# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 22:17:05 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-[2-(2,3-difluoro-5-{2-[(2R)-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)c(F)c(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
 KN4  KN4  6-[2-(2,3-difluoro-5-{2-[(2R)-1-methylpyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  53  26  .  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_KN4
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
 KN4  C12  C  CR6   0   0.354  -0.3517   2.6454   0.0207
 KN4  C13  C  CR6   0   0.425   0.7918   3.3187   0.4085
 KN4  C11  C  CR6   0  -0.045  -0.3656   1.2645  -0.0832
 KN4  C14  C  CR16  0  -0.490   1.9523   2.6361   0.7070
 KN4  C23  C  CH2   0  -0.463   5.5453  -2.5312  -1.6158
 KN4  C15  C  CR6   0   0.170   1.9708   1.2469   0.6196
 KN4  C17  C  CH2   0  -0.524   3.2302   0.4749   0.8941
 KN4  C18  C  CH2   0  -0.396   3.9715   0.1210  -0.3938
 KN4  C02  C  CR6   0   0.441  -5.7300  -0.5205  -0.8279
 KN4  C03  C  CR16  0  -0.447  -5.9614  -1.8590  -0.4627
 KN4  C04  C  CR6   0   0.204  -5.0433  -2.5033   0.3399
 KN4  C05  C  CR16  0  -0.431  -3.9161  -1.7860   0.7587
 KN4  C06  C  CR6   0   0.272  -3.7659  -0.4737   0.3500
 KN4  C09  C  CH2   0  -0.503  -1.6144   0.5234  -0.4654
 KN4  C16  C  CR16  0  -0.369   0.8107   0.5869   0.2254
 KN4  C22  C  CH2   0  -0.257   5.6442  -2.9838  -0.1703
 KN4  C24  C  CH2   0  -0.475   5.9243  -1.0583  -1.4949
 KN4  C25  C  CR15  0  -0.059   5.2832  -0.6274  -0.1662
 KN4  F12  F  F     0  -0.307  -1.4583   3.3541  -0.2510
 KN4  F13  F  F     0  -0.310   0.7550   4.6547   0.4951
 KN4  N01  N  N     0  -0.482  -4.6538   0.1483  -0.4290
 KN4  N02  N  NH2   0  -0.839  -6.6432   0.1622  -1.5783
 KN4  N21  N  NR5   0  -0.424   5.0757  -1.8760   0.5804
 KN4  H1   H  HCR6  0   0.277   2.8344   3.1877   1.0090
 KN4  H2   H  HCH2  0   0.237   6.2028  -3.0926  -2.2796
 KN4  H3   H  HCH2  0   0.226   4.5227  -2.6442  -1.9839
 KN4  H4   H  HCH2  0   0.239   3.8880   1.0580   1.5448
 KN4  H5   H  HCH2  0   0.246   2.9837  -0.4444   1.4301
 KN4  H6   H  HCH2  0   0.219   3.3166  -0.4833  -1.0312
 KN4  H7   H  HCH2  0   0.221   4.1886   1.0399  -0.9479
 KN4  H8   H  HCR6  0   0.255  -6.8512  -2.3701  -0.8105
 KN4  H9   H  HCR6  0   0.243  -3.1699  -2.2529   1.3894
 KN4  H10  H  HCH3  0   0.253  -4.5072  -4.5732   0.2341
 KN4  H11  H  HCH3  0   0.249  -5.0642  -4.0613   1.8158
 KN4  H12  H  HCH3  0   0.246  -6.2267  -4.2976   0.5065
 KN4  H15  H  HCH2  0   0.258  -2.1521   1.0438  -1.2597
 KN4  H16  H  HCH2  0   0.259  -1.3324  -0.4525  -0.8656
 KN4  H17  H  HCR6  0   0.251   0.8164  -0.4951   0.1519
 KN4  H18  H  HCH2  0   0.225   5.1052  -3.9134   0.0335
 KN4  H19  H  HCH2  0   0.185   6.7017  -3.1610   0.0883
 KN4  H20  H  HCH2  0   0.232   7.0109  -0.9628  -1.4380
 KN4  H21  H  HCH2  0   0.238   5.5893  -0.4503  -2.3372
 KN4  H22  H  HCR5  0   0.216   5.9656   0.0364   0.3842
 KN4  H26  H  HNH2  0   0.388  -7.2893  -0.3758  -2.1307
 KN4  H27  H  HNH2  0   0.379  -6.3125   0.9992  -2.0292
 KN4  C26  C  CH3   0  -0.526   5.4908  -1.8458   1.9607
 KN4  C08  C  CH2   0  -0.488  -2.5522   0.3233   0.7340
