# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 07:22:56 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2,6-difluoro-4-{4-[4-(4-methylpiperazin-1-yl)phenyl]pyridin-3-yl}phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc(cc2)c3ccncc3c4cc(F)c(O)c(F)c4
#
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
 2NK  2NK  2,6-difluoro-4-{4-[4-(4-methylpiperazin-1-yl)phenyl]pyridin-3-yl}phenol  ligand  49  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2NK
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
 2NK  C1   C  CR16  0  -0.086   4.3988  -1.7127  -0.0052
 2NK  N1   N  N     0  -0.406   4.7119  -2.9982   0.0539
 2NK  C2   C  CR16  0  -0.059   3.7065  -3.8644   0.1076
 2NK  C3   C  CR16  0  -0.383   2.3774  -3.4818   0.1203
 2NK  C4   C  CR6   0   0.202   2.0398  -2.1298   0.0734
 2NK  C5   C  CR6   0  -0.030   3.0980  -1.2114  -0.0074
 2NK  C6   C  CR6   0  -0.002   2.9015   0.2472  -0.1328
 2NK  C7   C  CR6   0  -0.004   0.6237  -1.7259   0.1251
 2NK  C8   C  CR16  0  -0.463   3.5523   1.1190   0.7365
 2NK  C9   C  CR6   0   0.491   3.3749   2.4792   0.6005
 2NK  C10  C  CR6   0   0.064   2.5651   3.0356  -0.3819
 2NK  C11  C  CR6   0   0.481   1.9381   2.1351  -1.2367
 2NK  C12  C  CR16  0  -0.443   2.0893   0.7717  -1.1348
 2NK  F1   F  F     0  -0.309   3.9925   3.3175   1.4429
 2NK  C13  C  CR16  0  -0.269   0.1815  -0.6964   0.9596
 2NK  C14  C  CR16  0  -0.315  -1.1462  -0.3297   1.0084
 2NK  C15  C  CR6   0   0.364  -2.1111  -0.9665   0.2081
 2NK  C16  C  CR16  0  -0.349  -1.6675  -2.0060  -0.6194
 2NK  C17  C  CR16  0  -0.287  -0.3320  -2.3786  -0.6460
 2NK  O1   O  OH1   0  -0.614   2.4364   4.3680  -0.4495
 2NK  F2   F  F     0  -0.317   1.1549   2.6488  -2.2012
 2NK  N2   N  NT    0  -0.515  -3.4431  -0.5802   0.2743
 2NK  C18  C  CH2   0  -0.306  -3.7268   0.8497   0.2625
 2NK  C19  C  CH2   0  -0.284  -5.1499   1.1272   0.7012
 2NK  N3   N  NT    0  -0.412  -6.0927   0.4057  -0.1259
 2NK  C20  C  CH2   0  -0.280  -5.8253  -1.0133  -0.0373
 2NK  C21  C  CH2   0  -0.314  -4.4139  -1.3362  -0.4920
 2NK  C22  C  CH3   0  -0.518  -7.4590   0.7158   0.2278
 2NK  H1   H  HCR6  0   0.264   5.2300  -1.0179  -0.0761
 2NK  H2   H  HCR6  0   0.266   3.9685  -4.9155   0.1529
 2NK  H3   H  HCR6  0   0.270   1.6057  -4.2360   0.1974
 2NK  H4   H  HCR6  0   0.283   4.1802   0.7444   1.5349
 2NK  H5   H  HCR6  0   0.282   1.5732   0.1271  -1.8341
 2NK  H6   H  HCR6  0   0.254   0.8817  -0.1827   1.6059
 2NK  H7   H  HCR6  0   0.263  -1.4361   0.4506   1.6988
 2NK  H8   H  HCR6  0   0.270  -2.3521  -2.5252  -1.2748
 2NK  H9   H  HCR6  0   0.254  -0.0331  -3.1761  -1.3162
 2NK  H10  H  HOH1  0   0.483   1.8394   4.6218  -1.1632
 2NK  H11  H  HCH2  0   0.256  -3.0554   1.3741   0.9386
 2NK  H12  H  HCH2  0   0.219  -3.5649   1.2619  -0.7437
 2NK  H13  H  HCH2  0   0.195  -5.2591   0.8648   1.7683
 2NK  H14  H  HCH2  0   0.242  -5.3354   2.2002   0.6122
 2NK  H16  H  HCH2  0   0.194  -5.9699  -1.3903   0.9906
 2NK  H17  H  HCH2  0   0.242  -6.5247  -1.5539  -0.6790
 2NK  H18  H  HCH2  0   0.215  -4.3217  -1.1400  -1.5707
 2NK  H19  H  HCH2  0   0.253  -4.2497  -2.4031  -0.3381
