# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 23:58:49 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-[2-(2,3-difluoro-5-{2-[(2S)-1-methylazetidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC[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
 KNV  KNV  6-[2-(2,3-difluoro-5-{2-[(2S)-1-methylazetidin-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 OK
;

data_comp_KNV
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
 KNV  C11  C  CR6   0  -0.046  -0.2037   0.8522  -0.2647
 KNV  C12  C  CR6   0   0.355  -0.0263   2.2256  -0.2450
 KNV  C13  C  CR6   0   0.425   1.2035   2.7806   0.0565
 KNV  C15  C  CR6   0   0.168   2.1443   0.5994   0.3448
 KNV  C16  C  CR16  0  -0.368   0.9000   0.0586   0.0362
 KNV  C21  C  CH3   0  -0.530   6.5804  -1.3305   1.5720
 KNV  C22  C  C     0  -0.035   5.1440  -1.7233  -0.4432
 KNV  C23  C  C     0  -0.499   5.9866  -2.1363  -1.6606
 KNV  C24  C  C     0  -0.266   7.2022  -1.9158  -0.7524
 KNV  C17  C  CH2   0  -0.526   3.3219  -0.2930   0.6190
 KNV  C18  C  CH2   0  -0.416   3.9798  -0.7830  -0.6722
 KNV  C02  C  CR6   0   0.440  -5.7609  -0.1505  -0.7355
 KNV  C03  C  CR16  0  -0.447  -6.2395  -1.3736  -0.2326
 KNV  C04  C  CR6   0   0.206  -5.4377  -2.1107   0.6136
 KNV  C05  C  CR16  0  -0.436  -4.1740  -1.6006   0.9348
 KNV  C06  C  CR6   0   0.277  -3.7847  -0.3866   0.3993
 KNV  C08  C  CH2   0  -0.488  -2.4347   0.2003   0.6988
 KNV  C09  C  CH2   0  -0.504  -1.5472   0.2471  -0.5533
 KNV  C14  C  CR16  0  -0.488   2.2896   1.9836   0.3508
 KNV  F12  F  F     0  -0.307  -1.0547   3.0436  -0.5154
 KNV  F13  F  F     0  -0.310   1.3262   4.1141   0.0622
 KNV  N01  N  N     0  -0.482  -4.5624   0.3258  -0.4187
 KNV  N02  N  NH2   0  -0.839  -6.5091   0.5811  -1.6127
 KNV  N21  N  N     0  -0.414   6.3547  -1.1458   0.1621
 KNV  H1   H  HCR6  0   0.252   0.7775  -1.0188   0.0285
 KNV  H2   H  HCH3  0   0.233   7.5766  -0.9718   1.8369
 KNV  H3   H  HCH3  0   0.232   5.8623  -0.7570   2.1590
 KNV  H4   H  HCH3  0   0.190   6.5092  -2.3832   1.8880
 KNV  H5   H  H     0   0.200   4.8005  -2.6129   0.1101
 KNV  H6   H  H     0   0.241   5.8332  -3.1386  -2.0549
 KNV  H7   H  H     0   0.232   5.9242  -1.4149  -2.4765
 KNV  H8   H  H     0   0.200   7.5598  -2.8586  -0.3165
 KNV  H9   H  H     0   0.220   8.0605  -1.3753  -1.1588
 KNV  H10  H  HCH2  0   0.250   4.0536   0.2510   1.2196
 KNV  H11  H  HCH2  0   0.244   3.0003  -1.1539   1.2118
 KNV  H12  H  HCH2  0   0.221   4.3233   0.0760  -1.2567
 KNV  H13  H  HCH2  0   0.231   3.2350  -1.3029  -1.2837
 KNV  H14  H  HCR6  0   0.255  -7.2267  -1.7245  -0.5089
 KNV  H15  H  HCR6  0   0.244  -3.5130  -2.1426   1.5995
 KNV  H16  H  HCH3  0   0.254  -5.3465  -4.2480   0.6965
 KNV  H17  H  HCH3  0   0.249  -5.7021  -3.4906   2.2378
 KNV  H18  H  HCH3  0   0.247  -6.9541  -3.5921   0.9958
 KNV  H19  H  HCH2  0   0.251  -2.5631   1.2124   1.0911
 KNV  H20  H  HCH2  0   0.251  -1.9378  -0.3843   1.4750
