# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:32:14 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-[2-(3-fluoro-5-{2-[(2R,4S)-4-fluoropyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cc(F)cc(CC[C@@H]3C[C@H](F)CN3)c2)c1
#
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
 KLA  KLA  6-[2-(3-fluoro-5-{2-[(2R,4S)-4-fluoropyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  50  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_KLA
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
 KLA  C02  C  CR6   0   0.439  -6.1521  -0.1925   0.2509
 KLA  C03  C  CR16  0  -0.447  -6.3989  -1.5579   0.0251
 KLA  C04  C  CR6   0   0.204  -5.3327  -2.4311  -0.0289
 KLA  C05  C  CR16  0  -0.434  -4.0444  -1.9093   0.1428
 KLA  C06  C  CR6   0   0.278  -3.8926  -0.5523   0.3567
 KLA  C07  C  CH3   0  -0.725  -5.5319  -3.8962  -0.2701
 KLA  C08  C  CH2   0  -0.488  -2.5307   0.0636   0.5077
 KLA  C09  C  CH2   0  -0.512  -2.1801   0.9686  -0.6817
 KLA  C11  C  CR6   0   0.169  -0.8195   1.5853  -0.5222
 KLA  C12  C  CR16  0  -0.493  -0.6783   2.8225   0.1014
 KLA  C13  C  CR6   0   0.561   0.5898   3.3402   0.2699
 KLA  C14  C  CR16  0  -0.495   1.7271   2.6858  -0.1611
 KLA  C15  C  CR6   0   0.176   1.5921   1.4505  -0.7886
 KLA  C16  C  CR16  0  -0.386   0.3185   0.9147  -0.9594
 KLA  C17  C  CH2   0  -0.519   2.8072   0.6821  -1.2280
 KLA  C18  C  CH2   0  -0.418   3.2584  -0.3175  -0.1637
 KLA  C22  C  CR15  0  -0.056   4.4201  -1.1892  -0.6137
 KLA  C23  C  CH2   0  -0.529   4.8973  -2.1733   0.4766
 KLA  C24  C  CR15  0   0.191   6.4013  -1.9603   0.5915
 KLA  C25  C  CH2   0  -0.332   6.7542  -1.2709  -0.7065
 KLA  F13  F  F     0  -0.320   0.7231   4.5351   0.8734
 KLA  F24  F  F     0  -0.390   6.6836  -1.1087   1.6671
 KLA  N01  N  N     0  -0.485  -4.9267   0.2907   0.4130
 KLA  N02  N  NH2   0  -0.838  -7.1815   0.7067   0.2676
 KLA  N21  N  NR15  0  -0.621   5.6123  -0.3991  -0.9167
 KLA  H1   H  HCR6  0   0.255  -7.4160  -1.9101  -0.0963
 KLA  H2   H  HCR6  0   0.244  -3.1778  -2.5578   0.1110
 KLA  H3   H  HCH3  0   0.252  -5.0626  -4.1965  -1.2083
 KLA  H4   H  HCH3  0   0.251  -5.0687  -4.4886   0.5197
 KLA  H5   H  HCH3  0   0.246  -6.5866  -4.1615  -0.3197
 KLA  H6   H  HCH2  0   0.249  -2.5004   0.6541   1.4275
 KLA  H7   H  HCH2  0   0.248  -1.7749  -0.7186   0.6022
 KLA  H8   H  HCH2  0   0.251  -2.2118   0.3760  -1.5995
 KLA  H9   H  HCH2  0   0.252  -2.9403   1.7460  -0.7772
 KLA  H10  H  HCR6  0   0.266  -1.5463   3.3721   0.4470
 KLA  H11  H  HCR6  0   0.266   2.7038   3.1307  -0.0132
 KLA  H12  H  HCR6  0   0.240   0.2096  -0.0448  -1.4545
 KLA  H13  H  HCH2  0   0.242   2.5856   0.1490  -2.1569
 KLA  H14  H  HCH2  0   0.244   3.6207   1.3786  -1.4444
 KLA  H15  H  HCH2  0   0.223   3.5497   0.2168   0.7462
 KLA  H16  H  HCH2  0   0.230   2.4180  -0.9653   0.1036
 KLA  H17  H  HCR5  0   0.213   4.0937  -1.7691  -1.4902
 KLA  H18  H  HCH2  0   0.254   4.4124  -2.0027   1.4395
