# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 18:06:04 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-[2-(3-fluoro-5-{2-[(2S)-1-methylpyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@@H]1CCc2cc(F)cc(CCc3cc(C)cc(N)n3)c2
#
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
 KKY  KKY  6-[2-(3-fluoro-5-{2-[(2S)-1-methylpyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  53  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KKY
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
 KKY  C13  C  CR6   0   0.560  -0.7984  -2.9668   0.2421
 KKY  C15  C  CR6   0   0.181  -1.7529  -0.7963   0.5224
 KKY  C17  C  CH2   0  -0.516  -2.9294   0.0928   0.8093
 KKY  C22  C  CR15  0  -0.058  -4.8229   1.4461  -0.2360
 KKY  C02  C  CR6   0   0.441   6.1069  -0.0708  -0.7923
 KKY  C03  C  CR16  0  -0.448   6.5887   1.1899  -0.3960
 KKY  C04  C  CR6   0   0.205   5.7956   1.9916   0.3976
 KKY  C05  C  CR16  0  -0.435   4.5364   1.5078   0.7732
 KKY  C06  C  CR6   0   0.278   4.1430   0.2542   0.3424
 KKY  C09  C  CH2   0  -0.512   1.8894  -0.4438  -0.5298
 KKY  C11  C  CR6   0   0.169   0.5623  -1.0523  -0.1755
 KKY  C14  C  CR16  0  -0.498  -1.8868  -2.1807   0.5673
 KKY  C23  C  CH2   0  -0.468  -5.4619   1.9218  -1.5572
 KKY  C25  C  CH2   0  -0.300  -7.0608   0.6922  -0.3452
 KKY  C12  C  CR16  0  -0.491   0.4206  -2.4377  -0.1284
 KKY  C16  C  CR16  0  -0.389  -0.5254  -0.2500   0.1531
 KKY  C18  C  CH2   0  -0.402  -3.6202   0.5435  -0.4770
 KKY  C24  C  CH2   0  -0.455  -6.9587   1.8976  -1.2735
 KKY  F13  F  F     0  -0.320  -0.9341  -4.3048   0.2885
 KKY  N01  N  N     0  -0.485   4.9133  -0.5216  -0.4240
 KKY  N02  N  NH2   0  -0.839   6.8470  -0.8695  -1.6161
 KKY  N21  N  NR5   0  -0.421  -5.8861   0.7627   0.5211
 KKY  H1   H  HCH2  0   0.244  -3.6505  -0.4355   1.4365
 KKY  H2   H  HCH2  0   0.237  -2.5983   0.9719   1.3705
 KKY  H3   H  HCR5  0   0.217  -4.4879   2.3214   0.3357
 KKY  H4   H  HCR6  0   0.255   7.5709   1.5187  -0.7137
 KKY  H5   H  HCR6  0   0.244   3.8825   2.1007   1.4005
 KKY  H6   H  HCH3  0   0.253   5.6438   4.1291   0.3963
 KKY  H7   H  HCH3  0   0.250   6.1645   3.4504   1.9273
 KKY  H8   H  HCH3  0   0.247   7.2930   3.5301   0.5711
 KKY  H11  H  HCH2  0   0.251   1.7386   0.5414  -0.9780
 KKY  H12  H  HCH2  0   0.252   2.3968  -1.0611  -1.2739
 KKY  H13  H  HCR6  0   0.265  -2.8260  -2.6395   0.8522
 KKY  H14  H  HCH2  0   0.240  -5.0898   2.9014  -1.8578
 KKY  H15  H  HCH2  0   0.222  -5.2240   1.2198  -2.3624
 KKY  H16  H  HCH2  0   0.231  -7.9778   0.6688   0.2461
 KKY  H17  H  HCH2  0   0.220  -7.0384  -0.2306  -0.9363
 KKY  H18  H  HCR6  0   0.266   1.2482  -3.0912  -0.3783
 KKY  H19  H  HCR6  0   0.240  -0.4163   0.8287   0.1159
 KKY  H20  H  HCH2  0   0.224  -2.9011   1.0749  -1.1093
 KKY  H21  H  HCH2  0   0.220  -3.9449  -0.3349  -1.0451
 KKY  H22  H  HCH2  0   0.223  -7.2715   2.8075  -0.7550
 KKY  H23  H  HCH2  0   0.231  -7.5700   1.8026  -2.1719
 KKY  H27  H  HNH2  0   0.379   6.5878  -1.8420  -1.6419
 KKY  H28  H  HNH2  0   0.388   7.8393  -0.7073  -1.6535
 KKY  C26  C  CH3   0  -0.532  -6.1580   1.3791   1.8032