 KNV  H21  H  HCH2  0   0.258  -2.0650   0.8021  -1.3368
 KNV  H22  H  HCH2  0   0.258  -1.4034  -0.7681  -0.9289
 KNV  H23  H  HCR6  0   0.278   3.2405   2.4447   0.5889
 KNV  H24  H  HNH2  0   0.388  -7.5017   0.4165  -1.6272
 KNV  H25  H  HNH2  0   0.379  -6.2520   1.5492  -1.7139
 KNV  C07  C  CH3   0  -0.727  -5.8914  -3.4271   1.1661

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
 KNV  C21  N21  single    1.440  0.020  1.440
 KNV  N21  C24  single    1.465  0.020  1.465
 KNV  N21  C22  single    1.472  0.020  1.472
 KNV  C24  C23  single    1.533  0.020  1.533
 KNV  C18  C22  single    1.514  0.020  1.514
 KNV  C18  C17  single    1.530  0.020  1.530
 KNV  C22  C23  single    1.537  0.020  1.537
 KNV  C17  C15  single    1.503  0.020  1.503
 KNV  C15  C16  aromatic  1.391  0.020  1.391
 KNV  C15  C14  aromatic  1.392  0.020  1.392
 KNV  C16  C11  aromatic  1.392  0.020  1.392
 KNV  C14  C13  aromatic  1.379  0.020  1.379
 KNV  C08  C06  single    1.502  0.020  1.502
 KNV  C08  C09  single    1.535  0.020  1.535
 KNV  C11  C09  single    1.501  0.020  1.501
 KNV  C11  C12  aromatic  1.385  0.020  1.385
 KNV  C13  C12  aromatic  1.383  0.020  1.383
 KNV  C13  F13  single    1.339  0.020  1.339
 KNV  N01  C06  aromatic  1.335  0.020  1.335
 KNV  N01  C02  aromatic  1.328  0.020  1.328
 KNV  N02  C02  single    1.365  0.020  1.365
 KNV  C06  C05  aromatic  1.383  0.020  1.383
 KNV  C12  F12  single    1.342  0.020  1.342
 KNV  C02  C03  aromatic  1.406  0.020  1.406
 KNV  C05  C04  aromatic  1.400  0.020  1.400
 KNV  C03  C04  aromatic  1.379  0.020  1.379
 KNV  C04  C07  single    1.498  0.020  1.498
 KNV  C16  H1   single    0.930  0.020  1.080
 KNV  C21  H2   single    0.970  0.020  1.090
 KNV  C21  H3   single    0.970  0.020  1.090
 KNV  C21  H4   single    0.970  0.020  1.090
 KNV  C22  H5   single    0.970  0.020  1.090
 KNV  C23  H6   single    0.970  0.020  1.090
 KNV  C23  H7   single    0.970  0.020  1.090
 KNV  C24  H8   single    0.970  0.020  1.090
 KNV  C24  H9   single    0.970  0.020  1.090
 KNV  C17  H10  single    0.970  0.020  1.090
 KNV  C17  H11  single    0.970  0.020  1.090
 KNV  C18  H12  single    0.970  0.020  1.090
 KNV  C18  H13  single    0.970  0.020  1.090
 KNV  C03  H14  single    0.930  0.020  1.080
 KNV  C05  H15  single    0.930  0.020  1.080
 KNV  C07  H16  single    0.970  0.020  1.090
 KNV  C07  H17  single    0.970  0.020  1.090
 KNV  C07  H18  single    0.970  0.020  1.090
 KNV  C08  H19  single    0.970  0.020  1.090
 KNV  C08  H20  single    0.970  0.020  1.090
 KNV  C09  H21  single    0.970  0.020  1.090
 KNV  C09  H22  single    0.970  0.020  1.090
 KNV  C14  H23  single    0.930  0.020  1.080
 KNV  N02  H24  single    0.890  0.020  1.040
 KNV  N02  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
 KNV  C09  C11  C16  121.41  3.000
 KNV  C09  C11  C12  121.13  3.000
 KNV  C16  C11  C12  117.43  3.000
 KNV  F12  C12  C13  118.76  3.000
 KNV  F12  C12  C11  120.23  3.000
 KNV  C13  C12  C11  121.01  3.000
