# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:47:58 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-(2-{3-[3-(dimethylamino)propyl]-2,5-difluorophenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCc1cc(F)cc(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
 KMJ  KMJ  6-(2-{3-[3-(dimethylamino)propyl]-2,5-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_KMJ
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
 KMJ  C02  C  CR6   0   0.441  -5.5889   0.1688  -0.7411
 KMJ  C03  C  CR16  0  -0.447  -6.0631  -1.1084  -0.3922
 KMJ  C04  C  CR6   0   0.205  -5.2609  -1.9396   0.3606
 KMJ  C05  C  CR16  0  -0.435  -3.9992  -1.4677   0.7435
 KMJ  C06  C  CR6   0   0.279  -3.6128  -0.1974   0.3584
 KMJ  C07  C  CH3   0  -0.726  -5.7118  -3.3126   0.7552
 KMJ  C08  C  CH2   0  -0.490  -2.2637   0.3509   0.7274
 KMJ  C09  C  CH2   0  -0.509  -1.3779   0.5522  -0.5105
 KMJ  C11  C  CR6   0  -0.044  -0.0552   1.1683  -0.1559
 KMJ  C12  C  CR6   0   0.488   1.0094   0.4049   0.2980
 KMJ  C13  C  CR6   0  -0.037   2.2385   0.9309   0.6699
 KMJ  C14  C  CR16  0  -0.473   2.3959   2.3106   0.5820
 KMJ  C15  C  CR6   0   0.550   1.3458   3.0869   0.1354
 KMJ  C16  C  CR16  0  -0.471   0.1315   2.5456  -0.2330
 KMJ  C17  C  CH2   0  -0.505   3.3727   0.0477   1.1030
 KMJ  C18  C  CH2   0  -0.444   4.1303  -0.5424  -0.0899
 KMJ  C19  C  CH2   0  -0.254   5.2851  -1.4161   0.3768
 KMJ  C21  C  CH3   0  -0.527   6.6726  -1.1659  -1.5791
 KMJ  C22  C  CH3   0  -0.521   6.9081  -3.0715  -0.1739
 KMJ  F12  F  F     0  -0.311   0.8408  -0.9303   0.3836
 KMJ  F15  F  F     0  -0.319   1.5125   4.4185   0.0542
 KMJ  N01  N  N     0  -0.485  -4.3921   0.6070  -0.3683
 KMJ  N02  N  NH2   0  -0.839  -6.3412   0.9989  -1.5219
 KMJ  N20  N  NT    0  -0.407   5.9850  -2.0893  -0.7015
 KMJ  H1   H  HCR6  0   0.256  -7.0477  -1.4261  -0.7136
 KMJ  H2   H  HCR6  0   0.244  -3.3386  -2.0822   1.3423
 KMJ  H3   H  HCH3  0   0.253  -5.1315  -4.0739   0.2310
 KMJ  H4   H  HCH3  0   0.250  -5.5668  -3.4794   1.8230
 KMJ  H5   H  HCH3  0   0.247  -6.7631  -3.4747   0.5233
 KMJ  H6   H  HCH2  0   0.252  -2.3895   1.3128   1.2319
 KMJ  H7   H  HCH2  0   0.250  -1.7723  -0.3200   1.4341
 KMJ  H8   H  HCH2  0   0.258  -1.2362  -0.4046  -1.0166
 KMJ  H9   H  HCH2  0   0.259  -1.8976   1.2064  -1.2120
 KMJ  H10  H  HCR6  0   0.279   3.3349   2.7703   0.8649
 KMJ  H11  H  HCR6  0   0.279  -0.6710   3.1842  -0.5817
 KMJ  H12  H  HCH2  0   0.251   4.0647   0.6330   1.7124
 KMJ  H13  H  HCH2  0   0.249   3.0062  -0.7601   1.7401
 KMJ  H14  H  HCH2  0   0.231   3.4535  -1.1381  -0.7077
 KMJ  H15  H  HCH2  0   0.236   4.4888   0.2792  -0.7150
 KMJ  H16  H  HCH2  0   0.185   5.9774  -0.8089   0.9888
 KMJ  H17  H  HCH2  0   0.227   4.8834  -2.1859   1.0433
 KMJ  H18  H  HCH3  0   0.233   7.2187  -1.7220  -2.3418
 KMJ  H19  H  HCH3  0   0.236   5.9693  -0.5153  -2.0979
