# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 06:43:31 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 6-[2-(2,3-difluoro-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)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
 KPJ  KPJ  6-[2-(2,3-difluoro-5-{2-[(2S)-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_KPJ
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
 KPJ  C11  C  CR6   0  -0.044  -0.5191  -0.9154   0.1495
 KPJ  C12  C  CR6   0   0.354  -0.3579  -2.2908   0.1427
 KPJ  C13  C  CR6   0   0.425   0.8573  -2.8638  -0.1838
 KPJ  C15  C  CR6   0   0.164   1.8180  -0.6974  -0.5167
 KPJ  C17  C  CH2   0  -0.515   3.0028   0.1797  -0.8062
 KPJ  C18  C  CH2   0  -0.401   3.6966   0.6287   0.4788
 KPJ  C03  C  CR16  0  -0.447  -6.5010   1.4332   0.3299
 KPJ  C04  C  CR6   0   0.205  -5.7454   2.0932  -0.6166
 KPJ  C05  C  CR16  0  -0.435  -4.5168   1.5325  -0.9869
 KPJ  C06  C  CR6   0   0.278  -4.1138   0.3492  -0.3958
 KPJ  C09  C  CH2   0  -0.503  -1.8449  -0.2896   0.4736
 KPJ  C22  C  CH2   0  -0.300   7.1398   0.7800   0.3407
 KPJ  C23  C  CH2   0  -0.455   7.0373   1.9852   1.2690
 KPJ  C24  C  CH2   0  -0.468   5.5415   2.0040   1.5574
 KPJ  C25  C  CH1   0  -0.059   4.9003   1.5298   0.2371
 KPJ  C02  C  CR6   0   0.439  -6.0126   0.2352   0.8810
 KPJ  C14  C  CR16  0  -0.487   1.9457  -2.0836  -0.5123
 KPJ  C16  C  CR16  0  -0.370   0.5866  -0.1392  -0.1876
 KPJ  F12  F  F     0  -0.307  -1.3879  -3.0932   0.4527
 KPJ  F13  F  F     0  -0.310   0.9641  -4.1989  -0.1763
 KPJ  N01  N  N     0  -0.483  -4.8467  -0.2876   0.5203
 KPJ  N21  N  NT    0  -0.421   5.9621   0.8464  -0.5220
 KPJ  H1   H  HCH2  0   0.246   3.7188  -0.3559  -1.4328
 KPJ  H2   H  HCH2  0   0.239   2.6786   1.0594  -1.3702
 KPJ  H3   H  HCH2  0   0.224   2.9787   1.1613   1.1117
 KPJ  H4   H  HCH2  0   0.220   4.0202  -0.2501   1.0467
 KPJ  H5   H  HNH2  0   0.387  -7.4528   0.0440   2.3055
 KPJ  H6   H  HNH2  0   0.379  -6.2492  -1.1374   2.3445
 KPJ  H7   H  HCR6  0   0.255  -7.4573   1.8281   0.6512
 KPJ  H8   H  HCR6  0   0.244  -3.8857   2.0205  -1.7191
 KPJ  H9   H  HCH2  0   0.251  -2.9622  -1.3078  -1.0713
 KPJ  H10  H  HCH2  0   0.250  -2.3239   0.2540  -1.5614
 KPJ  H11  H  HCH2  0   0.258  -2.3280  -0.8090   1.3026
 KPJ  H12  H  HCH2  0   0.257  -1.6765   0.7380   0.8022
 KPJ  H13  H  HCH2  0   0.231   8.0551   0.7581  -0.2533
 KPJ  H14  H  HCH2  0   0.220   7.1214  -0.1423   0.9329
 KPJ  H15  H  HCH2  0   0.232   7.6517   1.8923   2.1655
 KPJ  H16  H  HCH2  0   0.223   7.3448   2.8962   0.7495
 KPJ  H17  H  HCH2  0   0.222   5.3083   1.2992   2.3617
 KPJ  H18  H  HCH2  0   0.240   5.1667   2.9812   1.8624
 KPJ  H19  H  HCH1  0   0.217   4.5657   2.4066  -0.3329
 KPJ  H20  H  HCH3  0   0.194   6.5794   2.5035  -1.7462
 KPJ  H21  H  HCH3  0   0.229   6.9842   0.8877  -2.3453
 KPJ  H22  H  HCH3  0   0.230   5.3252   1.4561  -2.4161
 KPJ  H23  H  HCH3  0   0.253  -6.4629   3.2150  -2.2945
 KPJ  H24  H  HCH3  0   0.247  -7.1087   3.7561  -0.7458
 KPJ  H25  H  HCH3  0   0.250  -5.4461   4.1363  -1.2024
 KPJ  H26  H  HCR6  0   0.277   2.8857  -2.5590  -0.7653
