# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 22:45:46 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 4-azanyl-6-[1-[(3-fluorophenyl)methyl]pyrazol-4-yl]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc(c2cnn(Cc3cccc(F)c3)c2)c1C#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
 PZK  PZK  4-azanyl-6-[1-[(3-fluorophenyl)methyl]pyrazol-4-yl]pyrimidine-5-carbonitrile  ligand  33  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PZK
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
 PZK  C10  C  CR5   0  -0.204  20.3702  15.0089  34.0622
 PZK  N12  N  NR5   0  -0.285  21.0457  14.4526  36.0636
 PZK  C15  C  CH2   0  -0.486  21.3782  13.7283  37.2755
 PZK  C17  C  CR16  0  -0.288  23.7357  13.0079  36.7754
 PZK  C20  C  CR6   0   0.642  24.7146  14.5704  38.8125
 PZK  C21  C  CR16  0  -0.514  23.3525  14.5520  38.5790
 PZK  C02  C  CR6   0   0.486  18.7305  14.2569  30.7314
 PZK  N03  N  N     0  -0.511  18.8731  15.4626  30.1719
 PZK  C04  C  CR16  0   0.060  19.4738  16.3840  30.8953
 PZK  N05  N  N     0  -0.273  19.9592  16.2691  32.1184
 PZK  C06  C  CR6   0   0.289  19.8358  15.0801  32.7170
 PZK  C07  C  CR6   0  -0.286  19.2190  14.0181  32.0446
 PZK  C08  C  CSP   0   0.009  19.0466  12.7338  32.6080
 PZK  N09  N  NS    0  -0.194  18.8907  11.6660  33.0185
 PZK  C11  C  CR15  0  -0.028  20.4804  13.9570  34.9606
 PZK  N13  N  N     0  -0.264  21.3228  15.7546  35.9651
 PZK  C14  C  CR15  0  -0.052  20.9243  16.1042  34.7656
 PZK  C16  C  CR6   0   0.313  22.8577  13.7597  37.5510
 PZK  C18  C  CR16  0  -0.251  25.0988  13.0508  37.0271
 PZK  C19  C  CR16  0  -0.466  25.6048  13.8378  38.0538
 PZK  H1   H  HCH2  0   0.294  20.8205  14.1622  38.1057
 PZK  H2   H  HCH2  0   0.329  21.0285  12.7053  37.1406
 PZK  H3   H  HCR6  0   0.256  23.3542  12.3876  35.9736
 PZK  H4   H  HCR6  0   0.261  22.6868  15.1448  39.1944
 PZK  H5   H  HNH2  0   0.389  17.7952  13.5374  29.0903
 PZK  H6   H  HNH2  0   0.405  17.9614  12.3839  30.3575
 PZK  H7   H  HCR6  0   0.311  19.5846  17.3574  30.4283
 PZK  H8   H  HCR5  0   0.279  20.2107  12.9162  34.9038
 PZK  H9   H  HCR5  0   0.283  21.0306  17.1214  34.4240
 PZK  H10  H  HCR6  0   0.264  25.7793  12.4653  36.4232
 PZK  H11  H  HCR6  0   0.285  26.6666  13.8781  38.2580
 PZK  F22  F  F     0  -0.333  25.1847  15.3321  39.8121
 PZK  N01  N  NH2   0  -0.722  18.1182  13.3178  30.0181

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
 PZK  N01  C02  single    1.329  0.020  1.329
 PZK  N03  C02  aromatic  1.337  0.020  1.337
 PZK  N03  C04  aromatic  1.316  0.020  1.316
 PZK  C02  C07  aromatic  1.421  0.020  1.421
 PZK  C04  N05  aromatic  1.321  0.020  1.321
 PZK  C07  C08  single    1.413  0.020  1.413
 PZK  C07  C06  aromatic  1.400  0.020  1.400
 PZK  N05  C06  aromatic  1.337  0.020  1.337
 PZK  C08  N09  triple    1.155  0.020  1.155
 PZK  C06  C10  single    1.449  0.020  1.449
 PZK  C10  C14  aromatic  1.415  0.020  1.415
 PZK  C10  C11  aromatic  1.388  0.020  1.388
 PZK  C14  N13  aromatic  1.311  0.020  1.311
 PZK  C11  N12  aromatic  1.335  0.020  1.335
 PZK  N13  N12  aromatic  1.335  0.020  1.335
