# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:31:44 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-[[6-[3,3-bis(fluoranyl)pyrrolidin-1-yl]-4-[1-(oxetan-3-yl)piperidin-4-yl]pyridin-2-yl]amino]pyridine-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC1(F)CCN(C1)c2cc(cc(Nc3cc(ccn3)C#N)n2)C4CCN(CC4)C5COC5
#
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
 50D  50D  2-[[6-[3,3-bis(fluoranyl)pyrrolidin-1-yl]-4-[1-(oxetan-3-yl)piperidin-4-yl]pyridin-2-yl]amino]pyridine-4-carbonitrile  ligand  58  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_50D
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
 50D  C4   C  CR6   0   0.541  -2.4932  -2.3990  -0.1056
 50D  C14  C  CR6   0   0.559  -0.9398   1.5070   0.3034
 50D  C5   C  CR16  0  -0.410  -2.9431  -3.6494   0.3487
 50D  C6   C  CR6   0   0.119  -4.2173  -4.0467  -0.0080
 50D  C11  C  CR16  0  -0.526   0.7329  -0.6424   0.1433
 50D  C7   C  CSP   0   0.069  -4.7102  -5.3164   0.4297
 50D  C10  C  CR6   0   0.524  -0.6541  -0.7526   0.2032
 50D  C12  C  CR6   0   0.326   1.2904   0.6337   0.1758
 50D  C13  C  CR16  0  -0.532   0.4470   1.7300   0.2464
 50D  N3   N  N     0  -0.408  -3.2488  -1.6087  -0.8557
 50D  C1   C  CR16  0  -0.350  -5.0259  -3.2114  -0.7793
 50D  C2   C  CR16  0  -0.048  -4.4762  -2.0043  -1.1667
 50D  N8   N  NS    0  -0.236  -5.1126  -6.3365   0.7795
 50D  N9   N  NH1   0  -0.773  -1.2125  -2.0228   0.2115
 50D  N15  N  N     0  -0.487  -1.4668   0.2843   0.3006
 50D  N16  N  NT    0  -0.536  -1.8223   2.5323   0.3819
 50D  C17  C  CH2   0  -0.282  -1.4380   3.9339   0.3868
 50D  C18  C  CH2   0  -0.589  -2.7553   4.6590   0.6358
 50D  C19  C  CT    0   0.711  -3.7626   3.7192   0.0168
 50D  C20  C  CH2   0  -0.352  -3.2529   2.3247   0.3317
 50D  F21  F  F     0  -0.338  -5.0340   3.9183   0.4517
 50D  F22  F  F     0  -0.349  -3.8029   3.9048  -1.3396
 50D  C23  C  CH1   0  -0.357   2.7812   0.8280   0.1175
 50D  C24  C  CH2   0  -0.417   3.4958   0.1959   1.3131
 50D  C25  C  CH2   0  -0.291   4.9984   0.3993   1.2070
 50D  N26  N  NT    0  -0.425   5.5144  -0.1486  -0.0360
 50D  C27  C  CH2   0  -0.292   4.8964   0.4897  -1.1860
 50D  C28  C  CH2   0  -0.417   3.3897   0.2877  -1.1778
 50D  C29  C  C     0  -0.175   6.9493  -0.0500  -0.0931
 50D  C30  C  C     0  -0.140   7.7273  -0.9671   0.8573
 50D  O31  O  O     0  -0.514   8.4236  -1.5824  -0.2335
 50D  C32  C  C     0  -0.140   7.6374  -0.8656  -1.1930
 50D  H1   H  HCR6  0   0.300  -2.3136  -4.2781   0.9638
 50D  H3   H  HCR6  0   0.261   0.8563   2.7312   0.2568
 50D  H4   H  HCR6  0   0.288  -6.0281  -3.4922  -1.0672
 50D  H5   H  HCR6  0   0.273  -5.0559  -1.3216  -1.7769
 50D  H6   H  HNH1  0   0.416  -0.5951  -2.7668   0.4959
 50D  H7   H  HCH2  0   0.257  -0.7071   4.1473   1.1685
