# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:02:57 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-[2-(3-fluoro-5-{2-[(2S)-pyrrolidin-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]3CCCN3)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
 KL4  KL4  6-[2-(3-fluoro-5-{2-[(2S)-pyrrolidin-2-yl]ethyl}phenyl)ethyl]-4-methylpyridin-2-amine  ligand  50  24  .  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_KL4
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
 KL4  C02  C  CR6   0   0.441   5.6799  -0.1483  -0.3494
 KL4  C03  C  CR16  0  -0.448   5.9249  -1.5171  -0.1375
 KL4  C04  C  CR6   0   0.205   4.8564  -2.3869  -0.0711
 KL4  C05  C  CR16  0  -0.433   3.5677  -1.8597  -0.2182
 KL4  C06  C  CR6   0   0.276   3.4173  -0.5000  -0.4186
 KL4  C07  C  CH3   0  -0.727   5.0571  -3.8557   0.1430
 KL4  C08  C  CH2   0  -0.489   2.0542   0.1205  -0.5331
 KL4  C09  C  CH2   0  -0.512   1.7121   0.9620   0.7049
 KL4  C11  C  CR6   0   0.172   0.3414   1.5687   0.6023
 KL4  C12  C  CR16  0  -0.497   0.1770   2.8856   0.1865
 KL4  C13  C  CR6   0   0.561  -1.1045   3.3902   0.0709
 KL4  C14  C  CR16  0  -0.490  -2.2299   2.6428   0.3482
 KL4  C15  C  CR6   0   0.175  -2.0727   1.3216   0.7643
 KL4  C16  C  CR16  0  -0.392  -0.7880   0.8034   0.8861
 KL4  C17  C  CH2   0  -0.506  -3.2758   0.4607   1.0256
 KL4  C18  C  CH2   0  -0.437  -3.8799  -0.0739  -0.2745
 KL4  C22  C  CH1   0  -0.093  -5.0877  -0.9673  -0.0595
 KL4  C23  C  CH2   0  -0.442  -5.7350  -1.4680  -1.3607
 KL4  C24  C  CH2   0  -0.472  -6.4247  -2.7824  -0.9579
 KL4  C25  C  CH2   0  -0.317  -5.8952  -3.0643   0.4692
 KL4  F13  F  F     0  -0.320  -1.2583   4.6667  -0.3258
 KL4  N01  N  N     0  -0.484   4.4523   0.3407  -0.4831
 KL4  N02  N  NH2   0  -0.839   6.7161   0.7325  -0.4716
 KL4  N21  N  NH1   0  -0.584  -4.7654  -2.1712   0.7013
 KL4  H1   H  HCR6  0   0.255   6.9413  -1.8753  -0.0254
 KL4  H2   H  HCR6  0   0.244   2.6994  -2.5047  -0.1693
 KL4  H3   H  HCH3  0   0.253   4.7684  -4.4172  -0.7473
 KL4  H4   H  HCH3  0   0.247   6.0951  -4.0936   0.3687
 KL4  H5   H  HCH3  0   0.250   4.4374  -4.2196   0.9632
 KL4  H6   H  HCH2  0   0.249   2.0159   0.7577  -1.4209
 KL4  H7   H  HCH2  0   0.248   1.3007  -0.6589  -0.6629
 KL4  H8   H  HCH2  0   0.252   1.7673   0.3268   1.5929
 KL4  H9   H  HCH2  0   0.252   2.4647   1.7436   0.8233
 KL4  H10  H  HCR6  0   0.266   1.0333   3.5108  -0.0362
 KL4  H11  H  HCR6  0   0.266  -3.2156   3.0807   0.2439
 KL4  H12  H  HCR6  0   0.241  -0.6616  -0.2235   1.2125
 KL4  H13  H  HCH2  0   0.246  -2.9964  -0.3752   1.6694
 KL4  H14  H  HCH2  0   0.241  -4.0356   1.0337   1.5643
 KL4  H15  H  HCH2  0   0.238  -4.1732   0.7663  -0.9108
 KL4  H16  H  HCH2  0   0.224  -3.1181  -0.6286  -0.8343
 KL4  H17  H  HCH1  0   0.219  -5.8395  -0.4087   0.5139
 KL4  H18  H  HCH2  0   0.231  -6.4224  -0.7390  -1.7921
 KL4  H19  H  HCH2  0   0.219  -4.9547  -1.6516  -2.1051
 KL4  H20  H  HCH2  0   0.230  -7.5118  -2.6930  -0.9632
