# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 20:38:44 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: 2-{3-[3-chloro-5-(cyclopropylmethoxy)phenyl]-2-oxo[2H-[1,3'-bipyridine]]-5-yl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(OCC2CC2)cc(c1)C3=CC(=CN(C3=O)c4cccnc4)c5ccccc5C#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
 XFD  XFD  2-{3-[3-chloro-5-(cyclopropylmethoxy)phenyl]-2-oxo[2H-[1,3'-bipyridine]]-5-yl}benzonitrile  ligand  53  33  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XFD
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
 XFD  C9   C   CR6   0   0.143  -24.2035  -4.7336  -25.2472
 XFD  C3   C   CR16  0  -0.051  -18.6502  -3.7739  -25.6167
 XFD  C4   C   CR16  0  -0.054  -16.9161  -5.1587  -25.1179
 XFD  N1   N   NR6   0  -0.622  -20.7280  -4.5947  -26.5823
 XFD  C2   C   CR6   0   0.175  -19.4108  -4.8331  -26.0875
 XFD  C19  C   CR16  0  -0.298  -23.2878  -2.5047  -30.0030
 XFD  C20  C   CR6   0  -0.004  -23.5557  -2.1451  -31.3153
 XFD  C21  C   CR16  0  -0.323  -23.0158  -2.8250  -32.3862
 XFD  C22  C   CR6   0   0.411  -22.1775  -3.9159  -32.1397
 XFD  C23  C   CH2   0  -0.188  -20.9058  -5.7058  -33.0735
 XFD  C24  C   CH1   0  -0.280  -20.5833  -6.2264  -34.4373
 XFD  C25  C   CR16  0  -0.416  -21.8917  -4.2937  -30.8317
 XFD  C7   C   CR16  0   0.027  -21.7771  -4.7487  -25.7364
 XFD  C12  C   CR16  0  -0.229  -25.3771  -4.3305  -23.1493
 XFD  C13  C   CR16  0  -0.256  -26.4128  -5.1478  -23.5624
 XFD  C18  C   CR6   0   0.114  -22.4524  -3.5905  -29.7643
 XFD  C17  C   CR6   0  -0.174  -22.2094  -4.0117  -28.3707
 XFD  C14  C   CR16  0  -0.216  -26.3579  -5.7460  -24.8150
 XFD  C15  C   CR16  0  -0.305  -25.2662  -5.5407  -25.6436
 XFD  C16  C   CR16  0  -0.181  -23.2466  -4.1698  -27.5038
 XFD  C1   C   CR6   0   0.547  -20.8459  -4.2201  -27.9238
 XFD  C10  C   CR6   0  -0.018  -24.2829  -4.1166  -23.9897
 XFD  C11  C   CSP   0  -0.004  -23.2686  -3.2083  -23.5588
 XFD  C26  C   CH2   0  -0.479  -19.4488  -5.6279  -35.2101
 XFD  C27  C   CH2   0  -0.490  -19.3151  -7.0007  -34.6274
 XFD  C5   C   CR16  0  -0.329  -17.6042  -6.2783  -25.5615
 XFD  C6   C   CR16  0  -0.137  -18.8851  -6.1127  -26.0635
 XFD  C8   C   CR6   0  -0.086  -23.0552  -4.5383  -26.1473
 XFD  N2   N   N     0  -0.398  -17.4244  -3.9316  -25.1410
 XFD  N3   N   NS    0  -0.238  -22.4757  -2.4583  -23.1890
 XFD  CL1  CL  CL    0  -0.126  -24.5965  -0.7924  -31.6179
 XFD  H1   H   HCR6  0   0.280  -19.0557  -2.7674  -25.6268
 XFD  H2   H   HCR6  0   0.274  -15.9108  -5.2581  -24.7249
 XFD  H3   H   HCR6  0   0.276  -23.7098  -1.9423  -29.1812
 XFD  H4   H   HCR6  0   0.283  -23.2324  -2.5308  -33.4048
 XFD  H5   H   HCH2  0   0.236  -21.4566  -6.4562  -32.4956
 XFD  H6   H   HCH2  0   0.226  -19.9845  -5.4724  -32.5268
