# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 21:02:35 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 6-(2-{3-[3-(dimethylamino)propyl]-5-(trifluoromethyl)phenyl}ethyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCc1cc(CCc2cc(C)cc(N)n2)cc(c1)C(F)(F)F
#
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
 BY7  BY7  6-(2-{3-[3-(dimethylamino)propyl]-5-(trifluoromethyl)phenyl}ethyl)-4-methylpyridin-2-amine  ligand  52  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BY7
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
 BY7  F20  F  F     0  -0.317   1.6831  -4.4179   1.2581
 BY7  C17  C  CT    0   1.050   1.6816  -3.8482   0.0417
 BY7  F18  F  F     0  -0.313   2.8910  -4.0843  -0.4863
 BY7  F19  F  F     0  -0.304   0.7962  -4.5226  -0.6987
 BY7  C13  C  CR6   0  -0.151   1.3790  -2.3855   0.1219
 BY7  C14  C  CR16  0  -0.369   2.3613  -1.5258   0.6030
 BY7  C15  C  CR6   0   0.183   2.1010  -0.1678   0.7308
 BY7  C21  C  CH2   0  -0.511   3.1644   0.7814   1.2050
 BY7  C22  C  CH2   0  -0.439   3.8841   1.4689   0.0445
 BY7  C23  C  CH2   0  -0.256   4.9439   2.4379   0.5525
 BY7  N24  N  NT    0  -0.408   5.6950   3.0877  -0.5056
 BY7  C26  C  CH3   0  -0.524   4.9017   4.0489  -1.2405
 BY7  C25  C  CH3   0  -0.520   6.8941   3.7085   0.0138
 BY7  C12  C  CR16  0  -0.375   0.1303  -1.8985  -0.2338
 BY7  C11  C  CR6   0   0.177  -0.1477  -0.5389  -0.1172
 BY7  C16  C  CR16  0  -0.369   0.8429   0.3063   0.3667
 BY7  C09  C  CH2   0  -0.514  -1.5102  -0.0089  -0.4615
 BY7  C08  C  CH2   0  -0.489  -2.4452  -0.0193   0.7563
 BY7  C06  C  CR6   0   0.274  -3.7969   0.5449   0.4232
 BY7  N01  N  N     0  -0.484  -3.8469   1.8626   0.2145
 BY7  C02  C  CR6   0   0.441  -5.0118   2.4120  -0.1103
 BY7  N02  N  NH2   0  -0.839  -5.0181   3.7535  -0.3657
 BY7  C03  C  CR16  0  -0.447  -6.1911   1.6558  -0.2332
 BY7  C04  C  CR6   0   0.205  -6.1407   0.2943  -0.0179
 BY7  C05  C  CR16  0  -0.432  -4.9061  -0.2739   0.3181
 BY7  C07  C  CH3   0  -0.726  -7.3621  -0.5624  -0.1511
 BY7  H1   H  HCR6  0   0.262   3.3376  -1.9036   0.8837
 BY7  H2   H  HCH2  0   0.245   2.7132   1.5420   1.8482
 BY7  H3   H  HCH2  0   0.245   3.8923   0.2448   1.8185
 BY7  H4   H  HCH2  0   0.229   4.3576   0.7199  -0.5961
 BY7  H5   H  HCH2  0   0.234   3.1455   1.9882  -0.5726
 BY7  H6   H  HCH2  0   0.185   4.4682   3.1740   1.2261
 BY7  H7   H  HCH2  0   0.227   5.6529   1.8770   1.1688
 BY7  H9   H  HCH3  0   0.188   4.5352   4.8775  -0.6133
 BY7  H10  H  HCH3  0   0.232   5.4983   4.4824  -2.0443
 BY7  H11  H  HCH3  0   0.234   4.0364   3.5731  -1.7010
 BY7  H12  H  HCH3  0   0.231   7.5251   2.9620   0.4986
 BY7  H13  H  HCH3  0   0.231   7.4697   4.1507  -0.8011
 BY7  H14  H  HCH3  0   0.189   6.6925   4.5041   0.7486
 BY7  H15  H  HCR6  0   0.260  -0.6407  -2.5607  -0.6075
 BY7  H16  H  HCR6  0   0.247   0.6309   1.3665   0.4622
 BY7  H17  H  HCH2  0   0.254  -1.4294   1.0124  -0.8392
 BY7  H18  H  HCH2  0   0.253  -1.9510  -0.6118  -1.2590
 BY7  H19  H  HCH2  0   0.249  -2.5478  -1.0409   1.1286
