# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:17:14 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: 2-[3-(3-chloro-5-propoxyphenyl)-2-oxo[2H-[1,3'-bipyridine]]-5-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1cc(Cl)cc(c1)C2=CC(=CN(C2=O)c3cccnc3)c4ccccc4C#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
 XF1  XF1  2-[3-(3-chloro-5-propoxyphenyl)-2-oxo[2H-[1,3'-bipyridine]]-5-yl]benzonitrile  ligand  52  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XF1
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
 XF1  C7   C   CR16  0   0.023  -21.6901  -4.5337  -25.8178
 XF1  C8   C   CR6   0  -0.092  -22.9503  -4.3266  -26.2806
 XF1  C9   C   CR6   0   0.141  -24.1322  -4.5208  -25.4252
 XF1  C10  C   CR6   0  -0.016  -24.2614  -3.8935  -24.1772
 XF1  C11  C   CSP   0  -0.003  -23.2619  -2.9830  -23.7169
 XF1  C12  C   CR16  0  -0.229  -25.3869  -4.1035  -23.3786
 XF1  C1   C   CR6   0   0.549  -20.6715  -4.0195  -27.9677
 XF1  C2   C   CR6   0   0.188  -19.3113  -4.5637  -26.0469
 XF1  C3   C   CR16  0  -0.060  -18.8454  -3.6477  -25.1167
 XF1  C4   C   CR16  0  -0.055  -16.9023  -4.7994  -24.8540
 XF1  C5   C   CR16  0  -0.331  -17.2833  -5.7643  -25.7766
 XF1  C6   C   CR16  0  -0.138  -18.5182  -5.6464  -26.3893
 XF1  O2   O   O2    0  -0.469  -21.4944  -4.5306  -33.2935
 XF1  C13  C   CR16  0  -0.255  -26.4029  -4.9284  -23.8247
 XF1  C14  C   CR16  0  -0.216  -26.2974  -5.5381  -25.0684
 XF1  C15  C   CR16  0  -0.305  -25.1752  -5.3355  -25.8561
 XF1  C16  C   CR16  0  -0.172  -23.0887  -3.9645  -27.6455
 XF1  C17  C   CR6   0  -0.185  -22.0159  -3.8169  -28.4677
 XF1  C18  C   CR6   0   0.108  -22.1944  -3.4051  -29.8742
 XF1  C19  C   CR16  0  -0.292  -22.9192  -2.2535  -30.1541
 XF1  C20  C   CR6   0  -0.004  -23.1245  -1.9049  -31.4813
 XF1  C21  C   CR16  0  -0.322  -22.6388  -2.6665  -32.5229
 XF1  C22  C   CR6   0   0.412  -21.9149  -3.8272  -32.2323
 XF1  C23  C   CH2   0  -0.192  -20.7433  -5.7198  -33.0861
 XF1  C24  C   CH2   0  -0.457  -20.3896  -6.3036  -34.4367
 XF1  C25  C   CH3   0  -0.662  -19.5054  -5.4004  -35.2847
 XF1  C26  C   CR16  0  -0.411  -21.6827  -4.1880  -30.9090
 XF1  N1   N   NR6   0  -0.623  -20.6043  -4.3845  -26.6188
 XF1  N2   N   N     0  -0.396  -17.6644  -3.7640  -24.5261
 XF1  N3   N   NS    0  -0.239  -22.4757  -2.2346  -23.3293
 XF1  CL1  CL  CL    0  -0.126  -24.0151  -0.4614  -31.8374
 XF1  H1   H   HCR6  0   0.326  -21.4833  -4.8561  -24.8064
 XF1  H2   H   HCR6  0   0.284  -25.4631  -3.6091  -22.4195
 XF1  H3   H   HCR6  0   0.282  -19.4573  -2.7940  -24.8407
 XF1  H4   H   HCR6  0   0.274  -15.9405  -4.8687  -24.3592
 XF1  H5   H   HCR6  0   0.282  -16.6257  -6.5915  -26.0044
