# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 17:13:15 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 6-({[5-({[2-(3-fluorophenyl)ethyl]amino}methyl)pyridin-3-yl]oxy}methyl)-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(COc2cncc(CNCCc3cccc(F)c3)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
 QJ7  QJ7  6-({[5-({[2-(3-fluorophenyl)ethyl]amino}methyl)pyridin-3-yl]oxy}methyl)-4-methylpyridin-2-amine  ligand  50  27  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QJ7
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
 QJ7  F23  F  F     0  -0.318  -7.4157   3.2520  -0.7276
 QJ7  C23  C  CR6   0   0.539  -7.2094   2.0361  -0.1919
 QJ7  C24  C  CR16  0  -0.426  -8.2989   1.2232   0.0533
 QJ7  C25  C  CR16  0  -0.224  -8.0638  -0.0273   0.6090
 QJ7  C26  C  CR16  0  -0.319  -6.7717  -0.4380   0.9063
 QJ7  C22  C  CR16  0  -0.464  -5.9144   1.6507   0.0942
 QJ7  C21  C  CR6   0   0.138  -5.6845   0.3960   0.6539
 QJ7  C20  C  CH2   0  -0.532  -4.2812  -0.0617   0.9329
 QJ7  C19  C  CH2   0  -0.249  -3.6658  -0.7405  -0.2875
 QJ7  N18  N  NH1   0  -0.591  -2.3085  -1.1689  -0.0086
 QJ7  C17  C  CH2   0  -0.335  -1.6986  -1.8496  -1.1363
 QJ7  C15  C  CR6   0   0.026  -0.2836  -2.2374  -0.8159
 QJ7  C14  C  CR16  0  -0.289   0.6922  -1.2742  -0.6227
 QJ7  C16  C  CR16  0  -0.129   0.0870  -3.5716  -0.6733
 QJ7  N11  N  N     0  -0.386   1.3168  -3.9552  -0.3685
 QJ7  C12  C  CR16  0  -0.189   2.2545  -3.0328  -0.1934
 QJ7  C13  C  CR6   0   0.353   1.9905  -1.6684  -0.3181
 QJ7  O09  O  O2    0  -0.475   2.9050  -0.6948  -0.1666
 QJ7  C08  C  CH2   0  -0.210   4.2334  -1.0527   0.1394
 QJ7  C06  C  CR6   0   0.204   5.0970   0.1776   0.1752
 QJ7  N01  N  N     0  -0.493   6.3474  -0.0729   0.5647
 QJ7  C02  C  CR6   0   0.451   7.2108   0.9337   0.6117
 QJ7  N02  N  NH2   0  -0.839   8.4680   0.6571   1.0611
 QJ7  C03  C  CR16  0  -0.443   6.8471   2.2472   0.2603
 QJ7  C04  C  CR6   0   0.209   5.5540   2.4990  -0.1422
 QJ7  C05  C  CR16  0  -0.419   4.6466   1.4301  -0.1842
 QJ7  C07  C  CH3   0  -0.728   5.1104   3.8746  -0.5342
 QJ7  H1   H  HCR6  0   0.277  -9.3012   1.5576  -0.1785
 QJ7  H2   H  HCR6  0   0.266  -8.9000  -0.6827   0.8139
 QJ7  H3   H  HCR6  0   0.253  -6.6053  -1.4150   1.3438
 QJ7  H4   H  HCR6  0   0.270  -5.0912   2.3248  -0.1115
 QJ7  H5   H  HCH2  0   0.249  -3.6566   0.7861   1.2238
 QJ7  H6   H  HCH2  0   0.248  -4.2847  -0.7613   1.7734
 QJ7  H7   H  HCH2  0   0.202  -4.3164  -1.5693  -0.6089
