# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 22:34:37 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 3-[2-(2-amino-4-methylquinolin-7-yl)ethyl]-5-[(methylamino)methyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1cc(CCc2ccc3c(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
 8F7  8F7  3-[2-(2-amino-4-methylquinolin-7-yl)ethyl]-5-[(methylamino)methyl]benzonitrile  ligand  47  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_8F7
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
 8F7  N28  N  NS    0  -0.249   5.0333  -3.9725  -1.0690
 8F7  C27  C  CSP   0   0.052   4.6192  -2.9184  -0.8563
 8F7  C23  C  CR6   0   0.055   4.1013  -1.6147  -0.5898
 8F7  C24  C  CR16  0  -0.292   4.9573  -0.6149  -0.1420
 8F7  C25  C  CR6   0   0.134   4.4522   0.6528   0.1230
 8F7  C29  C  CH2   0  -0.312   5.3661   1.7373   0.6261
 8F7  N30  N  NH1   0  -0.577   6.5451   1.8573  -0.2040
 8F7  C31  C  CH3   0  -0.501   7.4929   2.8255   0.3068
 8F7  C22  C  CR16  0  -0.312   2.7425  -1.3639  -0.7869
 8F7  C21  C  CR6   0   0.183   2.2309  -0.1009  -0.5383
 8F7  C26  C  CR16  0  -0.333   3.1003   0.8909  -0.0849
 8F7  C13  C  CH2   0  -0.504   0.7682   0.1883  -0.7154
 8F7  C12  C  CH2   0  -0.498   0.0065   0.1106   0.6157
 8F7  C08  C  CR6   0   0.145  -1.4622   0.3733   0.4433
 8F7  C09  C  CR16  0  -0.370  -2.3850  -0.6343   0.5840
 8F7  C07  C  CR16  0  -0.278  -1.9121   1.6670   0.1052
 8F7  C06  C  CR16  0  -0.305  -3.2447   1.9161  -0.0905
 8F7  C05  C  CR66  0   0.012  -4.2016   0.8917   0.0488
 8F7  C04  C  CR6   0   0.219  -5.6027   1.0923  -0.1443
 8F7  C11  C  CH3   0  -0.721  -6.1389   2.4324  -0.5357
 8F7  C03  C  CR16  0  -0.425  -6.4317   0.0287   0.0371
 8F7  C02  C  CR6   0   0.462  -5.8954  -1.2411   0.4026
 8F7  N02  N  NH2   0  -0.817  -6.7476  -2.2766   0.6270
 8F7  N01  N  N     0  -0.521  -4.6133  -1.4501   0.5710
 8F7  C10  C  CR66  0   0.240  -3.7657  -0.4075   0.4008
 8F7  H1   H  HCR6  0   0.260   6.0106  -0.8191  -0.0032
 8F7  H2   H  HCH2  0   0.208   4.8004   2.6768   0.7211
 8F7  H3   H  HCH2  0   0.240   5.6923   1.4809   1.6392
 8F7  H4   H  HNH1  0   0.337   6.2652   2.1257  -1.1387
 8F7  H6   H  HCH3  0   0.222   7.8988   2.4814   1.2598
 8F7  H7   H  HCH3  0   0.227   8.3256   2.9241  -0.3884
 8F7  H8   H  HCH3  0   0.190   7.0725   3.8271   0.4707
 8F7  H9   H  HCR6  0   0.243   2.0967  -2.1577  -1.1396
 8F7  H10  H  HCR6  0   0.223   2.7096   1.8852   0.1056
 8F7  H11  H  HCH2  0   0.244   0.6399   1.1807  -1.1541
 8F7  H12  H  HCH2  0   0.251   0.3277  -0.5179  -1.4222
 8F7  H13  H  HCH2  0   0.247   0.1595  -0.8757   1.0578
 8F7  H14  H  HCH2  0   0.243   0.4341   0.8310   1.3193
 8F7  H15  H  HCR6  0   0.223  -2.0669  -1.6357   0.8500
 8F7  H16  H  HCR6  0   0.220  -1.1980   2.4750   0.0037
 8F7  H17  H  HCR6  0   0.234  -3.5623   2.9174  -0.3507
 8F7  H18  H  HCH3  0   0.246  -5.9179   3.1853   0.2222
 8F7  H19  H  HCH3  0   0.244  -5.6963   2.7769  -1.4712
 8F7  H20  H  HCH3  0   0.246  -7.2181   2.4038  -0.6688