 50D  H8   H  HCH2  0   0.246  -0.9938   4.2294  -0.5695
 50D  H9   H  HCH2  0   0.277  -2.9535   4.7330   1.7063
 50D  H10  H  HCH2  0   0.287  -2.7843   5.6604   0.2085
 50D  H11  H  HCH2  0   0.274  -3.5399   1.5936  -0.4262
 50D  H12  H  HCH2  0   0.252  -3.6579   1.9855   1.2908
 50D  H13  H  HCH1  0   0.240   2.9770   1.9064   0.1480
 50D  H14  H  HCH2  0   0.241   3.1358   0.6367   2.2454
 50D  H15  H  HCH2  0   0.226   3.2791  -0.8750   1.3599
 50D  H16  H  HCH2  0   0.195   5.2293   1.4758   1.2991
 50D  H17  H  HCH2  0   0.244   5.4907  -0.0975   2.0467
 50D  H19  H  HCH2  0   0.195   5.1202   1.5712  -1.2166
 50D  H20  H  HCH2  0   0.244   5.3127   0.0590  -2.1000
 50D  H21  H  HCH2  0   0.225   3.1697  -0.7783  -1.2834
 50D  H22  H  HCH2  0   0.241   2.9506   0.7924  -2.0413
 50D  H23  H  H     0   0.232   7.2982   0.9945  -0.0567
 50D  H24  H  H     0   0.223   8.4036  -0.4778   1.5626
 50D  H25  H  H     0   0.209   7.0954  -1.6774   1.4007
 50D  H26  H  H     0   0.209   6.9584  -1.5216  -1.7476
 50D  H27  H  H     0   0.223   8.2508  -0.3052  -1.9026
 50D  H2   H  HCR6  0   0.256   1.3509  -1.5284   0.0693

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
 50D  C30  C29  single    1.533  0.020  1.533
 50D  C30  O31  single    1.433  0.020  1.433
 50D  C25  C24  single    1.520  0.020  1.520
 50D  C25  N26  single    1.453  0.020  1.453
 50D  C29  N26  single    1.439  0.020  1.439
 50D  C29  C32  single    1.532  0.020  1.532
 50D  O31  C32  single    1.433  0.020  1.433
 50D  C24  C23  single    1.530  0.020  1.530
 50D  N26  C27  single    1.453  0.020  1.453
 50D  C23  C12  single    1.505  0.020  1.505
 50D  C23  C28  single    1.530  0.020  1.530
 50D  C18  C17  single    1.524  0.020  1.524
 50D  C18  C19  single    1.510  0.020  1.510
 50D  C27  C28  single    1.520  0.020  1.520
 50D  C17  N16  single    1.453  0.020  1.453
 50D  C13  C12  aromatic  1.385  0.020  1.385
 50D  C13  C14  aromatic  1.406  0.020  1.406
 50D  C12  C11  aromatic  1.393  0.020  1.393
 50D  N16  C14  single    1.355  0.020  1.355
 50D  N16  C20  single    1.446  0.020  1.446
 50D  C14  N15  aromatic  1.331  0.020  1.331
 50D  C11  C10  aromatic  1.393  0.020  1.393
 50D  F22  C19  single    1.370  0.020  1.370
 50D  C20  C19  single    1.518  0.020  1.518
 50D  C19  F21  single    1.358  0.020  1.358
 50D  N15  C10  aromatic  1.321  0.020  1.321
 50D  C10  N9   single    1.388  0.020  1.388
 50D  N9   C4   single    1.372  0.020  1.372
 50D  C4   N3   aromatic  1.326  0.020  1.326
 50D  C4   C5   aromatic  1.404  0.020  1.404
 50D  N3   C2   aromatic  1.327  0.020  1.327
 50D  C5   C6   aromatic  1.382  0.020  1.382
 50D  C2   C1   aromatic  1.382  0.020  1.382
 50D  C6   C1   aromatic  1.395  0.020  1.395
