# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 20:32:30 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-(2-{5-[3-(dimethylamino)propyl]-2,3-difluorophenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCc1cc(F)c(F)c(CCc2cc(C)cc(N)n2)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
 KL1  KL1  6-(2-{5-[3-(dimethylamino)propyl]-2,3-difluorophenyl}ethyl)-4-methylpyridin-2-amine  ligand  49  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_KL1
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
 KL1  C11  C  CR6   0  -0.046   0.0383  -0.8197   0.0081
 KL1  C13  C  CR6   0   0.157   2.3246  -0.5947  -0.8108
 KL1  C14  C  CR16  0  -0.483   2.4725  -1.9786  -0.7731
 KL1  C15  C  CR6   0   0.425   1.4171  -2.7613  -0.3562
 KL1  C16  C  CR6   0   0.356   0.2167  -2.1927   0.0282
 KL1  C02  C  CR6   0   0.439  -5.4145   0.2520   1.0719
 KL1  C05  C  CR16  0  -0.439  -4.0915   1.5309  -0.9326
 KL1  C06  C  CR6   0   0.279  -3.6032   0.3873  -0.3245
 KL1  C08  C  CH2   0  -0.488  -2.2918  -0.2164  -0.7392
 KL1  C17  C  CH2   0  -0.509   3.4804   0.2846  -1.1955
 KL1  C18  C  CH2   0  -0.440   4.2750   0.7388   0.0313
 KL1  C03  C  CR16  0  -0.444  -5.9868   1.4038   0.5068
 KL1  C04  C  CR6   0   0.204  -5.3185   2.0544  -0.5114
 KL1  C09  C  CH2   0  -0.504  -1.2711  -0.2026   0.4047
 KL1  C12  C  CR16  0  -0.369   1.1106  -0.0403  -0.4185
 KL1  C19  C  CH2   0  -0.255   5.4862   1.5694  -0.3667
 KL1  C21  C  CH3   0  -0.526   6.8394   1.1243   1.5785
 KL1  C22  C  CH3   0  -0.521   7.1845   3.1002   0.3022
 KL1  F15  F  F     0  -0.310   1.5420  -4.0941  -0.3152
 KL1  F16  F  F     0  -0.307  -0.7802  -2.9984   0.4241
 KL1  N01  N  N     0  -0.483  -4.2514  -0.2396   0.6570
 KL1  N02  N  NH2   0  -0.838  -6.0212  -0.3852   2.1171
 KL1  N20  N  NT    0  -0.407   6.2059   2.1361   0.7598
 KL1  H1   H  HCR6  0   0.278   3.4004  -2.4499  -1.0739
 KL1  H2   H  HCR6  0   0.244  -3.5259   2.0139  -1.7195
 KL1  H3   H  HCH3  0   0.255  -6.5068   2.9854  -2.0272
 KL1  H4   H  HCH3  0   0.247  -6.5404   3.8281  -0.4848
 KL1  H5   H  HCH3  0   0.247  -5.1182   3.9380  -1.5295
 KL1  H6   H  HCH2  0   0.251  -2.4646  -1.2463  -1.0632
 KL1  H7   H  HCH2  0   0.251  -1.8880   0.3239  -1.5973
 KL1  H8   H  HCH2  0   0.245   4.1420  -0.2541  -1.8790
 KL1  H9   H  HCH2  0   0.245   3.1152   1.1622  -1.7355
 KL1  H10  H  HCH2  0   0.228   3.6274   1.3317   0.6839
 KL1  H11  H  HCH2  0   0.234   4.5762  -0.1431   0.6023
 KL1  H12  H  HCR6  0   0.254  -6.9394   1.7715   0.8697
 KL1  H13  H  HCH2  0   0.259  -1.6957  -0.7089   1.2727
 KL1  H14  H  HCH2  0   0.257  -1.0901   0.8315   0.7055
 KL1  H15  H  HCR6  0   0.252   0.9905   1.0373  -0.4339
 KL1  H16  H  HCH2  0   0.185   6.1520   0.9606  -1.0057
 KL1  H17  H  HCH2  0   0.226   5.1429   2.4017  -0.9890
 KL1  H18  H  HCH3  0   0.189   7.5513   0.4976   1.0170
 KL1  H19  H  HCH3  0   0.232   7.3886   1.6013   2.3915
