# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 03:59:54 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-[(5-azanyl-3-methyl-pyrazol-1-yl)methyl]-~{N}-[(2-chloranyl-4-fluoranyl-phenyl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)n(Cc2ccc(cc2)C(=O)NCc3ccc(F)cc3Cl)n1
#
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
 9WK  9WK  4-[(5-azanyl-3-methyl-pyrazol-1-yl)methyl]-~{N}-[(2-chloranyl-4-fluoranyl-phenyl)methyl]benzamide  ligand  44  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9WK
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
 9WK  C10  C   CR16  0  -0.258   1.4853   2.2185   0.4225
 9WK  C13  C   CR16  0  -0.279   2.1956   1.0844  -2.0025
 9WK  C17  C   CH2   0  -0.354  -3.2754   1.7935  -0.5809
 9WK  C20  C   CR16  0  -0.393  -5.4475  -1.3269  -0.5273
 9WK  C21  C   CR6   0   0.522  -5.2022  -1.7918   0.7481
 9WK  C24  C   CR6   0  -0.085  -3.7411   0.0251   1.1847
 9WK  C02  C   CR5   0   0.289   5.4615  -1.5240   1.0602
 9WK  C03  C   CR15  0  -0.575   5.0042  -2.3995   0.0546
 9WK  C04  C   CR5   0   0.579   4.6740  -1.5740  -1.0023
 9WK  N05  N   NH2   0  -0.856   4.1003  -1.8512  -2.2217
 9WK  N06  N   NR5   0  -0.319   4.9497  -0.3137  -0.6045
 9WK  C07  C   CH2   0  -0.422   4.6060   0.9112  -1.2871
 9WK  C08  C   CR6   0   0.135   3.1724   1.3051  -1.0396
 9WK  C09  C   CR16  0  -0.278   2.8024   1.8723   0.1779
 9WK  C11  C   CR6   0  -0.044   0.5028   1.9746  -0.5353
 9WK  C12  C   CR16  0  -0.278   0.8699   1.4100  -1.7532
 9WK  C14  C   C     0   0.529  -0.9045   2.3739  -0.2261
 9WK  O15  O   O     0  -0.485  -1.1438   3.3443   0.4774
 9WK  N16  N   NH1   0  -0.633  -1.8560   1.5901  -0.7634
 9WK  C18  C   CR6   0   0.167  -3.9517   0.5407  -0.0927
 9WK  C19  C   CR16  0  -0.300  -4.8120  -0.1621  -0.9302
 9WK  C23  C   CR16  0  -0.358  -4.3570  -1.1363   1.6222
 9WK  CL2  CL  CL    0  -0.107  -2.6926   0.8503   2.2852
 9WK  N26  N   N     0  -0.338   5.4233  -0.2708   0.6586
 9WK  H1   H   HCR6  0   0.260   1.2150   2.6718   1.3670
 9WK  H2   H   HCR6  0   0.257   2.4681   0.6596  -2.9602
 9WK  H3   H   HCH2  0   0.274  -3.4154   2.6123   0.1234
 9WK  H4   H   HCH2  0   0.275  -3.7348   2.0982  -1.5238
 9WK  H5   H   HCR6  0   0.288  -6.1160  -1.8570  -1.1920
 9WK  H6   H   HCH3  0   0.243   6.7957  -2.5794   2.3639
 9WK  H7   H   HCH3  0   0.242   6.2819  -1.0021   2.9643
 9WK  H8   H   HCH3  0   0.243   5.1748  -2.3746   3.0044
 9WK  H9   H   HCR5  0   0.254   4.9387  -3.4751   0.0874
 9WK  H10  H   HNH2  0   0.390   4.1342  -2.8314  -2.4553
 9WK  H11  H   HNH2  0   0.384   4.4487  -1.3042  -2.9954
 9WK  H12  H   HCH2  0   0.292   5.2891   1.6811  -0.9297
 9WK  H13  H   HCH2  0   0.276   4.7922   0.7960  -2.3557
 9WK  H14  H   HCR6  0   0.258   3.5528   2.0473   0.9391
 9WK  H15  H   HCR6  0   0.264   0.1356   1.2419  -2.5314
 9WK  H16  H   HNH1  0   0.408  -1.5785   0.7705  -1.2792
 9WK  H17  H   HCR6  0   0.277  -4.9912   0.2141  -1.9294