 XFD  H7   H   HCH1  0   0.264  -21.4407  -6.5629  -35.0113
 XFD  H8   H   HCR6  0   0.280  -21.2519  -5.1393  -30.6256
 XFD  H9   H   HCR6  0   0.325  -21.5254  -5.0706  -24.7352
 XFD  H10  H   HCR6  0   0.284  -25.4135  -3.8435  -22.1842
 XFD  H11  H   HCR6  0   0.276  -27.2612  -5.3120  -22.9126
 XFD  H12  H   HCR6  0   0.276  -27.1664  -6.3846  -25.1450
 XFD  H13  H   HCR6  0   0.273  -25.2280  -6.0308  -26.6083
 XFD  H14  H   HCR6  0   0.283  -24.2583  -4.0080  -27.8581
 XFD  H15  H   HCH2  0   0.248  -18.8889  -4.8235  -34.7484
 XFD  H16  H   HCH2  0   0.253  -19.5586  -5.5329  -36.2823
 XFD  H17  H   HCH2  0   0.255  -19.3389  -7.8505  -35.2966
 XFD  H18  H   HCH2  0   0.249  -18.6632  -7.1297  -33.7722
 XFD  H19  H   HCR6  0   0.282  -17.1456  -7.2562  -25.5169
 XFD  H20  H   HCR6  0   0.289  -19.4614  -6.9540  -26.4272
 XFD  O1   O   O     0  -0.456  -19.8435  -4.0869  -28.6063
 XFD  O2   O   O2    0  -0.469  -21.6979  -4.5338  -33.2297

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
 XFD  C26  C27  single    1.497  0.020  1.497
 XFD  C26  C24  single    1.497  0.020  1.497
 XFD  C27  C24  single    1.498  0.020  1.498
 XFD  C24  C23  single    1.495  0.020  1.495
 XFD  O2   C23  single    1.423  0.020  1.423
 XFD  O2   C22  single    1.342  0.020  1.342
 XFD  C21  C22  aromatic  1.398  0.020  1.398
 XFD  C21  C20  aromatic  1.379  0.020  1.379
 XFD  C22  C25  aromatic  1.391  0.020  1.391
 XFD  CL1  C20  single    1.733  0.020  1.733
 XFD  C20  C19  aromatic  1.387  0.020  1.387
 XFD  C25  C18  aromatic  1.396  0.020  1.396
 XFD  C19  C18  aromatic  1.391  0.020  1.391
 XFD  C18  C17  single    1.476  0.020  1.476
 XFD  O1   C1   double    1.220  0.020  1.220
 XFD  C17  C1   single    1.450  0.020  1.450
 XFD  C17  C16  double    1.361  0.020  1.361
 XFD  C1   N1   single    1.398  0.020  1.398
 XFD  C16  C8   single    1.419  0.020  1.419
 XFD  N1   C2   single    1.427  0.020  1.427
 XFD  N1   C7   single    1.356  0.020  1.356
 XFD  C8   C7   double    1.359  0.020  1.359
 XFD  C8   C9   single    1.472  0.020  1.472
 XFD  C3   C2   aromatic  1.386  0.020  1.386
 XFD  C3   N2   aromatic  1.324  0.020  1.324
 XFD  C2   C6   aromatic  1.384  0.020  1.384
 XFD  N2   C4   aromatic  1.328  0.020  1.328
 XFD  C15  C9   aromatic  1.392  0.020  1.392
 XFD  C15  C14  aromatic  1.386  0.020  1.386
 XFD  C6   C5   aromatic  1.386  0.020  1.386
 XFD  C9   C10  aromatic  1.403  0.020  1.403
 XFD  C4   C5   aromatic  1.387  0.020  1.387
 XFD  C14  C13  aromatic  1.389  0.020  1.389
 XFD  C10  C11  single    1.428  0.020  1.428
 XFD  C10  C12  aromatic  1.396  0.020  1.396
 XFD  C13  C12  aromatic  1.383  0.020  1.383
 XFD  C11  N3   triple    1.152  0.020  1.152
 XFD  C3   H1   single    0.930  0.020  1.080
 XFD  C4   H2   single    0.930  0.020  1.080