 BY7  H20  H  HCH2  0   0.249  -1.9933   0.5725   1.5567
 BY7  H21  H  HNH2  0   0.379  -4.2408   4.2793  -0.0006
 BY7  H22  H  HNH2  0   0.387  -5.9009   4.2325  -0.3050
 BY7  H23  H  HCR6  0   0.255  -7.1228   2.1425  -0.4960
 BY7  H24  H  HCR6  0   0.243  -4.8172  -1.3381   0.4978
 BY7  H25  H  HCH3  0   0.254  -7.2863  -1.2018  -1.0322
 BY7  H26  H  HCH3  0   0.249  -7.4748  -1.2204   0.7112
 BY7  H27  H  HCH3  0   0.247  -8.2678   0.0343  -0.2474

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
 BY7  C07  C04  single    1.498  0.020  1.498
 BY7  C04  C03  aromatic  1.379  0.020  1.379
 BY7  C04  C05  aromatic  1.400  0.020  1.400
 BY7  C03  C02  aromatic  1.406  0.020  1.406
 BY7  C05  C06  aromatic  1.383  0.020  1.383
 BY7  C02  N02  single    1.366  0.020  1.366
 BY7  C02  N01  aromatic  1.328  0.020  1.328
 BY7  C06  N01  aromatic  1.335  0.020  1.335
 BY7  C06  C08  single    1.502  0.020  1.502
 BY7  C09  C08  single    1.535  0.020  1.535
 BY7  C09  C11  single    1.502  0.020  1.502
 BY7  C16  C11  aromatic  1.389  0.020  1.389
 BY7  C16  C15  aromatic  1.393  0.020  1.393
 BY7  C11  C12  aromatic  1.393  0.020  1.393
 BY7  C21  C15  single    1.502  0.020  1.502
 BY7  C21  C22  single    1.529  0.020  1.529
 BY7  C15  C14  aromatic  1.389  0.020  1.389
 BY7  C25  N24  single    1.447  0.020  1.447
 BY7  C22  C23  single    1.523  0.020  1.523
 BY7  C12  C13  aromatic  1.387  0.020  1.387
 BY7  C23  N24  single    1.451  0.020  1.451
 BY7  N24  C26  single    1.447  0.020  1.447
 BY7  C14  C13  aromatic  1.391  0.020  1.391
 BY7  C13  C17  single    1.496  0.020  1.496
 BY7  F19  C17  single    1.337  0.020  1.337
 BY7  C17  F20  single    1.343  0.020  1.343
 BY7  C17  F18  single    1.341  0.020  1.341
 BY7  C14  H1   single    0.930  0.020  1.080
 BY7  C21  H2   single    0.970  0.020  1.090
 BY7  C21  H3   single    0.970  0.020  1.090
 BY7  C22  H4   single    0.970  0.020  1.090
 BY7  C22  H5   single    0.970  0.020  1.090
 BY7  C23  H6   single    0.970  0.020  1.090
 BY7  C23  H7   single    0.970  0.020  1.090
 BY7  C26  H9   single    0.970  0.020  1.090
 BY7  C26  H10  single    0.970  0.020  1.090
 BY7  C26  H11  single    0.970  0.020  1.090
 BY7  C25  H12  single    0.970  0.020  1.090
 BY7  C25  H13  single    0.970  0.020  1.090
 BY7  C25  H14  single    0.970  0.020  1.090
 BY7  C12  H15  single    0.930  0.020  1.080
 BY7  C16  H16  single    0.930  0.020  1.080
 BY7  C09  H17  single    0.970  0.020  1.090
 BY7  C09  H18  single    0.970  0.020  1.090
 BY7  C08  H19  single    0.970  0.020  1.090
 BY7  C08  H20  single    0.970  0.020  1.090
 BY7  N02  H21  single    0.890  0.020  1.040
 BY7  N02  H22  single    0.890  0.020  1.040
 BY7  C03  H23  single    0.930  0.020  1.080
 BY7  C05  H24  single    0.930  0.020  1.080
 BY7  C07  H25  single    0.970  0.020  1.090
 BY7  C07  H26  single    0.970  0.020  1.090
 BY7  C07  H27  single    0.970  0.020  1.090

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
 BY7  C13  C17  F19  112.89  3.000
 BY7  F19  C17  F18  106.89  3.000