 2NK  H20  H  HCH3  0   0.234  -7.6382   1.7862   0.1174
 2NK  H21  H  HCH3  0   0.234  -8.1465   0.1915  -0.4374
 2NK  H22  H  HCH3  0   0.193  -7.7119   0.4367   1.2623

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
 2NK  F2   C11  single    1.344  0.020  1.344
 2NK  C12  C11  aromatic  1.376  0.020  1.376
 2NK  C12  C6   aromatic  1.392  0.020  1.392
 2NK  N1   C2   aromatic  1.328  0.020  1.328
 2NK  N1   C1   aromatic  1.324  0.020  1.324
 2NK  C2   C3   aromatic  1.383  0.020  1.383
 2NK  C1   C5   aromatic  1.394  0.020  1.394
 2NK  C11  C10  aromatic  1.391  0.020  1.391
 2NK  C13  C14  aromatic  1.378  0.020  1.378
 2NK  C13  C7   aromatic  1.397  0.020  1.397
 2NK  C3   C4   aromatic  1.394  0.020  1.394
 2NK  C5   C4   aromatic  1.403  0.020  1.403
 2NK  C5   C6   single    1.477  0.020  1.477
 2NK  C4   C7   single    1.473  0.020  1.473
 2NK  C14  C15  aromatic  1.406  0.020  1.406
 2NK  C6   C8   aromatic  1.393  0.020  1.393
 2NK  C7   C17  aromatic  1.391  0.020  1.391
 2NK  C10  O1   single    1.340  0.020  1.340
 2NK  C10  C9   aromatic  1.389  0.020  1.389
 2NK  C18  C19  single    1.515  0.020  1.515
 2NK  C18  N2   single    1.458  0.020  1.458
 2NK  C8   C9   aromatic  1.378  0.020  1.378
 2NK  C15  N2   single    1.388  0.020  1.388
 2NK  C15  C16  aromatic  1.401  0.020  1.401
 2NK  C19  N3   single    1.447  0.020  1.447
 2NK  C9   F1   single    1.339  0.020  1.339
 2NK  C17  C16  aromatic  1.387  0.020  1.387
 2NK  N2   C21  single    1.449  0.020  1.449
 2NK  N3   C22  single    1.445  0.020  1.445
 2NK  N3   C20  single    1.447  0.020  1.447
 2NK  C21  C20  single    1.518  0.020  1.518
 2NK  C1   H1   single    0.930  0.020  1.080
 2NK  C2   H2   single    0.930  0.020  1.080
 2NK  C3   H3   single    0.930  0.020  1.080
 2NK  C8   H4   single    0.930  0.020  1.080
 2NK  C12  H5   single    0.930  0.020  1.080
 2NK  C13  H6   single    0.930  0.020  1.080
 2NK  C14  H7   single    0.930  0.020  1.080
 2NK  C16  H8   single    0.930  0.020  1.080
 2NK  C17  H9   single    0.930  0.020  1.080
 2NK  O1   H10  single    0.850  0.020  0.980
 2NK  C18  H11  single    0.970  0.020  1.090
 2NK  C18  H12  single    0.970  0.020  1.090
 2NK  C19  H13  single    0.970  0.020  1.090
 2NK  C19  H14  single    0.970  0.020  1.090
 2NK  C20  H16  single    0.970  0.020  1.090
 2NK  C20  H17  single    0.970  0.020  1.090
 2NK  C21  H18  single    0.970  0.020  1.090
 2NK  C21  H19  single    0.970  0.020  1.090
 2NK  C22  H20  single    0.970  0.020  1.090
 2NK  C22  H21  single    0.970  0.020  1.090
 2NK  C22  H22  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
 2NK  H1   C1   C5   118.96  3.000
 2NK  H1   C1   N1   116.30  3.000
 2NK  C5   C1   N1   124.73  3.000
 2NK  C2   N1   C1   117.12  3.000
 2NK  H2   C2   C3   120.00  3.000
 2NK  H2   C2   N1   116.81  3.000
 2NK  C3   C2   N1   123.19  3.000
 2NK  H3   C3   C4   120.38  3.000
 2NK  H3   C3   C2   119.56  3.000
 2NK  C4   C3   C2   120.04  3.000
 2NK  C7   C4   C5   123.18  3.000
 2NK  C7   C4   C3   119.82  3.000
 2NK  C5   C4   C3   117.00  3.000
 2NK  C6   C5   C4   123.42  3.000
 2NK  C6   C5   C1   118.64  3.000