 KKY  C08  C  CH2   0  -0.488   2.7961  -0.3061   0.7014
 KKY  C07  C  CH3   0  -0.726   6.2558   3.3452   0.8456
 KKY  H9   H  HCH2  0   0.249   2.9253  -1.2905   1.1601
 KKY  H10  H  HCH2  0   0.248   2.3116   0.3324   1.4426
 KKY  H24  H  HCH3  0   0.194  -6.5063   2.4216   1.7413
 KKY  H25  H  HCH3  0   0.229  -6.9166   0.8066   2.3390
 KKY  H26  H  HCH3  0   0.230  -5.2570   1.3725   2.4178

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
 KKY  C07  C04  single    1.498  0.020  1.498
 KKY  C04  C03  aromatic  1.379  0.020  1.379
 KKY  C04  C05  aromatic  1.400  0.020  1.400
 KKY  C03  C02  aromatic  1.407  0.020  1.407
 KKY  C05  C06  aromatic  1.383  0.020  1.383
 KKY  C02  N02  single    1.365  0.020  1.365
 KKY  C02  N01  aromatic  1.328  0.020  1.328
 KKY  C06  N01  aromatic  1.335  0.020  1.335
 KKY  C06  C08  single    1.502  0.020  1.502
 KKY  F13  C13  single    1.346  0.020  1.346
 KKY  C08  C09  single    1.535  0.020  1.535
 KKY  C13  C14  aromatic  1.381  0.020  1.381
 KKY  C13  C12  aromatic  1.380  0.020  1.380
 KKY  C14  C15  aromatic  1.392  0.020  1.392
 KKY  C12  C11  aromatic  1.393  0.020  1.393
 KKY  C15  C17  single    1.502  0.020  1.502
 KKY  C15  C16  aromatic  1.393  0.020  1.393
 KKY  C11  C16  aromatic  1.391  0.020  1.391
 KKY  C11  C09  single    1.502  0.020  1.502
 KKY  C17  C18  single    1.528  0.020  1.528
 KKY  C18  C22  single    1.523  0.020  1.523
 KKY  C23  C22  single    1.543  0.020  1.543
 KKY  C23  C24  single    1.524  0.020  1.524
 KKY  C22  N21  single    1.473  0.020  1.473
 KKY  C24  C25  single    1.525  0.020  1.525
 KKY  N21  C25  single    1.461  0.020  1.461
 KKY  N21  C26  single    1.448  0.020  1.448
 KKY  C17  H1   single    0.970  0.020  1.090
 KKY  C17  H2   single    0.970  0.020  1.090
 KKY  C22  H3   single    0.970  0.020  1.090
 KKY  C03  H4   single    0.930  0.020  1.080
 KKY  C05  H5   single    0.930  0.020  1.080
 KKY  C07  H6   single    0.970  0.020  1.090
 KKY  C07  H7   single    0.970  0.020  1.090
 KKY  C07  H8   single    0.970  0.020  1.090
 KKY  C08  H9   single    0.970  0.020  1.090
 KKY  C08  H10  single    0.970  0.020  1.090
 KKY  C09  H11  single    0.970  0.020  1.090
 KKY  C09  H12  single    0.970  0.020  1.090
 KKY  C14  H13  single    0.930  0.020  1.080
 KKY  C23  H14  single    0.970  0.020  1.090
 KKY  C23  H15  single    0.970  0.020  1.090
 KKY  C25  H16  single    0.970  0.020  1.090
 KKY  C25  H17  single    0.970  0.020  1.090
 KKY  C12  H18  single    0.930  0.020  1.080
 KKY  C16  H19  single    0.930  0.020  1.080
 KKY  C18  H20  single    0.970  0.020  1.090
 KKY  C18  H21  single    0.970  0.020  1.090
 KKY  C24  H22  single    0.970  0.020  1.090
 KKY  C24  H23  single    0.970  0.020  1.090
 KKY  C26  H24  single    0.970  0.020  1.090
 KKY  C26  H25  single    0.970  0.020  1.090
 KKY  C26  H26  single    0.970  0.020  1.090
 KKY  N02  H27  single    0.890  0.020  1.040
 KKY  N02  H28  single    0.890  0.020  1.040

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
 KKY  F13  C13  C12  118.67  3.000
 KKY  C12  C13  C14  122.76  3.000
 KKY  F13  C13  C14  118.57  3.000