 9WK  H18  H   HCR6  0   0.302  -4.1870  -1.5208   2.6186
 9WK  F22  F   F     0  -0.309  -5.8016  -2.9154   1.1629
 9WK  C01  C   CH3   0  -0.736   5.9553  -1.8864   2.4189

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
 9WK  C01  C02  single    1.490  0.020  1.490
 9WK  N26  C02  aromatic  1.317  0.020  1.317
 9WK  N26  N06  aromatic  1.350  0.020  1.350
 9WK  C02  C03  aromatic  1.410  0.020  1.410
 9WK  C07  N06  single    1.444  0.020  1.444
 9WK  C07  C08  single    1.507  0.020  1.507
 9WK  N06  C04  aromatic  1.350  0.020  1.350
 9WK  C08  C09  aromatic  1.393  0.020  1.393
 9WK  C08  C13  aromatic  1.389  0.020  1.389
 9WK  C03  C04  aromatic  1.381  0.020  1.381
 9WK  C09  C10  aromatic  1.384  0.020  1.384
 9WK  C04  N05  single    1.376  0.020  1.376
 9WK  C13  C12  aromatic  1.388  0.020  1.388
 9WK  C10  C11  aromatic  1.394  0.020  1.394
 9WK  C12  C11  aromatic  1.392  0.020  1.392
 9WK  C11  C14  single    1.495  0.020  1.495
 9WK  C14  N16  single    1.345  0.020  1.345
 9WK  C14  O15  double    1.222  0.020  1.222
 9WK  N16  C17  single    1.445  0.020  1.445
 9WK  C17  C18  single    1.505  0.020  1.505
 9WK  CL2  C24  single    1.730  0.020  1.730
 9WK  C18  C24  aromatic  1.394  0.020  1.394
 9WK  C18  C19  aromatic  1.391  0.020  1.391
 9WK  C24  C23  aromatic  1.385  0.020  1.385
 9WK  C19  C20  aromatic  1.387  0.020  1.387
 9WK  C23  C21  aromatic  1.381  0.020  1.381
 9WK  C20  C21  aromatic  1.379  0.020  1.379
 9WK  C21  F22  single    1.339  0.020  1.339
 9WK  C10  H1   single    0.930  0.020  1.080
 9WK  C13  H2   single    0.930  0.020  1.080
 9WK  C17  H3   single    0.970  0.020  1.090
 9WK  C17  H4   single    0.970  0.020  1.090
 9WK  C20  H5   single    0.930  0.020  1.080
 9WK  C01  H6   single    0.970  0.020  1.090
 9WK  C01  H7   single    0.970  0.020  1.090
 9WK  C01  H8   single    0.970  0.020  1.090
 9WK  C03  H9   single    0.930  0.020  1.080
 9WK  N05  H10  single    0.890  0.020  1.040
 9WK  N05  H11  single    0.890  0.020  1.040
 9WK  C07  H12  single    0.970  0.020  1.090
 9WK  C07  H13  single    0.970  0.020  1.090
 9WK  C09  H14  single    0.930  0.020  1.080
 9WK  C12  H15  single    0.930  0.020  1.080
 9WK  N16  H16  single    0.860  0.020  1.020
 9WK  C19  H17  single    0.930  0.020  1.080
 9WK  C23  H18  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
 9WK  H1   C10  C11  119.81  3.000
 9WK  H1   C10  C09  119.80  3.000
 9WK  C11  C10  C09  120.38  3.000
 9WK  H2   C13  C12  119.44  3.000
 9WK  H2   C13  C08  119.90  3.000
 9WK  C12  C13  C08  120.66  3.000
 9WK  H4   C17  H3   107.13  3.000
 9WK  H4   C17  C18  108.86  3.000
 9WK  H3   C17  C18  111.00  3.000
 9WK  H4   C17  N16  110.08  3.000
 9WK  H3   C17  N16  108.28  3.000
 9WK  C18  C17  N16  111.41  3.000
 9WK  H5   C20  C19  121.09  3.000
 9WK  H5   C20  C21  120.86  3.000
 9WK  C19  C20  C21  118.05  3.000
 9WK  C23  C21  F22  118.42  3.000
 9WK  F22  C21  C20  119.31  3.000
