# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 18:15:54 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-(2-{3-[3-(dimethylamino)propyl]-2,6-difluorophenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCc1ccc(F)c(CCc2cc(C)cc(N)n2)c1F
#
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
 KL7  KL7  6-(2-{3-[3-(dimethylamino)propyl]-2,6-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_KL7
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
 KL7  C22  C  CH3   0  -0.526   6.7621  -0.7874  -1.6692
 KL7  C21  C  CH3   0  -0.520   7.1410  -2.7198  -0.3318
 KL7  C19  C  CH2   0  -0.254   5.4679  -1.1586   0.3305
 KL7  C18  C  CH2   0  -0.443   4.2531  -0.3305  -0.0620
 KL7  C17  C  CH2   0  -0.501   3.5057   0.1725   1.1755
 KL7  C16  C  CR6   0   0.522   1.1215   0.4998   0.4108
 KL7  C14  C  CR16  0  -0.298   2.4119   2.4279   0.8566
 KL7  C15  C  CR6   0  -0.070   2.3311   1.0400   0.8236
 KL7  C13  C  CR16  0  -0.410   1.3387   3.2299   0.4975
 KL7  C12  C  CR6   0   0.513   0.1687   2.6199   0.0966
 KL7  C11  C  CR6   0  -0.259   0.0125   1.2423   0.0294
 KL7  C02  C  CR6   0   0.442  -5.4560   0.0220  -0.7987
 KL7  C03  C  CR16  0  -0.447  -5.8764  -1.2821  -0.4813
 KL7  C04  C  CR6   0   0.206  -5.0660  -2.0756   0.3033
 KL7  C05  C  CR16  0  -0.435  -3.8510  -1.5405   0.7482
 KL7  C06  C  CR6   0   0.277  -3.5141  -0.2493   0.3859
 KL7  C09  C  CH2   0  -0.495  -1.2803   0.6005  -0.3855
 KL7  F12  F  F     0  -0.309  -0.8766   3.3923  -0.2436
 KL7  N01  N  N     0  -0.483  -4.2992   0.5171  -0.3737
 KL7  N02  N  NH2   0  -0.839  -6.2565   0.8531  -1.5279
 KL7  N20  N  NT    0  -0.407   6.1545  -1.7667  -0.7941
 KL7  H1   H  HCH3  0   0.189   7.4759  -0.1269  -1.1501
 KL7  H2   H  HCH3  0   0.233   7.3032  -1.2951  -2.4685
 KL7  H3   H  HCH3  0   0.235   6.0090  -0.1568  -2.1412
 KL7  H4   H  HCH3  0   0.231   6.6625  -3.4874   0.2784
 KL7  H5   H  HCH3  0   0.231   7.6130  -3.2141  -1.1822
 KL7  H6   H  HCH3  0   0.189   7.9396  -2.2631   0.2749
 KL7  H7   H  HCH2  0   0.185   6.1550  -0.5345   0.9314
 KL7  H8   H  HCH2  0   0.226   5.1355  -1.9665   0.9899
 KL7  H9   H  HCH2  0   0.234   4.5488   0.5329  -0.6633
 KL7  H10  H  HCH2  0   0.229   3.5884  -0.9360  -0.6835
 KL7  H11  H  HCH2  0   0.245   3.1860  -0.6777   1.7831
 KL7  H12  H  HCH2  0   0.248   4.1935   0.7518   1.7960
 KL7  H13  H  HCR6  0   0.268   3.3356   2.8933   1.1769
 KL7  H14  H  HCR6  0   0.278   1.4109   4.3086   0.5312
 KL7  H15  H  HCR6  0   0.255  -6.8253  -1.6512  -0.8514
 KL7  H16  H  HCR6  0   0.244  -3.1825  -2.1274   1.3655
 KL7  H17  H  HCH3  0   0.254  -5.7178  -3.5117   1.7504
 KL7  H18  H  HCH3  0   0.247  -6.3428  -3.8024   0.1288
 KL7  H19  H  HCH3  0   0.249  -4.6607  -4.1737   0.5175
 KL7  H20  H  HCH2  0   0.252  -2.4076   1.3183   1.3077
 KL7  H21  H  HCH2  0   0.250  -1.7177  -0.2819   1.5413
 KL7  H22  H  HCH2  0   0.261  -1.7918   1.2298  -1.1136