 50D  C6   C7   single    1.431  0.020  1.431
 50D  C7   N8   triple    1.151  0.020  1.151
 50D  C5   H1   single    0.930  0.020  1.080
 50D  C11  H2   single    0.930  0.020  1.080
 50D  C13  H3   single    0.930  0.020  1.080
 50D  C1   H4   single    0.930  0.020  1.080
 50D  C2   H5   single    0.930  0.020  1.080
 50D  N9   H6   single    0.860  0.020  1.020
 50D  C17  H7   single    0.970  0.020  1.090
 50D  C17  H8   single    0.970  0.020  1.090
 50D  C18  H9   single    0.970  0.020  1.090
 50D  C18  H10  single    0.970  0.020  1.090
 50D  C20  H11  single    0.970  0.020  1.090
 50D  C20  H12  single    0.970  0.020  1.090
 50D  C23  H13  single    0.970  0.020  1.090
 50D  C24  H14  single    0.970  0.020  1.090
 50D  C24  H15  single    0.970  0.020  1.090
 50D  C25  H16  single    0.970  0.020  1.090
 50D  C25  H17  single    0.970  0.020  1.090
 50D  C27  H19  single    0.970  0.020  1.090
 50D  C27  H20  single    0.970  0.020  1.090
 50D  C28  H21  single    0.970  0.020  1.090
 50D  C28  H22  single    0.970  0.020  1.090
 50D  C29  H23  single    0.970  0.020  1.090
 50D  C30  H24  single    0.970  0.020  1.090
 50D  C30  H25  single    0.970  0.020  1.090
 50D  C32  H26  single    0.970  0.020  1.090
 50D  C32  H27  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
 50D  N9   C4   N3   119.95  3.000
 50D  N3   C4   C5   122.08  3.000
 50D  N9   C4   C5   117.93  3.000
 50D  N16  C14  N15  115.93  3.000
 50D  N15  C14  C13  122.41  3.000
 50D  N16  C14  C13  121.65  3.000
 50D  H1   C5   C6   121.09  3.000
 50D  H1   C5   C4   121.00  3.000
 50D  C6   C5   C4   117.90  3.000
 50D  C1   C6   C7   120.05  3.000
 50D  C7   C6   C5   119.60  3.000
 50D  C1   C6   C5   120.34  3.000
 50D  H2   C11  C12  121.52  3.000
 50D  H2   C11  C10  120.44  3.000
 50D  C12  C11  C10  118.04  3.000
 50D  N8   C7   C6   180.00  3.000
 50D  N15  C10  N9   118.07  3.000
 50D  N9   C10  C11  118.26  3.000
 50D  N15  C10  C11  123.63  3.000
 50D  C23  C12  C13  120.20  3.000
 50D  C13  C12  C11  118.86  3.000
 50D  C23  C12  C11  120.93  3.000
 50D  H3   C13  C12  120.18  3.000
 50D  H3   C13  C14  121.31  3.000
 50D  C12  C13  C14  118.50  3.000
 50D  C2   N3   C4   118.82  3.000
 50D  H4   C1   C2   121.44  3.000
 50D  H4   C1   C6   121.98  3.000
 50D  C2   C1   C6   116.58  3.000
 50D  H5   C2   C1   119.70  3.000
 50D  H5   C2   N3   116.04  3.000
 50D  C1   C2   N3   124.25  3.000
 50D  H6   N9   C10  115.53  3.000
 50D  H6   N9   C4   115.76  3.000
 50D  C10  N9   C4   128.70  3.000
 50D  C10  N15  C14  118.52  3.000
 50D  C20  N16  C17  113.58  3.000
 50D  C20  N16  C14  122.24  3.000
 50D  C17  N16  C14  123.90  3.000
 50D  H8   C17  H7   107.53  3.000
 50D  H8   C17  C18  111.40  3.000
 50D  H7   C17  C18  111.65  3.000