 KN4  C07  C  CH3   0  -0.725  -5.2286  -3.9334   0.7457
 KN4  H13  H  HCH2  0   0.250  -2.8652   1.2963   1.1198
 KN4  H14  H  HCH2  0   0.251  -2.0098  -0.1829   1.5348
 KN4  H23  H  HCH3  0   0.192   6.5758  -1.7013   2.0855
 KN4  H24  H  HCH3  0   0.233   4.9861  -1.0453   2.5020
 KN4  H25  H  HCH3  0   0.227   5.2254  -2.7841   2.4521

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
 KN4  C22  C23  single    1.518  0.020  1.518
 KN4  C22  N21  single    1.454  0.020  1.454
 KN4  C26  N21  single    1.442  0.020  1.442
 KN4  C23  C24  single    1.526  0.020  1.526
 KN4  N21  C25  single    1.470  0.020  1.470
 KN4  C24  C25  single    1.537  0.020  1.537
 KN4  C25  C18  single    1.527  0.020  1.527
 KN4  C18  C17  single    1.528  0.020  1.528
 KN4  C17  C15  single    1.502  0.020  1.502
 KN4  C15  C16  aromatic  1.392  0.020  1.392
 KN4  C15  C14  aromatic  1.392  0.020  1.392
 KN4  C16  C11  aromatic  1.392  0.020  1.392
 KN4  C08  C06  single    1.502  0.020  1.502
 KN4  C08  C09  single    1.536  0.020  1.536
 KN4  N01  C06  aromatic  1.335  0.020  1.335
 KN4  N01  C02  aromatic  1.328  0.020  1.328
 KN4  N02  C02  single    1.365  0.020  1.365
 KN4  C14  C13  aromatic  1.379  0.020  1.379
 KN4  C06  C05  aromatic  1.383  0.020  1.383
 KN4  C02  C03  aromatic  1.407  0.020  1.407
 KN4  C11  C09  single    1.502  0.020  1.502
 KN4  C11  C12  aromatic  1.385  0.020  1.385
 KN4  C13  C12  aromatic  1.383  0.020  1.383
 KN4  C13  F13  single    1.339  0.020  1.339
 KN4  C12  F12  single    1.342  0.020  1.342
 KN4  C05  C04  aromatic  1.400  0.020  1.400
 KN4  C03  C04  aromatic  1.379  0.020  1.379
 KN4  C04  C07  single    1.498  0.020  1.498
 KN4  C14  H1   single    0.930  0.020  1.080
 KN4  C23  H2   single    0.970  0.020  1.090
 KN4  C23  H3   single    0.970  0.020  1.090
 KN4  C17  H4   single    0.970  0.020  1.090
 KN4  C17  H5   single    0.970  0.020  1.090
 KN4  C18  H6   single    0.970  0.020  1.090
 KN4  C18  H7   single    0.970  0.020  1.090
 KN4  C03  H8   single    0.930  0.020  1.080
 KN4  C05  H9   single    0.930  0.020  1.080
 KN4  C07  H10  single    0.970  0.020  1.090
 KN4  C07  H11  single    0.970  0.020  1.090
 KN4  C07  H12  single    0.970  0.020  1.090
 KN4  C08  H13  single    0.970  0.020  1.090
 KN4  C08  H14  single    0.970  0.020  1.090
 KN4  C09  H15  single    0.970  0.020  1.090
 KN4  C09  H16  single    0.970  0.020  1.090
 KN4  C16  H17  single    0.930  0.020  1.080
 KN4  C22  H18  single    0.970  0.020  1.090
 KN4  C22  H19  single    0.970  0.020  1.090
 KN4  C24  H20  single    0.970  0.020  1.090
 KN4  C24  H21  single    0.970  0.020  1.090
 KN4  C25  H22  single    0.970  0.020  1.090
 KN4  C26  H23  single    0.970  0.020  1.090
 KN4  C26  H24  single    0.970  0.020  1.090
 KN4  C26  H25  single    0.970  0.020  1.090
 KN4  N02  H26  single    0.890  0.020  1.040
 KN4  N02  H27  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
 KN4  F12  C12  C11  120.21  3.000
 KN4  F12  C12  C13  118.79  3.000
 KN4  C11  C12  C13  120.99  3.000
 KN4  F13  C13  C14  120.19  3.000
 KN4  F13  C13  C12  118.77  3.000
 KN4  C14  C13  C12  121.04  3.000