 XF1  H6   H   HCR6  0   0.288  -18.8598  -6.3819  -27.1058
 XF1  H7   H   HCR6  0   0.276  -27.2755  -5.0898  -23.2070
 XF1  H8   H   HCR6  0   0.276  -27.0899  -6.1830  -25.4241
 XF1  H9   H   HCR6  0   0.272  -25.0977  -5.8329  -26.8146
 XF1  H10  H   HCR6  0   0.282  -24.0842  -3.8000  -28.0420
 XF1  H11  H   HCR6  0   0.275  -23.3028  -1.6353  -29.3539
 XF1  H12  H   HCR6  0   0.283  -22.8114  -2.3822  -33.5527
 XF1  H13  H   HCH2  0   0.235  -21.3296  -6.4393  -32.5044
 XF1  H14  H   HCH2  0   0.223  -19.8309  -5.4953  -32.5214
 XF1  H15  H   HCH2  0   0.232  -21.3056  -6.5584  -34.9761
 XF1  H16  H   HCH2  0   0.235  -19.8758  -7.2488  -34.2462
 XF1  H17  H   HCH3  0   0.232  -19.2270  -5.8955  -36.2150
 XF1  H18  H   HCH3  0   0.226  -20.0077  -4.4695  -35.5468
 XF1  H19  H   HCH3  0   0.220  -18.5840  -5.1457  -34.7579
 XF1  H20  H   HCR6  0   0.280  -21.1314  -5.0841  -30.6633
 XF1  O1   O   O     0  -0.455  -19.6478  -3.8794  -28.6156

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
 XF1  C25  C24  single    1.522  0.020  1.522
 XF1  C24  C23  single    1.513  0.020  1.513
 XF1  O2   C23  single    1.422  0.020  1.422
 XF1  O2   C22  single    1.341  0.020  1.341
 XF1  C21  C22  aromatic  1.399  0.020  1.399
 XF1  C21  C20  aromatic  1.379  0.020  1.379
 XF1  C22  C26  aromatic  1.391  0.020  1.391
 XF1  CL1  C20  single    1.733  0.020  1.733
 XF1  C20  C19  aromatic  1.387  0.020  1.387
 XF1  C26  C18  aromatic  1.395  0.020  1.395
 XF1  C19  C18  aromatic  1.389  0.020  1.389
 XF1  C18  C17  single    1.476  0.020  1.476
 XF1  O1   C1   double    1.220  0.020  1.220
 XF1  C17  C1   single    1.449  0.020  1.449
 XF1  C17  C16  double    1.360  0.020  1.360
 XF1  C1   N1   single    1.399  0.020  1.399
 XF1  C16  C8   single    1.419  0.020  1.419
 XF1  N1   C2   single    1.425  0.020  1.425
 XF1  N1   C7   single    1.358  0.020  1.358
 XF1  C3   C2   aromatic  1.386  0.020  1.386
 XF1  C3   N2   aromatic  1.326  0.020  1.326
 XF1  C8   C7   double    1.358  0.020  1.358
 XF1  C8   C9   single    1.472  0.020  1.472
 XF1  C2   C6   aromatic  1.385  0.020  1.385
 XF1  N2   C4   aromatic  1.327  0.020  1.327
 XF1  C15  C9   aromatic  1.392  0.020  1.392
 XF1  C15  C14  aromatic  1.386  0.020  1.386
 XF1  C6   C5   aromatic  1.384  0.020  1.384
 XF1  C9   C10  aromatic  1.403  0.020  1.403
 XF1  C4   C5   aromatic  1.388  0.020  1.388
 XF1  C14  C13  aromatic  1.389  0.020  1.389
 XF1  C10  C11  single    1.428  0.020  1.428
 XF1  C10  C12  aromatic  1.396  0.020  1.396
 XF1  C13  C12  aromatic  1.383  0.020  1.383
 XF1  C11  N3   triple    1.153  0.020  1.153
 XF1  C7   H1   single    0.930  0.020  1.080
 XF1  C12  H2   single    0.930  0.020  1.080