 KMJ  H20  H  HCH3  0   0.189   7.3965  -0.5247  -1.0502
 KMJ  H21  H  HCH3  0   0.189   7.7039  -2.6321   0.4493
 KMJ  H22  H  HCH3  0   0.231   6.3730  -3.7984   0.4392
 KMJ  H23  H  HCH3  0   0.232   7.3885  -3.6125  -0.9905
 KMJ  H24  H  HNH2  0   0.388  -7.3336   0.8355  -1.5505
 KMJ  H25  H  HNH2  0   0.379  -6.0860   1.9728  -1.5073

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
 KMJ  F15  C15  single    1.345  0.020  1.345
 KMJ  C14  C15  aromatic  1.380  0.020  1.380
 KMJ  C14  C13  aromatic  1.391  0.020  1.391
 KMJ  C17  C13  single    1.501  0.020  1.501
 KMJ  C17  C18  single    1.531  0.020  1.531
 KMJ  C15  C16  aromatic  1.380  0.020  1.380
 KMJ  C13  C12  aromatic  1.388  0.020  1.388
 KMJ  C16  C11  aromatic  1.392  0.020  1.392
 KMJ  C12  C11  aromatic  1.386  0.020  1.386
 KMJ  C12  F12  single    1.348  0.020  1.348
 KMJ  C08  C09  single    1.535  0.020  1.535
 KMJ  C08  C06  single    1.502  0.020  1.502
 KMJ  C11  C09  single    1.502  0.020  1.502
 KMJ  C18  C19  single    1.521  0.020  1.521
 KMJ  C22  N20  single    1.448  0.020  1.448
 KMJ  C21  N20  single    1.448  0.020  1.448
 KMJ  N01  C06  aromatic  1.335  0.020  1.335
 KMJ  N01  C02  aromatic  1.328  0.020  1.328
 KMJ  N02  C02  single    1.366  0.020  1.366
 KMJ  C06  C05  aromatic  1.382  0.020  1.382
 KMJ  N20  C19  single    1.451  0.020  1.451
 KMJ  C02  C03  aromatic  1.406  0.020  1.406
 KMJ  C05  C04  aromatic  1.400  0.020  1.400
 KMJ  C03  C04  aromatic  1.379  0.020  1.379
 KMJ  C04  C07  single    1.498  0.020  1.498
 KMJ  C03  H1   single    0.930  0.020  1.080
 KMJ  C05  H2   single    0.930  0.020  1.080
 KMJ  C07  H3   single    0.970  0.020  1.090
 KMJ  C07  H4   single    0.970  0.020  1.090
 KMJ  C07  H5   single    0.970  0.020  1.090
 KMJ  C08  H6   single    0.970  0.020  1.090
 KMJ  C08  H7   single    0.970  0.020  1.090
 KMJ  C09  H8   single    0.970  0.020  1.090
 KMJ  C09  H9   single    0.970  0.020  1.090
 KMJ  C14  H10  single    0.930  0.020  1.080
 KMJ  C16  H11  single    0.930  0.020  1.080
 KMJ  C17  H12  single    0.970  0.020  1.090
 KMJ  C17  H13  single    0.970  0.020  1.090
 KMJ  C18  H14  single    0.970  0.020  1.090
 KMJ  C18  H15  single    0.970  0.020  1.090
 KMJ  C19  H16  single    0.970  0.020  1.090
 KMJ  C19  H17  single    0.970  0.020  1.090
 KMJ  C21  H18  single    0.970  0.020  1.090
 KMJ  C21  H19  single    0.970  0.020  1.090
 KMJ  C21  H20  single    0.970  0.020  1.090
 KMJ  C22  H21  single    0.970  0.020  1.090
 KMJ  C22  H22  single    0.970  0.020  1.090
 KMJ  C22  H23  single    0.970  0.020  1.090
 KMJ  N02  H24  single    0.890  0.020  1.040
 KMJ  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
 KMJ  N02  C02  N01  117.16  3.000
 KMJ  N02  C02  C03  120.54  3.000
 KMJ  N01  C02  C03  122.28  3.000
 KMJ  H1   C03  C04  120.93  3.000
 KMJ  H1   C03  C02  119.95  3.000
 KMJ  C04  C03  C02  119.12  3.000