 KN4  C16  C11  C09  121.26  3.000
 KN4  C09  C11  C12  121.30  3.000
 KN4  C16  C11  C12  117.40  3.000
 KN4  H1   C14  C15  120.99  3.000
 KN4  H1   C14  C13  119.57  3.000
 KN4  C15  C14  C13  119.45  3.000
 KN4  H3   C23  H2   107.82  3.000
 KN4  H3   C23  C24  111.04  3.000
 KN4  H2   C23  C24  113.31  3.000
 KN4  H3   C23  C22  110.54  3.000
 KN4  H2   C23  C22  112.77  3.000
 KN4  C24  C23  C22  101.32  3.000
 KN4  C16  C15  C17  120.45  3.000
 KN4  C16  C15  C14  118.68  3.000
 KN4  C17  C15  C14  120.82  3.000
 KN4  H5   C17  H4   107.01  3.000
 KN4  H5   C17  C18  109.16  3.000
 KN4  H4   C17  C18  109.47  3.000
 KN4  H5   C17  C15  109.44  3.000
 KN4  H4   C17  C15  109.81  3.000
 KN4  C18  C17  C15  111.82  3.000
 KN4  H7   C18  H6   106.68  3.000
 KN4  H7   C18  C25  108.44  3.000
 KN4  H6   C18  C25  109.26  3.000
 KN4  H7   C18  C17  109.18  3.000
 KN4  H6   C18  C17  109.17  3.000
 KN4  C25  C18  C17  113.87  3.000
 KN4  N02  C02  N01  117.08  3.000
 KN4  N02  C02  C03  120.57  3.000
 KN4  N01  C02  C03  122.30  3.000
 KN4  H8   C03  C04  120.87  3.000
 KN4  H8   C03  C02  120.04  3.000
 KN4  C04  C03  C02  119.09  3.000
 KN4  C07  C04  C05  120.51  3.000
 KN4  C07  C04  C03  121.42  3.000
 KN4  C05  C04  C03  118.07  3.000
 KN4  H9   C05  C06  120.44  3.000
 KN4  H9   C05  C04  120.53  3.000
 KN4  C06  C05  C04  119.03  3.000
 KN4  N01  C06  C08  116.07  3.000
 KN4  N01  C06  C05  122.85  3.000
 KN4  C08  C06  C05  121.05  3.000
 KN4  H16  C09  H15  106.66  3.000
 KN4  H16  C09  C08  109.11  3.000
 KN4  H15  C09  C08  109.25  3.000
 KN4  H16  C09  C11  108.64  3.000
 KN4  H15  C09  C11  111.09  3.000
 KN4  C08  C09  C11  111.92  3.000
 KN4  H17  C16  C15  119.21  3.000
 KN4  H17  C16  C11  118.36  3.000
 KN4  C15  C16  C11  122.43  3.000
 KN4  H19  C22  H18  107.00  3.000
 KN4  H19  C22  N21  112.10  3.000
 KN4  H18  C22  N21  111.02  3.000
 KN4  H19  C22  C23  109.49  3.000
 KN4  H18  C22  C23  113.50  3.000
 KN4  N21  C22  C23  103.83  3.000
 KN4  H21  C24  H20  107.27  3.000
 KN4  H21  C24  C25  112.52  3.000
 KN4  H20  C24  C25  110.21  3.000
 KN4  H21  C24  C23  113.60  3.000
 KN4  H20  C24  C23  109.61  3.000
 KN4  C25  C24  C23  103.63  3.000
 KN4  H22  C25  N21  110.26  3.000
 KN4  H22  C25  C24  110.07  3.000
 KN4  N21  C25  C24  105.07  3.000
 KN4  H22  C25  C18  108.17  3.000
 KN4  C24  C25  C18  111.52  3.000
 KN4  N21  C25  C18  111.76  3.000
 KN4  C06  N01  C02  118.65  3.000
 KN4  H27  N02  H26  114.18  3.000
 KN4  H27  N02  C02  116.26  3.000
 KN4  H26  N02  C02  117.65  3.000
 KN4  C26  N21  C25  115.34  3.000
 KN4  C25  N21  C22  109.26  3.000
 KN4  C26  N21  C22  113.43  3.000
 KN4  H25  C26  H24  107.16  3.000
 KN4  H25  C26  H23  107.53  3.000
 KN4  H24  C26  H23  107.66  3.000
 KN4  H25  C26  N21  110.05  3.000
 KN4  H24  C26  N21  110.94  3.000
 KN4  H23  C26  N21  113.25  3.000
 KN4  H14  C08  H13  107.23  3.000
 KN4  H14  C08  C09  109.27  3.000
 KN4  H13  C08  C09  109.55  3.000
 KN4  H14  C08  C06  110.06  3.000
 KN4  H13  C08  C06  109.36  3.000
 KN4  C09  C08  C06  111.28  3.000
 KN4  H12  C07  H11  108.34  3.000
 KN4  H12  C07  H10  107.87  3.000