 KL4  H21  H  HCH2  0   0.230  -6.1699  -3.5894  -1.6456
 KL4  H22  H  HCH2  0   0.220  -6.6752  -2.8488   1.2043
 KL4  H23  H  HCH2  0   0.234  -5.5960  -4.1019   0.6181
 KL4  H24  H  HNH2  0   0.379   6.4876   1.7047  -0.3445
 KL4  H25  H  HNH2  0   0.388   7.6034   0.4651  -0.0797
 KL4  H26  H  HNH1  0   0.333  -3.9380  -2.5888   0.2851

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
 KL4  C07  C04  single    1.498  0.020  1.498
 KL4  C04  C05  aromatic  1.400  0.020  1.400
 KL4  C04  C03  aromatic  1.379  0.020  1.379
 KL4  C05  C06  aromatic  1.383  0.020  1.383
 KL4  C03  C02  aromatic  1.407  0.020  1.407
 KL4  C06  N01  aromatic  1.335  0.020  1.335
 KL4  C06  C08  single    1.502  0.020  1.502
 KL4  C02  N01  aromatic  1.328  0.020  1.328
 KL4  C02  N02  single    1.365  0.020  1.365
 KL4  F13  C13  single    1.346  0.020  1.346
 KL4  C08  C09  single    1.536  0.020  1.536
 KL4  C13  C12  aromatic  1.382  0.020  1.382
 KL4  C13  C14  aromatic  1.379  0.020  1.379
 KL4  C12  C11  aromatic  1.391  0.020  1.391
 KL4  C14  C15  aromatic  1.394  0.020  1.394
 KL4  C11  C09  single    1.502  0.020  1.502
 KL4  C11  C16  aromatic  1.394  0.020  1.394
 KL4  C15  C16  aromatic  1.391  0.020  1.391
 KL4  C15  C17  single    1.502  0.020  1.502
 KL4  C17  C18  single    1.530  0.020  1.530
 KL4  C18  C22  single    1.518  0.020  1.518
 KL4  C23  C24  single    1.538  0.020  1.538
 KL4  C23  C22  single    1.537  0.020  1.537
 KL4  C24  C25  single    1.548  0.020  1.548
 KL4  C22  N21  single    1.460  0.020  1.460
 KL4  N21  C25  single    1.459  0.020  1.459
 KL4  C03  H1   single    0.930  0.020  1.080
 KL4  C05  H2   single    0.930  0.020  1.080
 KL4  C07  H3   single    0.970  0.020  1.090
 KL4  C07  H4   single    0.970  0.020  1.090
 KL4  C07  H5   single    0.970  0.020  1.090
 KL4  C08  H6   single    0.970  0.020  1.090
 KL4  C08  H7   single    0.970  0.020  1.090
 KL4  C09  H8   single    0.970  0.020  1.090
 KL4  C09  H9   single    0.970  0.020  1.090
 KL4  C12  H10  single    0.930  0.020  1.080
 KL4  C14  H11  single    0.930  0.020  1.080
 KL4  C16  H12  single    0.930  0.020  1.080
 KL4  C17  H13  single    0.970  0.020  1.090
 KL4  C17  H14  single    0.970  0.020  1.090
 KL4  C18  H15  single    0.970  0.020  1.090
 KL4  C18  H16  single    0.970  0.020  1.090
 KL4  C22  H17  single    0.970  0.020  1.090
 KL4  C23  H18  single    0.970  0.020  1.090
 KL4  C23  H19  single    0.970  0.020  1.090
 KL4  C24  H20  single    0.970  0.020  1.090
 KL4  C24  H21  single    0.970  0.020  1.090
 KL4  C25  H22  single    0.970  0.020  1.090
 KL4  C25  H23  single    0.970  0.020  1.090
 KL4  N02  H24  single    0.890  0.020  1.040
 KL4  N02  H25  single    0.890  0.020  1.040
 KL4  N21  H26  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
 KL4  N02  C02  N01  117.06  3.000
 KL4  N02  C02  C03  120.60  3.000
 KL4  N01  C02  C03  122.31  3.000
 KL4  H1   C03  C04  120.88  3.000
 KL4  H1   C03  C02  120.04  3.000