 QJ7  H8   H  HCH2  0   0.228  -3.6382  -0.0301  -1.1192
 QJ7  H9   H  HNH1  0   0.345  -2.3217  -1.8045   0.7815
 QJ7  H11  H  HCH2  0   0.220  -2.2581  -2.7419  -1.4545
 QJ7  H12  H  HCH2  0   0.244  -1.7012  -1.1647  -1.9893
 QJ7  H13  H  HCR6  0   0.271   0.4560  -0.2206  -0.7191
 QJ7  H14  H  HCR6  0   0.255  -0.6492  -4.3570  -0.8115
 QJ7  H15  H  HCR6  0   0.279   3.2439  -3.3990   0.0543
 QJ7  H16  H  HCH2  0   0.251   4.2870  -1.5623   1.1085
 QJ7  H17  H  HCH2  0   0.251   4.6369  -1.7426  -0.6120
 QJ7  H18  H  HNH2  0   0.381   8.7427  -0.3115   1.0518
 QJ7  H19  H  HNH2  0   0.390   9.2040   1.2972   0.8143
 QJ7  H20  H  HCR6  0   0.258   7.5804   3.0430   0.3074
 QJ7  H21  H  HCR6  0   0.250   3.6257   1.5963  -0.4980
 QJ7  H22  H  HCH3  0   0.253   4.7593   3.8867  -1.5670
 QJ7  H23  H  HCH3  0   0.253   4.2775   4.2055   0.0878
 QJ7  H24  H  HCH3  0   0.248   5.9134   4.6034  -0.4409

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
 QJ7  C07  C04  single    1.498  0.020  1.498
 QJ7  C04  C03  aromatic  1.378  0.020  1.378
 QJ7  C04  C05  aromatic  1.403  0.020  1.403
 QJ7  C03  C02  aromatic  1.407  0.020  1.407
 QJ7  C05  C06  aromatic  1.379  0.020  1.379
 QJ7  C02  N02  single    1.363  0.020  1.363
 QJ7  C02  N01  aromatic  1.327  0.020  1.327
 QJ7  C06  N01  aromatic  1.333  0.020  1.333
 QJ7  C06  C08  single    1.504  0.020  1.504
 QJ7  O09  C13  single    1.344  0.020  1.344
 QJ7  O09  C08  single    1.409  0.020  1.409
 QJ7  C13  C14  aromatic  1.391  0.020  1.391
 QJ7  C13  C12  aromatic  1.395  0.020  1.395
 QJ7  C14  C15  aromatic  1.385  0.020  1.385
 QJ7  C12  N11  aromatic  1.327  0.020  1.327
 QJ7  C15  C17  single    1.502  0.020  1.502
 QJ7  C15  C16  aromatic  1.392  0.020  1.392
 QJ7  C17  N18  single    1.452  0.020  1.452
 QJ7  N11  C16  aromatic  1.324  0.020  1.324
 QJ7  N18  C19  single    1.450  0.020  1.450
 QJ7  C19  C20  single    1.526  0.020  1.526
 QJ7  C20  C21  single    1.502  0.020  1.502
 QJ7  C21  C26  aromatic  1.393  0.020  1.393
 QJ7  C21  C22  aromatic  1.393  0.020  1.393
 QJ7  C26  C25  aromatic  1.388  0.020  1.388
 QJ7  C22  C23  aromatic  1.381  0.020  1.381
 QJ7  C25  C24  aromatic  1.388  0.020  1.388
 QJ7  C23  C24  aromatic  1.381  0.020  1.381
 QJ7  C23  F23  single    1.345  0.020  1.345
 QJ7  C24  H1   single    0.930  0.020  1.080
 QJ7  C25  H2   single    0.930  0.020  1.080
 QJ7  C26  H3   single    0.930  0.020  1.080
 QJ7  C22  H4   single    0.930  0.020  1.080
 QJ7  C20  H5   single    0.970  0.020  1.090