 PZK  N12  C15  single    1.450  0.020  1.450
 PZK  C18  C17  aromatic  1.387  0.020  1.387
 PZK  C18  C19  aromatic  1.389  0.020  1.389
 PZK  C17  C16  aromatic  1.392  0.020  1.392
 PZK  C19  C20  aromatic  1.380  0.020  1.380
 PZK  C16  C15  single    1.505  0.020  1.505
 PZK  C16  C21  aromatic  1.389  0.020  1.389
 PZK  C20  C21  aromatic  1.382  0.020  1.382
 PZK  C20  F22  single    1.342  0.020  1.342
 PZK  C15  H1   single    0.970  0.020  1.090
 PZK  C15  H2   single    0.970  0.020  1.090
 PZK  C17  H3   single    0.930  0.020  1.080
 PZK  C21  H4   single    0.930  0.020  1.080
 PZK  N01  H5   single    0.860  0.020  1.020
 PZK  N01  H6   single    0.860  0.020  1.020
 PZK  C04  H7   single    0.930  0.020  1.080
 PZK  C11  H8   single    0.930  0.020  1.080
 PZK  C14  H9   single    0.930  0.020  1.080
 PZK  C18  H10  single    0.930  0.020  1.080
 PZK  C19  H11  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
 PZK  C14  C10  C11  103.53  3.000
 PZK  C11  C10  C06  131.87  3.000
 PZK  C14  C10  C06  124.60  3.000
 PZK  N13  N12  C11  112.90  3.000
 PZK  N13  N12  C15  120.08  3.000
 PZK  C11  N12  C15  127.02  3.000
 PZK  H2   C15  H1   107.68  3.000
 PZK  H2   C15  C16  110.96  3.000
 PZK  H1   C15  C16  110.80  3.000
 PZK  H2   C15  N12  106.97  3.000
 PZK  H1   C15  N12  108.67  3.000
 PZK  C16  C15  N12  111.59  3.000
 PZK  H3   C17  C18  119.88  3.000
 PZK  H3   C17  C16  119.97  3.000
 PZK  C18  C17  C16  120.15  3.000
 PZK  F22  C20  C19  119.01  3.000
 PZK  F22  C20  C21  118.60  3.000
 PZK  C19  C20  C21  122.39  3.000
 PZK  H4   C21  C16  120.91  3.000
 PZK  H4   C21  C20  120.16  3.000
 PZK  C16  C21  C20  118.93  3.000
 PZK  C07  C02  N03  120.11  3.000
 PZK  C07  C02  N01  122.38  3.000
 PZK  N03  C02  N01  117.51  3.000
 PZK  C04  N03  C02  116.74  3.000
 PZK  H7   C04  N05  116.04  3.000
 PZK  H7   C04  N03  115.97  3.000
 PZK  N05  C04  N03  127.99  3.000
 PZK  C06  N05  C04  117.26  3.000
 PZK  C07  C06  N05  120.01  3.000
 PZK  N05  C06  C10  115.17  3.000
 PZK  C07  C06  C10  124.81  3.000
 PZK  C08  C07  C06  123.48  3.000
 PZK  C06  C07  C02  117.88  3.000
 PZK  C08  C07  C02  118.63  3.000
 PZK  N09  C08  C07  180.00  3.000
 PZK  H8   C11  N12  120.57  3.000
 PZK  H8   C11  C10  132.74  3.000
 PZK  N12  C11  C10  106.69  3.000
 PZK  C14  N13  N12  105.34  3.000
 PZK  H9   C14  N13  120.75  3.000
 PZK  H9   C14  C10  127.69  3.000
 PZK  N13  C14  C10  111.55  3.000
 PZK  C21  C16  C17  119.72  3.000
 PZK  C21  C16  C15  119.84  3.000
 PZK  C17  C16  C15  120.44  3.000
 PZK  H10  C18  C19  119.34  3.000
 PZK  H10  C18  C17  120.02  3.000
 PZK  C19  C18  C17  120.64  3.000
 PZK  H11  C19  C18  121.20  3.000
 PZK  H11  C19  C20  120.63  3.000
 PZK  C18  C19  C20  118.17  3.000
 PZK  H6   N01  H5   117.61  3.000
 PZK  H6   N01  C02  123.15  3.000
 PZK  H5   N01  C02  119.24  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
 PZK  CONST_01  C02  C07  C06  C10  180.00   0.0  0
 PZK  CONST_02  C04  N05  C06  C10  180.00   0.0  0
 PZK  CONST_03  N12  N13  C14  C10    0.00   0.0  0
 PZK  CONST_04  N13  N12  C11  C10    0.00   0.0  0
 PZK  CONST_05  C06  C10  C11  N12  180.00   0.0  0