 KL1  H20  H  HCH3  0   0.236   6.1013   0.4645   2.0337
 KL1  H21  H  HCH3  0   0.231   6.6960   3.8828  -0.2802
 KL1  H22  H  HCH3  0   0.231   7.6740   3.5723   1.1554
 KL1  H23  H  HCH3  0   0.189   7.9708   2.6564  -0.3297
 KL1  H24  H  HNH2  0   0.379  -5.7246  -1.3316   2.2913
 KL1  H25  H  HNH2  0   0.387  -7.0100  -0.2411   2.2358
 KL1  C07  C  CH3   0  -0.724  -5.8991   3.2708  -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
 KL1  C07  C04  single    1.499  0.020  1.499
 KL1  C04  C05  aromatic  1.399  0.020  1.399
 KL1  C04  C03  aromatic  1.381  0.020  1.381
 KL1  C05  C06  aromatic  1.384  0.020  1.384
 KL1  C03  C02  aromatic  1.405  0.020  1.405
 KL1  C06  C08  single    1.502  0.020  1.502
 KL1  C06  N01  aromatic  1.333  0.020  1.333
 KL1  F15  C15  single    1.339  0.020  1.339
 KL1  C02  N01  aromatic  1.329  0.020  1.329
 KL1  C02  N02  single    1.366  0.020  1.366
 KL1  F16  C16  single    1.342  0.020  1.342
 KL1  C08  C09  single    1.533  0.020  1.533
 KL1  C15  C16  aromatic  1.383  0.020  1.383
 KL1  C15  C14  aromatic  1.379  0.020  1.379
 KL1  C16  C11  aromatic  1.385  0.020  1.385
 KL1  C14  C13  aromatic  1.392  0.020  1.392
 KL1  C11  C09  single    1.501  0.020  1.501
 KL1  C11  C12  aromatic  1.393  0.020  1.393
 KL1  C13  C12  aromatic  1.391  0.020  1.391
 KL1  C13  C17  single    1.502  0.020  1.502
 KL1  C17  C18  single    1.531  0.020  1.531
 KL1  C18  C19  single    1.522  0.020  1.522
 KL1  C19  N20  single    1.452  0.020  1.452
 KL1  N20  C21  single    1.448  0.020  1.448
 KL1  N20  C22  single    1.448  0.020  1.448
 KL1  C14  H1   single    0.930  0.020  1.080
 KL1  C05  H2   single    0.930  0.020  1.080
 KL1  C07  H3   single    0.970  0.020  1.090
 KL1  C07  H4   single    0.970  0.020  1.090
 KL1  C07  H5   single    0.970  0.020  1.090
 KL1  C08  H6   single    0.970  0.020  1.090
 KL1  C08  H7   single    0.970  0.020  1.090
 KL1  C17  H8   single    0.970  0.020  1.090
 KL1  C17  H9   single    0.970  0.020  1.090
 KL1  C18  H10  single    0.970  0.020  1.090
 KL1  C18  H11  single    0.970  0.020  1.090
 KL1  C03  H12  single    0.930  0.020  1.080
 KL1  C09  H13  single    0.970  0.020  1.090
 KL1  C09  H14  single    0.970  0.020  1.090
 KL1  C12  H15  single    0.930  0.020  1.080
 KL1  C19  H16  single    0.970  0.020  1.090
 KL1  C19  H17  single    0.970  0.020  1.090
 KL1  C21  H18  single    0.970  0.020  1.090
 KL1  C21  H19  single    0.970  0.020  1.090
 KL1  C21  H20  single    0.970  0.020  1.090
 KL1  C22  H21  single    0.970  0.020  1.090
 KL1  C22  H22  single    0.970  0.020  1.090
 KL1  C22  H23  single    0.970  0.020  1.090
 KL1  N02  H24  single    0.890  0.020  1.040
 KL1  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
 KL1  C12  C11  C09  121.50  3.000
 KL1  C12  C11  C16  117.40  3.000
 KL1  C09  C11  C16  121.08  3.000
 KL1  C12  C13  C17  120.69  3.000