 9WK  C23  C21  C20  122.27  3.000
 9WK  CL2  C24  C23  117.94  3.000
 9WK  C23  C24  C18  122.17  3.000
 9WK  CL2  C24  C18  119.89  3.000
 9WK  N26  C02  C03  111.36  3.000
 9WK  C03  C02  C01  127.36  3.000
 9WK  N26  C02  C01  121.27  3.000
 9WK  H9   C03  C04  127.24  3.000
 9WK  H9   C03  C02  128.15  3.000
 9WK  C04  C03  C02  104.61  3.000
 9WK  N06  C04  N05  122.30  3.000
 9WK  N05  C04  C03  131.11  3.000
 9WK  N06  C04  C03  106.48  3.000
 9WK  H11  N05  H10  109.73  3.000
 9WK  H11  N05  C04  115.23  3.000
 9WK  H10  N05  C04  112.79  3.000
 9WK  N26  N06  C07  119.94  3.000
 9WK  C07  N06  C04  127.16  3.000
 9WK  N26  N06  C04  112.16  3.000
 9WK  H13  C07  H12  106.79  3.000
 9WK  H13  C07  C08  110.54  3.000
 9WK  H12  C07  C08  110.97  3.000
 9WK  H13  C07  N06  109.45  3.000
 9WK  H12  C07  N06  107.17  3.000
 9WK  C08  C07  N06  111.74  3.000
 9WK  C09  C08  C07  120.17  3.000
 9WK  C09  C08  C13  118.92  3.000
 9WK  C07  C08  C13  120.89  3.000
 9WK  H14  C09  C08  119.73  3.000
 9WK  H14  C09  C10  119.66  3.000
 9WK  C08  C09  C10  120.61  3.000
 9WK  C14  C11  C12  122.52  3.000
 9WK  C14  C11  C10  118.34  3.000
 9WK  C12  C11  C10  119.11  3.000
 9WK  H15  C12  C11  120.86  3.000
 9WK  H15  C12  C13  118.83  3.000
 9WK  C11  C12  C13  120.29  3.000
 9WK  N16  C14  O15  123.66  3.000
 9WK  O15  C14  C11  121.02  3.000
 9WK  N16  C14  C11  115.32  3.000
 9WK  H16  N16  C14  118.94  3.000
 9WK  H16  N16  C17  116.72  3.000
 9WK  C14  N16  C17  124.22  3.000
 9WK  C19  C18  C24  117.28  3.000
 9WK  C19  C18  C17  120.21  3.000
 9WK  C24  C18  C17  122.51  3.000
 9WK  H17  C19  C18  118.85  3.000
 9WK  H17  C19  C20  118.96  3.000
 9WK  C18  C19  C20  122.20  3.000
 9WK  H18  C23  C24  121.27  3.000
 9WK  H18  C23  C21  120.70  3.000
 9WK  C24  C23  C21  118.03  3.000
 9WK  N06  N26  C02  105.39  3.000
 9WK  H8   C01  H7   108.00  3.000
 9WK  H8   C01  H6   107.09  3.000
 9WK  H7   C01  H6   108.07  3.000
 9WK  H8   C01  C02  111.16  3.000
 9WK  H7   C01  C02  111.01  3.000
 9WK  H6   C01  C02  111.34  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
 9WK  CONST_01  C13  C08  C09  C10     0.00   0.0  0
 9WK  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 9WK  CONST_03  C24  C18  C19  C20     0.00   0.0  0
 9WK  CONST_04  C24  C23  C21  C20     0.00   0.0  0
 9WK  CONST_05  C18  C24  C23  C21     0.00   0.0  0
 9WK  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 9WK  CONST_07  C04  N06  N26  C02     0.00   0.0  0
 9WK  CONST_08  N06  C04  C03  C02     0.00   0.0  0
 9WK  CONST_09  N06  N26  C02  C03     0.00   0.0  0
 9WK  CONST_10  N26  N06  C04  C03     0.00   0.0  0
 9WK  CONST_11  N26  C02  C03  C04     0.00   0.0  0
 9WK  CONST_12  C11  C10  C09  C08     0.00   0.0  0
 9WK  CONST_13  C11  C12  C13  C08     0.00   0.0  0
 9WK  CONST_14  C12  C13  C08  C09     0.00   0.0  0
 9WK  CONST_15  C12  C11  C10  C09     0.00   0.0  0
 9WK  CONST_16  C23  C24  C18  C19     0.00   0.0  0