 2NK  C4   C5   C1   117.91  3.000
 2NK  C12  C6   C8   119.07  3.000
 2NK  C8   C6   C5   120.20  3.000
 2NK  C12  C6   C5   120.71  3.000
 2NK  C17  C7   C13  117.35  3.000
 2NK  C17  C7   C4   120.82  3.000
 2NK  C13  C7   C4   121.82  3.000
 2NK  H4   C8   C9   119.26  3.000
 2NK  H4   C8   C6   120.98  3.000
 2NK  C9   C8   C6   119.74  3.000
 2NK  F1   C9   C10  117.57  3.000
 2NK  F1   C9   C8   119.76  3.000
 2NK  C10  C9   C8   122.68  3.000
 2NK  O1   C10  C11  124.70  3.000
 2NK  O1   C10  C9   119.33  3.000
 2NK  C11  C10  C9   115.98  3.000
 2NK  F2   C11  C12  119.73  3.000
 2NK  C12  C11  C10  123.13  3.000
 2NK  F2   C11  C10  117.14  3.000
 2NK  H5   C12  C11  119.35  3.000
 2NK  H5   C12  C6   121.25  3.000
 2NK  C11  C12  C6   119.40  3.000
 2NK  H6   C13  C14  118.40  3.000
 2NK  H6   C13  C7   120.10  3.000
 2NK  C14  C13  C7   121.48  3.000
 2NK  H7   C14  C15  120.41  3.000
 2NK  H7   C14  C13  118.22  3.000
 2NK  C15  C14  C13  121.36  3.000
 2NK  N2   C15  C16  122.58  3.000
 2NK  C16  C15  C14  117.06  3.000
 2NK  N2   C15  C14  120.34  3.000
 2NK  H8   C16  C17  118.00  3.000
 2NK  H8   C16  C15  120.94  3.000
 2NK  C17  C16  C15  121.04  3.000
 2NK  H9   C17  C16  118.37  3.000
 2NK  H9   C17  C7   119.92  3.000
 2NK  C16  C17  C7   121.68  3.000
 2NK  H10  O1   C10  111.00  3.000
 2NK  C21  N2   C18  112.15  3.000
 2NK  C21  N2   C15  118.18  3.000
 2NK  C18  N2   C15  117.34  3.000
 2NK  H12  C18  H11  107.30  3.000
 2NK  H12  C18  C19  109.55  3.000
 2NK  H11  C18  C19  108.16  3.000
 2NK  H12  C18  N2   110.27  3.000
 2NK  H11  C18  N2   110.35  3.000
 2NK  C19  C18  N2   111.11  3.000
 2NK  H14  C19  H13  107.18  3.000
 2NK  H14  C19  N3   109.42  3.000
 2NK  H13  C19  N3   111.68  3.000
 2NK  H14  C19  C18  108.41  3.000
 2NK  H13  C19  C18  109.22  3.000
 2NK  N3   C19  C18  110.81  3.000
 2NK  C22  N3   C20  111.73  3.000
 2NK  C20  N3   C19  109.49  3.000
 2NK  C22  N3   C19  111.67  3.000
 2NK  H17  C20  H16  107.09  3.000
 2NK  H17  C20  C21  108.31  3.000
 2NK  H16  C20  C21  109.15  3.000
 2NK  H17  C20  N3   109.33  3.000
 2NK  H16  C20  N3   111.57  3.000
 2NK  C21  C20  N3   111.24  3.000
 2NK  H19  C21  H18  107.47  3.000
 2NK  H19  C21  C20  107.82  3.000
 2NK  H18  C21  C20  109.50  3.000
 2NK  H19  C21  N2   109.56  3.000
 2NK  H18  C21  N2   111.66  3.000
 2NK  C20  C21  N2   110.70  3.000
 2NK  H22  C22  H21  107.84  3.000
 2NK  H22  C22  H20  107.82  3.000
 2NK  H21  C22  H20  107.84  3.000
 2NK  H22  C22  N3   113.13  3.000
 2NK  H21  C22  N3   110.09  3.000
 2NK  H20  C22  N3   109.95  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
 2NK  CONST_01  C3   C2   N1   C1      0.00   0.0  0
 2NK  CONST_02  C3   C4   C5   C1      0.00   0.0  0
 2NK  CONST_03  C7   C4   C5   C1    180.00   0.0  0
 2NK  CONST_06  C4   C3   C2   N1      0.00   0.0  0
 2NK  CONST_07  C4   C5   C1   N1      0.00   0.0  0
 2NK  CONST_08  C6   C5   C1   N1    180.00   0.0  0
 2NK  CONST_09  C5   C1   N1   C2      0.00   0.0  0
 2NK  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 2NK  CONST_11  C7   C4   C3   C2    180.00   0.0  0
 2NK  CONST_12  C6   C5   C4   C3    180.00   0.0  0