 XF1  C3   H3   single    0.930  0.020  1.080
 XF1  C4   H4   single    0.930  0.020  1.080
 XF1  C5   H5   single    0.930  0.020  1.080
 XF1  C6   H6   single    0.930  0.020  1.080
 XF1  C13  H7   single    0.930  0.020  1.080
 XF1  C14  H8   single    0.930  0.020  1.080
 XF1  C15  H9   single    0.930  0.020  1.080
 XF1  C16  H10  single    0.930  0.020  1.080
 XF1  C19  H11  single    0.930  0.020  1.080
 XF1  C21  H12  single    0.930  0.020  1.080
 XF1  C23  H13  single    0.970  0.020  1.090
 XF1  C23  H14  single    0.970  0.020  1.090
 XF1  C24  H15  single    0.970  0.020  1.090
 XF1  C24  H16  single    0.970  0.020  1.090
 XF1  C25  H17  single    0.970  0.020  1.090
 XF1  C25  H18  single    0.970  0.020  1.090
 XF1  C25  H19  single    0.970  0.020  1.090
 XF1  C26  H20  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
 XF1  H1   C7   N1   115.57  3.000
 XF1  H1   C7   C8   122.78  3.000
 XF1  N1   C7   C8   121.62  3.000
 XF1  C16  C8   C9   120.96  3.000
 XF1  C9   C8   C7   121.79  3.000
 XF1  C16  C8   C7   117.20  3.000
 XF1  C15  C9   C10  117.91  3.000
 XF1  C10  C9   C8   122.15  3.000
 XF1  C15  C9   C8   119.94  3.000
 XF1  C12  C10  C11  118.41  3.000
 XF1  C12  C10  C9   121.07  3.000
 XF1  C11  C10  C9   120.48  3.000
 XF1  N3   C11  C10  180.00  3.000
 XF1  H2   C12  C13  120.47  3.000
 XF1  H2   C12  C10  119.69  3.000
 XF1  C13  C12  C10  119.84  3.000
 XF1  N1   C1   C17  114.45  3.000
 XF1  N1   C1   O1   120.13  3.000
 XF1  C17  C1   O1   125.42  3.000
 XF1  N1   C2   C6   121.24  3.000
 XF1  C6   C2   C3   119.34  3.000
 XF1  N1   C2   C3   119.42  3.000
 XF1  H3   C3   N2   117.24  3.000
 XF1  H3   C3   C2   120.04  3.000
 XF1  N2   C3   C2   122.72  3.000
 XF1  H4   C4   N2   116.54  3.000
 XF1  H4   C4   C5   120.16  3.000
 XF1  N2   C4   C5   123.30  3.000
 XF1  H5   C5   C6   120.98  3.000
 XF1  H5   C5   C4   120.33  3.000
 XF1  C6   C5   C4   118.69  3.000
 XF1  H6   C6   C5   121.14  3.000
 XF1  H6   C6   C2   120.94  3.000
 XF1  C5   C6   C2   117.92  3.000
 XF1  C23  O2   C22  119.28  3.000
 XF1  H7   C13  C14  120.48  3.000
 XF1  H7   C13  C12  119.85  3.000
 XF1  C14  C13  C12  119.67  3.000
 XF1  H8   C14  C15  119.56  3.000
 XF1  H8   C14  C13  120.03  3.000
 XF1  C15  C14  C13  120.41  3.000
 XF1  H9   C15  C14  119.60  3.000
 XF1  H9   C15  C9   119.30  3.000
 XF1  C14  C15  C9   121.09  3.000
 XF1  H10  C16  C17  119.13  3.000
 XF1  H10  C16  C8   118.69  3.000
 XF1  C17  C16  C8   122.18  3.000
 XF1  C18  C17  C16  120.73  3.000
 XF1  C16  C17  C1   120.55  3.000
 XF1  C18  C17  C1   118.69  3.000
 XF1  C26  C18  C19  120.48  3.000
 XF1  C19  C18  C17  119.09  3.000
 XF1  C26  C18  C17  120.39  3.000