 KL1  C17  C13  C14  120.46  3.000
 KL1  C12  C13  C14  118.77  3.000
 KL1  H1   C14  C15  119.52  3.000
 KL1  H1   C14  C13  121.06  3.000
 KL1  C15  C14  C13  119.42  3.000
 KL1  F15  C15  C16  118.79  3.000
 KL1  C16  C15  C14  121.01  3.000
 KL1  F15  C15  C14  120.19  3.000
 KL1  F16  C16  C15  118.69  3.000
 KL1  C15  C16  C11  121.04  3.000
 KL1  F16  C16  C11  120.27  3.000
 KL1  N02  C02  N01  117.06  3.000
 KL1  N02  C02  C03  120.61  3.000
 KL1  N01  C02  C03  122.29  3.000
 KL1  H2   C05  C04  120.67  3.000
 KL1  H2   C05  C06  120.23  3.000
 KL1  C04  C05  C06  119.10  3.000
 KL1  N01  C06  C08  116.03  3.000
 KL1  N01  C06  C05  122.72  3.000
 KL1  C08  C06  C05  121.25  3.000
 KL1  H7   C08  H6   106.96  3.000
 KL1  H7   C08  C09  109.62  3.000
 KL1  H6   C08  C09  109.56  3.000
 KL1  H7   C08  C06  109.94  3.000
 KL1  H6   C08  C06  108.81  3.000
 KL1  C09  C08  C06  111.82  3.000
 KL1  H9   C17  H8   106.79  3.000
 KL1  H9   C17  C18  109.33  3.000
 KL1  H8   C17  C18  109.47  3.000
 KL1  H9   C17  C13  109.84  3.000
 KL1  H8   C17  C13  109.71  3.000
 KL1  C18  C17  C13  111.58  3.000
 KL1  H11  C18  H10  106.78  3.000
 KL1  H11  C18  C19  110.96  3.000
 KL1  H10  C18  C19  109.36  3.000
 KL1  H11  C18  C17  108.81  3.000
 KL1  H10  C18  C17  109.37  3.000
 KL1  C19  C18  C17  111.44  3.000
 KL1  H12  C03  C04  120.83  3.000
 KL1  H12  C03  C02  120.11  3.000
 KL1  C04  C03  C02  119.06  3.000
 KL1  C03  C04  C07  121.14  3.000
 KL1  C03  C04  C05  118.05  3.000
 KL1  C07  C04  C05  120.80  3.000
 KL1  H14  C09  H13  106.55  3.000
 KL1  H14  C09  C08  108.93  3.000
 KL1  H13  C09  C08  109.29  3.000
 KL1  H14  C09  C11  108.51  3.000
 KL1  H13  C09  C11  111.03  3.000
 KL1  C08  C09  C11  112.33  3.000
 KL1  H15  C12  C13  119.26  3.000
 KL1  H15  C12  C11  118.38  3.000
 KL1  C13  C12  C11  122.36  3.000
 KL1  H17  C19  H16  106.20  3.000
 KL1  H17  C19  N20  107.44  3.000
 KL1  H16  C19  N20  111.40  3.000
 KL1  H17  C19  C18  108.31  3.000
 KL1  H16  C19  C18  109.27  3.000
 KL1  N20  C19  C18  113.87  3.000
 KL1  H20  C21  H19  107.13  3.000
 KL1  H20  C21  H18  107.82  3.000
 KL1  H19  C21  H18  107.64  3.000
 KL1  H20  C21  N20  111.29  3.000
 KL1  H19  C21  N20  109.64  3.000
 KL1  H18  C21  N20  113.08  3.000
 KL1  H23  C22  H22  107.62  3.000
 KL1  H23  C22  H21  107.59  3.000
 KL1  H22  C22  H21  107.93  3.000
 KL1  H23  C22  N20  113.29  3.000
 KL1  H22  C22  N20  110.13  3.000
 KL1  H21  C22  N20  110.10  3.000
 KL1  C06  N01  C02  118.79  3.000
 KL1  H25  N02  H24  113.81  3.000
 KL1  H25  N02  C02  117.38  3.000
 KL1  H24  N02  C02  116.10  3.000
 KL1  C22  N20  C21  110.39  3.000
 KL1  C22  N20  C19  110.47  3.000
 KL1  C21  N20  C19  112.51  3.000
 KL1  H5   C07  H4   108.51  3.000
 KL1  H5   C07  H3   107.22  3.000
 KL1  H4   C07  H3   107.42  3.000
 KL1  H5   C07  C04  111.41  3.000
 KL1  H4   C07  C04  111.73  3.000