 QJ7  C20  H6   single    0.970  0.020  1.090
 QJ7  C19  H7   single    0.970  0.020  1.090
 QJ7  C19  H8   single    0.970  0.020  1.090
 QJ7  N18  H9   single    0.890  0.020  1.040
 QJ7  C17  H11  single    0.970  0.020  1.090
 QJ7  C17  H12  single    0.970  0.020  1.090
 QJ7  C14  H13  single    0.930  0.020  1.080
 QJ7  C16  H14  single    0.930  0.020  1.080
 QJ7  C12  H15  single    0.930  0.020  1.080
 QJ7  C08  H16  single    0.970  0.020  1.090
 QJ7  C08  H17  single    0.970  0.020  1.090
 QJ7  N02  H18  single    0.890  0.020  1.040
 QJ7  N02  H19  single    0.890  0.020  1.040
 QJ7  C03  H20  single    0.930  0.020  1.080
 QJ7  C05  H21  single    0.930  0.020  1.080
 QJ7  C07  H22  single    0.970  0.020  1.090
 QJ7  C07  H23  single    0.970  0.020  1.090
 QJ7  C07  H24  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
 QJ7  C22  C23  C24  122.59  3.000
 QJ7  C24  C23  F23  118.81  3.000
 QJ7  C22  C23  F23  118.61  3.000
 QJ7  H1   C24  C25  121.41  3.000
 QJ7  H1   C24  C23  120.72  3.000
 QJ7  C25  C24  C23  117.88  3.000
 QJ7  H2   C25  C26  119.97  3.000
 QJ7  H2   C25  C24  119.37  3.000
 QJ7  C26  C25  C24  120.65  3.000
 QJ7  H3   C26  C21  119.54  3.000
 QJ7  H3   C26  C25  119.77  3.000
 QJ7  C21  C26  C25  120.69  3.000
 QJ7  H4   C22  C21  120.75  3.000
 QJ7  H4   C22  C23  119.95  3.000
 QJ7  C21  C22  C23  119.30  3.000
 QJ7  C20  C21  C22  120.21  3.000
 QJ7  C22  C21  C26  118.90  3.000
 QJ7  C20  C21  C26  120.86  3.000
 QJ7  H6   C20  H5   107.07  3.000
 QJ7  H6   C20  C19  109.35  3.000
 QJ7  H5   C20  C19  109.12  3.000
 QJ7  H6   C20  C21  109.55  3.000
 QJ7  H5   C20  C21  110.32  3.000
 QJ7  C19  C20  C21  111.32  3.000
 QJ7  H8   C19  H7   106.36  3.000
 QJ7  H8   C19  N18  108.32  3.000
 QJ7  H7   C19  N18  112.74  3.000
 QJ7  H8   C19  C20  109.22  3.000
 QJ7  H7   C19  C20  109.26  3.000
 QJ7  N18  C19  C20  110.79  3.000
 QJ7  H9   N18  C17  108.47  3.000
 QJ7  H9   N18  C19  108.83  3.000
 QJ7  C17  N18  C19  112.47  3.000
 QJ7  H12  C17  H11  106.32  3.000
 QJ7  H12  C17  C15  109.28  3.000
 QJ7  H11  C17  C15  109.35  3.000
 QJ7  H12  C17  N18  108.14  3.000
 QJ7  H11  C17  N18  113.04  3.000
 QJ7  C15  C17  N18  110.56  3.000
 QJ7  C16  C15  C14  117.69  3.000
 QJ7  C16  C15  C17  121.35  3.000
 QJ7  C14  C15  C17  120.94  3.000
 QJ7  H13  C14  C13  119.90  3.000
 QJ7  H13  C14  C15  120.67  3.000
 QJ7  C13  C14  C15  119.43  3.000
 QJ7  H14  C16  N11  116.73  3.000
 QJ7  H14  C16  C15  119.99  3.000
