# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 06:35:17 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-[2-bromo-4-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-methylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Oc2ccc(Cc3n[nH]c4nnccc34)cc2Br)cc(c1)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
 PZ2  PZ2  3-[2-bromo-4-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-methylbenzonitrile  ligand  41  27  .  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_PZ2
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
 PZ2  C1    C   CR56  0  -0.011  -4.0386  -0.7733   0.0784
 PZ2  C2    C   CR16  0  -0.336  -3.2720  -1.9011  -0.1508
 PZ2  C3    C   CR16  0  -0.107  -3.7141  -2.7192  -1.1788
 PZ2  N4    N   N     0  -0.259  -4.7973  -2.4782  -1.9269
 PZ2  N5    N   N     0  -0.271  -5.5335  -1.4211  -1.7324
 PZ2  C6    C   CR56  0   0.481  -5.1551  -0.6045  -0.7605
 PZ2  C7    C   CR5   0   0.252  -4.0667   0.3622   0.9415
 PZ2  N8    N   NR15  0  -0.504  -5.7472   0.5455  -0.3757
 PZ2  N9    N   N     0  -0.231  -5.0892   1.1186   0.6348
 PZ2  C10   C   CR6   0   0.381   0.9824   0.5828   0.7271
 PZ2  C11   C   CR6   0  -0.191   0.0447   1.3702   0.0632
 PZ2  C12   C   CR16  0  -0.256  -1.2711   1.4147   0.4920
 PZ2  C13   C   CR6   0   0.099  -1.6817   0.6615   1.5874
 PZ2  C14   C   CR16  0  -0.308  -0.7422  -0.1228   2.2439
 PZ2  C15   C   CR16  0  -0.309   0.5790  -0.1616   1.8264
 PZ2  C16   C   CR6   0   0.114   5.1780  -1.4483   1.0157
 PZ2  C17   C   CR16  0  -0.308   4.7479  -2.6803   0.5431
 PZ2  C18   C   CR6   0   0.035   3.4724  -2.8086  -0.0068
 PZ2  C19   C   CR16  0  -0.319   2.6070  -1.7242  -0.0965
 PZ2  C20   C   CR6   0   0.370   3.0455  -0.5019   0.3899
 PZ2  C21   C   CR16  0  -0.344   4.3085  -0.3610   0.9391
 PZ2  C23   C   CSP   0   0.058   3.0452  -4.0799  -0.4980
 PZ2  N24   N   NS    0  -0.247   2.7025  -5.1060  -0.8937
 PZ2  BR26  BR  BR    0  -0.019   0.5816   2.3860  -1.4263
 PZ2  C27   C   CH2   0  -0.590  -3.1196   0.7004   2.0415
 PZ2  H2    H   HCR6  0   0.281  -2.3841  -2.1486   0.4151
 PZ2  H3    H   HCR6  0   0.287  -3.1803  -3.6247  -1.4336
 PZ2  HN8   H   HNR5  0   0.428  -6.5651   0.9861  -0.7663
 PZ2  H12   H   HCR6  0   0.280  -1.9869   2.0339  -0.0354
 PZ2  H14   H   HCR6  0   0.271  -1.0382  -0.7125   3.1023
 PZ2  H15   H   HCR6  0   0.294   1.2915  -0.7731   2.3651
 PZ2  H17   H   HCR6  0   0.279   5.3980  -3.5433   0.5983
 PZ2  H19   H   HCR6  0   0.304   1.6241  -1.8373  -0.5351
 PZ2  H21   H   HCR6  0   0.281   4.6193   0.6087   1.3098
 PZ2  H22   H   HCH3  0   0.258   7.1527  -0.6136   0.9847
 PZ2  H22A  H   HCH3  0   0.256   6.4910  -0.8294   2.5965
 PZ2  H22B  H   HCH3  0   0.253   7.0683  -2.2271   1.6884
 PZ2  H27   H   HCH2  0   0.287  -3.3709   1.6906   2.4275
 PZ2  H27A  H   HCH2  0   0.282  -3.2524  -0.0023   2.8681
 PZ2  O25   O   O2    0  -0.497   2.2686   0.6177   0.2903
 PZ2  C22   C   CH3   0  -0.721   6.5460  -1.2761   1.6036