 2NK  CONST_17  C14  C13  C7   C4    180.00   0.0  0
 2NK  CONST_18  C16  C17  C7   C4    180.00   0.0  0
 2NK  CONST_21  C11  C12  C6   C5    180.00   0.0  0
 2NK  CONST_22  C9   C8   C6   C5    180.00   0.0  0
 2NK  CONST_23  C10  C11  C12  C6      0.00   0.0  0
 2NK  CONST_24  C7   C4   C5   C6      0.00   0.0  0
 2NK  CONST_25  C10  C9   C8   C6      0.00   0.0  0
 2NK  CONST_26  C15  C14  C13  C7      0.00   0.0  0
 2NK  CONST_27  C15  C16  C17  C7      0.00   0.0  0
 2NK  CONST_28  C11  C12  C6   C8      0.00   0.0  0
 2NK  CONST_29  C11  C10  C9   C8      0.00   0.0  0
 2NK  CONST_30  C12  C11  C10  C9      0.00   0.0  0
 2NK  CONST_31  C12  C6   C8   C9      0.00   0.0  0
 2NK  CONST_32  C16  C15  C14  C13     0.00   0.0  0
 2NK  CONST_33  C16  C17  C7   C13     0.00   0.0  0
 2NK  CONST_34  C17  C7   C13  C14     0.00   0.0  0
 2NK  CONST_35  C17  C16  C15  C14     0.00   0.0  0
 2NK  CONST_36  N2   C15  C14  C13   180.00   0.0  0
 2NK  CONST_37  N2   C15  C16  C17   180.00   0.0  0
 2NK  CONST_38  F2   C11  C12  C6    180.00   0.0  0
 2NK  CONST_39  F1   C9   C8   C6    180.00   0.0  0
 2NK  CONST_40  O1   C10  C9   C8    180.00   0.0  0
 2NK  CONST_41  F2   C11  C10  C9    180.00   0.0  0
 2NK  CONST_42  F1   C9   C10  C11   180.00   0.0  0
 2NK  CONST_43  O1   C10  C11  C12   180.00   0.0  0
 2NK  CONST_44  H2   C2   N1   C1    180.00   0.0  0
 2NK  CONST_45  H3   C3   C2   N1    180.00   0.0  0
 2NK  CONST_46  H1   C1   N1   C2    180.00   0.0  0
 2NK  CONST_47  H6   C13  C7   C4      0.00   0.0  0
 2NK  CONST_48  H9   C17  C7   C4      0.00   0.0  0
 2NK  CONST_49  H5   C12  C6   C5      0.00   0.0  0
 2NK  CONST_50  H4   C8   C6   C5      0.00   0.0  0
 2NK  CONST_51  H7   C14  C13  C7    180.00   0.0  0
 2NK  CONST_52  H8   C16  C17  C7    180.00   0.0  0
 2NK  Var_01    C18  N2   C15  C14    45.42  30.0  2
 2NK  Var_02    C19  C18  N2   C15  -165.04  30.0  1
 2NK  Var_03    C20  C21  N2   C15   165.63  30.0  1
 2NK  Var_04    N3   C19  C18  N2    -56.16  30.0  1
 2NK  Var_05    N3   C20  C21  N2     56.32  30.0  1
 2NK  Var_06    C20  N3   C19  C18    58.98  30.0  1
 2NK  Var_07    C21  C20  N3   C19   -59.23  30.0  1
 2NK  Var_08    H20  C22  N3   C19    58.97  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
 2NK  plan-1  C1   0.020
 2NK  plan-1  N1   0.020
 2NK  plan-1  C2   0.020
 2NK  plan-1  C3   0.020
 2NK  plan-1  C4   0.020
 2NK  plan-1  C5   0.020
 2NK  plan-1  C6   0.020
 2NK  plan-1  C7   0.020
 2NK  plan-1  H1   0.020
 2NK  plan-1  H2   0.020
 2NK  plan-1  H3   0.020
 2NK  plan-2  C5   0.020
 2NK  plan-2  C6   0.020
 2NK  plan-2  C8   0.020
 2NK  plan-2  C9   0.020
 2NK  plan-2  C10  0.020
 2NK  plan-2  C11  0.020
 2NK  plan-2  C12  0.020
 2NK  plan-2  F1   0.020
 2NK  plan-2  O1   0.020
 2NK  plan-2  F2   0.020
 2NK  plan-2  H4   0.020
 2NK  plan-2  H5   0.020
 2NK  plan-3  C4   0.020
 2NK  plan-3  C7   0.020
 2NK  plan-3  C13  0.020
 2NK  plan-3  C14  0.020
 2NK  plan-3  C15  0.020
 2NK  plan-3  C16  0.020
 2NK  plan-3  C17  0.020
 2NK  plan-3  N2   0.020
 2NK  plan-3  H6   0.020
 2NK  plan-3  H7   0.020
 2NK  plan-3  H8   0.020
 2NK  plan-3  H9   0.020