 QJ7  N11  C16  C15  123.28  3.000
 QJ7  C12  N11  C16  119.04  3.000
 QJ7  H15  C12  C13  121.58  3.000
 QJ7  H15  C12  N11  116.13  3.000
 QJ7  C13  C12  N11  122.30  3.000
 QJ7  O09  C13  C12  124.71  3.000
 QJ7  C12  C13  C14  118.26  3.000
 QJ7  O09  C13  C14  117.03  3.000
 QJ7  C08  O09  C13  118.80  3.000
 QJ7  H17  C08  H16  107.17  3.000
 QJ7  H17  C08  C06  108.64  3.000
 QJ7  H16  C08  C06  109.35  3.000
 QJ7  H17  C08  O09  110.96  3.000
 QJ7  H16  C08  O09  110.85  3.000
 QJ7  C06  C08  O09  109.80  3.000
 QJ7  C05  C06  N01  123.58  3.000
 QJ7  N01  C06  C08  113.07  3.000
 QJ7  C05  C06  C08  123.33  3.000
 QJ7  C02  N01  C06  118.56  3.000
 QJ7  C03  C02  N02  120.66  3.000
 QJ7  N02  C02  N01  117.24  3.000
 QJ7  C03  C02  N01  122.07  3.000
 QJ7  H19  N02  H18  114.22  3.000
 QJ7  H19  N02  C02  117.68  3.000
 QJ7  H18  N02  C02  116.34  3.000
 QJ7  H20  C03  C04  120.93  3.000
 QJ7  H20  C03  C02  119.99  3.000
 QJ7  C04  C03  C02  119.08  3.000
 QJ7  C07  C04  C05  120.03  3.000
 QJ7  C05  C04  C03  118.48  3.000
 QJ7  C07  C04  C03  121.50  3.000
 QJ7  H21  C05  C04  120.16  3.000
 QJ7  H21  C05  C06  121.60  3.000
 QJ7  C04  C05  C06  118.23  3.000
 QJ7  H24  C07  H23  108.14  3.000
 QJ7  H24  C07  H22  108.13  3.000
 QJ7  H23  C07  H22  106.91  3.000
 QJ7  H24  C07  C04  111.96  3.000
 QJ7  H23  C07  C04  110.83  3.000
 QJ7  H22  C07  C04  110.69  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
 QJ7  CONST_01  C26  C21  C22  C23    0.00   0.0  0
 QJ7  CONST_02  C26  C25  C24  C23    0.00   0.0  0
 QJ7  CONST_03  C21  C26  C25  C24    0.00   0.0  0
 QJ7  CONST_04  C21  C22  C23  C24    0.00   0.0  0
 QJ7  CONST_05  C22  C21  C26  C25    0.00   0.0  0
 QJ7  CONST_06  C22  C23  C24  C25    0.00   0.0  0
 QJ7  CONST_07  C12  C13  C14  C15    0.00   0.0  0
 QJ7  CONST_08  C12  N11  C16  C15    0.00   0.0  0
 QJ7  CONST_09  N11  C12  C13  C14    0.00   0.0  0
 QJ7  CONST_10  N11  C16  C15  C14    0.00   0.0  0
 QJ7  CONST_11  C13  C14  C15  C16    0.00   0.0  0
 QJ7  CONST_12  C13  C12  N11  C16    0.00   0.0  0
 QJ7  CONST_13  C03  C04  C05  C06    0.00   0.0  0
 QJ7  CONST_14  C03  C02  N01  C06    0.00   0.0  0
 QJ7  CONST_15  C04  C03  C02  N01    0.00   0.0  0
 QJ7  CONST_16  C04  C05  C06  N01    0.00   0.0  0
 QJ7  CONST_17  C05  C04  C03  C02    0.00   0.0  0
 QJ7  CONST_18  C05  C06  N01  C02    0.00   0.0  0
 QJ7  CONST_19  C21  C22  C23  F23  180.00   0.0  0
 QJ7  CONST_20  C25  C24  C23  F23  180.00   0.0  0