 XF1  H11  C19  C20  120.77  3.000
 XF1  H11  C19  C18  120.65  3.000
 XF1  C20  C19  C18  118.57  3.000
 XF1  CL1  C20  C21  119.07  3.000
 XF1  CL1  C20  C19  118.81  3.000
 XF1  C21  C20  C19  122.12  3.000
 XF1  H12  C21  C22  119.88  3.000
 XF1  H12  C21  C20  121.18  3.000
 XF1  C22  C21  C20  118.94  3.000
 XF1  C26  C22  C21  119.95  3.000
 XF1  C26  C22  O2   124.37  3.000
 XF1  C21  C22  O2   115.68  3.000
 XF1  H14  C23  H13  107.84  3.000
 XF1  H14  C23  C24  110.13  3.000
 XF1  H13  C23  C24  110.22  3.000
 XF1  H14  C23  O2   110.09  3.000
 XF1  H13  C23  O2   110.13  3.000
 XF1  C24  C23  O2   108.42  3.000
 XF1  H16  C24  H15  106.17  3.000
 XF1  H16  C24  C25  109.71  3.000
 XF1  H15  C24  C25  110.50  3.000
 XF1  H16  C24  C23  106.74  3.000
 XF1  H15  C24  C23  109.54  3.000
 XF1  C25  C24  C23  113.83  3.000
 XF1  H19  C25  H18  107.82  3.000
 XF1  H19  C25  H17  107.60  3.000
 XF1  H18  C25  H17  107.49  3.000
 XF1  H19  C25  C24  111.10  3.000
 XF1  H18  C25  C24  111.90  3.000
 XF1  H17  C25  C24  110.75  3.000
 XF1  H20  C26  C22  121.10  3.000
 XF1  H20  C26  C18  118.94  3.000
 XF1  C22  C26  C18  119.93  3.000
 XF1  C2   N1   C1   117.60  3.000
 XF1  C2   N1   C7   118.36  3.000
 XF1  C1   N1   C7   124.00  3.000
 XF1  C4   N2   C3   118.04  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
 XF1  CONST_01  C13  C14  C15  C9      0.00   0.0  0
 XF1  CONST_02  C13  C12  C10  C9      0.00   0.0  0
 XF1  CONST_03  C14  C15  C9   C10     0.00   0.0  0
 XF1  CONST_04  C14  C13  C12  C10     0.00   0.0  0
 XF1  CONST_05  C15  C9   C10  C12     0.00   0.0  0
 XF1  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 XF1  CONST_07  C4   N2   C3   C2      0.00   0.0  0
 XF1  CONST_08  C4   C5   C6   C2      0.00   0.0  0
 XF1  CONST_09  C5   C6   C2   C3      0.00   0.0  0
 XF1  CONST_10  C5   C4   N2   C3      0.00   0.0  0
 XF1  CONST_11  N2   C3   C2   C6      0.00   0.0  0
 XF1  CONST_12  N2   C4   C5   C6      0.00   0.0  0
 XF1  CONST_13  C21  C22  C26  C18     0.00   0.0  0
 XF1  CONST_14  C21  C20  C19  C18     0.00   0.0  0
 XF1  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 XF1  CONST_16  C22  C26  C18  C19     0.00   0.0  0
 XF1  CONST_17  C26  C22  C21  C20     0.00   0.0  0
 XF1  CONST_18  C26  C18  C19  C20     0.00   0.0  0
 XF1  CONST_19  C14  C15  C9   C8    180.00   0.0  0
 XF1  CONST_20  C12  C10  C9   C8    180.00   0.0  0
 XF1  CONST_21  N1   C2   C6   C5    180.00   0.0  0
 XF1  CONST_22  C22  C26  C18  C17   180.00   0.0  0
 XF1  CONST_23  C20  C19  C18  C17   180.00   0.0  0
 XF1  CONST_24  N2   C3   C2   N1    180.00   0.0  0
 XF1  CONST_25  C17  C1   N1   C7      0.00   0.0  0