 KPJ  H27  H  HCR6  0   0.251   0.4776   0.9396  -0.1878
 KPJ  C26  C  CH3   0  -0.533   6.2292   1.4616  -1.8059
 KPJ  C08  C  CH2   0  -0.488  -2.7927  -0.2819  -0.7340
 KPJ  C07  C  CH3   0  -0.726  -6.2200   3.3694  -1.2417
 KPJ  N02  N  NH2   0  -0.838  -6.7544  -0.4654   1.7900

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
 KPJ  C07  C04  single    1.498  0.020  1.498
 KPJ  C04  C05  aromatic  1.400  0.020  1.400
 KPJ  C04  C03  aromatic  1.379  0.020  1.379
 KPJ  C05  C06  aromatic  1.383  0.020  1.383
 KPJ  C03  C02  aromatic  1.406  0.020  1.406
 KPJ  C06  C08  single    1.503  0.020  1.503
 KPJ  C06  N01  aromatic  1.335  0.020  1.335
 KPJ  C02  N01  aromatic  1.328  0.020  1.328
 KPJ  C02  N02  single    1.367  0.020  1.367
 KPJ  F13  C13  single    1.339  0.020  1.339
 KPJ  F12  C12  single    1.342  0.020  1.342
 KPJ  C08  C09  single    1.535  0.020  1.535
 KPJ  C13  C12  aromatic  1.383  0.020  1.383
 KPJ  C13  C14  aromatic  1.379  0.020  1.379
 KPJ  C12  C11  aromatic  1.385  0.020  1.385
 KPJ  C14  C15  aromatic  1.392  0.020  1.392
 KPJ  C11  C09  single    1.501  0.020  1.501
 KPJ  C11  C16  aromatic  1.392  0.020  1.392
 KPJ  C15  C16  aromatic  1.391  0.020  1.391
 KPJ  C15  C17  single    1.502  0.020  1.502
 KPJ  C17  C18  single    1.528  0.020  1.528
 KPJ  C18  C25  single    1.523  0.020  1.523
 KPJ  C24  C25  single    1.542  0.020  1.542
 KPJ  C24  C23  single    1.523  0.020  1.523
 KPJ  C25  N21  single    1.473  0.020  1.473
 KPJ  C23  C22  single    1.525  0.020  1.525
 KPJ  N21  C22  single    1.461  0.020  1.461
 KPJ  N21  C26  single    1.449  0.020  1.449
 KPJ  C17  H1   single    0.970  0.020  1.090
 KPJ  C17  H2   single    0.970  0.020  1.090
 KPJ  C18  H3   single    0.970  0.020  1.090
 KPJ  C18  H4   single    0.970  0.020  1.090
 KPJ  N02  H5   single    0.890  0.020  1.040
 KPJ  N02  H6   single    0.890  0.020  1.040
 KPJ  C03  H7   single    0.930  0.020  1.080
 KPJ  C05  H8   single    0.930  0.020  1.080
 KPJ  C08  H9   single    0.970  0.020  1.090
 KPJ  C08  H10  single    0.970  0.020  1.090
 KPJ  C09  H11  single    0.970  0.020  1.090
 KPJ  C09  H12  single    0.970  0.020  1.090
 KPJ  C22  H13  single    0.970  0.020  1.090
 KPJ  C22  H14  single    0.970  0.020  1.090
 KPJ  C23  H15  single    0.970  0.020  1.090
 KPJ  C23  H16  single    0.970  0.020  1.090
 KPJ  C24  H17  single    0.970  0.020  1.090
 KPJ  C24  H18  single    0.970  0.020  1.090
 KPJ  C25  H19  single    0.970  0.020  1.090
 KPJ  C26  H20  single    0.970  0.020  1.090
 KPJ  C26  H21  single    0.970  0.020  1.090
 KPJ  C26  H22  single    0.970  0.020  1.090
 KPJ  C07  H23  single    0.970  0.020  1.090
 KPJ  C07  H24  single    0.970  0.020  1.090
 KPJ  C07  H25  single    0.970  0.020  1.090
 KPJ  C14  H26  single    0.930  0.020  1.080
 KPJ  C16  H27  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
 KPJ  C16  C11  C09  121.41  3.000
 KPJ  C16  C11  C12  117.39  3.000
 KPJ  C09  C11  C12  121.18  3.000
 KPJ  F12  C12  C13  118.77  3.000
 KPJ  C13  C12  C11  121.00  3.000
 KPJ  F12  C12  C11  120.22  3.000
 KPJ  F13  C13  C14  120.16  3.000