 BY7  C13  C17  F18  112.08  3.000
 BY7  F18  C17  F20  106.32  3.000
 BY7  F19  C17  F20  106.76  3.000
 BY7  C13  C17  F20  111.50  3.000
 BY7  C12  C13  C14  120.50  3.000
 BY7  C14  C13  C17  118.68  3.000
 BY7  C12  C13  C17  120.79  3.000
 BY7  H1   C14  C15  119.07  3.000
 BY7  H1   C14  C13  120.68  3.000
 BY7  C15  C14  C13  120.25  3.000
 BY7  C16  C15  C21  120.45  3.000
 BY7  C21  C15  C14  120.95  3.000
 BY7  C16  C15  C14  118.56  3.000
 BY7  H3   C21  H2   106.62  3.000
 BY7  H3   C21  C22  109.47  3.000
 BY7  H2   C21  C22  109.15  3.000
 BY7  H3   C21  C15  109.78  3.000
 BY7  H2   C21  C15  109.46  3.000
 BY7  C22  C21  C15  112.20  3.000
 BY7  H5   C22  H4   106.69  3.000
 BY7  H5   C22  C23  110.86  3.000
 BY7  H4   C22  C23  109.26  3.000
 BY7  H5   C22  C21  108.89  3.000
 BY7  H4   C22  C21  109.91  3.000
 BY7  C23  C22  C21  111.13  3.000
 BY7  H7   C23  H6   106.09  3.000
 BY7  H7   C23  N24  107.75  3.000
 BY7  H6   C23  N24  111.64  3.000
 BY7  H7   C23  C22  108.22  3.000
 BY7  H6   C23  C22  109.11  3.000
 BY7  N24  C23  C22  113.69  3.000
 BY7  C25  N24  C26  110.59  3.000
 BY7  C26  N24  C23  112.59  3.000
 BY7  C25  N24  C23  111.06  3.000
 BY7  H11  C26  H10  107.24  3.000
 BY7  H11  C26  H9   107.74  3.000
 BY7  H10  C26  H9   107.61  3.000
 BY7  H11  C26  N24  111.10  3.000
 BY7  H10  C26  N24  109.78  3.000
 BY7  H9   C26  N24  113.13  3.000
 BY7  H14  C25  H13  107.58  3.000
 BY7  H14  C25  H12  107.67  3.000
 BY7  H13  C25  H12  107.70  3.000
 BY7  H14  C25  N24  113.43  3.000
 BY7  H13  C25  N24  110.06  3.000
 BY7  H12  C25  N24  110.20  3.000
 BY7  H15  C12  C11  118.93  3.000
 BY7  H15  C12  C13  120.99  3.000
 BY7  C11  C12  C13  120.07  3.000
 BY7  C09  C11  C16  120.80  3.000
 BY7  C16  C11  C12  118.74  3.000
 BY7  C09  C11  C12  120.42  3.000
 BY7  H16  C16  C11  119.05  3.000
 BY7  H16  C16  C15  119.07  3.000
 BY7  C11  C16  C15  121.88  3.000
 BY7  H18  C09  H17  107.07  3.000
 BY7  H18  C09  C08  109.24  3.000
 BY7  H17  C09  C08  109.02  3.000
 BY7  H18  C09  C11  109.79  3.000
 BY7  H17  C09  C11  110.01  3.000
 BY7  C08  C09  C11  111.61  3.000
 BY7  H20  C08  H19  107.19  3.000
 BY7  H20  C08  C06  109.33  3.000
 BY7  H19  C08  C06  110.02  3.000
 BY7  H20  C08  C09  108.99  3.000
 BY7  H19  C08  C09  109.51  3.000
 BY7  C06  C08  C09  111.69  3.000
 BY7  C05  C06  N01  122.85  3.000
 BY7  N01  C06  C08  116.04  3.000
 BY7  C05  C06  C08  121.09  3.000
 BY7  C02  N01  C06  118.64  3.000
 BY7  C03  C02  N02  120.53  3.000
 BY7  N02  C02  N01  117.13  3.000
 BY7  C03  C02  N01  122.31  3.000
 BY7  H22  N02  H21  114.00  3.000
 BY7  H22  N02  C02  117.41  3.000
 BY7  H21  N02  C02  116.20  3.000
 BY7  H23  C03  C04  120.84  3.000
 BY7  H23  C03  C02  120.05  3.000
 BY7  C04  C03  C02  119.11  3.000
 BY7  C07  C04  C05  120.55  3.000
 BY7  C05  C04  C03  118.05  3.000
 BY7  C07  C04  C03  121.39  3.000
 BY7  H24  C05  C04  120.74  3.000
 BY7  H24  C05  C06  120.23  3.000
 BY7  C04  C05  C06  119.04  3.000
 BY7  H27  C07  H26  108.34  3.000
 BY7  H27  C07  H25  107.91  3.000