 KLA  H19  H  HCH2  0   0.253   4.6852  -3.2023   0.1880
 KLA  H20  H  HCR5  0   0.221   6.9638  -2.8786   0.7590
 KLA  H21  H  HCH2  0   0.244   7.6903  -0.7111  -0.6502
 KLA  H22  H  HCH2  0   0.207   6.8761  -2.0405  -1.4840
 KLA  H23  H  HNH2  0   0.378  -6.9859   1.5899   0.7105
 KLA  H24  H  HNH2  0   0.387  -8.1034   0.3520   0.4605
 KLA  H25  H  HNR5  0   0.353   5.5903  -0.0398  -1.8616

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
 KLA  C07  C04  single    1.498  0.020  1.498
 KLA  C04  C03  aromatic  1.379  0.020  1.379
 KLA  C04  C05  aromatic  1.401  0.020  1.401
 KLA  C03  C02  aromatic  1.406  0.020  1.406
 KLA  C05  C06  aromatic  1.382  0.020  1.382
 KLA  C02  N02  single    1.367  0.020  1.367
 KLA  C02  N01  aromatic  1.327  0.020  1.327
 KLA  C06  N01  aromatic  1.335  0.020  1.335
 KLA  C06  C08  single    1.502  0.020  1.502
 KLA  F13  C13  single    1.345  0.020  1.345
 KLA  C08  C09  single    1.535  0.020  1.535
 KLA  C12  C13  aromatic  1.380  0.020  1.380
 KLA  C12  C11  aromatic  1.393  0.020  1.393
 KLA  C13  C14  aromatic  1.381  0.020  1.381
 KLA  C09  C11  single    1.502  0.020  1.502
 KLA  C11  C16  aromatic  1.391  0.020  1.391
 KLA  C14  C15  aromatic  1.392  0.020  1.392
 KLA  C16  C15  aromatic  1.392  0.020  1.392
 KLA  C15  C17  single    1.503  0.020  1.503
 KLA  C17  C18  single    1.528  0.020  1.528
 KLA  C18  C22  single    1.520  0.020  1.520
 KLA  C22  C23  single    1.544  0.020  1.544
 KLA  C22  N21  single    1.462  0.020  1.462
 KLA  C23  C24  single    1.523  0.020  1.523
 KLA  N21  C25  single    1.452  0.020  1.452
 KLA  C24  C25  single    1.511  0.020  1.511
 KLA  C24  F24  single    1.401  0.020  1.401
 KLA  C03  H1   single    0.930  0.020  1.080
 KLA  C05  H2   single    0.930  0.020  1.080
 KLA  C07  H3   single    0.970  0.020  1.090
 KLA  C07  H4   single    0.970  0.020  1.090
 KLA  C07  H5   single    0.970  0.020  1.090
 KLA  C08  H6   single    0.970  0.020  1.090
 KLA  C08  H7   single    0.970  0.020  1.090
 KLA  C09  H8   single    0.970  0.020  1.090
 KLA  C09  H9   single    0.970  0.020  1.090
 KLA  C12  H10  single    0.930  0.020  1.080
 KLA  C14  H11  single    0.930  0.020  1.080
 KLA  C16  H12  single    0.930  0.020  1.080
 KLA  C17  H13  single    0.970  0.020  1.090
 KLA  C17  H14  single    0.970  0.020  1.090
 KLA  C18  H15  single    0.970  0.020  1.090
 KLA  C18  H16  single    0.970  0.020  1.090
 KLA  C22  H17  single    0.970  0.020  1.090
 KLA  C23  H18  single    0.970  0.020  1.090
 KLA  C23  H19  single    0.970  0.020  1.090
 KLA  C24  H20  single    0.970  0.020  1.090
 KLA  C25  H21  single    0.970  0.020  1.090
 KLA  C25  H22  single    0.970  0.020  1.090
 KLA  N02  H23  single    0.890  0.020  1.040
 KLA  N02  H24  single    0.890  0.020  1.040
 KLA  N21  H25  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
 KLA  N02  C02  N01  117.03  3.000
 KLA  N01  C02  C03  122.37  3.000
 KLA  N02  C02  C03  120.57  3.000
 KLA  H1   C03  C04  121.04  3.000