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
 PZ2  C1   C2    aromatic  1.383  0.020  1.383
 PZ2  C1   C6    aromatic  1.407  0.020  1.407
 PZ2  C1   C7    aromatic  1.427  0.020  1.427
 PZ2  C2   C3    aromatic  1.386  0.020  1.386
 PZ2  C3   N4    aromatic  1.338  0.020  1.338
 PZ2  N4   N5    aromatic  1.303  0.020  1.303
 PZ2  N5   C6    aromatic  1.325  0.020  1.325
 PZ2  C6   N8    aromatic  1.350  0.020  1.350
 PZ2  C7   N9    aromatic  1.308  0.020  1.308
 PZ2  C7   C27   single    1.490  0.020  1.490
 PZ2  N8   N9    aromatic  1.335  0.020  1.335
 PZ2  C10  C11   aromatic  1.393  0.020  1.393
 PZ2  C10  C15   aromatic  1.388  0.020  1.388
 PZ2  C10  O25   single    1.359  0.020  1.359
 PZ2  C11  C12   aromatic  1.385  0.020  1.385
 PZ2  C11  BR26  single    1.881  0.020  1.881
 PZ2  C12  C13   aromatic  1.391  0.020  1.391
 PZ2  C13  C14   aromatic  1.389  0.020  1.389
 PZ2  C13  C27   single    1.508  0.020  1.508
 PZ2  C14  C15   aromatic  1.386  0.020  1.386
 PZ2  C16  C17   aromatic  1.388  0.020  1.388
 PZ2  C16  C21   aromatic  1.394  0.020  1.394
 PZ2  C16  C22   single    1.499  0.020  1.499
 PZ2  C17  C18   aromatic  1.395  0.020  1.395
 PZ2  C18  C19   aromatic  1.390  0.020  1.390
 PZ2  C18  C23   single    1.428  0.020  1.428
 PZ2  C19  C20   aromatic  1.387  0.020  1.387
 PZ2  C20  C21   aromatic  1.384  0.020  1.384
 PZ2  C20  O25   single    1.366  0.020  1.366
 PZ2  C23  N24   triple    1.152  0.020  1.152
 PZ2  C2   H2    single    0.930  0.020  1.080
 PZ2  C3   H3    single    0.930  0.020  1.080
 PZ2  N8   HN8   single    0.860  0.020  1.020
 PZ2  C12  H12   single    0.930  0.020  1.080
 PZ2  C14  H14   single    0.930  0.020  1.080
 PZ2  C15  H15   single    0.930  0.020  1.080
 PZ2  C17  H17   single    0.930  0.020  1.080
 PZ2  C19  H19   single    0.930  0.020  1.080
 PZ2  C21  H21   single    0.930  0.020  1.080
 PZ2  C22  H22   single    0.970  0.020  1.090
 PZ2  C22  H22A  single    0.970  0.020  1.090
 PZ2  C22  H22B  single    0.970  0.020  1.090
 PZ2  C27  H27   single    0.970  0.020  1.090
 PZ2  C27  H27A  single    0.970  0.020  1.090

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
 PZ2  C7    C1   C6    104.46  3.000
 PZ2  C7    C1   C2    139.50  3.000
 PZ2  C6    C1   C2    116.04  3.000
 PZ2  H2    C2   C3    120.99  3.000
 PZ2  H2    C2   C1    123.71  3.000
 PZ2  C3    C2   C1    115.30  3.000
 PZ2  H3    C3   N4    114.74  3.000
 PZ2  H3    C3   C2    120.75  3.000
 PZ2  N4    C3   C2    124.50  3.000
 PZ2  N5    N4   C3    121.33  3.000
 PZ2  C6    N5   N4    116.64  3.000
 PZ2  N8    C6   N5    127.53  3.000
 PZ2  N8    C6   C1    106.29  3.000
 PZ2  N5    C6   C1    126.18  3.000
 PZ2  C27   C7   N9    122.58  3.000
 PZ2  C27   C7   C1    127.93  3.000
 PZ2  N9    C7   C1    109.49  3.000
 PZ2  HN8   N8   N9    120.38  3.000
 PZ2  HN8   N8   C6    128.18  3.000
 PZ2  N9    N8   C6    111.43  3.000
 PZ2  N8    N9   C7    108.33  3.000