 KKY  C16  C15  C14  118.90  3.000
 KKY  C16  C15  C17  120.56  3.000
 KKY  C14  C15  C17  120.48  3.000
 KKY  H2   C17  H1   107.09  3.000
 KKY  H2   C17  C18  109.36  3.000
 KKY  H1   C17  C18  109.13  3.000
 KKY  H2   C17  C15  109.66  3.000
 KKY  H1   C17  C15  109.91  3.000
 KKY  C18  C17  C15  111.58  3.000
 KKY  H3   C22  N21  108.81  3.000
 KKY  H3   C22  C18  108.30  3.000
 KKY  N21  C22  C18  112.11  3.000
 KKY  H3   C22  C23  109.06  3.000
 KKY  N21  C22  C23  106.51  3.000
 KKY  C18  C22  C23  111.98  3.000
 KKY  N02  C02  N01  117.12  3.000
 KKY  N01  C02  C03  122.28  3.000
 KKY  N02  C02  C03  120.57  3.000
 KKY  H4   C03  C04  120.91  3.000
 KKY  H4   C03  C02  120.00  3.000
 KKY  C04  C03  C02  119.09  3.000
 KKY  C07  C04  C05  120.54  3.000
 KKY  C05  C04  C03  118.08  3.000
 KKY  C07  C04  C03  121.38  3.000
 KKY  H5   C05  C06  120.34  3.000
 KKY  H5   C05  C04  120.61  3.000
 KKY  C06  C05  C04  119.05  3.000
 KKY  N01  C06  C08  115.96  3.000
 KKY  C08  C06  C05  121.25  3.000
 KKY  N01  C06  C05  122.79  3.000
 KKY  H12  C09  H11  107.12  3.000
 KKY  H12  C09  C11  110.02  3.000
 KKY  H11  C09  C11  109.88  3.000
 KKY  H12  C09  C08  108.83  3.000
 KKY  H11  C09  C08  109.24  3.000
 KKY  C11  C09  C08  111.65  3.000
 KKY  C16  C11  C12  119.07  3.000
 KKY  C16  C11  C09  120.86  3.000
 KKY  C12  C11  C09  120.03  3.000
 KKY  H13  C14  C15  120.88  3.000
 KKY  H13  C14  C13  120.26  3.000
 KKY  C15  C14  C13  118.86  3.000
 KKY  H15  C23  H14  107.41  3.000
 KKY  H15  C23  C24  109.90  3.000
 KKY  H14  C23  C24  113.63  3.000
 KKY  H15  C23  C22  110.01  3.000
 KKY  H14  C23  C22  111.83  3.000
 KKY  C24  C23  C22  104.04  3.000
 KKY  H17  C25  H16  106.93  3.000
 KKY  H17  C25  N21  110.12  3.000
 KKY  H16  C25  N21  110.81  3.000
 KKY  H17  C25  C24  109.63  3.000
 KKY  H16  C25  C24  113.77  3.000
 KKY  N21  C25  C24  105.61  3.000
 KKY  H18  C12  C11  120.93  3.000
 KKY  H18  C12  C13  120.36  3.000
 KKY  C11  C12  C13  118.70  3.000
 KKY  H19  C16  C11  119.13  3.000
 KKY  H19  C16  C15  119.17  3.000
 KKY  C11  C16  C15  121.70  3.000
 KKY  H21  C18  H20  106.52  3.000
 KKY  H21  C18  C22  108.86  3.000
 KKY  H20  C18  C22  108.81  3.000
 KKY  H21  C18  C17  109.52  3.000
 KKY  H20  C18  C17  109.41  3.000
 KKY  C22  C18  C17  113.49  3.000
 KKY  H23  C24  H22  107.63  3.000
 KKY  H23  C24  C25  113.27  3.000
 KKY  H22  C24  C25  110.50  3.000
 KKY  H23  C24  C23  113.49  3.000
 KKY  H22  C24  C23  110.87  3.000
 KKY  C25  C24  C23  101.05  3.000
 KKY  C06  N01  C02  118.71  3.000
 KKY  H28  N02  H27  114.12  3.000
 KKY  H28  N02  C02  117.56  3.000
 KKY  H27  N02  C02  116.17  3.000
 KKY  C26  N21  C25  113.23  3.000
 KKY  C26  N21  C22  113.14  3.000
 KKY  C25  N21  C22  107.33  3.000
 KKY  H26  C26  H25  107.13  3.000
 KKY  H26  C26  H24  107.38  3.000
 KKY  H25  C26  H24  107.73  3.000
 KKY  H26  C26  N21  109.95  3.000
 KKY  H25  C26  N21  109.99  3.000
 KKY  H24  C26  N21  114.37  3.000
 KKY  H10  C08  H9   107.10  3.000
 KKY  H10  C08  C09  109.56  3.000
 KKY  H9   C08  C09  108.98  3.000
 KKY  H10  C08  C06  110.00  3.000
 KKY  H9   C08  C06  109.27  3.000
