# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:27:59 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: N-[(4R)-4-(3H-imidazo[4,5-c]pyridin-2-yl)-4H-fluoren-9-yl]quinoline-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC1=C2C=CC=CC2=C3[C@@H](C=CC=C13)c4[nH]c5cnccc5n4)c6cccc7ncccc67
#
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
 YKE  YKE  N-[(4R)-4-(3H-imidazo[4,5-c]pyridin-2-yl)-4H-fluoren-9-yl]quinoline-5-carboxamide  ligand  54  35  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YKE
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
 YKE  C1   C  CR16  0  -0.267   2.4111   3.7330  -1.0195
 YKE  C2   C  CR16  0  -0.261   1.0658   3.9707  -1.4753
 YKE  C3   C  CR16  0  -0.302   0.0249   3.2048  -1.0625
 YKE  C4   C  CR16  0  -0.319   2.7011   2.7272  -0.1569
 YKE  C5   C  CR56  0   0.061   1.6435   1.8872   0.3087
 YKE  C6   C  CR56  0   0.069   0.2763   2.1317  -0.1557
 YKE  C7   C  CR5   0   0.189  -0.5606   1.2069   0.4173
 YKE  C8   C  CR5   0   0.049   1.6230   0.8115   1.1574
 YKE  C9   C  CR5   0   0.120   0.2501   0.3616   1.2529
 YKE  C10  C  C1    0  -0.288  -0.0806  -0.6891   2.0451
 YKE  C11  C  C1    0  -0.245   0.9331  -1.3797   2.8030
 YKE  C12  C  C1    0  -0.161   2.2250  -1.0204   2.7389
 YKE  C13  C  CH1   0  -0.550   2.7182   0.1177   1.8959
 YKE  C14  C  CR5   0   0.516   3.7851  -0.3706   0.9594
 YKE  N15  N  N     0  -0.469   5.0140   0.0710   0.9305
 YKE  N16  N  NR15  0  -0.697   3.5360  -1.3216   0.0270
 YKE  C17  C  CR56  0   0.246   4.6985  -1.5132  -0.6684
 YKE  C18  C  CR56  0   0.232   5.6157  -0.6273  -0.0845
 YKE  C19  C  CR16  0  -0.391   6.9132  -0.5896  -0.5876
 YKE  C20  C  CR16  0  -0.098   7.1917  -1.4453  -1.6372
 YKE  N21  N  N     0  -0.413   6.3082  -2.2898  -2.1885
 YKE  C22  C  CR16  0  -0.104   5.0725  -2.3352  -1.7217
 YKE  N23  N  NH1   0  -0.740  -1.9518   1.1276   0.2642
 YKE  C24  C  C     0   0.460  -2.5684   0.1201  -0.3940
 YKE  C25  C  CR6   0  -0.083  -4.0490   0.2849  -0.5312
 YKE  O26  O  O     0  -0.455  -1.9765  -0.8402  -0.8545
 YKE  C27  C  CR16  0  -0.287  -4.5475   1.4667  -1.0201
 YKE  C28  C  CR16  0  -0.288  -6.7988   0.6239  -0.9622
 YKE  C29  C  CR16  0  -0.249  -5.9271   1.6364  -1.2437
 YKE  C30  C  CR66  0   0.074  -4.9346  -0.7879  -0.2319
 YKE  C31  C  CR66  0   0.205  -6.3260  -0.6043  -0.4449
 YKE  N32  N  N     0  -0.430  -7.2408  -1.5638  -0.1681
 YKE  C33  C  CR16  0  -0.080  -6.8225  -2.6978   0.3239
 YKE  C34  C  CR16  0  -0.319  -5.4680  -2.9799   0.5886
 YKE  C35  C  CR16  0  -0.194  -4.5275  -2.0299   0.3100
 YKE  H1   H  HCR6  0   0.257   3.1992   4.3813  -1.3801
 YKE  H2   H  HCR6  0   0.258   0.8946   4.7868  -2.1655
 YKE  H4   H  HCR6  0   0.244   3.7174   2.5593   0.1784
 YKE  H3   H  HCR6  0   0.245  -0.9813   3.3962  -1.4147
 YKE  H23  H  HNH1  0   0.414  -2.5213   1.8592   0.6636
 YKE  H10  H  H     0   0.277  -1.1069  -1.0263   2.1260