 KL7  H23  H  HCH2  0   0.260  -1.0818  -0.3494  -0.8833
 KL7  H24  H  HNH2  0   0.379  -5.8045   1.6477  -1.9495
 KL7  H25  H  HNH2  0   0.388  -6.9711   0.4337  -2.0985
 KL7  F16  F  F     0  -0.306   1.0081  -0.8401   0.3760
 KL7  C08  C  CH2   0  -0.488  -2.2106   0.3639   0.8126
 KL7  C07  C  CH3   0  -0.726  -5.4717  -3.4653   0.6881

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
 KL7  C07  C04  single    1.498  0.020  1.498
 KL7  C04  C05  aromatic  1.400  0.020  1.400
 KL7  C04  C03  aromatic  1.379  0.020  1.379
 KL7  C05  C06  aromatic  1.383  0.020  1.383
 KL7  C03  C02  aromatic  1.406  0.020  1.406
 KL7  C06  C08  single    1.502  0.020  1.502
 KL7  C06  N01  aromatic  1.334  0.020  1.334
 KL7  C02  N01  aromatic  1.328  0.020  1.328
 KL7  C02  N02  single    1.365  0.020  1.365
 KL7  C08  C09  single    1.535  0.020  1.535
 KL7  C14  C13  aromatic  1.387  0.020  1.387
 KL7  C14  C15  aromatic  1.391  0.020  1.391
 KL7  C13  C12  aromatic  1.379  0.020  1.379
 KL7  C15  C17  single    1.502  0.020  1.502
 KL7  C15  C16  aromatic  1.388  0.020  1.388
 KL7  C17  C18  single    1.531  0.020  1.531
 KL7  C12  F12  single    1.344  0.020  1.344
 KL7  C12  C11  aromatic  1.388  0.020  1.388
 KL7  C16  C11  aromatic  1.388  0.020  1.388
 KL7  C16  F16  single    1.345  0.020  1.345
 KL7  C11  C09  single    1.502  0.020  1.502
 KL7  C18  C19  single    1.522  0.020  1.522
 KL7  C19  N20  single    1.451  0.020  1.451
 KL7  N20  C22  single    1.447  0.020  1.447
 KL7  N20  C21  single    1.448  0.020  1.448
 KL7  C22  H1   single    0.970  0.020  1.090
 KL7  C22  H2   single    0.970  0.020  1.090
 KL7  C22  H3   single    0.970  0.020  1.090
 KL7  C21  H4   single    0.970  0.020  1.090
 KL7  C21  H5   single    0.970  0.020  1.090
 KL7  C21  H6   single    0.970  0.020  1.090
 KL7  C19  H7   single    0.970  0.020  1.090
 KL7  C19  H8   single    0.970  0.020  1.090
 KL7  C18  H9   single    0.970  0.020  1.090
 KL7  C18  H10  single    0.970  0.020  1.090
 KL7  C17  H11  single    0.970  0.020  1.090
 KL7  C17  H12  single    0.970  0.020  1.090
 KL7  C14  H13  single    0.930  0.020  1.080
 KL7  C13  H14  single    0.930  0.020  1.080
 KL7  C03  H15  single    0.930  0.020  1.080
 KL7  C05  H16  single    0.930  0.020  1.080
 KL7  C07  H17  single    0.970  0.020  1.090
 KL7  C07  H18  single    0.970  0.020  1.090
 KL7  C07  H19  single    0.970  0.020  1.090
 KL7  C08  H20  single    0.970  0.020  1.090
 KL7  C08  H21  single    0.970  0.020  1.090
 KL7  C09  H22  single    0.970  0.020  1.090
 KL7  C09  H23  single    0.970  0.020  1.090
 KL7  N02  H24  single    0.890  0.020  1.040
 KL7  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
 KL7  H3   C22  H2   107.15  3.000
 KL7  H3   C22  H1   107.74  3.000
 KL7  H2   C22  H1   107.63  3.000
 KL7  H3   C22  N20  111.30  3.000
 KL7  H2   C22  N20  109.66  3.000