 KMJ  C07  C04  C05  120.53  3.000
 KMJ  C07  C04  C03  121.41  3.000
 KMJ  C05  C04  C03  118.06  3.000
 KMJ  H2   C05  C06  120.33  3.000
 KMJ  H2   C05  C04  120.63  3.000
 KMJ  C06  C05  C04  119.03  3.000
 KMJ  N01  C06  C08  115.98  3.000
 KMJ  N01  C06  C05  122.83  3.000
 KMJ  C08  C06  C05  121.19  3.000
 KMJ  H5   C07  H4   108.32  3.000
 KMJ  H5   C07  H3   107.90  3.000
 KMJ  H4   C07  H3   107.03  3.000
 KMJ  H5   C07  C04  111.78  3.000
 KMJ  H4   C07  C04  110.98  3.000
 KMJ  H3   C07  C04  110.65  3.000
 KMJ  H7   C08  H6   107.09  3.000
 KMJ  H7   C08  C09  110.05  3.000
 KMJ  H6   C08  C09  108.84  3.000
 KMJ  H7   C08  C06  109.82  3.000
 KMJ  H6   C08  C06  109.33  3.000
 KMJ  C09  C08  C06  111.59  3.000
 KMJ  H9   C09  H8   106.82  3.000
 KMJ  H9   C09  C11  108.99  3.000
 KMJ  H8   C09  C11  110.78  3.000
 KMJ  H9   C09  C08  108.80  3.000
 KMJ  H8   C09  C08  109.49  3.000
 KMJ  C11  C09  C08  111.81  3.000
 KMJ  C16  C11  C12  117.38  3.000
 KMJ  C12  C11  C09  121.86  3.000
 KMJ  C16  C11  C09  120.73  3.000
 KMJ  F12  C12  C13  117.97  3.000
 KMJ  F12  C12  C11  118.03  3.000
 KMJ  C13  C12  C11  124.00  3.000
 KMJ  C17  C13  C14  121.07  3.000
 KMJ  C17  C13  C12  121.56  3.000
 KMJ  C14  C13  C12  117.33  3.000
 KMJ  H10  C14  C15  120.36  3.000
 KMJ  H10  C14  C13  120.16  3.000
 KMJ  C15  C14  C13  119.47  3.000
 KMJ  F15  C15  C16  118.80  3.000
 KMJ  C16  C15  C14  122.37  3.000
 KMJ  F15  C15  C14  118.83  3.000
 KMJ  H11  C16  C15  120.44  3.000
 KMJ  H11  C16  C11  120.11  3.000
 KMJ  C15  C16  C11  119.44  3.000
 KMJ  H13  C17  H12  106.47  3.000
 KMJ  H13  C17  C18  109.60  3.000
 KMJ  H12  C17  C18  109.13  3.000
 KMJ  H13  C17  C13  110.48  3.000
 KMJ  H12  C17  C13  108.93  3.000
 KMJ  C18  C17  C13  112.07  3.000
 KMJ  H15  C18  H14  106.83  3.000
 KMJ  H15  C18  C19  110.99  3.000
 KMJ  H14  C18  C19  109.29  3.000
 KMJ  H15  C18  C17  108.55  3.000
 KMJ  H14  C18  C17  110.12  3.000
 KMJ  C19  C18  C17  110.97  3.000
 KMJ  H17  C19  H16  106.20  3.000
 KMJ  H17  C19  N20  107.65  3.000
 KMJ  H16  C19  N20  111.35  3.000
 KMJ  H17  C19  C18  108.18  3.000
 KMJ  H16  C19  C18  109.25  3.000
 KMJ  N20  C19  C18  113.86  3.000
 KMJ  H20  C21  H19  107.76  3.000
 KMJ  H20  C21  H18  107.66  3.000
 KMJ  H19  C21  H18  107.15  3.000
 KMJ  H20  C21  N20  113.09  3.000
 KMJ  H19  C21  N20  111.28  3.000
 KMJ  H18  C21  N20  109.67  3.000
 KMJ  H23  C22  H22  107.83  3.000
 KMJ  H23  C22  H21  107.64  3.000
 KMJ  H22  C22  H21  107.58  3.000
 KMJ  H23  C22  N20  110.15  3.000
 KMJ  H22  C22  N20  110.13  3.000
 KMJ  H21  C22  N20  113.33  3.000
 KMJ  C06  N01  C02  118.69  3.000
 KMJ  H25  N02  H24  114.05  3.000
 KMJ  H25  N02  C02  116.11  3.000
 KMJ  H24  N02  C02  117.45  3.000
 KMJ  C22  N20  C21  110.54  3.000
 KMJ  C21  N20  C19  112.56  3.000
 KMJ  C22  N20  C19  110.58  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