 YKE  H11  H  H     0   0.282   0.6324  -2.2061   3.4324
 YKE  H12  H  H     0   0.299   2.9699  -1.5563   3.3133
 YKE  H13  H  HCH1  0   0.335   3.2244   0.8203   2.5716
 YKE  H16  H  HNR5  0   0.424   2.6559  -1.7894  -0.1297
 YKE  H22  H  HCR6  0   0.274   4.3783  -3.0275  -2.1854
 YKE  H19  H  HCR6  0   0.270   7.6697   0.0708  -0.1864
 YKE  H20  H  HCR6  0   0.261   8.1868  -1.4580  -2.0665
 YKE  H27  H  HCR6  0   0.273  -3.8761   2.2807  -1.2636
 YKE  H29  H  HCR6  0   0.272  -6.2884   2.5741  -1.6433
 YKE  H28  H  HCR6  0   0.269  -7.8626   0.7377  -1.1248
 YKE  H35  H  HCR6  0   0.271  -3.4845  -2.2339   0.5038
 YKE  H33  H  HCR6  0   0.268  -7.5777  -3.4471   0.5368
 YKE  H34  H  HCR6  0   0.276  -5.1882  -3.9365   1.0071

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
 YKE  C1   C2   single    1.440  0.020  1.440
 YKE  C1   C4   double    1.356  0.020  1.356
 YKE  C2   C3   double    1.357  0.020  1.357
 YKE  C3   C6   single    1.427  0.020  1.427
 YKE  C4   C5   single    1.429  0.020  1.429
 YKE  C5   C6   single    1.464  0.020  1.464
 YKE  C5   C8   double    1.370  0.020  1.370
 YKE  C6   C7   double    1.373  0.020  1.373
 YKE  C7   C9   single    1.439  0.020  1.439
 YKE  C7   N23  single    1.402  0.020  1.402
 YKE  C8   C9   single    1.448  0.020  1.448
 YKE  C8   C13  single    1.492  0.020  1.492
 YKE  C9   C10  double    1.357  0.020  1.357
 YKE  C10  C11  single    1.442  0.020  1.442
 YKE  C11  C12  double    1.342  0.020  1.342
 YKE  C12  C13  single    1.500  0.020  1.500
 YKE  C13  C14  single    1.501  0.020  1.501
 YKE  C14  N15  aromatic  1.306  0.020  1.306
 YKE  C14  N16  aromatic  1.355  0.020  1.355
 YKE  N15  C18  aromatic  1.371  0.020  1.371
 YKE  N16  C17  aromatic  1.368  0.020  1.368
 YKE  C17  C18  aromatic  1.402  0.020  1.402
 YKE  C17  C22  aromatic  1.387  0.020  1.387
 YKE  C18  C19  aromatic  1.392  0.020  1.392
 YKE  C19  C20  aromatic  1.383  0.020  1.383
 YKE  C20  N21  aromatic  1.341  0.020  1.341
 YKE  N21  C22  aromatic  1.322  0.020  1.322
 YKE  N23  C24  single    1.352  0.020  1.352
 YKE  C24  C25  single    1.496  0.020  1.496
 YKE  C24  O26  double    1.218  0.020  1.218
 YKE  C25  C27  aromatic  1.373  0.020  1.373
 YKE  C25  C30  aromatic  1.423  0.020  1.423
 YKE  C27  C29  aromatic  1.408  0.020  1.408
 YKE  C28  C29  aromatic  1.365  0.020  1.365
 YKE  C28  C31  aromatic  1.414  0.020  1.414
 YKE  C30  C31  aromatic  1.419  0.020  1.419
 YKE  C30  C35  aromatic  1.415  0.020  1.415
 YKE  C31  N32  aromatic  1.354  0.020  1.354
 YKE  N32  C33  aromatic  1.305  0.020  1.305
 YKE  C33  C34  aromatic  1.409  0.020  1.409
 YKE  C34  C35  aromatic  1.366  0.020  1.366
 YKE  C1   H1   single    0.930  0.020  1.080
 YKE  C2   H2   single    0.930  0.020  1.080
 YKE  C4   H4   single    0.930  0.020  1.080
 YKE  C3   H3   single    0.930  0.020  1.080
 YKE  N23  H23  single    0.860  0.020  1.020
 YKE  C10  H10  single    0.930  0.020  1.080