 KL7  H1   C22  N20  113.12  3.000
 KL7  H6   C21  H5   107.66  3.000
 KL7  H6   C21  H4   107.54  3.000
 KL7  H5   C21  H4   107.87  3.000
 KL7  H6   C21  N20  113.38  3.000
 KL7  H5   C21  N20  110.14  3.000
 KL7  H4   C21  N20  110.06  3.000
 KL7  H8   C19  H7   106.13  3.000
 KL7  H8   C19  N20  107.53  3.000
 KL7  H7   C19  N20  111.33  3.000
 KL7  H8   C19  C18  108.34  3.000
 KL7  H7   C19  C18  109.21  3.000
 KL7  N20  C19  C18  113.95  3.000
 KL7  H10  C18  H9   106.82  3.000
 KL7  H10  C18  C17  110.16  3.000
 KL7  H9   C18  C17  108.50  3.000
 KL7  H10  C18  C19  109.31  3.000
 KL7  H9   C18  C19  110.85  3.000
 KL7  C17  C18  C19  111.11  3.000
 KL7  H12  C17  H11  106.31  3.000
 KL7  H12  C17  C15  108.61  3.000
 KL7  H11  C17  C15  110.53  3.000
 KL7  H12  C17  C18  109.03  3.000
 KL7  H11  C17  C18  109.68  3.000
 KL7  C15  C17  C18  112.48  3.000
 KL7  F16  C16  C11  117.29  3.000
 KL7  F16  C16  C15  117.97  3.000
 KL7  C11  C16  C15  124.75  3.000
 KL7  H13  C14  C13  119.22  3.000
 KL7  H13  C14  C15  119.05  3.000
 KL7  C13  C14  C15  121.73  3.000
 KL7  C14  C15  C16  116.50  3.000
 KL7  C16  C15  C17  121.77  3.000
 KL7  C14  C15  C17  121.70  3.000
 KL7  H14  C13  C12  120.45  3.000
 KL7  H14  C13  C14  121.13  3.000
 KL7  C12  C13  C14  118.42  3.000
 KL7  F12  C12  C11  118.09  3.000
 KL7  C11  C12  C13  123.27  3.000
 KL7  F12  C12  C13  118.64  3.000
 KL7  C09  C11  C12  122.31  3.000
 KL7  C09  C11  C16  122.35  3.000
 KL7  C12  C11  C16  115.32  3.000
 KL7  N02  C02  N01  117.05  3.000
 KL7  N02  C02  C03  120.65  3.000
 KL7  N01  C02  C03  122.26  3.000
 KL7  H15  C03  C04  120.86  3.000
 KL7  H15  C03  C02  120.04  3.000
 KL7  C04  C03  C02  119.10  3.000
 KL7  C07  C04  C05  120.53  3.000
 KL7  C05  C04  C03  118.08  3.000
 KL7  C07  C04  C03  121.38  3.000
 KL7  H16  C05  C06  120.34  3.000
 KL7  H16  C05  C04  120.64  3.000
 KL7  C06  C05  C04  119.02  3.000
 KL7  N01  C06  C08  115.96  3.000
 KL7  N01  C06  C05  122.82  3.000
 KL7  C08  C06  C05  121.21  3.000
 KL7  H23  C09  H22  106.46  3.000
 KL7  H23  C09  C08  109.41  3.000
 KL7  H22  C09  C08  109.02  3.000
 KL7  H23  C09  C11  109.98  3.000
 KL7  H22  C09  C11  109.99  3.000
 KL7  C08  C09  C11  111.83  3.000
 KL7  C06  N01  C02  118.72  3.000
 KL7  H25  N02  H24  114.23  3.000
 KL7  H25  N02  C02  117.76  3.000
 KL7  H24  N02  C02  116.17  3.000
 KL7  C19  N20  C21  110.54  3.000
 KL7  C21  N20  C22  110.64  3.000
 KL7  C19  N20  C22  112.56  3.000
 KL7  H21  C08  H20  107.20  3.000
 KL7  H21  C08  C09  109.79  3.000
 KL7  H20  C08  C09  109.16  3.000
 KL7  H21  C08  C06  109.88  3.000
 KL7  H20  C08  C06  109.19  3.000
 KL7  C09  C08  C06  111.53  3.000
 KL7  H19  C07  H18  108.27  3.000
 KL7  H19  C07  H17  107.01  3.000
 KL7  H18  C07  H17  107.85  3.000
 KL7  H19  C07  C04  111.17  3.000
 KL7  H18  C07  C04  111.84  3.000
 KL7  H17  C07  C04  110.52  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