 KNV  F13  C13  C14  120.16  3.000
 KNV  F13  C13  C12  118.83  3.000
 KNV  C14  C13  C12  121.01  3.000
 KNV  C14  C15  C17  120.53  3.000
 KNV  C14  C15  C16  118.74  3.000
 KNV  C17  C15  C16  120.69  3.000
 KNV  H1   C16  C15  119.26  3.000
 KNV  H1   C16  C11  118.37  3.000
 KNV  C15  C16  C11  122.36  3.000
 KNV  H4   C21  H3   107.80  3.000
 KNV  H4   C21  H2   107.66  3.000
 KNV  H3   C21  H2   107.31  3.000
 KNV  H4   C21  N21  113.17  3.000
 KNV  H3   C21  N21  110.88  3.000
 KNV  H2   C21  N21  109.79  3.000
 KNV  H5   C22  N21  111.50  3.000
 KNV  H5   C22  C18  109.72  3.000
 KNV  N21  C22  C18  116.81  3.000
 KNV  H5   C22  C23  110.58  3.000
 KNV  C18  C22  C23  117.95  3.000
 KNV  N21  C22  C23   88.86  3.000
 KNV  H7   C23  H6   109.27  3.000
 KNV  H7   C23  C24  113.16  3.000
 KNV  H6   C23  C24  117.32  3.000
 KNV  H7   C23  C22  112.54  3.000
 KNV  H6   C23  C22  117.21  3.000
 KNV  C24  C23  C22   85.81  3.000
 KNV  H9   C24  H8   108.45  3.000
 KNV  H9   C24  N21  115.24  3.000
 KNV  H8   C24  N21  113.06  3.000
 KNV  H9   C24  C23  118.26  3.000
 KNV  H8   C24  C23  111.70  3.000
 KNV  N21  C24  C23   89.24  3.000
 KNV  H11  C17  H10  106.92  3.000
 KNV  H11  C17  C18  109.38  3.000
 KNV  H10  C17  C18  109.62  3.000
 KNV  H11  C17  C15  109.62  3.000
 KNV  H10  C17  C15  109.25  3.000
 KNV  C18  C17  C15  111.91  3.000
 KNV  H13  C18  H12  106.74  3.000
 KNV  H13  C18  C17  109.33  3.000
 KNV  H12  C18  C17  109.53  3.000
 KNV  H13  C18  C22  108.22  3.000
 KNV  H12  C18  C22  109.08  3.000
 KNV  C17  C18  C22  113.70  3.000
 KNV  N02  C02  N01  117.11  3.000
 KNV  N02  C02  C03  120.61  3.000
 KNV  N01  C02  C03  122.26  3.000
 KNV  H14  C03  C04  120.86  3.000
 KNV  H14  C03  C02  120.04  3.000
 KNV  C04  C03  C02  119.10  3.000
 KNV  C07  C04  C05  120.59  3.000
 KNV  C07  C04  C03  121.32  3.000
 KNV  C05  C04  C03  118.08  3.000
 KNV  H15  C05  C06  120.35  3.000
 KNV  H15  C05  C04  120.63  3.000
 KNV  C06  C05  C04  119.02  3.000
 KNV  N01  C06  C08  115.93  3.000
 KNV  N01  C06  C05  122.81  3.000
 KNV  C08  C06  C05  121.25  3.000
 KNV  H20  C08  H19  107.11  3.000
 KNV  H20  C08  C09  109.45  3.000
 KNV  H19  C08  C09  109.41  3.000
 KNV  H20  C08  C06  109.98  3.000
 KNV  H19  C08  C06  109.13  3.000
 KNV  C09  C08  C06  111.64  3.000
 KNV  H22  C09  H21  106.76  3.000
 KNV  H22  C09  C08  109.16  3.000
 KNV  H21  C09  C08  109.08  3.000
 KNV  H22  C09  C11  108.84  3.000
 KNV  H21  C09  C11  110.96  3.000
 KNV  C08  C09  C11  111.89  3.000
 KNV  H23  C14  C15  121.06  3.000
 KNV  H23  C14  C13  119.49  3.000
 KNV  C15  C14  C13  119.45  3.000
 KNV  C06  N01  C02  118.73  3.000
 KNV  H25  N02  H24  114.07  3.000
 KNV  H25  N02  C02  116.09  3.000
 KNV  H24  N02  C02  117.52  3.000
 KNV  C24  N21  C22   90.74  3.000
 KNV  C22  N21  C21  118.78  3.000
 KNV  C24  N21  C21  116.94  3.000
 KNV  H18  C07  H17  108.32  3.000
 KNV  H18  C07  H16  107.82  3.000
 KNV  H17  C07  H16  107.01  3.000