 KL4  C04  C03  C02  119.08  3.000
 KL4  C07  C04  C05  120.50  3.000
 KL4  C05  C04  C03  118.06  3.000
 KL4  C07  C04  C03  121.43  3.000
 KL4  H2   C05  C06  120.34  3.000
 KL4  H2   C05  C04  120.60  3.000
 KL4  C06  C05  C04  119.06  3.000
 KL4  N01  C06  C08  116.08  3.000
 KL4  C08  C06  C05  121.07  3.000
 KL4  N01  C06  C05  122.82  3.000
 KL4  H5   C07  H4   108.24  3.000
 KL4  H5   C07  H3   106.95  3.000
 KL4  H4   C07  H3   108.00  3.000
 KL4  H5   C07  C04  111.01  3.000
 KL4  H4   C07  C04  111.81  3.000
 KL4  H3   C07  C04  110.64  3.000
 KL4  H7   C08  H6   107.18  3.000
 KL4  H7   C08  C09  109.46  3.000
 KL4  H6   C08  C09  109.12  3.000
 KL4  H7   C08  C06  109.90  3.000
 KL4  H6   C08  C06  109.54  3.000
 KL4  C09  C08  C06  111.54  3.000
 KL4  H9   C09  H8   107.05  3.000
 KL4  H9   C09  C11  110.32  3.000
 KL4  H8   C09  C11  109.65  3.000
 KL4  H9   C09  C08  109.04  3.000
 KL4  H8   C09  C08  108.98  3.000
 KL4  C11  C09  C08  111.68  3.000
 KL4  C16  C11  C12  119.02  3.000
 KL4  C16  C11  C09  120.25  3.000
 KL4  C12  C11  C09  120.70  3.000
 KL4  H10  C12  C13  120.33  3.000
 KL4  H10  C12  C11  120.96  3.000
 KL4  C13  C12  C11  118.70  3.000
 KL4  F13  C13  C14  118.70  3.000
 KL4  C14  C13  C12  122.81  3.000
 KL4  F13  C13  C12  118.49  3.000
 KL4  H11  C14  C15  120.95  3.000
 KL4  H11  C14  C13  120.26  3.000
 KL4  C15  C14  C13  118.79  3.000
 KL4  C17  C15  C16  120.74  3.000
 KL4  C17  C15  C14  120.31  3.000
 KL4  C16  C15  C14  118.91  3.000
 KL4  H12  C16  C15  119.12  3.000
 KL4  H12  C16  C11  119.12  3.000
 KL4  C15  C16  C11  121.75  3.000
 KL4  H14  C17  H13  106.77  3.000
 KL4  H14  C17  C18  109.11  3.000
 KL4  H13  C17  C18  109.55  3.000
 KL4  H14  C17  C15  109.99  3.000
 KL4  H13  C17  C15  109.66  3.000
 KL4  C18  C17  C15  111.63  3.000
 KL4  H16  C18  H15  106.14  3.000
 KL4  H16  C18  C22  109.12  3.000
 KL4  H15  C18  C22  108.73  3.000
 KL4  H16  C18  C17  109.66  3.000
 KL4  H15  C18  C17  109.38  3.000
 KL4  C22  C18  C17  113.55  3.000
 KL4  H17  C22  N21  107.37  3.000
 KL4  H17  C22  C23  108.62  3.000
 KL4  N21  C22  C23  105.39  3.000
 KL4  H17  C22  C18  108.62  3.000
 KL4  N21  C22  C18  112.55  3.000
 KL4  C23  C22  C18  114.02  3.000
 KL4  H19  C23  H18  107.01  3.000
 KL4  H19  C23  C24  110.78  3.000
 KL4  H18  C23  C24  113.09  3.000
 KL4  H19  C23  C22  109.29  3.000
 KL4  H18  C23  C22  112.48  3.000
 KL4  C24  C23  C22  104.21  3.000
 KL4  H21  C24  H20  106.88  3.000
 KL4  H21  C24  C25  111.52  3.000
 KL4  H20  C24  C25  111.12  3.000
 KL4  H21  C24  C23  111.25  3.000
 KL4  H20  C24  C23  112.06  3.000
 KL4  C25  C24  C23  104.11  3.000
 KL4  H23  C25  H22  106.96  3.000
 KL4  H23  C25  N21  110.39  3.000
 KL4  H22  C25  N21  108.96  3.000
 KL4  H23  C25  C24  113.15  3.000
 KL4  H22  C25  C24  109.87  3.000
 KL4  N21  C25  C24  107.46  3.000
 KL4  C06  N01  C02  118.67  3.000
 KL4  H25  N02  H24  114.05  3.000
 KL4  H25  N02  C02  117.57  3.000
 KL4  H24  N02  C02  116.06  3.000