 KL7  CONST_01  C13  C14  C15  C16     0.00   0.0  0
 KL7  CONST_02  C13  C12  C11  C16     0.00   0.0  0
 KL7  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 KL7  CONST_04  C11  C16  C15  C14     0.00   0.0  0
 KL7  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 KL7  CONST_06  C12  C11  C16  C15     0.00   0.0  0
 KL7  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 KL7  CONST_08  C05  C06  N01  C02     0.00   0.0  0
 KL7  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 KL7  CONST_10  C06  N01  C02  C03     0.00   0.0  0
 KL7  CONST_11  N01  C06  C05  C04     0.00   0.0  0
 KL7  CONST_12  N01  C02  C03  C04     0.00   0.0  0
 KL7  CONST_13  C13  C14  C15  C17   180.00   0.0  0
 KL7  CONST_14  C11  C16  C15  C17   180.00   0.0  0
 KL7  CONST_15  F12  C12  C11  C16   180.00   0.0  0
 KL7  CONST_16  F12  C12  C13  C14   180.00   0.0  0
 KL7  CONST_17  F16  C16  C15  C14   180.00   0.0  0
 KL7  CONST_18  C09  C11  C16  C15   180.00   0.0  0
 KL7  CONST_19  C09  C11  C12  C13   180.00   0.0  0
 KL7  CONST_20  F16  C16  C11  C12   180.00   0.0  0
 KL7  CONST_21  C07  C04  C03  C02   180.00   0.0  0
 KL7  CONST_22  C08  C06  N01  C02   180.00   0.0  0
 KL7  CONST_23  C08  C06  C05  C04   180.00   0.0  0
 KL7  CONST_24  N02  C02  C03  C04   180.00   0.0  0
 KL7  CONST_25  C07  C04  C05  C06   180.00   0.0  0
 KL7  CONST_26  N02  C02  N01  C06   180.00   0.0  0
 KL7  CONST_27  H13  C14  C15  C16   180.00   0.0  0
 KL7  CONST_28  H14  C13  C14  C15   180.00   0.0  0
 KL7  CONST_29  H16  C05  C04  C03   180.00   0.0  0
 KL7  CONST_30  H15  C03  C04  C05   180.00   0.0  0
 KL7  Var_01    C14  C15  C17  C18   -98.62  30.0  1
 KL7  Var_02    C08  C09  C11  C16    89.15  30.0  2
 KL7  Var_03    C06  C08  C09  C11   178.70  30.0  1
 KL7  Var_04    C09  C08  C06  C05   112.61  30.0  2
 KL7  Var_05    H17  C07  C04  C03  -109.21  30.0  2
 KL7  Var_06    C15  C17  C18  C19   177.72  30.0  1
 KL7  Var_07    C18  C19  N20  C22    65.89  30.0  1
 KL7  Var_08    N20  C19  C18  C17   174.78  30.0  3
 KL7  Var_09    H4   C21  N20  C22  -176.64  30.0  3
 KL7  Var_10    H1   C22  N20  C21   -67.06  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
 KL7  plan-1  C17  0.020
 KL7  plan-1  C16  0.020
 KL7  plan-1  C14  0.020
 KL7  plan-1  C15  0.020
 KL7  plan-1  C13  0.020
 KL7  plan-1  C12  0.020
 KL7  plan-1  C11  0.020
 KL7  plan-1  C09  0.020
 KL7  plan-1  F12  0.020
 KL7  plan-1  H13  0.020
 KL7  plan-1  H14  0.020
 KL7  plan-1  F16  0.020
 KL7  plan-2  C02  0.020
 KL7  plan-2  C03  0.020
 KL7  plan-2  C04  0.020
 KL7  plan-2  C05  0.020
 KL7  plan-2  C06  0.020
 KL7  plan-2  N01  0.020
 KL7  plan-2  N02  0.020
 KL7  plan-2  H15  0.020
 KL7  plan-2  H16  0.020
 KL7  plan-2  C08  0.020
 KL7  plan-2  C07  0.020
 KL7  plan-3  C02  0.020
 KL7  plan-3  N02  0.020
 KL7  plan-3  H24  0.020
 KL7  plan-3  H25  0.020