 XFD  C19  H3   single    0.930  0.020  1.080
 XFD  C21  H4   single    0.930  0.020  1.080
 XFD  C23  H5   single    0.970  0.020  1.090
 XFD  C23  H6   single    0.970  0.020  1.090
 XFD  C24  H7   single    0.970  0.020  1.090
 XFD  C25  H8   single    0.930  0.020  1.080
 XFD  C7   H9   single    0.930  0.020  1.080
 XFD  C12  H10  single    0.930  0.020  1.080
 XFD  C13  H11  single    0.930  0.020  1.080
 XFD  C14  H12  single    0.930  0.020  1.080
 XFD  C15  H13  single    0.930  0.020  1.080
 XFD  C16  H14  single    0.930  0.020  1.080
 XFD  C26  H15  single    0.970  0.020  1.090
 XFD  C26  H16  single    0.970  0.020  1.090
 XFD  C27  H17  single    0.970  0.020  1.090
 XFD  C27  H18  single    0.970  0.020  1.090
 XFD  C5   H19  single    0.930  0.020  1.080
 XFD  C6   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
 XFD  C8   C9   C10  122.27  3.000
 XFD  C10  C9   C15  117.84  3.000
 XFD  C8   C9   C15  119.89  3.000
 XFD  H1   C3   N2   117.37  3.000
 XFD  H1   C3   C2   120.03  3.000
 XFD  N2   C3   C2   122.60  3.000
 XFD  H2   C4   N2   116.48  3.000
 XFD  H2   C4   C5   120.14  3.000
 XFD  N2   C4   C5   123.38  3.000
 XFD  C1   N1   C7   124.31  3.000
 XFD  C7   N1   C2   118.60  3.000
 XFD  C1   N1   C2   117.08  3.000
 XFD  C6   C2   N1   120.74  3.000
 XFD  C6   C2   C3   119.49  3.000
 XFD  N1   C2   C3   119.77  3.000
 XFD  H3   C19  C18  120.66  3.000
 XFD  H3   C19  C20  120.58  3.000
 XFD  C18  C19  C20  118.75  3.000
 XFD  CL1  C20  C21  118.98  3.000
 XFD  CL1  C20  C19  118.92  3.000
 XFD  C21  C20  C19  122.10  3.000
 XFD  H4   C21  C22  119.89  3.000
 XFD  H4   C21  C20  121.24  3.000
 XFD  C22  C21  C20  118.87  3.000
 XFD  O2   C22  C25  124.42  3.000
 XFD  C25  C22  C21  120.07  3.000
 XFD  O2   C22  C21  115.51  3.000
 XFD  H6   C23  H5   107.77  3.000
 XFD  H6   C23  O2   110.31  3.000
 XFD  H5   C23  O2   110.01  3.000
 XFD  H6   C23  C24  110.35  3.000
 XFD  H5   C23  C24  110.55  3.000
 XFD  O2   C23  C24  107.86  3.000
 XFD  H7   C24  C27  116.20  3.000
 XFD  H7   C24  C26  116.71  3.000
 XFD  C27  C24  C26   59.98  3.000
 XFD  H7   C24  C23  114.83  3.000
 XFD  C27  C24  C23  118.58  3.000
 XFD  C26  C24  C23  119.67  3.000
 XFD  H8   C25  C18  119.11  3.000
 XFD  H8   C25  C22  120.91  3.000
 XFD  C18  C25  C22  119.97  3.000
 XFD  H9   C7   C8   123.02  3.000
 XFD  H9   C7   N1   115.54  3.000
 XFD  C8   C7   N1   121.42  3.000
 XFD  H10  C12  C10  119.64  3.000
 XFD  H10  C12  C13  120.50  3.000
 XFD  C10  C12  C13  119.85  3.000
 XFD  H11  C13  C14  120.49  3.000
 XFD  H11  C13  C12  119.87  3.000
 XFD  C14  C13  C12  119.63  3.000
 XFD  C17  C18  C25  120.80  3.000
 XFD  C17  C18  C19  118.93  3.000
 XFD  C25  C18  C19  120.23  3.000
 XFD  C1   C17  C16  120.24  3.000
 XFD  C16  C17  C18  120.60  3.000
 XFD  C1   C17  C18  119.14  3.000