 QJ7  CONST_21  C20  C21  C22  C23  180.00   0.0  0
 QJ7  CONST_22  C20  C21  C26  C25  180.00   0.0  0
 QJ7  CONST_23  C13  C14  C15  C17  180.00   0.0  0
 QJ7  CONST_24  N11  C16  C15  C17  180.00   0.0  0
 QJ7  CONST_25  O09  C13  C14  C15  180.00   0.0  0
 QJ7  CONST_26  O09  C13  C12  N11  180.00   0.0  0
 QJ7  CONST_27  C04  C05  C06  C08  180.00   0.0  0
 QJ7  CONST_28  C02  N01  C06  C08  180.00   0.0  0
 QJ7  CONST_29  C07  C04  C05  C06  180.00   0.0  0
 QJ7  CONST_30  N02  C02  N01  C06  180.00   0.0  0
 QJ7  CONST_31  C07  C04  C03  C02  180.00   0.0  0
 QJ7  CONST_32  C04  C03  C02  N02  180.00   0.0  0
 QJ7  CONST_33  H2   C25  C24  C23  180.00   0.0  0
 QJ7  CONST_34  H3   C26  C25  C24  180.00   0.0  0
 QJ7  CONST_35  H4   C22  C23  C24  180.00   0.0  0
 QJ7  CONST_36  H1   C24  C25  C26  180.00   0.0  0
 QJ7  CONST_37  H15  C12  C13  C14  180.00   0.0  0
 QJ7  CONST_38  H14  C16  C15  C14  180.00   0.0  0
 QJ7  CONST_39  H13  C14  C15  C16  180.00   0.0  0
 QJ7  CONST_40  H20  C03  C02  N01  180.00   0.0  0
 QJ7  CONST_41  H21  C05  C06  N01  180.00   0.0  0
 QJ7  Var_01    C19  C20  C21  C26   90.48  30.0  3
 QJ7  Var_02    C14  C15  C17  N18  -66.59  30.0  1
 QJ7  Var_03    C06  C08  O09  C13  176.35  30.0  3
 QJ7  Var_04    C05  C06  C08  O09   -6.29  30.0  1
 QJ7  Var_05    H22  C07  C04  C03  119.78  30.0  2
 QJ7  Var_06    N18  C19  C20  C21  179.59  30.0  2
 QJ7  Var_07    C15  C17  N18  C19  178.32  30.0  1
 QJ7  Var_08    C17  N18  C19  C20  178.59  30.0  1

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
 QJ7  plan-1  F23  0.020
 QJ7  plan-1  C23  0.020
 QJ7  plan-1  C24  0.020
 QJ7  plan-1  C25  0.020
 QJ7  plan-1  C26  0.020
 QJ7  plan-1  C22  0.020
 QJ7  plan-1  C21  0.020
 QJ7  plan-1  C20  0.020
 QJ7  plan-1  H1   0.020
 QJ7  plan-1  H2   0.020
 QJ7  plan-1  H3   0.020
 QJ7  plan-1  H4   0.020
 QJ7  plan-2  C17  0.020
 QJ7  plan-2  C15  0.020
 QJ7  plan-2  C14  0.020
 QJ7  plan-2  C16  0.020
 QJ7  plan-2  N11  0.020
 QJ7  plan-2  C12  0.020
 QJ7  plan-2  C13  0.020
 QJ7  plan-2  O09  0.020
 QJ7  plan-2  H13  0.020
 QJ7  plan-2  H14  0.020
 QJ7  plan-2  H15  0.020
 QJ7  plan-3  C08  0.020
 QJ7  plan-3  C06  0.020
 QJ7  plan-3  N01  0.020
 QJ7  plan-3  C02  0.020
 QJ7  plan-3  N02  0.020
 QJ7  plan-3  C03  0.020
 QJ7  plan-3  C04  0.020
 QJ7  plan-3  C05  0.020
 QJ7  plan-3  C07  0.020
 QJ7  plan-3  H20  0.020
 QJ7  plan-3  H21  0.020
 QJ7  plan-4  C02  0.020
 QJ7  plan-4  N02  0.020
 QJ7  plan-4  H18  0.020
 QJ7  plan-4  H19  0.020

