# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:31:01 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cc(OCc2ccc3c(C)cc(N)nc3c2)cc(c1)C#N
#
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
 8EY  8EY  3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-[(methylamino)methyl]benzonitrile  ligand  45  25  .  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_8EY
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
 8EY  C23  C  CR6   0   0.058  -4.1198   1.2014  -0.8373
 8EY  C24  C  CR16  0  -0.323  -4.9117   0.2041  -0.2852
 8EY  C25  C  CR6   0   0.107  -4.2998  -0.8478   0.3928
 8EY  C26  C  CR16  0  -0.388  -2.9186  -0.8758   0.4928
 8EY  C22  C  CR16  0  -0.398  -2.7270   1.1876  -0.7353
 8EY  C21  C  CR6   0   0.429  -2.1259   0.1339  -0.0593
 8EY  C12  C  CH2   0  -0.274   0.0540   1.0221  -0.3928
 8EY  C11  C  CH3   0  -0.749   5.9212  -0.3149   2.4595
 8EY  C08  C  CR6   0   0.096   1.4606   0.6735  -0.0132
 8EY  C07  C  CR16  0  -0.287   1.8154   0.5701   1.3472
 8EY  C06  C  CR16  0  -0.324   3.1075   0.2818   1.7013
 8EY  C09  C  CR16  0  -0.371   2.4129   0.4748  -0.9807
 8EY  C10  C  CR66  0   0.232   3.7531   0.1796  -0.6441
 8EY  N01  N  N     0  -0.514   4.6389   0.0033  -1.6519
 8EY  C05  C  CR66  0   0.013   4.1029   0.0839   0.7232
 8EY  C04  C  CR6   0   0.211   5.4685  -0.2020   1.0384
 8EY  C03  C  CR16  0  -0.448   6.3397  -0.3715   0.0074
 8EY  C02  C  CR6   0   0.450   5.8848  -0.2668  -1.3425
 8EY  N02  N  NH2   0  -0.839   6.7638  -0.4923  -2.3495
 8EY  N31  N  NS    0  -0.252  -5.2490   3.1466  -2.1037
 8EY  C30  C  CSP   0   0.050  -4.7447   2.2789  -1.5376
 8EY  C27  C  CH2   0  -0.306  -5.1245  -1.9258   1.0468
 8EY  N28  N  NH1   0  -0.592  -6.3400  -2.2043   0.3159
 8EY  C29  C  CH3   0  -0.518  -7.2000  -3.1429   1.0080
 8EY  O13  O  O2    0  -0.467  -0.7991  -0.0011   0.1028
 8EY  H1   H  HCR6  0   0.269  -5.9876   0.2372  -0.3836
 8EY  H2   H  HCR6  0   0.271  -2.4314  -1.6970   1.0062
 8EY  H3   H  HCR6  0   0.305  -2.1552   1.9856  -1.1868
 8EY  H4   H  HCH2  0   0.248  -0.2264   1.9868   0.0454
 8EY  H5   H  HCH2  0   0.252  -0.0390   1.1084  -1.4800
 8EY  H6   H  HCH3  0   0.254   5.6910   0.5898   3.0238
 8EY  H7   H  HCH3  0   0.256   5.4226  -1.1434   2.9658
 8EY  H8   H  HCH3  0   0.260   6.9947  -0.4836   2.5183
 8EY  H9   H  HCR6  0   0.252   1.0684   0.7263   2.1153
 8EY  H10  H  HCR6  0   0.257   3.3637   0.2096   2.7506
 8EY  H11  H  HCR6  0   0.251   2.1553   0.5467  -2.0310
 8EY  H12  H  HCR6  0   0.266   7.3844  -0.5866   0.1985
 8EY  H13  H  HNH2  0   0.397   7.7495  -0.4353  -2.1606
 8EY  H14  H  HNH2  0   0.386   6.4857  -0.2289  -3.2800
 8EY  H15  H  HCH2  0   0.221  -4.4951  -2.8149   1.2039
 8EY  H16  H  HCH2  0   0.250  -5.4057  -1.5807   2.0480
 8EY  H17  H  HNH1  0   0.349  -6.1013  -2.5791  -0.5939
 8EY  H19  H  HCH3  0   0.197  -6.7218  -4.1032   1.2427