 PZ2  O25   C10  C15   122.93  3.000
 PZ2  O25   C10  C11   118.00  3.000
 PZ2  C15   C10  C11   119.02  3.000
 PZ2  BR26  C11  C12   119.94  3.000
 PZ2  BR26  C11  C10   119.38  3.000
 PZ2  C12   C11  C10   120.69  3.000
 PZ2  H12   C12  C13   119.85  3.000
 PZ2  H12   C12  C11   119.70  3.000
 PZ2  C13   C12  C11   120.45  3.000
 PZ2  C27   C13  C14   121.14  3.000
 PZ2  C27   C13  C12   120.29  3.000
 PZ2  C14   C13  C12   118.57  3.000
 PZ2  H14   C14  C15   118.96  3.000
 PZ2  H14   C14  C13   119.83  3.000
 PZ2  C15   C14  C13   121.21  3.000
 PZ2  H15   C15  C14   119.56  3.000
 PZ2  H15   C15  C10   120.39  3.000
 PZ2  C14   C15  C10   120.05  3.000
 PZ2  C22   C16  C21   120.07  3.000
 PZ2  C22   C16  C17   121.22  3.000
 PZ2  C21   C16  C17   118.70  3.000
 PZ2  H17   C17  C18   119.75  3.000
 PZ2  H17   C17  C16   120.30  3.000
 PZ2  C18   C17  C16   119.95  3.000
 PZ2  C23   C18  C19   119.07  3.000
 PZ2  C23   C18  C17   119.40  3.000
 PZ2  C19   C18  C17   121.53  3.000
 PZ2  H19   C19  C20   121.43  3.000
 PZ2  H19   C19  C18   120.66  3.000
 PZ2  C20   C19  C18   117.91  3.000
 PZ2  O25   C20  C21   117.66  3.000
 PZ2  O25   C20  C19   121.12  3.000
 PZ2  C21   C20  C19   121.15  3.000
 PZ2  H21   C21  C20   119.23  3.000
 PZ2  H21   C21  C16   120.01  3.000
 PZ2  C20   C21  C16   120.75  3.000
 PZ2  N24   C23  C18   180.00  3.000
 PZ2  H27A  C27  H27   106.72  3.000
 PZ2  H27A  C27  C13   109.08  3.000
 PZ2  H27   C27  C13   110.44  3.000
 PZ2  H27A  C27  C7    109.58  3.000
 PZ2  H27   C27  C7    108.69  3.000
 PZ2  C13   C27  C7    112.19  3.000
 PZ2  C20   O25  C10   119.59  3.000
 PZ2  H22B  C22  H22A  108.14  3.000
 PZ2  H22B  C22  H22   107.94  3.000
 PZ2  H22A  C22  H22   107.21  3.000
 PZ2  H22B  C22  C16   111.60  3.000
 PZ2  H22A  C22  C16   111.00  3.000
 PZ2  H22   C22  C16   110.78  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
 PZ2  CONST_01  N4    C3   C2   C1     0.00   0.0  0
 PZ2  CONST_02  N4    N5   C6   C1     0.00   0.0  0
 PZ2  CONST_03  N9    N8   C6   C1     0.00   0.0  0
 PZ2  CONST_04  N8    N9   C7   C1     0.00   0.0  0
 PZ2  CONST_05  N5    C6   C1   C2     0.00   0.0  0
 PZ2  CONST_06  N8    C6   C1   C2   180.00   0.0  0
 PZ2  CONST_07  N9    C7   C1   C2   180.00   0.0  0
 PZ2  CONST_08  N5    N4   C3   C2     0.00   0.0  0
 PZ2  CONST_09  C6    C1   C2   C3     0.00   0.0  0
 PZ2  CONST_10  C7    C1   C2   C3   180.00   0.0  0
 PZ2  CONST_11  C6    N5   N4   C3     0.00   0.0  0
 PZ2  CONST_12  N8    C6   N5   N4   180.00   0.0  0
 PZ2  CONST_13  C7    C1   C6   N5   180.00   0.0  0
 PZ2  CONST_14  N9    N8   C6   N5   180.00   0.0  0
 PZ2  CONST_15  N9    C7   C1   C6     0.00   0.0  0
 PZ2  CONST_16  C7    N9   N8   C6     0.00   0.0  0
 PZ2  CONST_17  N8    C6   C1   C7     0.00   0.0  0
 PZ2  CONST_18  C13   C12  C11  C10    0.00   0.0  0
 PZ2  CONST_19  C13   C14  C15  C10    0.00   0.0  0
 PZ2  CONST_20  C14   C15  C10  C11    0.00   0.0  0