 KLA  H1   C03  C02  119.91  3.000
 KLA  C04  C03  C02  119.05  3.000
 KLA  C07  C04  C05  120.42  3.000
 KLA  C05  C04  C03  118.06  3.000
 KLA  C07  C04  C03  121.52  3.000
 KLA  H2   C05  C06  120.30  3.000
 KLA  H2   C05  C04  120.63  3.000
 KLA  C06  C05  C04  119.07  3.000
 KLA  N01  C06  C08  116.04  3.000
 KLA  C08  C06  C05  121.18  3.000
 KLA  N01  C06  C05  122.77  3.000
 KLA  H5   C07  H4   108.19  3.000
 KLA  H5   C07  H3   108.08  3.000
 KLA  H4   C07  H3   106.89  3.000
 KLA  H5   C07  C04  111.99  3.000
 KLA  H4   C07  C04  110.99  3.000
 KLA  H3   C07  C04  110.51  3.000
 KLA  H7   C08  H6   107.15  3.000
 KLA  H7   C08  C09  109.35  3.000
 KLA  H6   C08  C09  109.09  3.000
 KLA  H7   C08  C06  110.03  3.000
 KLA  H6   C08  C06  109.34  3.000
 KLA  C09  C08  C06  111.77  3.000
 KLA  H9   C09  H8   107.00  3.000
 KLA  H9   C09  C11  110.35  3.000
 KLA  H8   C09  C11  109.76  3.000
 KLA  H9   C09  C08  109.18  3.000
 KLA  H8   C09  C08  108.92  3.000
 KLA  C11  C09  C08  111.50  3.000
 KLA  C16  C11  C12  119.07  3.000
 KLA  C16  C11  C09  120.63  3.000
 KLA  C12  C11  C09  120.27  3.000
 KLA  H10  C12  C13  120.45  3.000
 KLA  H10  C12  C11  120.79  3.000
 KLA  C13  C12  C11  118.76  3.000
 KLA  F13  C13  C14  118.64  3.000
 KLA  C14  C13  C12  122.74  3.000
 KLA  F13  C13  C12  118.62  3.000
 KLA  H11  C14  C15  120.89  3.000
 KLA  H11  C14  C13  120.34  3.000
 KLA  C15  C14  C13  118.77  3.000
 KLA  C17  C15  C16  120.45  3.000
 KLA  C17  C15  C14  120.46  3.000
 KLA  C16  C15  C14  119.04  3.000
 KLA  H12  C16  C15  119.21  3.000
 KLA  H12  C16  C11  119.17  3.000
 KLA  C15  C16  C11  121.61  3.000
 KLA  H14  C17  H13  107.06  3.000
 KLA  H14  C17  C18  109.58  3.000
 KLA  H13  C17  C18  109.41  3.000
 KLA  H14  C17  C15  109.51  3.000
 KLA  H13  C17  C15  109.49  3.000
 KLA  C18  C17  C15  111.68  3.000
 KLA  H16  C18  H15  106.88  3.000
 KLA  H16  C18  C22  108.65  3.000
 KLA  H15  C18  C22  108.81  3.000
 KLA  H16  C18  C17  109.31  3.000
 KLA  H15  C18  C17  109.76  3.000
 KLA  C22  C18  C17  113.24  3.000
 KLA  H17  C22  N21  111.20  3.000
 KLA  H17  C22  C23  108.55  3.000
 KLA  N21  C22  C23  103.81  3.000
 KLA  H17  C22  C18  108.13  3.000
 KLA  N21  C22  C18  112.00  3.000
 KLA  C23  C22  C18  113.11  3.000
 KLA  H19  C23  H18  107.14  3.000
 KLA  H19  C23  C24  110.13  3.000
 KLA  H18  C23  C24  110.50  3.000
 KLA  H19  C23  C22  110.77  3.000
 KLA  H18  C23  C22  112.70  3.000
 KLA  C24  C23  C22  105.62  3.000
 KLA  H20  C24  F24  106.88  3.000
 KLA  H20  C24  C25  113.32  3.000
 KLA  F24  C24  C25  109.58  3.000
 KLA  H20  C24  C23  113.79  3.000
 KLA  F24  C24  C23  109.99  3.000
 KLA  C25  C24  C23  103.27  3.000
 KLA  H22  C25  H21  107.45  3.000
 KLA  H22  C25  N21  113.87  3.000
 KLA  H21  C25  N21  111.95  3.000
 KLA  H22  C25  C24  108.28  3.000
 KLA  H21  C25  C24  112.93  3.000
 KLA  N21  C25  C24  102.39  3.000
 KLA  C06  N01  C02  118.69  3.000
 KLA  H24  N02  H23  113.74  3.000