 8EY  H20  H  HCH3  0   0.226  -7.5367  -2.7069   1.9503
 8EY  H21  H  HCH3  0   0.236  -8.0838  -3.3464   0.4040

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
 8EY  C11  C04  single    1.496  0.020  1.496
 8EY  C04  C03  aromatic  1.360  0.020  1.360
 8EY  C04  C05  aromatic  1.430  0.020  1.430
 8EY  C03  C02  aromatic  1.428  0.020  1.428
 8EY  C06  C05  aromatic  1.409  0.020  1.409
 8EY  C06  C07  aromatic  1.370  0.020  1.370
 8EY  C05  C10  aromatic  1.415  0.020  1.415
 8EY  C02  N02  single    1.356  0.020  1.356
 8EY  C02  N01  aromatic  1.312  0.020  1.312
 8EY  C07  C08  aromatic  1.410  0.020  1.410
 8EY  N31  C30  triple    1.152  0.020  1.152
 8EY  C10  N01  aromatic  1.353  0.020  1.353
 8EY  C10  C09  aromatic  1.413  0.020  1.413
 8EY  C30  C23  single    1.429  0.020  1.429
 8EY  C22  C23  aromatic  1.397  0.020  1.397
 8EY  C22  C21  aromatic  1.389  0.020  1.389
 8EY  C08  C09  aromatic  1.372  0.020  1.372
 8EY  C08  C12  single    1.498  0.020  1.498
 8EY  O13  C21  single    1.343  0.020  1.343
 8EY  O13  C12  single    1.421  0.020  1.421
 8EY  C23  C24  aromatic  1.388  0.020  1.388
 8EY  C21  C26  aromatic  1.397  0.020  1.397
 8EY  C24  C25  aromatic  1.393  0.020  1.393
 8EY  C26  C25  aromatic  1.385  0.020  1.385
 8EY  C25  C27  single    1.507  0.020  1.507
 8EY  C29  N28  single    1.449  0.020  1.449
 8EY  C27  N28  single    1.445  0.020  1.445
 8EY  C24  H1   single    0.930  0.020  1.080
 8EY  C26  H2   single    0.930  0.020  1.080
 8EY  C22  H3   single    0.930  0.020  1.080
 8EY  C12  H4   single    0.970  0.020  1.090
 8EY  C12  H5   single    0.970  0.020  1.090
 8EY  C11  H6   single    0.970  0.020  1.090
 8EY  C11  H7   single    0.970  0.020  1.090
 8EY  C11  H8   single    0.970  0.020  1.090
 8EY  C07  H9   single    0.930  0.020  1.080
 8EY  C06  H10  single    0.930  0.020  1.080
 8EY  C09  H11  single    0.930  0.020  1.080
 8EY  C03  H12  single    0.930  0.020  1.080
 8EY  N02  H13  single    0.890  0.020  1.040
 8EY  N02  H14  single    0.890  0.020  1.040
 8EY  C27  H15  single    0.970  0.020  1.090
 8EY  C27  H16  single    0.970  0.020  1.090
 8EY  N28  H17  single    0.890  0.020  1.040
 8EY  C29  H19  single    0.970  0.020  1.090
 8EY  C29  H20  single    0.970  0.020  1.090
 8EY  C29  H21  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
 8EY  C30  C23  C22  118.64  3.000
 8EY  C22  C23  C24  122.20  3.000
 8EY  C30  C23  C24  119.16  3.000
 8EY  H1   C24  C25  120.30  3.000
 8EY  H1   C24  C23  120.64  3.000
 8EY  C25  C24  C23  119.05  3.000
 8EY  C27  C25  C26  120.00  3.000
 8EY  C27  C25  C24  120.74  3.000
 8EY  C26  C25  C24  119.23  3.000
 8EY  H2   C26  C21  118.65  3.000
 8EY  H2   C26  C25  119.84  3.000
 8EY  C21  C26  C25  121.50  3.000
 8EY  H3   C22  C21  122.33  3.000
 8EY  H3   C22  C23  119.33  3.000
 8EY  C21  C22  C23  118.34  3.000
 8EY  O13  C21  C22  124.23  3.000