 KPJ  C14  C13  C12  121.04  3.000
 KPJ  F13  C13  C12  118.81  3.000
 KPJ  C16  C15  C14  118.68  3.000
 KPJ  C16  C15  C17  120.61  3.000
 KPJ  C14  C15  C17  120.64  3.000
 KPJ  H2   C17  H1   107.03  3.000
 KPJ  H2   C17  C18  109.38  3.000
 KPJ  H1   C17  C18  109.21  3.000
 KPJ  H2   C17  C15  109.58  3.000
 KPJ  H1   C17  C15  109.96  3.000
 KPJ  C18  C17  C15  111.57  3.000
 KPJ  H4   C18  H3   106.51  3.000
 KPJ  H4   C18  C25  108.88  3.000
 KPJ  H3   C18  C25  108.79  3.000
 KPJ  H4   C18  C17  109.54  3.000
 KPJ  H3   C18  C17  109.34  3.000
 KPJ  C25  C18  C17  113.53  3.000
 KPJ  H7   C03  C02  120.06  3.000
 KPJ  H7   C03  C04  120.84  3.000
 KPJ  C02  C03  C04  119.10  3.000
 KPJ  C07  C04  C05  120.57  3.000
 KPJ  C05  C04  C03  118.07  3.000
 KPJ  C07  C04  C03  121.36  3.000
 KPJ  H8   C05  C06  120.32  3.000
 KPJ  H8   C05  C04  120.65  3.000
 KPJ  C06  C05  C04  119.03  3.000
 KPJ  N01  C06  C08  115.90  3.000
 KPJ  N01  C06  C05  122.79  3.000
 KPJ  C08  C06  C05  121.30  3.000
 KPJ  H12  C09  H11  106.71  3.000
 KPJ  H12  C09  C08  109.10  3.000
 KPJ  H11  C09  C08  109.07  3.000
 KPJ  H12  C09  C11  108.72  3.000
 KPJ  H11  C09  C11  110.89  3.000
 KPJ  C08  C09  C11  112.18  3.000
 KPJ  H14  C22  H13  106.93  3.000
 KPJ  H14  C22  N21  110.09  3.000
 KPJ  H13  C22  N21  110.82  3.000
 KPJ  H14  C22  C23  109.57  3.000
 KPJ  H13  C22  C23  113.81  3.000
 KPJ  N21  C22  C23  105.62  3.000
 KPJ  H16  C23  H15  107.65  3.000
 KPJ  H16  C23  C24  110.85  3.000
 KPJ  H15  C23  C24  113.49  3.000
 KPJ  H16  C23  C22  110.52  3.000
 KPJ  H15  C23  C22  113.28  3.000
 KPJ  C24  C23  C22  101.01  3.000
 KPJ  H18  C24  H17  107.36  3.000
 KPJ  H18  C24  C25  111.85  3.000
 KPJ  H17  C24  C25  110.03  3.000
 KPJ  H18  C24  C23  113.68  3.000
 KPJ  H17  C24  C23  109.90  3.000
 KPJ  C25  C24  C23  104.02  3.000
 KPJ  H19  C25  N21  108.82  3.000
 KPJ  H19  C25  C24  109.00  3.000
 KPJ  N21  C25  C24  106.50  3.000
 KPJ  H19  C25  C18  108.30  3.000
 KPJ  N21  C25  C18  112.14  3.000
 KPJ  C24  C25  C18  112.00  3.000
 KPJ  N01  C02  C03  122.27  3.000
 KPJ  N01  C02  N02  117.10  3.000
 KPJ  C03  C02  N02  120.59  3.000
 KPJ  H26  C14  C15  121.06  3.000
 KPJ  H26  C14  C13  119.49  3.000
 KPJ  C15  C14  C13  119.45  3.000
 KPJ  H27  C16  C15  119.21  3.000
 KPJ  H27  C16  C11  118.35  3.000
 KPJ  C15  C16  C11  122.44  3.000
 KPJ  C02  N01  C06  118.73  3.000
 KPJ  C26  N21  C25  113.11  3.000
 KPJ  C26  N21  C22  113.20  3.000
 KPJ  C25  N21  C22  107.32  3.000
 KPJ  H22  C26  H21  107.12  3.000
 KPJ  H22  C26  H20  107.39  3.000
 KPJ  H21  C26  H20  107.72  3.000
 KPJ  H22  C26  N21  109.93  3.000
 KPJ  H21  C26  N21  110.02  3.000
 KPJ  H20  C26  N21  114.37  3.000
 KPJ  H10  C08  H9   107.07  3.000
 KPJ  H10  C08  C09  109.48  3.000
 KPJ  H9   C08  C09  109.49  3.000
 KPJ  H10  C08  C06  110.00  3.000
 KPJ  H9   C08  C06  109.11  3.000
 KPJ  C09  C08  C06  111.58  3.000
 KPJ  H25  C07  H24  108.25  3.000
 KPJ  H25  C07  H23  106.99  3.000
 KPJ  H24  C07  H23  107.94  3.000
 KPJ  H25  C07  C04  111.06  3.000
 KPJ  H24  C07  C04  111.78  3.000