 XFD  H12  C14  C15  119.59  3.000
 XFD  H12  C14  C13  119.98  3.000
 XFD  C15  C14  C13  120.43  3.000
 XFD  H13  C15  C14  119.57  3.000
 XFD  H13  C15  C9   119.29  3.000
 XFD  C14  C15  C9   121.13  3.000
 XFD  H14  C16  C8   118.50  3.000
 XFD  H14  C16  C17  119.06  3.000
 XFD  C8   C16  C17  122.44  3.000
 XFD  O1   C1   C17  125.77  3.000
 XFD  C17  C1   N1   114.43  3.000
 XFD  O1   C1   N1   119.80  3.000
 XFD  C11  C10  C12  118.19  3.000
 XFD  C12  C10  C9   121.10  3.000
 XFD  C11  C10  C9   120.66  3.000
 XFD  N3   C11  C10  180.00  3.000
 XFD  H16  C26  H15  114.17  3.000
 XFD  H16  C26  C27  118.37  3.000
 XFD  H15  C26  C27  117.95  3.000
 XFD  H16  C26  C24  118.01  3.000
 XFD  H15  C26  C24  117.93  3.000
 XFD  C27  C26  C24   60.03  3.000
 XFD  H18  C27  H17  114.09  3.000
 XFD  H18  C27  C26  118.05  3.000
 XFD  H17  C27  C26  118.52  3.000
 XFD  H18  C27  C24  118.09  3.000
 XFD  H17  C27  C24  117.77  3.000
 XFD  C26  C27  C24   59.99  3.000
 XFD  H19  C5   C6   121.01  3.000
 XFD  H19  C5   C4   120.43  3.000
 XFD  C6   C5   C4   118.55  3.000
 XFD  H20  C6   C5   121.39  3.000
 XFD  H20  C6   C2   120.70  3.000
 XFD  C5   C6   C2   117.91  3.000
 XFD  C16  C8   C7   117.14  3.000
 XFD  C7   C8   C9   121.89  3.000
 XFD  C16  C8   C9   120.92  3.000
 XFD  C4   N2   C3   118.06  3.000
 XFD  C23  O2   C22  119.28  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
 XFD  CONST_01  C13  C14  C15  C9      0.00   0.0  0
 XFD  CONST_02  C13  C12  C10  C9      0.00   0.0  0
 XFD  CONST_03  C5   C6   C2   C3      0.00   0.0  0
 XFD  CONST_04  C5   C4   N2   C3      0.00   0.0  0
 XFD  CONST_05  C2   C3   N2   C4      0.00   0.0  0
 XFD  CONST_06  C2   C6   C5   C4      0.00   0.0  0
 XFD  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 XFD  CONST_08  C22  C25  C18  C19     0.00   0.0  0
 XFD  CONST_09  C25  C22  C21  C20     0.00   0.0  0
 XFD  CONST_10  C25  C18  C19  C20     0.00   0.0  0
 XFD  CONST_11  C18  C25  C22  C21     0.00   0.0  0
 XFD  CONST_12  C18  C19  C20  C21     0.00   0.0  0
 XFD  CONST_13  C15  C9   C10  C12     0.00   0.0  0
 XFD  CONST_14  C15  C14  C13  C12     0.00   0.0  0
 XFD  CONST_15  C10  C9   C15  C14     0.00   0.0  0
 XFD  CONST_16  C10  C12  C13  C14     0.00   0.0  0
 XFD  CONST_17  N2   C3   C2   C6      0.00   0.0  0
 XFD  CONST_18  N2   C4   C5   C6      0.00   0.0  0
 XFD  CONST_19  N2   C3   C2   N1    180.00   0.0  0
 XFD  CONST_20  C5   C6   C2   N1    180.00   0.0  0
 XFD  CONST_21  C17  C18  C19  C20   180.00   0.0  0
 XFD  CONST_22  C17  C18  C25  C22   180.00   0.0  0
 XFD  CONST_23  C8   C9   C10  C12   180.00   0.0  0
 XFD  CONST_24  C8   C9   C15  C14   180.00   0.0  0
 XFD  CONST_25  C17  C1   N1   C2    180.00   0.0  0
 XFD  CONST_26  C17  C1   N1   C7      0.00   0.0  0