 YKE  C11  H11  single    0.930  0.020  1.080
 YKE  C12  H12  single    0.930  0.020  1.080
 YKE  C13  H13  single    0.970  0.020  1.090
 YKE  N16  H16  single    0.860  0.020  1.020
 YKE  C22  H22  single    0.930  0.020  1.080
 YKE  C19  H19  single    0.930  0.020  1.080
 YKE  C20  H20  single    0.930  0.020  1.080
 YKE  C27  H27  single    0.930  0.020  1.080
 YKE  C29  H29  single    0.930  0.020  1.080
 YKE  C28  H28  single    0.930  0.020  1.080
 YKE  C35  H35  single    0.930  0.020  1.080
 YKE  C33  H33  single    0.930  0.020  1.080
 YKE  C34  H34  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
 YKE  H1   C1   C4   120.02  3.000
 YKE  H1   C1   C2   118.42  3.000
 YKE  C4   C1   C2   121.56  3.000
 YKE  H2   C2   C3   119.89  3.000
 YKE  H2   C2   C1   118.29  3.000
 YKE  C3   C2   C1   121.82  3.000
 YKE  H3   C3   C6   120.21  3.000
 YKE  H3   C3   C2   120.94  3.000
 YKE  C6   C3   C2   118.86  3.000
 YKE  H4   C4   C5   120.16  3.000
 YKE  H4   C4   C1   120.83  3.000
 YKE  C5   C4   C1   119.01  3.000
 YKE  C8   C5   C6   108.27  3.000
 YKE  C8   C5   C4   132.41  3.000
 YKE  C6   C5   C4   119.31  3.000
 YKE  C7   C6   C5   108.93  3.000
 YKE  C7   C6   C3   131.64  3.000
 YKE  C5   C6   C3   119.44  3.000
 YKE  N23  C7   C9   126.11  3.000
 YKE  N23  C7   C6   126.70  3.000
 YKE  C9   C7   C6   107.14  3.000
 YKE  C13  C8   C9   121.26  3.000
 YKE  C13  C8   C5   131.34  3.000
 YKE  C9   C8   C5   107.39  3.000
 YKE  C10  C9   C8   120.68  3.000
 YKE  C10  C9   C7   131.05  3.000
 YKE  C8   C9   C7   108.27  3.000
 YKE  H10  C10  C11  118.53  3.000
 YKE  H10  C10  C9   121.04  3.000
 YKE  C11  C10  C9   120.43  3.000
 YKE  H11  C11  C12  120.00  3.000
 YKE  H11  C11  C10  118.45  3.000
 YKE  C12  C11  C10  121.55  3.000
 YKE  H12  C12  C13  116.59  3.000
 YKE  H12  C12  C11  120.29  3.000
 YKE  C13  C12  C11  123.12  3.000
 YKE  H13  C13  C14  105.32  3.000
 YKE  H13  C13  C12  106.93  3.000
 YKE  C14  C13  C12  109.73  3.000
 YKE  H13  C13  C8   110.20  3.000
 YKE  C14  C13  C8   111.36  3.000
 YKE  C12  C13  C8   112.93  3.000
 YKE  N16  C14  N15  113.27  3.000
 YKE  N16  C14  C13  121.80  3.000
 YKE  N15  C14  C13  124.93  3.000
 YKE  C18  N15  C14  104.90  3.000
 YKE  H16  N16  C17  126.68  3.000
 YKE  H16  N16  C14  126.35  3.000
 YKE  C17  N16  C14  106.97  3.000
 YKE  C22  C17  C18  120.93  3.000
 YKE  C22  C17  N16  134.25  3.000
 YKE  C18  C17  N16  104.81  3.000
 YKE  C19  C18  C17  118.43  3.000
 YKE  C19  C18  N15  131.51  3.000
 YKE  C17  C18  N15  110.05  3.000
 YKE  H19  C19  C20  121.25  3.000
 YKE  H19  C19  C18  122.31  3.000
 YKE  C20  C19  C18  116.45  3.000
 YKE  H20  C20  N21  115.77  3.000
 YKE  H20  C20  C19  119.53  3.000
 YKE  N21  C20  C19  124.70  3.000
 YKE  C22  N21  C20  119.50  3.000
 YKE  H22  C22  N21  117.99  3.000
 YKE  H22  C22  C17  122.02  3.000
 YKE  N21  C22  C17  119.98  3.000
 YKE  H23  N23  C24  118.38  3.000