 50D  H8   C17  N16  111.38  3.000
 50D  H7   C17  N16  111.60  3.000
 50D  C18  C17  N16  103.34  3.000
 50D  H10  C18  H9   108.52  3.000
 50D  H10  C18  C19  113.18  3.000
 50D  H9   C18  C19  108.85  3.000
 50D  H10  C18  C17  113.35  3.000
 50D  H9   C18  C17  110.45  3.000
 50D  C19  C18  C17  102.33  3.000
 50D  F22  C19  F21  105.64  3.000
 50D  F21  C19  C20  112.49  3.000
 50D  F22  C19  C20  109.86  3.000
 50D  F21  C19  C18  113.70  3.000
 50D  C20  C19  C18  105.23  3.000
 50D  F22  C19  C18  109.95  3.000
 50D  H12  C20  H11  107.67  3.000
 50D  H12  C20  C19  110.01  3.000
 50D  H11  C20  C19  112.53  3.000
 50D  H12  C20  N16  112.32  3.000
 50D  H11  C20  N16  112.35  3.000
 50D  C19  C20  N16  101.97  3.000
 50D  H13  C23  C28  107.45  3.000
 50D  H13  C23  C24  107.53  3.000
 50D  C28  C23  C24  109.28  3.000
 50D  H13  C23  C12  107.63  3.000
 50D  C28  C23  C12  112.42  3.000
 50D  C24  C23  C12  112.29  3.000
 50D  H15  C24  H14  107.07  3.000
 50D  H15  C24  C25  109.26  3.000
 50D  H14  C24  C25  109.35  3.000
 50D  H15  C24  C23  110.22  3.000
 50D  H14  C24  C23  110.27  3.000
 50D  C25  C24  C23  110.61  3.000
 50D  H17  C25  H16  106.55  3.000
 50D  H17  C25  N26  109.02  3.000
 50D  H16  C25  N26  111.38  3.000
 50D  H17  C25  C24  109.32  3.000
 50D  H16  C25  C24  109.34  3.000
 50D  N26  C25  C24  111.12  3.000
 50D  C29  N26  C27  111.25  3.000
 50D  C27  N26  C25  111.12  3.000
 50D  C29  N26  C25  111.22  3.000
 50D  H20  C27  H19  106.58  3.000
 50D  H20  C27  C28  109.25  3.000
 50D  H19  C27  C28  109.33  3.000
 50D  H20  C27  N26  109.07  3.000
 50D  H19  C27  N26  111.45  3.000
 50D  C28  C27  N26  111.03  3.000
 50D  H22  C28  H21  107.05  3.000
 50D  H22  C28  C27  109.44  3.000
 50D  H21  C28  C27  109.17  3.000
 50D  H22  C28  C23  110.26  3.000
 50D  H21  C28  C23  110.25  3.000
 50D  C27  C28  C23  110.60  3.000
 50D  H23  C29  C32  112.71  3.000
 50D  H23  C29  C30  112.71  3.000
 50D  C32  C29  C30   84.18  3.000
 50D  H23  C29  N26  112.29  3.000
 50D  C32  C29  N26  116.08  3.000
 50D  C30  C29  N26  116.13  3.000
 50D  H25  C30  H24  109.11  3.000
 50D  H25  C30  O31  112.31  3.000
 50D  H24  C30  O31  112.51  3.000
 50D  H25  C30  C29  113.76  3.000
 50D  H24  C30  C29  116.51  3.000
 50D  O31  C30  C29   91.81  3.000
 50D  C32  O31  C30   91.62  3.000
 50D  H27  C32  H26  109.05  3.000
 50D  H27  C32  O31  112.55  3.000
 50D  H26  C32  O31  112.32  3.000
 50D  H27  C32  C29  116.43  3.000
 50D  H26  C32  C29  113.83  3.000
 50D  O31  C32  C29   91.84  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
 50D  CONST_01  C1   C2   N3   C4      0.00   0.0  0
 50D  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 50D  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 50D  CONST_04  C11  C10  N15  C14     0.00   0.0  0