 KKY  C09  C08  C06  111.80  3.000
 KKY  H8   C07  H7   108.27  3.000
 KKY  H8   C07  H6   107.97  3.000
 KKY  H7   C07  H6   106.98  3.000
 KKY  H8   C07  C04  111.75  3.000
 KKY  H7   C07  C04  110.98  3.000
 KKY  H6   C07  C04  110.71  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
 KKY  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 KKY  CONST_02  C16  C11  C12  C13    0.00   0.0  0
 KKY  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 KKY  CONST_04  C12  C11  C16  C15    0.00   0.0  0
 KKY  CONST_05  C05  C04  C03  C02    0.00   0.0  0
 KKY  CONST_06  C05  C06  N01  C02    0.00   0.0  0
 KKY  CONST_07  C06  C05  C04  C03    0.00   0.0  0
 KKY  CONST_08  C06  N01  C02  C03    0.00   0.0  0
 KKY  CONST_09  N01  C02  C03  C04    0.00   0.0  0
 KKY  CONST_10  N01  C06  C05  C04    0.00   0.0  0
 KKY  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 KKY  CONST_12  C14  C15  C16  C11    0.00   0.0  0
 KKY  CONST_13  C17  C15  C14  C13  180.00   0.0  0
 KKY  CONST_14  C09  C11  C12  C13  180.00   0.0  0
 KKY  CONST_15  F13  C13  C14  C15  180.00   0.0  0
 KKY  CONST_16  C09  C11  C16  C15  180.00   0.0  0
 KKY  CONST_17  C11  C16  C15  C17  180.00   0.0  0
 KKY  CONST_18  C07  C04  C03  C02  180.00   0.0  0
 KKY  CONST_19  C08  C06  N01  C02  180.00   0.0  0
 KKY  CONST_20  N02  C02  C03  C04  180.00   0.0  0
 KKY  CONST_21  C08  C06  C05  C04  180.00   0.0  0
 KKY  CONST_22  C07  C04  C05  C06  180.00   0.0  0
 KKY  CONST_23  N02  C02  N01  C06  180.00   0.0  0
 KKY  CONST_24  F13  C13  C12  C11  180.00   0.0  0
 KKY  CONST_25  H5   C05  C04  C03  180.00   0.0  0
 KKY  CONST_26  H4   C03  C04  C05  180.00   0.0  0
 KKY  CONST_27  H18  C12  C13  C14  180.00   0.0  0
 KKY  CONST_28  H19  C16  C15  C14  180.00   0.0  0
 KKY  CONST_29  H13  C14  C13  C12  180.00   0.0  0
 KKY  Var_01    C25  C24  C23  C22  -34.59  30.0  1
 KKY  Var_02    C24  C25  N21  C22  -28.51  30.0  1
 KKY  Var_03    N21  C25  C24  C23   39.29  30.0  1
 KKY  Var_04    C22  C18  C17  C15  179.87  30.0  3
 KKY  Var_05    C09  C08  C06  C05  112.72  30.0  2
 KKY  Var_06    C11  C09  C08  C06  177.86  30.0  3
 KKY  Var_07    C12  C11  C09  C08  -85.55  30.0  2
 KKY  Var_08    C18  C17  C15  C14  -96.48  30.0  2
 KKY  Var_09    H24  C26  N21  C22   61.33  30.0  3
 KKY  Var_10    H6   C07  C04  C03  113.55  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
 KKY  chir_01  C22  C18  C23  N21  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
 KKY  plan-1  C13  0.020
 KKY  plan-1  C15  0.020
 KKY  plan-1  C17  0.020
 KKY  plan-1  C09  0.020
 KKY  plan-1  C11  0.020
 KKY  plan-1  C14  0.020
 KKY  plan-1  C12  0.020
 KKY  plan-1  C16  0.020
 KKY  plan-1  F13  0.020
 KKY  plan-1  H13  0.020
 KKY  plan-1  H18  0.020
 KKY  plan-1  H19  0.020
 KKY  plan-2  C02  0.020
 KKY  plan-2  C03  0.020
 KKY  plan-2  C04  0.020
 KKY  plan-2  C05  0.020
 KKY  plan-2  C06  0.020
 KKY  plan-2  N01  0.020
 KKY  plan-2  N02  0.020
 KKY  plan-2  H4   0.020
 KKY  plan-2  H5   0.020
 KKY  plan-2  C08  0.020
 KKY  plan-2  C07  0.020
 KKY  plan-3  C02  0.020
 KKY  plan-3  N02  0.020
 KKY  plan-3  H27  0.020
 KKY  plan-3  H28  0.020