 YKE  H23  N23  C7   118.41  3.000
 YKE  C24  N23  C7   123.22  3.000
 YKE  O26  C24  C25  122.20  3.000
 YKE  O26  C24  N23  123.35  3.000
 YKE  C25  C24  N23  114.45  3.000
 YKE  C30  C25  C27  119.87  3.000
 YKE  C30  C25  C24  120.91  3.000
 YKE  C27  C25  C24  119.14  3.000
 YKE  H27  C27  C29  118.77  3.000
 YKE  H27  C27  C25  120.14  3.000
 YKE  C29  C27  C25  121.08  3.000
 YKE  H28  C28  C31  118.36  3.000
 YKE  H28  C28  C29  121.24  3.000
 YKE  C31  C28  C29  120.40  3.000
 YKE  H29  C29  C28  120.39  3.000
 YKE  H29  C29  C27  119.38  3.000
 YKE  C28  C29  C27  120.22  3.000
 YKE  C35  C30  C31  116.94  3.000
 YKE  C35  C30  C25  124.28  3.000
 YKE  C31  C30  C25  118.75  3.000
 YKE  N32  C31  C30  122.67  3.000
 YKE  N32  C31  C28  117.66  3.000
 YKE  C30  C31  C28  119.67  3.000
 YKE  C33  N32  C31  118.44  3.000
 YKE  H33  C33  C34  119.61  3.000
 YKE  H33  C33  N32  116.81  3.000
 YKE  C34  C33  N32  123.58  3.000
 YKE  H34  C34  C35  121.09  3.000
 YKE  H34  C34  C33  119.93  3.000
 YKE  C35  C34  C33  118.99  3.000
 YKE  H35  C35  C34  119.80  3.000
 YKE  H35  C35  C30  120.81  3.000
 YKE  C34  C35  C30  119.38  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
 YKE  CONST_01  C17  C18  N15  C14     0.00   0.0  0
 YKE  CONST_02  C19  C18  N15  C14   180.00   0.0  0
 YKE  CONST_03  C18  C17  N16  C14     0.00   0.0  0
 YKE  CONST_04  C22  C17  N16  C14   180.00   0.0  0
 YKE  CONST_05  C17  N16  C14  N15     0.00   0.0  0
 YKE  CONST_06  N16  C17  C18  N15     0.00   0.0  0
 YKE  CONST_07  C22  C17  C18  N15   180.00   0.0  0
 YKE  CONST_08  C20  C19  C18  N15   180.00   0.0  0
 YKE  CONST_09  C18  N15  C14  N16     0.00   0.0  0
 YKE  CONST_10  C19  C18  C17  N16   180.00   0.0  0
 YKE  CONST_11  N21  C22  C17  N16   180.00   0.0  0
 YKE  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 YKE  CONST_13  C20  N21  C22  C17     0.00   0.0  0
 YKE  CONST_14  N21  C22  C17  C18     0.00   0.0  0
 YKE  CONST_15  N21  C20  C19  C18     0.00   0.0  0
 YKE  CONST_16  C22  C17  C18  C19     0.00   0.0  0
 YKE  CONST_17  C22  N21  C20  C19     0.00   0.0  0
 YKE  CONST_18  C28  C29  C27  C25     0.00   0.0  0
 YKE  CONST_19  C28  C31  C30  C25     0.00   0.0  0
 YKE  CONST_20  N32  C31  C30  C25   180.00   0.0  0
 YKE  CONST_21  C34  C35  C30  C25   180.00   0.0  0
 YKE  CONST_22  C31  C30  C25  C27     0.00   0.0  0
 YKE  CONST_23  C35  C30  C25  C27   180.00   0.0  0
 YKE  CONST_24  C31  C28  C29  C27     0.00   0.0  0
 YKE  CONST_25  C35  C30  C31  C28   180.00   0.0  0
 YKE  CONST_26  C33  N32  C31  C28   180.00   0.0  0
 YKE  CONST_27  C30  C25  C27  C29     0.00   0.0  0
 YKE  CONST_28  C30  C31  C28  C29     0.00   0.0  0
 YKE  CONST_29  N32  C31  C28  C29   180.00   0.0  0
 YKE  CONST_30  C33  N32  C31  C30     0.00   0.0  0
 YKE  CONST_31  C33  C34  C35  C30     0.00   0.0  0
 YKE  CONST_32  C34  C35  C30  C31     0.00   0.0  0