 9WK  CONST_17  C23  C21  C20  C19     0.00   0.0  0
 9WK  CONST_18  C07  C08  C09  C10   180.00   0.0  0
 9WK  CONST_19  C14  C11  C12  C13   180.00   0.0  0
 9WK  CONST_20  C23  C24  C18  C17   180.00   0.0  0
 9WK  CONST_21  C20  C19  C18  C17   180.00   0.0  0
 9WK  CONST_22  CL2  C24  C23  C21   180.00   0.0  0
 9WK  CONST_23  F22  C21  C23  C24   180.00   0.0  0
 9WK  CONST_24  N06  N26  C02  C01   180.00   0.0  0
 9WK  CONST_25  C04  C03  C02  C01   180.00   0.0  0
 9WK  CONST_26  C07  N06  N26  C02   180.00   0.0  0
 9WK  CONST_27  N05  C04  C03  C02   180.00   0.0  0
 9WK  CONST_28  C07  N06  C04  C03   180.00   0.0  0
 9WK  CONST_29  N26  N06  C04  N05   180.00   0.0  0
 9WK  CONST_30  C12  C13  C08  C07   180.00   0.0  0
 9WK  CONST_31  C14  C11  C10  C09   180.00   0.0  0
 9WK  CONST_32  CL2  C24  C18  C19   180.00   0.0  0
 9WK  CONST_33  F22  C21  C20  C19   180.00   0.0  0
 9WK  CONST_34  H15  C12  C11  C10   180.00   0.0  0
 9WK  CONST_35  H14  C09  C08  C13   180.00   0.0  0
 9WK  CONST_36  H18  C23  C21  C20   180.00   0.0  0
 9WK  CONST_37  H17  C19  C20  C21   180.00   0.0  0
 9WK  CONST_38  H9   C03  C04  N06   180.00   0.0  0
 9WK  CONST_39  H1   C10  C09  C08   180.00   0.0  0
 9WK  CONST_40  H2   C13  C08  C09   180.00   0.0  0
 9WK  CONST_41  H5   C20  C19  C18   180.00   0.0  0
 9WK  CONST_44  C11  C14  N16  C17   180.00   0.0  0
 9WK  CONST_45  H16  N16  C14  C11     0.00   0.0  0
 9WK  CONST_46  O15  C14  N16  C17     0.00   0.0  0
 9WK  Var_01    N06  C07  C08  C13  -102.32  30.0  2
 9WK  Var_02    C08  C07  N06  C04    80.22  30.0  1
 9WK  Var_03    N16  C14  C11  C10  -147.69  30.0  2
 9WK  Var_04    N16  C17  C18  C24    69.04  30.0  3
 9WK  Var_05    H6   C01  C02  C03    57.16  30.0  2
 9WK  Var_06    C18  C17  N16  C14  -127.46  30.0  3

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
 9WK  plan-1  C02  0.020
 9WK  plan-1  C03  0.020
 9WK  plan-1  C04  0.020
 9WK  plan-1  N05  0.020
 9WK  plan-1  N06  0.020
 9WK  plan-1  C07  0.020
 9WK  plan-1  N26  0.020
 9WK  plan-1  H9   0.020
 9WK  plan-1  C01  0.020
 9WK  plan-2  C10  0.020
 9WK  plan-2  C13  0.020
 9WK  plan-2  C07  0.020
 9WK  plan-2  C08  0.020
 9WK  plan-2  C09  0.020
 9WK  plan-2  C11  0.020
 9WK  plan-2  C12  0.020
 9WK  plan-2  C14  0.020
 9WK  plan-2  H1   0.020
 9WK  plan-2  H2   0.020
 9WK  plan-2  H14  0.020
 9WK  plan-2  H15  0.020
 9WK  plan-3  C17  0.020
 9WK  plan-3  C20  0.020
 9WK  plan-3  C21  0.020
 9WK  plan-3  C24  0.020
 9WK  plan-3  C18  0.020
 9WK  plan-3  C19  0.020
 9WK  plan-3  C23  0.020
 9WK  plan-3  CL2  0.020
 9WK  plan-3  H5   0.020
 9WK  plan-3  H17  0.020
 9WK  plan-3  H18  0.020
 9WK  plan-3  F22  0.020
 9WK  plan-4  C17  0.020
 9WK  plan-4  C11  0.020
 9WK  plan-4  C14  0.020
 9WK  plan-4  O15  0.020
 9WK  plan-4  N16  0.020
 9WK  plan-4  H16  0.020
 9WK  plan-5  C04  0.020
 9WK  plan-5  N05  0.020
 9WK  plan-5  H10  0.020
 9WK  plan-5  H11  0.020