 KNV  H18  C07  C04  111.78  3.000
 KNV  H17  C07  C04  111.17  3.000
 KNV  H16  C07  C04  110.55  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
 KNV  CONST_01  C14  C15  C16  C11     0.00   0.0  0
 KNV  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 KNV  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 KNV  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 KNV  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 KNV  CONST_06  C16  C11  C12  C13     0.00   0.0  0
 KNV  CONST_07  C05  C06  N01  C02     0.00   0.0  0
 KNV  CONST_08  C05  C04  C03  C02     0.00   0.0  0
 KNV  CONST_09  C06  N01  C02  C03     0.00   0.0  0
 KNV  CONST_10  C06  C05  C04  C03     0.00   0.0  0
 KNV  CONST_11  N01  C06  C05  C04     0.00   0.0  0
 KNV  CONST_12  N01  C02  C03  C04     0.00   0.0  0
 KNV  CONST_13  C17  C15  C16  C11   180.00   0.0  0
 KNV  CONST_14  F13  C13  C12  C11   180.00   0.0  0
 KNV  CONST_15  C17  C15  C14  C13   180.00   0.0  0
 KNV  CONST_16  C09  C11  C12  C13   180.00   0.0  0
 KNV  CONST_17  C09  C11  C16  C15   180.00   0.0  0
 KNV  CONST_18  F13  C13  C14  C15   180.00   0.0  0
 KNV  CONST_19  F12  C12  C11  C16   180.00   0.0  0
 KNV  CONST_20  C08  C06  N01  C02   180.00   0.0  0
 KNV  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 KNV  CONST_22  C08  C06  C05  C04   180.00   0.0  0
 KNV  CONST_23  N02  C02  C03  C04   180.00   0.0  0
 KNV  CONST_24  N02  C02  N01  C06   180.00   0.0  0
 KNV  CONST_25  C07  C04  C05  C06   180.00   0.0  0
 KNV  CONST_26  F12  C12  C13  C14   180.00   0.0  0
 KNV  CONST_27  H1   C16  C11  C12   180.00   0.0  0
 KNV  CONST_28  H23  C14  C13  C12   180.00   0.0  0
 KNV  CONST_29  H15  C05  C04  C03   180.00   0.0  0
 KNV  CONST_30  H14  C03  C04  C05   180.00   0.0  0
 KNV  Var_01    C23  C24  N21  C22    17.78  30.0  1
 KNV  Var_02    C06  C08  C09  C11   179.13  30.0  1
 KNV  Var_03    C08  C09  C11  C12   -82.77  30.0  2
 KNV  Var_04    C22  C18  C17  C15  -178.08  30.0  1
 KNV  Var_05    C18  C17  C15  C16    81.52  30.0  2
 KNV  Var_06    C09  C08  C06  C05   113.27  30.0  1
 KNV  Var_07    H2   C21  N21  C22   172.00  30.0  3
 KNV  Var_08    H16  C07  C04  C03   107.90  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
 KNV  chir_01  C22  N21  C18  C23  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
 KNV  plan-1  C11  0.020
 KNV  plan-1  C12  0.020
 KNV  plan-1  C13  0.020
 KNV  plan-1  C15  0.020
 KNV  plan-1  C16  0.020
 KNV  plan-1  C17  0.020
 KNV  plan-1  C09  0.020
 KNV  plan-1  C14  0.020
 KNV  plan-1  F12  0.020
 KNV  plan-1  F13  0.020
 KNV  plan-1  H1   0.020
 KNV  plan-1  H23  0.020
 KNV  plan-2  C02  0.020
 KNV  plan-2  C03  0.020
 KNV  plan-2  C04  0.020
 KNV  plan-2  C05  0.020
 KNV  plan-2  C06  0.020
 KNV  plan-2  C08  0.020
 KNV  plan-2  N01  0.020
 KNV  plan-2  N02  0.020
 KNV  plan-2  H14  0.020
 KNV  plan-2  H15  0.020
 KNV  plan-2  C07  0.020
 KNV  plan-3  C02  0.020
 KNV  plan-3  N02  0.020
 KNV  plan-3  H24  0.020
 KNV  plan-3  H25  0.020