 8F7  H21  H  HCR6  0   0.229  -7.5012   0.1403  -0.0930
 8F7  H22  H  HNH2  0   0.368  -7.6790  -2.2314   0.2559
 8F7  H23  H  HNH2  0   0.367  -6.3537  -3.2005   0.6612

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
 8F7  C11  C04  single    1.496  0.020  1.496
 8F7  C04  C03  aromatic  1.361  0.020  1.361
 8F7  C04  C05  aromatic  1.428  0.020  1.428
 8F7  C03  C02  aromatic  1.426  0.020  1.426
 8F7  C06  C05  aromatic  1.409  0.020  1.409
 8F7  C06  C07  aromatic  1.370  0.020  1.370
 8F7  C05  C10  aromatic  1.415  0.020  1.415
 8F7  C02  N02  single    1.360  0.020  1.360
 8F7  C02  N01  aromatic  1.310  0.020  1.310
 8F7  C07  C08  aromatic  1.411  0.020  1.411
 8F7  C10  N01  aromatic  1.354  0.020  1.354
 8F7  C10  C09  aromatic  1.411  0.020  1.411
 8F7  C08  C09  aromatic  1.374  0.020  1.374
 8F7  C08  C12  single    1.502  0.020  1.502
 8F7  C13  C12  single    1.536  0.020  1.536
 8F7  C13  C21  single    1.501  0.020  1.501
 8F7  C22  C21  aromatic  1.385  0.020  1.385
 8F7  C22  C23  aromatic  1.396  0.020  1.396
 8F7  C21  C26  aromatic  1.395  0.020  1.395
 8F7  N28  C27  triple    1.152  0.020  1.152
 8F7  C27  C23  single    1.428  0.020  1.428
 8F7  C23  C24  aromatic  1.390  0.020  1.390
 8F7  C26  C25  aromatic  1.388  0.020  1.388
 8F7  C24  C25  aromatic  1.390  0.020  1.390
 8F7  C25  C29  single    1.505  0.020  1.505
 8F7  C31  N30  single    1.448  0.020  1.448
 8F7  C29  N30  single    1.447  0.020  1.447
 8F7  C24  H1   single    0.930  0.020  1.080
 8F7  C29  H2   single    0.970  0.020  1.090
 8F7  C29  H3   single    0.970  0.020  1.090
 8F7  N30  H4   single    0.890  0.020  1.040
 8F7  C31  H6   single    0.970  0.020  1.090
 8F7  C31  H7   single    0.970  0.020  1.090
 8F7  C31  H8   single    0.970  0.020  1.090
 8F7  C22  H9   single    0.930  0.020  1.080
 8F7  C26  H10  single    0.930  0.020  1.080
 8F7  C13  H11  single    0.970  0.020  1.090
 8F7  C13  H12  single    0.970  0.020  1.090
 8F7  C12  H13  single    0.970  0.020  1.090
 8F7  C12  H14  single    0.970  0.020  1.090
 8F7  C09  H15  single    0.930  0.020  1.080
 8F7  C07  H16  single    0.930  0.020  1.080
 8F7  C06  H17  single    0.930  0.020  1.080
 8F7  C11  H18  single    0.970  0.020  1.090
 8F7  C11  H19  single    0.970  0.020  1.090
 8F7  C11  H20  single    0.970  0.020  1.090
 8F7  C03  H21  single    0.930  0.020  1.080
 8F7  N02  H22  single    0.890  0.020  1.040
 8F7  N02  H23  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
 8F7  C23  C27  N28  180.00  3.000
 8F7  C22  C23  C24  121.04  3.000
 8F7  C24  C23  C27  119.57  3.000
 8F7  C22  C23  C27  119.39  3.000
 8F7  H1   C24  C25  120.09  3.000
 8F7  H1   C24  C23  120.34  3.000
 8F7  C25  C24  C23  119.57  3.000
 8F7  C26  C25  C29  121.19  3.000
 8F7  C29  C25  C24  120.02  3.000
 8F7  C26  C25  C24  118.79  3.000
 8F7  H3   C29  H2   105.85  3.000
 8F7  H3   C29  N30  107.91  3.000
 8F7  H2   C29  N30  113.43  3.000
 8F7  H3   C29  C25  108.75  3.000
 8F7  H2   C29  C25  109.38  3.000