 XFD  CONST_27  O2   C22  C21  C20   180.00   0.0  0
 XFD  CONST_28  CL1  C20  C21  C22   180.00   0.0  0
 XFD  CONST_29  C11  C10  C12  C13   180.00   0.0  0
 XFD  CONST_30  O2   C22  C25  C18   180.00   0.0  0
 XFD  CONST_31  CL1  C20  C19  C18   180.00   0.0  0
 XFD  CONST_32  C11  C10  C9   C15   180.00   0.0  0
 XFD  CONST_33  C8   C9   C10  C11     0.00   0.0  0
 XFD  CONST_34  O1   C1   N1   C2      0.00   0.0  0
 XFD  CONST_35  O1   C1   N1   C7    180.00   0.0  0
 XFD  CONST_36  H12  C14  C15  C9    180.00   0.0  0
 XFD  CONST_37  H10  C12  C10  C9    180.00   0.0  0
 XFD  CONST_38  H20  C6   C2   C3    180.00   0.0  0
 XFD  CONST_39  H2   C4   N2   C3    180.00   0.0  0
 XFD  CONST_40  H1   C3   N2   C4    180.00   0.0  0
 XFD  CONST_41  H19  C5   C6   C2    180.00   0.0  0
 XFD  CONST_42  H4   C21  C20  C19   180.00   0.0  0
 XFD  CONST_43  H8   C25  C18  C19   180.00   0.0  0
 XFD  CONST_44  H3   C19  C20  C21   180.00   0.0  0
 XFD  CONST_45  H13  C15  C14  C13   180.00   0.0  0
 XFD  CONST_46  H11  C13  C14  C15   180.00   0.0  0
 XFD  Var_01    C1   N1   C2   C3     85.65  30.0  2
 XFD  Var_02    C1   C17  C18  C19  -130.31  30.0  2
 XFD  Var_03    C15  C9   C8   C7   -127.78  30.0  2
 XFD  Var_04    C27  C26  C24  C23   107.86  30.0  1
 XFD  Var_05    H17  C27  C26  C24   107.36  30.0  1
 XFD  Var_06    C24  C23  O2   C22   176.51  30.0  3
 XFD  Var_07    C25  C22  O2   C23     3.99  30.0  2
 XFD  Var_08    O2   C23  C24  C26    81.94  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XFD  chir_01  C24  C26  C27  C23  both

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
 XFD  plan-1  C3   0.020
 XFD  plan-1  C4   0.020
 XFD  plan-1  N1   0.020
 XFD  plan-1  C2   0.020
 XFD  plan-1  C5   0.020
 XFD  plan-1  C6   0.020
 XFD  plan-1  N2   0.020
 XFD  plan-1  H1   0.020
 XFD  plan-1  H2   0.020
 XFD  plan-1  H19  0.020
 XFD  plan-1  H20  0.020
 XFD  plan-2  C19  0.020
 XFD  plan-2  C20  0.020
 XFD  plan-2  C21  0.020
 XFD  plan-2  C22  0.020
 XFD  plan-2  C25  0.020
 XFD  plan-2  C18  0.020
 XFD  plan-2  C17  0.020
 XFD  plan-2  CL1  0.020
 XFD  plan-2  H3   0.020
 XFD  plan-2  H4   0.020
 XFD  plan-2  H8   0.020
 XFD  plan-2  O2   0.020
 XFD  plan-3  C9   0.020
 XFD  plan-3  N1   0.020
 XFD  plan-3  C2   0.020
 XFD  plan-3  C7   0.020
 XFD  plan-3  C18  0.020
 XFD  plan-3  C17  0.020
 XFD  plan-3  C16  0.020
 XFD  plan-3  C1   0.020
 XFD  plan-3  C8   0.020
 XFD  plan-3  H9   0.020
 XFD  plan-3  H14  0.020
 XFD  plan-3  O1   0.020
 XFD  plan-4  C9   0.020
 XFD  plan-4  C12  0.020
 XFD  plan-4  C13  0.020
 XFD  plan-4  C14  0.020
 XFD  plan-4  C15  0.020
 XFD  plan-4  C10  0.020
 XFD  plan-4  C11  0.020
 XFD  plan-4  C8   0.020
 XFD  plan-4  N3   0.020
 XFD  plan-4  H10  0.020
 XFD  plan-4  H11  0.020
 XFD  plan-4  H12  0.020
 XFD  plan-4  H13  0.020