 KL4  H26  N21  C25  108.30  3.000
 KL4  H26  N21  C22  107.77  3.000
 KL4  C25  N21  C22  104.53  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
 KL4  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 KL4  CONST_02  C05  C06  N01  C02     0.00   0.0  0
 KL4  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 KL4  CONST_04  C06  N01  C02  C03     0.00   0.0  0
 KL4  CONST_05  N01  C06  C05  C04     0.00   0.0  0
 KL4  CONST_06  N01  C02  C03  C04     0.00   0.0  0
 KL4  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 KL4  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 KL4  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 KL4  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 KL4  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 KL4  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 KL4  CONST_13  C07  C04  C03  C02   180.00   0.0  0
 KL4  CONST_14  C08  C06  N01  C02   180.00   0.0  0
 KL4  CONST_15  C08  C06  C05  C04   180.00   0.0  0
 KL4  CONST_16  N02  C02  C03  C04   180.00   0.0  0
 KL4  CONST_17  C07  C04  C05  C06   180.00   0.0  0
 KL4  CONST_18  N02  C02  N01  C06   180.00   0.0  0
 KL4  CONST_19  C13  C12  C11  C09   180.00   0.0  0
 KL4  CONST_20  C15  C16  C11  C09   180.00   0.0  0
 KL4  CONST_21  F13  C13  C12  C11   180.00   0.0  0
 KL4  CONST_22  C17  C15  C16  C11   180.00   0.0  0
 KL4  CONST_23  C17  C15  C14  C13   180.00   0.0  0
 KL4  CONST_24  F13  C13  C14  C15   180.00   0.0  0
 KL4  CONST_25  H2   C05  C04  C03   180.00   0.0  0
 KL4  CONST_26  H1   C03  C04  C05   180.00   0.0  0
 KL4  CONST_27  H11  C14  C13  C12   180.00   0.0  0
 KL4  CONST_28  H12  C16  C11  C12   180.00   0.0  0
 KL4  CONST_29  H10  C12  C13  C14   180.00   0.0  0
 KL4  Var_01    C25  C24  C23  C22   -10.34  30.0  1
 KL4  Var_02    C24  C25  N21  C22    32.21  30.0  1
 KL4  Var_03    N21  C25  C24  C23   -12.85  30.0  1
 KL4  Var_04    C09  C08  C06  C05   108.81  30.0  2
 KL4  Var_05    C11  C09  C08  C06  -179.20  30.0  3
 KL4  Var_06    C12  C11  C09  C08   -98.31  30.0  3
 KL4  Var_07    C18  C17  C15  C14    79.01  30.0  2
 KL4  Var_08    C22  C18  C17  C15   179.14  30.0  3
 KL4  Var_09    H3   C07  C04  C03  -112.55  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
 KL4  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
 KL4  plan-1  C02  0.020
 KL4  plan-1  C03  0.020
 KL4  plan-1  C04  0.020
 KL4  plan-1  C05  0.020
 KL4  plan-1  C06  0.020
 KL4  plan-1  C07  0.020
 KL4  plan-1  C08  0.020
 KL4  plan-1  N01  0.020
 KL4  plan-1  N02  0.020
 KL4  plan-1  H1   0.020
 KL4  plan-1  H2   0.020
 KL4  plan-2  C09  0.020
 KL4  plan-2  C11  0.020
 KL4  plan-2  C12  0.020
 KL4  plan-2  C13  0.020
 KL4  plan-2  C14  0.020
 KL4  plan-2  C15  0.020
 KL4  plan-2  C16  0.020
 KL4  plan-2  C17  0.020
 KL4  plan-2  F13  0.020
 KL4  plan-2  H10  0.020
 KL4  plan-2  H11  0.020
 KL4  plan-2  H12  0.020
 KL4  plan-3  C02  0.020
 KL4  plan-3  N02  0.020
 KL4  plan-3  H24  0.020
 KL4  plan-3  H25  0.020