 KLA  H24  N02  C02  117.41  3.000
 KLA  H23  N02  C02  115.85  3.000
 KLA  H25  N21  C25  111.46  3.000
 KLA  H25  N21  C22  111.59  3.000
 KLA  C25  N21  C22  106.67  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
 KLA  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 KLA  CONST_02  C05  C06  N01  C02    0.00   0.0  0
 KLA  CONST_03  C06  C05  C04  C03    0.00   0.0  0
 KLA  CONST_04  C06  N01  C02  C03    0.00   0.0  0
 KLA  CONST_05  N01  C02  C03  C04    0.00   0.0  0
 KLA  CONST_06  N01  C06  C05  C04    0.00   0.0  0
 KLA  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 KLA  CONST_08  C14  C15  C16  C11    0.00   0.0  0
 KLA  CONST_09  C15  C14  C13  C12    0.00   0.0  0
 KLA  CONST_10  C15  C16  C11  C12    0.00   0.0  0
 KLA  CONST_11  C16  C11  C12  C13    0.00   0.0  0
 KLA  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 KLA  CONST_13  C07  C04  C03  C02  180.00   0.0  0
 KLA  CONST_14  C08  C06  N01  C02  180.00   0.0  0
 KLA  CONST_15  N02  C02  C03  C04  180.00   0.0  0
 KLA  CONST_16  C08  C06  C05  C04  180.00   0.0  0
 KLA  CONST_17  C07  C04  C05  C06  180.00   0.0  0
 KLA  CONST_18  N02  C02  N01  C06  180.00   0.0  0
 KLA  CONST_19  C13  C12  C11  C09  180.00   0.0  0
 KLA  CONST_20  C15  C16  C11  C09  180.00   0.0  0
 KLA  CONST_21  F13  C13  C12  C11  180.00   0.0  0
 KLA  CONST_22  C17  C15  C16  C11  180.00   0.0  0
 KLA  CONST_23  C17  C15  C14  C13  180.00   0.0  0
 KLA  CONST_24  F13  C13  C14  C15  180.00   0.0  0
 KLA  CONST_25  H2   C05  C04  C03  180.00   0.0  0
 KLA  CONST_26  H1   C03  C04  C05  180.00   0.0  0
 KLA  CONST_27  H11  C14  C13  C12  180.00   0.0  0
 KLA  CONST_28  H12  C16  C11  C12  180.00   0.0  0
 KLA  CONST_29  H10  C12  C13  C14  180.00   0.0  0
 KLA  Var_01    C24  C25  N21  C22  -43.71  30.0  1
 KLA  Var_02    C09  C08  C06  C05  111.56  30.0  2
 KLA  Var_03    C11  C09  C08  C06  179.79  30.0  3
 KLA  Var_04    C12  C11  C09  C08  -91.08  30.0  2
 KLA  Var_05    C18  C17  C15  C14   93.62  30.0  2
 KLA  Var_06    C22  C18  C17  C15  175.57  30.0  3
 KLA  Var_07    H3   C07  C04  C03  116.58  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
 KLA  chir_01  C22  C18  C23  N21  positiv
 KLA  chir_02  C24  F24  C25  C23  positiv

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
 KLA  plan-1  C02  0.020
 KLA  plan-1  C03  0.020
 KLA  plan-1  C04  0.020
 KLA  plan-1  C05  0.020
 KLA  plan-1  C06  0.020
 KLA  plan-1  C07  0.020
 KLA  plan-1  C08  0.020
 KLA  plan-1  N01  0.020
 KLA  plan-1  N02  0.020
 KLA  plan-1  H1   0.020
 KLA  plan-1  H2   0.020
 KLA  plan-2  C09  0.020
 KLA  plan-2  C11  0.020
 KLA  plan-2  C12  0.020
 KLA  plan-2  C13  0.020
 KLA  plan-2  C14  0.020
 KLA  plan-2  C15  0.020
 KLA  plan-2  C16  0.020
 KLA  plan-2  C17  0.020
 KLA  plan-2  F13  0.020
 KLA  plan-2  H10  0.020
 KLA  plan-2  H11  0.020
 KLA  plan-2  H12  0.020
 KLA  plan-3  C02  0.020
 KLA  plan-3  N02  0.020
 KLA  plan-3  H23  0.020
 KLA  plan-3  H24  0.020