 8EY  O13  C21  C26  116.10  3.000
 8EY  C22  C21  C26  119.67  3.000
 8EY  H5   C12  H4   107.82  3.000
 8EY  H5   C12  O13  110.61  3.000
 8EY  H4   C12  O13  109.91  3.000
 8EY  H5   C12  C08  110.48  3.000
 8EY  H4   C12  C08  110.11  3.000
 8EY  O13  C12  C08  107.92  3.000
 8EY  H8   C11  H7   107.93  3.000
 8EY  H8   C11  H6   107.99  3.000
 8EY  H7   C11  H6   107.05  3.000
 8EY  H8   C11  C04  111.20  3.000
 8EY  H7   C11  C04  111.08  3.000
 8EY  H6   C11  C04  111.41  3.000
 8EY  C09  C08  C07  119.68  3.000
 8EY  C09  C08  C12  120.45  3.000
 8EY  C07  C08  C12  119.86  3.000
 8EY  H9   C07  C06  119.84  3.000
 8EY  H9   C07  C08  120.02  3.000
 8EY  C06  C07  C08  120.14  3.000
 8EY  H10  C06  C05  119.75  3.000
 8EY  H10  C06  C07  119.18  3.000
 8EY  C05  C06  C07  121.07  3.000
 8EY  H11  C09  C10  118.04  3.000
 8EY  H11  C09  C08  120.58  3.000
 8EY  C10  C09  C08  121.38  3.000
 8EY  C05  C10  N01  123.31  3.000
 8EY  N01  C10  C09  118.08  3.000
 8EY  C05  C10  C09  118.61  3.000
 8EY  C02  N01  C10  118.22  3.000
 8EY  C04  C05  C10  117.55  3.000
 8EY  C10  C05  C06  119.12  3.000
 8EY  C04  C05  C06  123.33  3.000
 8EY  C03  C04  C05  117.99  3.000
 8EY  C05  C04  C11  120.89  3.000
 8EY  C03  C04  C11  121.12  3.000
 8EY  H12  C03  C02  119.23  3.000
 8EY  H12  C03  C04  120.56  3.000
 8EY  C02  C03  C04  120.21  3.000
 8EY  N02  C02  C03  118.91  3.000
 8EY  N02  C02  N01  118.35  3.000
 8EY  C03  C02  N01  122.72  3.000
 8EY  H14  N02  H13  115.46  3.000
 8EY  H14  N02  C02  117.66  3.000
 8EY  H13  N02  C02  119.12  3.000
 8EY  N31  C30  C23  180.00  3.000
 8EY  H16  C27  H15  105.71  3.000
 8EY  H16  C27  N28  107.87  3.000
 8EY  H15  C27  N28  113.42  3.000
 8EY  H16  C27  C25  108.17  3.000
 8EY  H15  C27  C25  109.08  3.000
 8EY  N28  C27  C25  112.25  3.000
 8EY  H17  N28  C29  109.23  3.000
 8EY  H17  N28  C27  109.11  3.000
 8EY  C29  N28  C27  112.48  3.000
 8EY  H21  C29  H20  107.63  3.000
 8EY  H21  C29  H19  107.96  3.000
 8EY  H20  C29  H19  107.41  3.000
 8EY  H21  C29  N28  109.73  3.000
 8EY  H20  C29  N28  109.68  3.000
 8EY  H19  C29  N28  114.21  3.000
 8EY  C12  O13  C21  118.58  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
 8EY  CONST_01  C26  C21  C22  C23     0.00   0.0  0
 8EY  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 8EY  CONST_03  C21  C22  C23  C24     0.00   0.0  0
 8EY  CONST_04  C21  C26  C25  C24     0.00   0.0  0
 8EY  CONST_05  C22  C23  C24  C25     0.00   0.0  0
 8EY  CONST_06  C22  C21  C26  C25     0.00   0.0  0
 8EY  CONST_07  C05  C06  C07  C08     0.00   0.0  0
 8EY  CONST_08  C05  C10  C09  C08     0.00   0.0  0
 8EY  CONST_09  N01  C10  C09  C08   180.00   0.0  0
 8EY  CONST_10  C04  C05  C06  C07   180.00   0.0  0
 8EY  CONST_11  C10  C05  C06  C07     0.00   0.0  0
 8EY  CONST_12  C10  C09  C08  C07     0.00   0.0  0
 8EY  CONST_13  C03  C04  C05  C06   180.00   0.0  0