 8F7  N30  C29  C25  111.28  3.000
 8F7  H4   N30  C31  109.24  3.000
 8F7  H4   N30  C29  109.05  3.000
 8F7  C31  N30  C29  112.74  3.000
 8F7  H8   C31  H7   107.78  3.000
 8F7  H8   C31  H6   107.43  3.000
 8F7  H7   C31  H6   107.55  3.000
 8F7  H8   C31  N30  114.32  3.000
 8F7  H7   C31  N30  109.62  3.000
 8F7  H6   C31  N30  109.91  3.000
 8F7  H9   C22  C21  120.45  3.000
 8F7  H9   C22  C23  119.68  3.000
 8F7  C21  C22  C23  119.87  3.000
 8F7  C13  C21  C26  120.57  3.000
 8F7  C26  C21  C22  118.46  3.000
 8F7  C13  C21  C22  120.95  3.000
 8F7  H10  C26  C21  118.96  3.000
 8F7  H10  C26  C25  118.78  3.000
 8F7  C21  C26  C25  122.26  3.000
 8F7  H12  C13  H11  106.27  3.000
 8F7  H12  C13  C12  109.16  3.000
 8F7  H11  C13  C12  109.62  3.000
 8F7  H12  C13  C21  110.17  3.000
 8F7  H11  C13  C21  109.67  3.000
 8F7  C12  C13  C21  111.80  3.000
 8F7  H14  C12  H13  106.24  3.000
 8F7  H14  C12  C08  109.93  3.000
 8F7  H13  C12  C08  109.97  3.000
 8F7  H14  C12  C13  109.28  3.000
 8F7  H13  C12  C13  109.10  3.000
 8F7  C08  C12  C13  112.13  3.000
 8F7  C07  C08  C09  118.88  3.000
 8F7  C09  C08  C12  121.13  3.000
 8F7  C07  C08  C12  119.98  3.000
 8F7  H15  C09  C10  117.87  3.000
 8F7  H15  C09  C08  120.38  3.000
 8F7  C10  C09  C08  121.75  3.000
 8F7  H16  C07  C06  119.50  3.000
 8F7  H16  C07  C08  119.76  3.000
 8F7  C06  C07  C08  120.75  3.000
 8F7  H17  C06  C05  119.82  3.000
 8F7  H17  C06  C07  119.22  3.000
 8F7  C05  C06  C07  120.96  3.000
 8F7  C10  C05  C04  117.69  3.000
 8F7  C10  C05  C06  118.88  3.000
 8F7  C04  C05  C06  123.42  3.000
 8F7  C03  C04  C11  121.12  3.000
 8F7  C03  C04  C05  118.02  3.000
 8F7  C11  C04  C05  120.85  3.000
 8F7  H20  C11  H19  107.81  3.000
 8F7  H20  C11  H18  107.70  3.000
 8F7  H19  C11  H18  107.20  3.000
 8F7  H20  C11  C04  111.36  3.000
 8F7  H19  C11  C04  111.23  3.000
 8F7  H18  C11  C04  111.35  3.000
 8F7  H21  C03  C02  119.60  3.000
 8F7  H21  C03  C04  120.33  3.000
 8F7  C02  C03  C04  120.07  3.000
 8F7  N01  C02  N02  118.08  3.000
 8F7  N01  C02  C03  122.90  3.000
 8F7  N02  C02  C03  118.99  3.000
 8F7  H23  N02  H22  114.70  3.000
 8F7  H23  N02  C02  117.39  3.000
 8F7  H22  N02  C02  119.09  3.000
 8F7  C10  N01  C02  118.27  3.000
 8F7  N01  C10  C05  123.04  3.000
 8F7  N01  C10  C09  118.18  3.000
 8F7  C05  C10  C09  118.77  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
 8F7  CONST_01  C26  C21  C22  C23     0.00   0.0  0
 8F7  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 8F7  CONST_03  C21  C22  C23  C24     0.00   0.0  0
 8F7  CONST_04  C21  C26  C25  C24     0.00   0.0  0
 8F7  CONST_05  C22  C21  C26  C25     0.00   0.0  0
 8F7  CONST_06  C22  C23  C24  C25     0.00   0.0  0
 8F7  CONST_07  C05  C06  C07  C08     0.00   0.0  0
 8F7  CONST_08  C05  C10  C09  C08     0.00   0.0  0
 8F7  CONST_09  N01  C10  C09  C08   180.00   0.0  0
 8F7  CONST_10  C04  C05  C10  C09   180.00   0.0  0
 8F7  CONST_11  C06  C05  C10  C09     0.00   0.0  0
 8F7  CONST_12  C02  N01  C10  C09   180.00   0.0  0