 50D  CONST_05  C2   N3   C4   C5      0.00   0.0  0
 50D  CONST_06  C2   C1   C6   C5      0.00   0.0  0
 50D  CONST_07  N3   C4   C5   C6      0.00   0.0  0
 50D  CONST_08  N3   C2   C1   C6      0.00   0.0  0
 50D  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 50D  CONST_10  C13  C14  N15  C10     0.00   0.0  0
 50D  CONST_11  N15  C14  C13  C12     0.00   0.0  0
 50D  CONST_12  N15  C10  C11  C12     0.00   0.0  0
 50D  CONST_13  C23  C12  C13  C14   180.00   0.0  0
 50D  CONST_14  C23  C12  C11  C10   180.00   0.0  0
 50D  CONST_15  N16  C14  N15  C10   180.00   0.0  0
 50D  CONST_16  N16  C14  C13  C12   180.00   0.0  0
 50D  CONST_17  C7   C6   C5   C4    180.00   0.0  0
 50D  CONST_18  N9   C10  N15  C14   180.00   0.0  0
 50D  CONST_19  N9   C4   C5   C6    180.00   0.0  0
 50D  CONST_20  C2   C1   C6   C7    180.00   0.0  0
 50D  CONST_21  N9   C10  C11  C12   180.00   0.0  0
 50D  CONST_22  N9   C4   N3   C2    180.00   0.0  0
 50D  CONST_23  H5   C2   N3   C4    180.00   0.0  0
 50D  CONST_24  H4   C1   C6   C5    180.00   0.0  0
 50D  CONST_25  H3   C13  C12  C11   180.00   0.0  0
 50D  CONST_26  H2   C11  C12  C13   180.00   0.0  0
 50D  CONST_27  H1   C5   C4   N3    180.00   0.0  0
 50D  Var_01    C18  C17  N16  C14  -174.26  30.0  1
 50D  Var_02    C19  C20  N16  C14  -162.99  30.0  1
 50D  Var_03    C17  N16  C14  C13     1.32  30.0  2
 50D  Var_04    C19  C18  C17  N16   -29.53  30.0  1
 50D  Var_05    C18  C19  C20  N16   -29.96  30.0  1
 50D  Var_06    C20  C19  C18  C17    37.33  30.0  1
 50D  Var_07    N26  C25  C24  C23   -57.14  30.0  1
 50D  Var_08    N26  C27  C28  C23    57.29  30.0  1
 50D  Var_09    C29  N26  C25  C24  -175.55  30.0  1
 50D  Var_10    C28  C27  N26  C25   -59.97  30.0  1
 50D  Var_11    C11  C10  N9   C4   -159.87  30.0  2
 50D  Var_12    C10  N9   C4   C5   -161.29  30.0  2
 50D  Var_13    H26  C32  O31  C30  -110.96  30.0  1
 50D  Var_14    H24  C30  O31  C32  -125.55  30.0  1

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
 50D  chir_01  C23  C24  C12  C28  positiv
 50D  chir_02  C29  N26  C30  C32  negativ

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
 50D  plan-1  C4   0.020
 50D  plan-1  C5   0.020
 50D  plan-1  C6   0.020
 50D  plan-1  C7   0.020
 50D  plan-1  N3   0.020
 50D  plan-1  C1   0.020
 50D  plan-1  C2   0.020
 50D  plan-1  N8   0.020
 50D  plan-1  N9   0.020
 50D  plan-1  H1   0.020
 50D  plan-1  H4   0.020
 50D  plan-1  H5   0.020
 50D  plan-2  C14  0.020
 50D  plan-2  C11  0.020
 50D  plan-2  C10  0.020
 50D  plan-2  C12  0.020
 50D  plan-2  C13  0.020
 50D  plan-2  N9   0.020
 50D  plan-2  N15  0.020
 50D  plan-2  N16  0.020
 50D  plan-2  C23  0.020
 50D  plan-2  H3   0.020
 50D  plan-2  H2   0.020