 8EY  CONST_14  N01  C10  C05  C06   180.00   0.0  0
 8EY  CONST_15  C09  C10  C05  C06     0.00   0.0  0
 8EY  CONST_16  C09  C08  C07  C06     0.00   0.0  0
 8EY  CONST_17  C04  C05  C10  C09   180.00   0.0  0
 8EY  CONST_18  C02  N01  C10  C09   180.00   0.0  0
 8EY  CONST_19  C03  C04  C05  C10     0.00   0.0  0
 8EY  CONST_20  C03  C02  N01  C10     0.00   0.0  0
 8EY  CONST_21  C04  C03  C02  N01     0.00   0.0  0
 8EY  CONST_22  C04  C05  C10  N01     0.00   0.0  0
 8EY  CONST_23  C02  C03  C04  C05     0.00   0.0  0
 8EY  CONST_24  C02  N01  C10  C05     0.00   0.0  0
 8EY  CONST_25  O13  C21  C22  C23   180.00   0.0  0
 8EY  CONST_26  C27  C25  C24  C23   180.00   0.0  0
 8EY  CONST_27  C30  C23  C24  C25   180.00   0.0  0
 8EY  CONST_28  O13  C21  C26  C25   180.00   0.0  0
 8EY  CONST_29  C30  C23  C22  C21   180.00   0.0  0
 8EY  CONST_30  C27  C25  C26  C21   180.00   0.0  0
 8EY  CONST_31  C06  C07  C08  C12   180.00   0.0  0
 8EY  CONST_32  C10  C09  C08  C12   180.00   0.0  0
 8EY  CONST_33  C02  C03  C04  C11   180.00   0.0  0
 8EY  CONST_34  C06  C05  C04  C11     0.00   0.0  0
 8EY  CONST_35  C10  C05  C04  C11   180.00   0.0  0
 8EY  CONST_36  N02  C02  N01  C10   180.00   0.0  0
 8EY  CONST_37  N02  C02  C03  C04   180.00   0.0  0
 8EY  CONST_38  H3   C22  C23  C24   180.00   0.0  0
 8EY  CONST_39  H2   C26  C25  C24   180.00   0.0  0
 8EY  CONST_40  H1   C24  C25  C26   180.00   0.0  0
 8EY  CONST_41  H10  C06  C07  C08   180.00   0.0  0
 8EY  CONST_42  H11  C09  C08  C07   180.00   0.0  0
 8EY  CONST_43  H9   C07  C08  C09   180.00   0.0  0
 8EY  CONST_44  H12  C03  C02  N01   180.00   0.0  0
 8EY  CONST_46  H14  N02  C02  N01     0.00   0.0  0
 8EY  Var_01    N28  C27  C25  C24    33.48  30.0  2
 8EY  Var_02    C08  C12  O13  C21   176.58  30.0  3
 8EY  Var_03    O13  C12  C08  C07   -61.68  30.0  2
 8EY  Var_04    H6   C11  C04  C05   -56.52  30.0  2
 8EY  Var_05    C29  N28  C27  C25  -174.25  30.0  3
 8EY  Var_06    H19  C29  N28  C27   -56.71  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
 8EY  plan-1  C23  0.020
 8EY  plan-1  C24  0.020
 8EY  plan-1  C25  0.020
 8EY  plan-1  C26  0.020
 8EY  plan-1  C22  0.020
 8EY  plan-1  C21  0.020
 8EY  plan-1  N31  0.020
 8EY  plan-1  C30  0.020
 8EY  plan-1  C27  0.020
 8EY  plan-1  O13  0.020
 8EY  plan-1  H1   0.020
 8EY  plan-1  H2   0.020
 8EY  plan-1  H3   0.020
 8EY  plan-2  C12  0.020
 8EY  plan-2  C11  0.020
 8EY  plan-2  C08  0.020
 8EY  plan-2  C07  0.020
 8EY  plan-2  C06  0.020
 8EY  plan-2  C09  0.020
 8EY  plan-2  C10  0.020
 8EY  plan-2  N01  0.020
 8EY  plan-2  C05  0.020
 8EY  plan-2  C04  0.020
 8EY  plan-2  C03  0.020
 8EY  plan-2  C02  0.020
 8EY  plan-2  N02  0.020
 8EY  plan-2  H9   0.020
 8EY  plan-2  H10  0.020
 8EY  plan-2  H11  0.020
 8EY  plan-2  H12  0.020
 8EY  plan-3  C02  0.020
 8EY  plan-3  N02  0.020
 8EY  plan-3  H13  0.020
 8EY  plan-3  H14  0.020