 8F7  CONST_13  C06  C07  C08  C09     0.00   0.0  0
 8F7  CONST_14  C04  C05  C06  C07   180.00   0.0  0
 8F7  CONST_15  C10  C05  C06  C07     0.00   0.0  0
 8F7  CONST_16  C10  C09  C08  C07     0.00   0.0  0
 8F7  CONST_17  C03  C04  C05  C06   180.00   0.0  0
 8F7  CONST_18  N01  C10  C05  C06   180.00   0.0  0
 8F7  CONST_19  C02  C03  C04  C05     0.00   0.0  0
 8F7  CONST_20  C02  N01  C10  C05     0.00   0.0  0
 8F7  CONST_21  N01  C02  C03  C04     0.00   0.0  0
 8F7  CONST_22  N01  C10  C05  C04     0.00   0.0  0
 8F7  CONST_23  C10  C05  C04  C03     0.00   0.0  0
 8F7  CONST_24  C10  N01  C02  C03     0.00   0.0  0
 8F7  CONST_25  C21  C22  C23  C27   180.00   0.0  0
 8F7  CONST_26  C25  C24  C23  C27   180.00   0.0  0
 8F7  CONST_27  C13  C21  C22  C23   180.00   0.0  0
 8F7  CONST_28  C29  C25  C24  C23   180.00   0.0  0
 8F7  CONST_29  C13  C21  C26  C25   180.00   0.0  0
 8F7  CONST_30  C21  C26  C25  C29   180.00   0.0  0
 8F7  CONST_31  C06  C07  C08  C12   180.00   0.0  0
 8F7  CONST_32  C10  C09  C08  C12   180.00   0.0  0
 8F7  CONST_33  C11  C04  C05  C06     0.00   0.0  0
 8F7  CONST_34  N02  C02  C03  C04   180.00   0.0  0
 8F7  CONST_35  C02  C03  C04  C11   180.00   0.0  0
 8F7  CONST_36  C10  C05  C04  C11   180.00   0.0  0
 8F7  CONST_37  C10  N01  C02  N02   180.00   0.0  0
 8F7  CONST_38  H9   C22  C23  C24   180.00   0.0  0
 8F7  CONST_39  H10  C26  C25  C24   180.00   0.0  0
 8F7  CONST_40  H1   C24  C23  C22   180.00   0.0  0
 8F7  CONST_41  H17  C06  C07  C08   180.00   0.0  0
 8F7  CONST_42  H16  C07  C08  C09   180.00   0.0  0
 8F7  CONST_43  H15  C09  C08  C07   180.00   0.0  0
 8F7  CONST_44  H21  C03  C04  C05   180.00   0.0  0
 8F7  CONST_46  H23  N02  C02  C03   180.00   0.0  0
 8F7  Var_01    N30  C29  C25  C24    50.67  30.0  2
 8F7  Var_02    C12  C13  C21  C22    97.34  30.0  3
 8F7  Var_03    C08  C12  C13  C21  -178.93  30.0  3
 8F7  Var_04    C07  C08  C12  C13   -69.25  30.0  2
 8F7  Var_05    H18  C11  C04  C05   -61.44  30.0  2
 8F7  Var_06    C31  N30  C29  C25  -175.80  30.0  3
 8F7  Var_07    H6   C31  N30  C29    65.79  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
 8F7  plan-1  N28  0.020
 8F7  plan-1  C27  0.020
 8F7  plan-1  C23  0.020
 8F7  plan-1  C24  0.020
 8F7  plan-1  C25  0.020
 8F7  plan-1  C29  0.020
 8F7  plan-1  C22  0.020
 8F7  plan-1  C21  0.020
 8F7  plan-1  C26  0.020
 8F7  plan-1  C13  0.020
 8F7  plan-1  H1   0.020
 8F7  plan-1  H9   0.020
 8F7  plan-1  H10  0.020
 8F7  plan-2  C12  0.020
 8F7  plan-2  C08  0.020
 8F7  plan-2  C09  0.020
 8F7  plan-2  C07  0.020
 8F7  plan-2  C06  0.020
 8F7  plan-2  C05  0.020
 8F7  plan-2  C04  0.020
 8F7  plan-2  C11  0.020
 8F7  plan-2  C03  0.020
 8F7  plan-2  C02  0.020
 8F7  plan-2  N02  0.020
 8F7  plan-2  N01  0.020
 8F7  plan-2  C10  0.020
 8F7  plan-2  H15  0.020
 8F7  plan-2  H16  0.020
 8F7  plan-2  H17  0.020
 8F7  plan-2  H21  0.020
 8F7  plan-3  C02  0.020
 8F7  plan-3  N02  0.020
 8F7  plan-3  H22  0.020
 8F7  plan-3  H23  0.020