 YKE  CONST_33  C34  C33  N32  C31     0.00   0.0  0
 YKE  CONST_34  C35  C30  C31  N32     0.00   0.0  0
 YKE  CONST_35  C35  C34  C33  N32     0.00   0.0  0
 YKE  CONST_36  C18  N15  C14  C13   180.00   0.0  0
 YKE  CONST_37  C17  N16  C14  C13   180.00   0.0  0
 YKE  CONST_38  C29  C27  C25  C24   180.00   0.0  0
 YKE  CONST_39  C31  C30  C25  C24   180.00   0.0  0
 YKE  CONST_40  C35  C30  C25  C24     0.00   0.0  0
 YKE  CONST_41  H16  N16  C14  C13     0.00   0.0  0
 YKE  CONST_42  H19  C19  C18  N15     0.00   0.0  0
 YKE  CONST_43  H22  C22  C17  N16     0.00   0.0  0
 YKE  CONST_44  H20  C20  C19  C18   180.00   0.0  0
 YKE  CONST_45  H29  C29  C27  C25   180.00   0.0  0
 YKE  CONST_46  H35  C35  C30  C25     0.00   0.0  0
 YKE  CONST_47  H28  C28  C29  C27   180.00   0.0  0
 YKE  CONST_48  H27  C27  C29  C28   180.00   0.0  0
 YKE  CONST_49  H34  C34  C35  C30   180.00   0.0  0
 YKE  CONST_50  H33  C33  N32  C31   180.00   0.0  0
 YKE  CONST_51  C25  C24  N23  C7    180.00   0.0  0
 YKE  CONST_52  O26  C24  N23  C7      0.00   0.0  0
 YKE  CONST_53  H23  N23  C24  C25     0.00   0.0  0
 YKE  Var_01    C9   C7   C6   C3   -179.99  30.0  1
 YKE  Var_02    C9   C8   C5   C4   -179.96  30.0  1
 YKE  Var_03    C7   C9   C8   C5      0.38  30.0  1
 YKE  Var_04    C8   C9   C7   C6     -0.26  30.0  1
 YKE  Var_05    C11  C10  C9   C7   -179.63  30.0  1
 YKE  Var_06    C12  C11  C10  C9     -0.78  30.0  1
 YKE  Var_07    C13  C12  C11  C10     0.46  30.0  1
 YKE  Var_08    C24  N23  C7   C6    111.83  30.0  2
 YKE  Var_09    C27  C25  C24  N23    50.66  30.0  2

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
 YKE  chir_01  C13  C8  C12  C14  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
 YKE  plan-1  C13  0.020
 YKE  plan-1  C14  0.020
 YKE  plan-1  N15  0.020
 YKE  plan-1  N16  0.020
 YKE  plan-1  C17  0.020
 YKE  plan-1  C18  0.020
 YKE  plan-1  C19  0.020
 YKE  plan-1  C20  0.020
 YKE  plan-1  N21  0.020
 YKE  plan-1  C22  0.020
 YKE  plan-1  H16  0.020
 YKE  plan-1  H22  0.020
 YKE  plan-1  H19  0.020
 YKE  plan-1  H20  0.020
 YKE  plan-2  C24  0.020
 YKE  plan-2  C25  0.020
 YKE  plan-2  C27  0.020
 YKE  plan-2  C28  0.020
 YKE  plan-2  C29  0.020
 YKE  plan-2  C30  0.020
 YKE  plan-2  C31  0.020
 YKE  plan-2  N32  0.020
 YKE  plan-2  C33  0.020
 YKE  plan-2  C34  0.020
 YKE  plan-2  C35  0.020
 YKE  plan-2  H27  0.020
 YKE  plan-2  H29  0.020
 YKE  plan-2  H28  0.020
 YKE  plan-2  H35  0.020
 YKE  plan-2  H33  0.020
 YKE  plan-2  H34  0.020
 YKE  plan-3  C1   0.020
 YKE  plan-3  C2   0.020
 YKE  plan-3  C3   0.020
 YKE  plan-3  C4   0.020
 YKE  plan-3  C5   0.020
 YKE  plan-3  C6   0.020
 YKE  plan-3  C7   0.020
 YKE  plan-3  C8   0.020
 YKE  plan-3  H1   0.020
 YKE  plan-3  H2   0.020
 YKE  plan-3  H4   0.020
 YKE  plan-3  H3   0.020
 YKE  plan-4  C7   0.020
 YKE  plan-4  N23  0.020
 YKE  plan-4  C24  0.020
 YKE  plan-4  C25  0.020
 YKE  plan-4  O26  0.020
 YKE  plan-4  H23  0.020