 KPJ  H23  C07  C04  110.64  3.000
 KPJ  H6   N02  H5   113.82  3.000
 KPJ  H6   N02  C02  115.85  3.000
 KPJ  H5   N02  C02  117.25  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
 KPJ  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 KPJ  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 KPJ  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 KPJ  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 KPJ  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 KPJ  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 KPJ  CONST_07  C06  C05  C04  C03     0.00   0.0  0
 KPJ  CONST_08  C06  N01  C02  C03     0.00   0.0  0
 KPJ  CONST_09  N01  C06  C05  C04     0.00   0.0  0
 KPJ  CONST_10  N01  C02  C03  C04     0.00   0.0  0
 KPJ  CONST_11  C02  C03  C04  C05     0.00   0.0  0
 KPJ  CONST_12  C02  N01  C06  C05     0.00   0.0  0
 KPJ  CONST_13  F13  C13  C12  C11   180.00   0.0  0
 KPJ  CONST_14  C17  C15  C16  C11   180.00   0.0  0
 KPJ  CONST_15  C09  C11  C12  C13   180.00   0.0  0
 KPJ  CONST_16  C17  C15  C14  C13   180.00   0.0  0
 KPJ  CONST_17  F13  C13  C14  C15   180.00   0.0  0
 KPJ  CONST_18  C09  C11  C16  C15   180.00   0.0  0
 KPJ  CONST_19  C04  C03  C02  N02   180.00   0.0  0
 KPJ  CONST_20  C06  N01  C02  N02   180.00   0.0  0
 KPJ  CONST_21  C08  C06  C05  C04   180.00   0.0  0
 KPJ  CONST_22  C07  C04  C05  C06   180.00   0.0  0
 KPJ  CONST_23  C02  N01  C06  C08   180.00   0.0  0
 KPJ  CONST_24  C07  C04  C03  C02   180.00   0.0  0
 KPJ  CONST_25  F12  C12  C13  C14   180.00   0.0  0
 KPJ  CONST_26  F12  C12  C11  C16   180.00   0.0  0
 KPJ  CONST_27  H26  C14  C13  C12   180.00   0.0  0
 KPJ  CONST_28  H27  C16  C11  C12   180.00   0.0  0
 KPJ  CONST_29  H8   C05  C04  C03   180.00   0.0  0
 KPJ  CONST_30  H7   C03  C04  C05   180.00   0.0  0
 KPJ  Var_01    C25  C24  C23  C22   -34.75  30.0  1
 KPJ  Var_02    C25  N21  C22  C23   -28.37  30.0  1
 KPJ  Var_03    N21  C22  C23  C24    39.30  30.0  1
 KPJ  Var_04    C06  C08  C09  C11  -179.89  30.0  1
 KPJ  Var_05    C08  C09  C11  C12   -81.11  30.0  2
 KPJ  Var_06    C25  C18  C17  C15  -179.59  30.0  3
 KPJ  Var_07    C14  C15  C17  C18   -94.36  30.0  1
 KPJ  Var_08    C09  C08  C06  C05   114.49  30.0  2
 KPJ  Var_09    H23  C07  C04  C03  -111.20  30.0  2
 KPJ  Var_10    H20  C26  N21  C22   -60.84  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
 KPJ  chir_01  C25  C18  C24  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
 KPJ  plan-1  C11  0.020
 KPJ  plan-1  C12  0.020
 KPJ  plan-1  C13  0.020
 KPJ  plan-1  C15  0.020
 KPJ  plan-1  C17  0.020
 KPJ  plan-1  C09  0.020
 KPJ  plan-1  C14  0.020
 KPJ  plan-1  C16  0.020
 KPJ  plan-1  F12  0.020
 KPJ  plan-1  F13  0.020
 KPJ  plan-1  H26  0.020
 KPJ  plan-1  H27  0.020
 KPJ  plan-2  C03  0.020
 KPJ  plan-2  C04  0.020
 KPJ  plan-2  C05  0.020
 KPJ  plan-2  C06  0.020
 KPJ  plan-2  C02  0.020
 KPJ  plan-2  N01  0.020
 KPJ  plan-2  H7   0.020
 KPJ  plan-2  H8   0.020
 KPJ  plan-2  C08  0.020
 KPJ  plan-2  C07  0.020
 KPJ  plan-2  N02  0.020
 KPJ  plan-3  C02  0.020
 KPJ  plan-3  H5   0.020
 KPJ  plan-3  H6   0.020
 KPJ  plan-3  N02  0.020