 KMJ  CONST_01  C05  C06  N01  C02     0.00   0.0  0
 KMJ  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 KMJ  CONST_03  C06  N01  C02  C03     0.00   0.0  0
 KMJ  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 KMJ  CONST_05  N01  C06  C05  C04     0.00   0.0  0
 KMJ  CONST_06  N01  C02  C03  C04     0.00   0.0  0
 KMJ  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 KMJ  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 KMJ  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 KMJ  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 KMJ  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 KMJ  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 KMJ  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 KMJ  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 KMJ  CONST_15  C08  C06  C05  C04   180.00   0.0  0
 KMJ  CONST_16  N02  C02  C03  C04   180.00   0.0  0
 KMJ  CONST_17  N02  C02  N01  C06   180.00   0.0  0
 KMJ  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 KMJ  CONST_19  C15  C16  C11  C09   180.00   0.0  0
 KMJ  CONST_20  C13  C12  C11  C09   180.00   0.0  0
 KMJ  CONST_21  F15  C15  C16  C11   180.00   0.0  0
 KMJ  CONST_22  C17  C13  C12  C11   180.00   0.0  0
 KMJ  CONST_23  F15  C15  C14  C13   180.00   0.0  0
 KMJ  CONST_24  F12  C12  C13  C14   180.00   0.0  0
 KMJ  CONST_25  C17  C13  C14  C15   180.00   0.0  0
 KMJ  CONST_26  F12  C12  C11  C16   180.00   0.0  0
 KMJ  CONST_27  H2   C05  C04  C03   180.00   0.0  0
 KMJ  CONST_28  H1   C03  C04  C05   180.00   0.0  0
 KMJ  CONST_29  H10  C14  C13  C12   180.00   0.0  0
 KMJ  CONST_30  H11  C16  C11  C12   180.00   0.0  0
 KMJ  Var_01    C09  C08  C06  C05   113.39  30.0  1
 KMJ  Var_02    C11  C09  C08  C06   176.96  30.0  3
 KMJ  Var_03    C16  C11  C09  C08   -94.45  30.0  1
 KMJ  Var_04    C18  C17  C13  C12    81.75  30.0  2
 KMJ  Var_05    H3   C07  C04  C03   110.82  30.0  2
 KMJ  Var_06    C19  C18  C17  C13   179.19  30.0  3
 KMJ  Var_07    N20  C19  C18  C17   175.59  30.0  3
 KMJ  Var_08    C22  N20  C19  C18  -170.07  30.0  2
 KMJ  Var_09    H21  C22  N20  C19   -62.57  30.0  3
 KMJ  Var_10    H18  C21  N20  C19   177.37  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
 KMJ  plan-1  C09  0.020
 KMJ  plan-1  C11  0.020
 KMJ  plan-1  C12  0.020
 KMJ  plan-1  C13  0.020
 KMJ  plan-1  C14  0.020
 KMJ  plan-1  C15  0.020
 KMJ  plan-1  C16  0.020
 KMJ  plan-1  C17  0.020
 KMJ  plan-1  F12  0.020
 KMJ  plan-1  F15  0.020
 KMJ  plan-1  H10  0.020
 KMJ  plan-1  H11  0.020
 KMJ  plan-2  C02  0.020
 KMJ  plan-2  C03  0.020
 KMJ  plan-2  C04  0.020
 KMJ  plan-2  C05  0.020
 KMJ  plan-2  C06  0.020
 KMJ  plan-2  C07  0.020
 KMJ  plan-2  C08  0.020
 KMJ  plan-2  N01  0.020
 KMJ  plan-2  N02  0.020
 KMJ  plan-2  H1   0.020
 KMJ  plan-2  H2   0.020
 KMJ  plan-3  C02  0.020
 KMJ  plan-3  N02  0.020
 KMJ  plan-3  H24  0.020
 KMJ  plan-3  H25  0.020