 KL1  H3   C07  C04  110.36  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
 KL1  CONST_01  C14  C15  C16  C11    0.00   0.0  0
 KL1  CONST_02  C14  C13  C12  C11    0.00   0.0  0
 KL1  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 KL1  CONST_04  C16  C11  C12  C13    0.00   0.0  0
 KL1  CONST_05  C12  C11  C16  C15    0.00   0.0  0
 KL1  CONST_06  C12  C13  C14  C15    0.00   0.0  0
 KL1  CONST_07  C05  C04  C03  C02    0.00   0.0  0
 KL1  CONST_08  C05  C06  N01  C02    0.00   0.0  0
 KL1  CONST_09  C03  C04  C05  C06    0.00   0.0  0
 KL1  CONST_10  C03  C02  N01  C06    0.00   0.0  0
 KL1  CONST_11  N01  C06  C05  C04    0.00   0.0  0
 KL1  CONST_12  N01  C02  C03  C04    0.00   0.0  0
 KL1  CONST_13  F15  C15  C16  C11  180.00   0.0  0
 KL1  CONST_14  C17  C13  C12  C11  180.00   0.0  0
 KL1  CONST_15  F15  C15  C14  C13  180.00   0.0  0
 KL1  CONST_16  C09  C11  C12  C13  180.00   0.0  0
 KL1  CONST_17  F16  C16  C15  C14  180.00   0.0  0
 KL1  CONST_18  C09  C11  C16  C15  180.00   0.0  0
 KL1  CONST_19  C17  C13  C14  C15  180.00   0.0  0
 KL1  CONST_20  C07  C04  C03  C02  180.00   0.0  0
 KL1  CONST_21  C08  C06  N01  C02  180.00   0.0  0
 KL1  CONST_22  C07  C04  C05  C06  180.00   0.0  0
 KL1  CONST_23  N02  C02  N01  C06  180.00   0.0  0
 KL1  CONST_24  C04  C05  C06  C08  180.00   0.0  0
 KL1  CONST_25  N02  C02  C03  C04  180.00   0.0  0
 KL1  CONST_26  F16  C16  C11  C12  180.00   0.0  0
 KL1  CONST_27  H15  C12  C13  C14  180.00   0.0  0
 KL1  CONST_28  H1   C14  C15  C16  180.00   0.0  0
 KL1  CONST_29  H12  C03  C04  C05  180.00   0.0  0
 KL1  CONST_30  H2   C05  C04  C03  180.00   0.0  0
 KL1  Var_01    C06  C08  C09  C11  179.26  30.0  1
 KL1  Var_02    C18  C17  C13  C14  -92.26  30.0  2
 KL1  Var_03    C08  C09  C11  C16  -82.12  30.0  2
 KL1  Var_04    C09  C08  C06  C05  117.16  30.0  2
 KL1  Var_05    H3   C07  C04  C05   88.20  30.0  2
 KL1  Var_06    C19  C18  C17  C13  177.05  30.0  3
 KL1  Var_07    N20  C19  C18  C17  174.39  30.0  3
 KL1  Var_08    C21  N20  C19  C18   66.56  30.0  3
 KL1  Var_09    H18  C21  N20  C19   58.25  30.0  3
 KL1  Var_10    H21  C22  N20  C19   57.22  30.0  3

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
 KL1  plan-1  C11  0.020
 KL1  plan-1  C13  0.020
 KL1  plan-1  C14  0.020
 KL1  plan-1  C15  0.020
 KL1  plan-1  C16  0.020
 KL1  plan-1  C17  0.020
 KL1  plan-1  C09  0.020
 KL1  plan-1  C12  0.020
 KL1  plan-1  F15  0.020
 KL1  plan-1  F16  0.020
 KL1  plan-1  H1   0.020
 KL1  plan-1  H15  0.020
 KL1  plan-2  C02  0.020
 KL1  plan-2  C05  0.020
 KL1  plan-2  C06  0.020
 KL1  plan-2  C08  0.020
 KL1  plan-2  C03  0.020
 KL1  plan-2  C04  0.020
 KL1  plan-2  N01  0.020
 KL1  plan-2  N02  0.020
 KL1  plan-2  H2   0.020
 KL1  plan-2  H12  0.020
 KL1  plan-2  C07  0.020
 KL1  plan-3  C02  0.020
 KL1  plan-3  N02  0.020
 KL1  plan-3  H24  0.020
 KL1  plan-3  H25  0.020