 KN4  H11  C07  H10  106.96  3.000
 KN4  H12  C07  C04  111.90  3.000
 KN4  H11  C07  C04  111.05  3.000
 KN4  H10  C07  C04  110.53  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
 KN4  CONST_01  C15  C16  C11  C12     0.00   0.0  0
 KN4  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 KN4  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 KN4  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 KN4  CONST_05  C14  C15  C16  C11     0.00   0.0  0
 KN4  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 KN4  CONST_07  C05  C06  N01  C02     0.00   0.0  0
 KN4  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 KN4  CONST_09  C06  N01  C02  C03     0.00   0.0  0
 KN4  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 KN4  CONST_11  N01  C06  C05  C04     0.00   0.0  0
 KN4  CONST_12  N01  C02  C03  C04     0.00   0.0  0
 KN4  CONST_13  C17  C15  C14  C13   180.00   0.0  0
 KN4  CONST_14  C09  C11  C12  C13   180.00   0.0  0
 KN4  CONST_15  C17  C15  C16  C11   180.00   0.0  0
 KN4  CONST_16  F13  C13  C12  C11   180.00   0.0  0
 KN4  CONST_17  F12  C12  C13  C14   180.00   0.0  0
 KN4  CONST_18  C09  C11  C16  C15   180.00   0.0  0
 KN4  CONST_19  F13  C13  C14  C15   180.00   0.0  0
 KN4  CONST_20  C08  C06  N01  C02   180.00   0.0  0
 KN4  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 KN4  CONST_22  C08  C06  C05  C04   180.00   0.0  0
 KN4  CONST_23  N02  C02  C03  C04   180.00   0.0  0
 KN4  CONST_24  N02  C02  N01  C06   180.00   0.0  0
 KN4  CONST_25  C07  C04  C05  C06   180.00   0.0  0
 KN4  CONST_26  F12  C12  C11  C16   180.00   0.0  0
 KN4  CONST_27  H17  C16  C11  C12   180.00   0.0  0
 KN4  CONST_28  H1   C14  C13  C12   180.00   0.0  0
 KN4  CONST_29  H9   C05  C04  C03   180.00   0.0  0
 KN4  CONST_30  H8   C03  C04  C05   180.00   0.0  0
 KN4  Var_01    C25  N21  C22  C23   -28.34  30.0  1
 KN4  Var_02    C25  C24  C23  C22   -37.23  30.0  1
 KN4  Var_03    N21  C22  C23  C24    40.29  30.0  1
 KN4  Var_04    C08  C09  C11  C12   -81.55  30.0  2
 KN4  Var_05    C06  C08  C09  C11  -177.38  30.0  1
 KN4  Var_06    C18  C17  C15  C14   -97.21  30.0  3
 KN4  Var_07    C25  C18  C17  C15   178.19  30.0  1
 KN4  Var_08    C09  C08  C06  C05   107.02  30.0  1
 KN4  Var_09    H10  C07  C04  C03   108.85  30.0  2
 KN4  Var_10    H23  C26  N21  C22    62.93  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
 KN4  chir_01  C25  N21  C24  C18  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
 KN4  plan-1  C12  0.020
 KN4  plan-1  C13  0.020
 KN4  plan-1  C11  0.020
 KN4  plan-1  C14  0.020
 KN4  plan-1  C15  0.020
 KN4  plan-1  C17  0.020
 KN4  plan-1  C09  0.020
 KN4  plan-1  C16  0.020
 KN4  plan-1  F12  0.020
 KN4  plan-1  F13  0.020
 KN4  plan-1  H1   0.020
 KN4  plan-1  H17  0.020
 KN4  plan-2  C02  0.020
 KN4  plan-2  C03  0.020
 KN4  plan-2  C04  0.020
 KN4  plan-2  C05  0.020
 KN4  plan-2  C06  0.020
 KN4  plan-2  N01  0.020
 KN4  plan-2  N02  0.020
 KN4  plan-2  H8   0.020
 KN4  plan-2  H9   0.020
 KN4  plan-2  C08  0.020
 KN4  plan-2  C07  0.020
 KN4  plan-3  C02  0.020
 KN4  plan-3  N02  0.020
 KN4  plan-3  H26  0.020
 KN4  plan-3  H27  0.020

