZL  CONST_46  C23   C25  C26  C18     0.00   0.0  0
 PZL  CONST_47  H14   C14  C13  C12   180.00   0.0  0
 PZL  CONST_48  H10   C10  C11  C12   180.00   0.0  0
 PZL  CONST_49  H12   C12  C11  C10   180.00   0.0  0
 PZL  CONST_50  H1    C1   C4   C3    180.00   0.0  0
 PZL  CONST_51  H7    C7   C1   C4    180.00   0.0  0
 PZL  CONST_52  HN28  N28  N27  C26   180.00   0.0  0
 PZL  CONST_53  H23   C23  C25  C26     0.00   0.0  0
 PZL  CONST_54  H22   C22  N21  N20   180.00   0.0  0
 PZL  Var_01    C4    C3   O8   C9    124.96  30.0  2
 PZL  Var_02    C26   C18  C6   C2     78.31  30.0  2
 PZL  Var_03    N27   C26  C18  C6     84.39  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
 PZL  plan-1  N19   0.020
 PZL  plan-1  C16   0.020
 PZL  plan-1  C13   0.020
 PZL  plan-1  C12   0.020
 PZL  plan-1  C11   0.020
 PZL  plan-1  CL15  0.020
 PZL  plan-1  C10   0.020
 PZL  plan-1  C14   0.020
 PZL  plan-1  C9    0.020
 PZL  plan-1  O8    0.020
 PZL  plan-1  H12   0.020
 PZL  plan-1  H10   0.020
 PZL  plan-1  H14   0.020
 PZL  plan-2  O8    0.020
 PZL  plan-2  C3    0.020
 PZL  plan-2  C4    0.020
 PZL  plan-2  BR17  0.020
 PZL  plan-2  C2    0.020
 PZL  plan-2  F5    0.020
 PZL  plan-2  C6    0.020
 PZL  plan-2  C7    0.020
 PZL  plan-2  C1    0.020
 PZL  plan-2  C18   0.020
 PZL  plan-2  H7    0.020
 PZL  plan-2  H1    0.020
 PZL  plan-3  C18   0.020
 PZL  plan-3  C26   0.020
 PZL  plan-3  N27   0.020
 PZL  plan-3  N28   0.020
 PZL  plan-3  C24   0.020
 PZL  plan-3  N20   0.020
 PZL  plan-3  C25   0.020
 PZL  plan-3  C23   0.020
 PZL  plan-3  C22   0.020
 PZL  plan-3  N21   0.020
 PZL  plan-3  HN28  0.020
 PZL  plan-3  H23   0.020
 PZL  plan-3  H22   0.020