 XF1  CONST_26  C17  C1   N1   C2    180.00   0.0  0
 XF1  CONST_27  C11  C10  C9   C8      0.00   0.0  0
 XF1  CONST_28  C15  C9   C10  C11   180.00   0.0  0
 XF1  CONST_29  C13  C12  C10  C11   180.00   0.0  0
 XF1  CONST_30  C20  C21  C22  O2    180.00   0.0  0
 XF1  CONST_31  C18  C26  C22  O2    180.00   0.0  0
 XF1  CONST_32  CL1  C20  C19  C18   180.00   0.0  0
 XF1  CONST_33  CL1  C20  C21  C22   180.00   0.0  0
 XF1  CONST_34  O1   C1   N1   C7    180.00   0.0  0
 XF1  CONST_35  C2   N1   C1   O1      0.00   0.0  0
 XF1  CONST_36  H9   C15  C9   C8      0.00   0.0  0
 XF1  CONST_37  H8   C14  C15  C9    180.00   0.0  0
 XF1  CONST_38  H2   C12  C10  C9    180.00   0.0  0
 XF1  CONST_39  H7   C13  C12  C10   180.00   0.0  0
 XF1  CONST_40  H5   C5   C6   C2    180.00   0.0  0
 XF1  CONST_41  H6   C6   C2   C3    180.00   0.0  0
 XF1  CONST_42  H4   C4   N2   C3    180.00   0.0  0
 XF1  CONST_43  H3   C3   N2   C4    180.00   0.0  0
 XF1  CONST_44  H20  C26  C18  C17     0.00   0.0  0
 XF1  CONST_45  H11  C19  C18  C17     0.00   0.0  0
 XF1  CONST_46  H12  C21  C20  C19   180.00   0.0  0
 XF1  Var_01    C3   C2   N1   C7    -67.95  30.0  2
 XF1  Var_02    C15  C9   C8   C7   -127.51  30.0  2
 XF1  Var_03    C26  C18  C17  C1     57.58  30.0  3
 XF1  Var_04    C26  C22  O2   C23    -0.88  30.0  2
 XF1  Var_05    C24  C23  O2   C22  -179.53  30.0  3
 XF1  Var_06    C25  C24  C23  O2     62.67  30.0  2
 XF1  Var_07    H17  C25  C24  C23   176.18  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
 XF1  plan-1  C2   0.020
 XF1  plan-1  C3   0.020
 XF1  plan-1  C4   0.020
 XF1  plan-1  C5   0.020
 XF1  plan-1  C6   0.020
 XF1  plan-1  N1   0.020
 XF1  plan-1  N2   0.020
 XF1  plan-1  H3   0.020
 XF1  plan-1  H4   0.020
 XF1  plan-1  H5   0.020
 XF1  plan-1  H6   0.020
 XF1  plan-2  C8   0.020
 XF1  plan-2  C9   0.020
 XF1  plan-2  C10  0.020
 XF1  plan-2  C11  0.020
 XF1  plan-2  C12  0.020
 XF1  plan-2  C13  0.020
 XF1  plan-2  C14  0.020
 XF1  plan-2  C15  0.020
 XF1  plan-2  N3   0.020
 XF1  plan-2  H2   0.020
 XF1  plan-2  H7   0.020
 XF1  plan-2  H8   0.020
 XF1  plan-2  H9   0.020
 XF1  plan-3  C7   0.020
 XF1  plan-3  C8   0.020
 XF1  plan-3  C9   0.020
 XF1  plan-3  C1   0.020
 XF1  plan-3  C2   0.020
 XF1  plan-3  C16  0.020
 XF1  plan-3  C17  0.020
 XF1  plan-3  C18  0.020
 XF1  plan-3  N1   0.020
 XF1  plan-3  H1   0.020
 XF1  plan-3  H10  0.020
 XF1  plan-3  O1   0.020
 XF1  plan-4  O2   0.020
 XF1  plan-4  C17  0.020
 XF1  plan-4  C18  0.020
 XF1  plan-4  C19  0.020
 XF1  plan-4  C20  0.020
 XF1  plan-4  C21  0.020
 XF1  plan-4  C22  0.020
 XF1  plan-4  C26  0.020
 XF1  plan-4  CL1  0.020
 XF1  plan-4  H11  0.020
 XF1  plan-4  H12  0.020
 XF1  plan-4  H20  0.020