 BY7  H26  C07  H25  106.97  3.000
 BY7  H27  C07  C04  111.88  3.000
 BY7  H26  C07  C04  111.04  3.000
 BY7  H25  C07  C04  110.50  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
 BY7  CONST_01  C16  C11  C12  C13     0.00   0.0  0
 BY7  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 BY7  CONST_03  C11  C16  C15  C14     0.00   0.0  0
 BY7  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 BY7  CONST_05  C12  C11  C16  C15     0.00   0.0  0
 BY7  CONST_06  C12  C13  C14  C15     0.00   0.0  0
 BY7  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 BY7  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 BY7  CONST_09  C04  C03  C02  N01     0.00   0.0  0
 BY7  CONST_10  C04  C05  C06  N01     0.00   0.0  0
 BY7  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 BY7  CONST_12  C05  C06  N01  C02     0.00   0.0  0
 BY7  CONST_13  C11  C12  C13  C17   180.00   0.0  0
 BY7  CONST_14  C15  C14  C13  C17   180.00   0.0  0
 BY7  CONST_15  C09  C11  C12  C13   180.00   0.0  0
 BY7  CONST_16  C21  C15  C14  C13   180.00   0.0  0
 BY7  CONST_17  C09  C11  C16  C15   180.00   0.0  0
 BY7  CONST_18  C11  C16  C15  C21   180.00   0.0  0
 BY7  CONST_19  C04  C05  C06  C08   180.00   0.0  0
 BY7  CONST_20  C02  N01  C06  C08   180.00   0.0  0
 BY7  CONST_21  C07  C04  C05  C06   180.00   0.0  0
 BY7  CONST_22  N02  C02  N01  C06   180.00   0.0  0
 BY7  CONST_23  C07  C04  C03  C02   180.00   0.0  0
 BY7  CONST_24  C04  C03  C02  N02   180.00   0.0  0
 BY7  CONST_25  H16  C16  C15  C14   180.00   0.0  0
 BY7  CONST_26  H15  C12  C13  C14   180.00   0.0  0
 BY7  CONST_27  H1   C14  C13  C12   180.00   0.0  0
 BY7  CONST_28  H23  C03  C02  N01   180.00   0.0  0
 BY7  CONST_29  H24  C05  C06  N01   180.00   0.0  0
 BY7  Var_01    C12  C13  C17  F20  -104.10  30.0  3
 BY7  Var_02    C22  C21  C15  C14    96.32  30.0  2
 BY7  Var_03    C08  C09  C11  C12    89.64  30.0  1
 BY7  Var_04    C06  C08  C09  C11   178.46  30.0  3
 BY7  Var_05    C05  C06  C08  C09   107.66  30.0  2
 BY7  Var_06    H25  C07  C04  C03   109.93  30.0  2
 BY7  Var_07    C23  C22  C21  C15   179.28  30.0  3
 BY7  Var_08    N24  C23  C22  C21   177.95  30.0  3
 BY7  Var_09    C25  N24  C23  C22  -164.89  30.0  3
 BY7  Var_10    H12  C25  N24  C23    58.68  30.0  3
 BY7  Var_11    H9   C26  N24  C23    61.79  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
 BY7  plan-1  C17  0.020
 BY7  plan-1  C13  0.020
 BY7  plan-1  C14  0.020
 BY7  plan-1  C15  0.020
 BY7  plan-1  C21  0.020
 BY7  plan-1  C12  0.020
 BY7  plan-1  C11  0.020
 BY7  plan-1  C16  0.020
 BY7  plan-1  C09  0.020
 BY7  plan-1  H1   0.020
 BY7  plan-1  H15  0.020
 BY7  plan-1  H16  0.020
 BY7  plan-2  C08  0.020
 BY7  plan-2  C06  0.020
 BY7  plan-2  N01  0.020
 BY7  plan-2  C02  0.020
 BY7  plan-2  N02  0.020
 BY7  plan-2  C03  0.020
 BY7  plan-2  C04  0.020
 BY7  plan-2  C05  0.020
 BY7  plan-2  C07  0.020
 BY7  plan-2  H23  0.020
 BY7  plan-2  H24  0.020
 BY7  plan-3  C02  0.020
 BY7  plan-3  N02  0.020
 BY7  plan-3  H21  0.020
 BY7  plan-3  H22  0.020