 PZK  CONST_06  C14  C10  C11  N12    0.00   0.0  0
 PZK  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 PZK  CONST_08  C20  C21  C16  C17    0.00   0.0  0
 PZK  CONST_09  C18  C17  C16  C21    0.00   0.0  0
 PZK  CONST_10  C18  C19  C20  C21    0.00   0.0  0
 PZK  CONST_11  N05  C04  N03  C02    0.00   0.0  0
 PZK  CONST_12  N05  C06  C07  C02    0.00   0.0  0
 PZK  CONST_13  C06  C07  C02  N03    0.00   0.0  0
 PZK  CONST_14  C06  N05  C04  N03    0.00   0.0  0
 PZK  CONST_15  C07  C02  N03  C04    0.00   0.0  0
 PZK  CONST_16  C07  C06  N05  C04    0.00   0.0  0
 PZK  CONST_17  C14  C10  C06  N05    0.00   0.0  0
 PZK  CONST_18  C11  C10  C06  N05  180.00   0.0  0
 PZK  CONST_19  N13  C14  C10  C06  180.00   0.0  0
 PZK  CONST_20  C14  C10  C06  C07  180.00   0.0  0
 PZK  CONST_21  C11  C10  C06  C07    0.00   0.0  0
 PZK  CONST_22  N13  C14  C10  C11    0.00   0.0  0
 PZK  CONST_23  C14  N13  N12  C11    0.00   0.0  0
 PZK  CONST_24  C19  C18  C17  C16    0.00   0.0  0
 PZK  CONST_25  C19  C20  C21  C16    0.00   0.0  0
 PZK  CONST_26  C08  C07  C06  C10    0.00   0.0  0
 PZK  CONST_27  C15  N12  C11  C10  180.00   0.0  0
 PZK  CONST_28  C14  N13  N12  C15  180.00   0.0  0
 PZK  CONST_29  C18  C17  C16  C15  180.00   0.0  0
 PZK  CONST_30  C20  C21  C16  C15  180.00   0.0  0
 PZK  CONST_31  C04  N03  C02  N01  180.00   0.0  0
 PZK  CONST_32  C06  C07  C02  N01  180.00   0.0  0
 PZK  CONST_33  C08  C07  C02  N03  180.00   0.0  0
 PZK  CONST_34  C08  C07  C06  N05  180.00   0.0  0
 PZK  CONST_35  F22  C20  C21  C16  180.00   0.0  0
 PZK  CONST_36  F22  C20  C19  C18  180.00   0.0  0
 PZK  CONST_37  H9   C14  N13  N12  180.00   0.0  0
 PZK  CONST_38  H11  C19  C18  C17  180.00   0.0  0
 PZK  CONST_39  H4   C21  C16  C17  180.00   0.0  0
 PZK  CONST_40  H10  C18  C19  C20  180.00   0.0  0
 PZK  CONST_41  H3   C17  C16  C21  180.00   0.0  0
 PZK  CONST_42  H7   C04  N03  C02  180.00   0.0  0
 PZK  CONST_43  H8   C11  C10  C06    0.00   0.0  0
 PZK  CONST_44  H5   N01  C02  N03    0.00   0.0  0
 PZK  CONST_45  H6   N01  C02  N03  180.00   0.0  0
 PZK  Var_01    C17  C16  C15  N12  -72.76  30.0  2
 PZK  Var_02    C16  C15  N12  C11  118.45  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
 PZK  plan-1  C10  0.020
 PZK  plan-1  N12  0.020
 PZK  plan-1  C15  0.020
 PZK  plan-1  C06  0.020
 PZK  plan-1  C11  0.020
 PZK  plan-1  N13  0.020
 PZK  plan-1  C14  0.020
 PZK  plan-1  H8   0.020
 PZK  plan-1  H9   0.020
 PZK  plan-2  C10  0.020
 PZK  plan-2  C02  0.020
 PZK  plan-2  N03  0.020
 PZK  plan-2  C04  0.020
 PZK  plan-2  N05  0.020
 PZK  plan-2  C06  0.020
 PZK  plan-2  C07  0.020
 PZK  plan-2  C08  0.020
 PZK  plan-2  N09  0.020
 PZK  plan-2  H7   0.020
 PZK  plan-2  N01  0.020
 PZK  plan-3  C15  0.020
 PZK  plan-3  C17  0.020
 PZK  plan-3  C20  0.020
 PZK  plan-3  C21  0.020
 PZK  plan-3  C16  0.020
 PZK  plan-3  C18  0.020
 PZK  plan-3  C19  0.020
 PZK  plan-3  H3   0.020
 PZK  plan-3  H4   0.020
 PZK  plan-3  H10  0.020
 PZK  plan-3  H11  0.020
 PZK  plan-3  F22  0.020
 PZK  plan-4  C02  0.020
 PZK  plan-4  H5   0.020
 PZK  plan-4  H6   0.020
 PZK  plan-4  N01  0.020