 PZ2  CONST_21  C14   C13  C12  C11    0.00   0.0  0
 PZ2  CONST_22  C15   C10  C11  C12    0.00   0.0  0
 PZ2  CONST_23  C15   C14  C13  C12    0.00   0.0  0
 PZ2  CONST_24  C19   C18  C17  C16    0.00   0.0  0
 PZ2  CONST_25  C19   C20  C21  C16    0.00   0.0  0
 PZ2  CONST_26  C20   C21  C16  C17    0.00   0.0  0
 PZ2  CONST_27  C20   C19  C18  C17    0.00   0.0  0
 PZ2  CONST_28  C21   C16  C17  C18    0.00   0.0  0
 PZ2  CONST_29  C21   C20  C19  C18    0.00   0.0  0
 PZ2  CONST_30  C27   C7   C1   C2     0.00   0.0  0
 PZ2  CONST_31  C27   C7   C1   C6   180.00   0.0  0
 PZ2  CONST_32  C27   C7   N9   N8   180.00   0.0  0
 PZ2  CONST_33  C27   C13  C12  C11  180.00   0.0  0
 PZ2  CONST_34  O25   C10  C11  C12  180.00   0.0  0
 PZ2  CONST_35  BR26  C11  C12  C13  180.00   0.0  0
 PZ2  CONST_36  O25   C10  C15  C14  180.00   0.0  0
 PZ2  CONST_37  BR26  C11  C10  C15  180.00   0.0  0
 PZ2  CONST_38  C27   C13  C14  C15  180.00   0.0  0
 PZ2  CONST_39  C23   C18  C17  C16  180.00   0.0  0
 PZ2  CONST_40  O25   C20  C21  C16  180.00   0.0  0
 PZ2  CONST_41  C22   C16  C17  C18  180.00   0.0  0
 PZ2  CONST_42  O25   C20  C19  C18  180.00   0.0  0
 PZ2  CONST_43  C23   C18  C19  C20  180.00   0.0  0
 PZ2  CONST_44  C22   C16  C21  C20  180.00   0.0  0
 PZ2  CONST_45  H3    C3   C2   C1   180.00   0.0  0
 PZ2  CONST_46  HN8   N8   C6   C1   180.00   0.0  0
 PZ2  CONST_47  H2    C2   C3   N4   180.00   0.0  0
 PZ2  CONST_48  H12   C12  C11  C10  180.00   0.0  0
 PZ2  CONST_49  H14   C14  C15  C10  180.00   0.0  0
 PZ2  CONST_50  H15   C15  C10  C11  180.00   0.0  0
 PZ2  CONST_51  H21   C21  C16  C17  180.00   0.0  0
 PZ2  CONST_52  H19   C19  C18  C17  180.00   0.0  0
 PZ2  CONST_53  H17   C17  C18  C19  180.00   0.0  0
 PZ2  Var_01    C13   C27  C7   C1    51.61  30.0  2
 PZ2  Var_02    C12   C13  C27  C7    54.78  30.0  3
 PZ2  Var_03    C19   C20  O25  C10   51.40  30.0  2
 PZ2  Var_04    H22   C22  C16  C17  114.72  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
 PZ2  plan-1  C10   0.020
 PZ2  plan-1  C11   0.020
 PZ2  plan-1  C12   0.020
 PZ2  plan-1  C13   0.020
 PZ2  plan-1  C14   0.020
 PZ2  plan-1  C15   0.020
 PZ2  plan-1  BR26  0.020
 PZ2  plan-1  C27   0.020
 PZ2  plan-1  H12   0.020
 PZ2  plan-1  H14   0.020
 PZ2  plan-1  H15   0.020
 PZ2  plan-1  O25   0.020
 PZ2  plan-2  C16   0.020
 PZ2  plan-2  C17   0.020
 PZ2  plan-2  C18   0.020
 PZ2  plan-2  C19   0.020
 PZ2  plan-2  C20   0.020
 PZ2  plan-2  C21   0.020
 PZ2  plan-2  C23   0.020
 PZ2  plan-2  N24   0.020
 PZ2  plan-2  H17   0.020
 PZ2  plan-2  H19   0.020
 PZ2  plan-2  H21   0.020
 PZ2  plan-2  O25   0.020
 PZ2  plan-2  C22   0.020
 PZ2  plan-3  C1    0.020
 PZ2  plan-3  C2    0.020
 PZ2  plan-3  C3    0.020
 PZ2  plan-3  N4    0.020
 PZ2  plan-3  N5    0.020
 PZ2  plan-3  C6    0.020
 PZ2  plan-3  C7    0.020
 PZ2  plan-3  N8    0.020
 PZ2  plan-3  N9    0.020
 PZ2  plan-3  C27   0.020
 PZ2  plan-3  H2    0.020
 PZ2  plan-3  H3    0.020
 PZ2  plan-3  HN8   0.020

