# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 14:25:19 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4-(2-{[(2-aminoquinolin-7-yl)methyl]amino}ethyl)-2-methylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CCNCc2ccc3ccc(N)nc3c2)ccc1C#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
 9P7  9P7  4-(2-{[(2-aminoquinolin-7-yl)methyl]amino}ethyl)-2-methylbenzonitrile  ligand  44  24  .  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_9P7
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
 9P7  C10  C  CR66  0   0.235  -4.6768  -0.3168   0.3618
 9P7  C11  C  CH2   0  -0.324  -0.9453   0.2332   0.9239
 9P7  C13  C  CH2   0  -0.248   1.3611   0.2739   0.2102
 9P7  C14  C  CH2   0  -0.534   2.2840   0.4900  -0.9887
 9P7  N29  N  NS    0  -0.256   8.8201  -0.0285   1.0213
 9P7  C24  C  CR6   0  -0.046   6.3662   0.1547   0.2491
 9P7  C25  C  CR16  0  -0.216   5.7383   1.4001   0.2583
 9P7  C23  C  CR6   0   0.161   5.6892  -0.9970  -0.1776
 9P7  C27  C  CH3   0  -0.744   6.3663  -2.3330  -0.1919
 9P7  C22  C  CR16  0  -0.361   4.3712  -0.8510  -0.5881
 9P7  C21  C  CR6   0   0.159   3.7249   0.3833  -0.5865
 9P7  C26  C  CR16  0  -0.321   4.4251   1.5089  -0.1574
 9P7  N12  N  NH1   0  -0.594  -0.0266   0.3965  -0.1857
 9P7  C08  C  CR6   0   0.092  -2.3696   0.4364   0.4844
 9P7  C09  C  CR16  0  -0.381  -3.3319  -0.5059   0.7529
 9P7  C07  C  CR16  0  -0.294  -2.7232   1.6170  -0.2073
 9P7  C06  C  CR16  0  -0.306  -4.0182   1.8284  -0.5982
 9P7  C05  C  CR66  0   0.043  -5.0165   0.8720  -0.3242
 9P7  C04  C  CR16  0  -0.180  -6.3726   1.0293  -0.7063
 9P7  C03  C  CR16  0  -0.378  -7.2774   0.0629  -0.4084
 9P7  C02  C  CR6   0   0.435  -6.8329  -1.1038   0.2891
 9P7  N02  N  NH2   0  -0.835  -7.7407  -2.0538   0.6279
 9P7  N01  N  N     0  -0.508  -5.5832  -1.2796   0.6520
 9P7  H1   H  HCH2  0   0.217  -0.8529  -0.7422   1.4242
 9P7  H2   H  HCH2  0   0.240  -0.6953   0.9867   1.6785
 9P7  H3   H  HCH2  0   0.203   1.5926  -0.6985   0.6725
 9P7  H4   H  HCH2  0   0.229   1.5711   1.0345   0.9685
 9P7  H5   H  HCH2  0   0.251   2.0573  -0.2533  -1.7577
 9P7  H6   H  HCH2  0   0.252   2.0837   1.4738  -1.4178
 9P7  H7   H  HCR6  0   0.277   6.2816   2.2759   0.5869
 9P7  H8   H  HCH3  0   0.258   6.7141  -2.6127   0.8037
 9P7  H9   H  HCH3  0   0.262   5.6896  -3.1102  -0.5409
 9P7  H10  H  HCH3  0   0.258   7.2379  -2.3283  -0.8487
 9P7  H11  H  HCR6  0   0.256   3.8315  -1.7289  -0.9249
 9P7  H12  H  HCR6  0   0.262   3.9408   2.4774  -0.1538
 9P7  H13  H  HNH1  0   0.344  -0.2334  -0.3042  -0.8886
 9P7  H15  H  HCR6  0   0.244  -3.0723  -1.4202   1.2751
 9P7  H16  H  HCR6  0   0.244  -1.9588   2.3513  -0.4260
 9P7  H17  H  HCR6  0   0.253  -4.2914   2.7357  -1.1247
 9P7  H18  H  HCR6  0   0.267  -6.6803   1.9242  -1.2340
 9P7  H19  H  HCR6  0   0.272  -8.3184   0.1615  -0.6882
 9P7  H20  H  HNH2  0   0.396  -8.6194  -2.0791   0.1398
 9P7  H21  H  HNH2  0   0.386  -7.3874  -2.9482   0.9248
 9P7  C28  C  CSP   0   0.029   7.7229   0.0561   0.6768

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
 9P7  C04  C03  aromatic  1.357  0.020  1.357
 9P7  C04  C05  aromatic  1.418  0.020  1.418
 9P7  C03  C02  aromatic  1.430  0.020  1.430
 9P7  C06  C05  aromatic  1.409  0.020  1.409
 9P7  C06  C07  aromatic  1.369  0.020  1.369
 9P7  C05  C10  aromatic  1.414  0.020  1.414
 9P7  C02  N02  single    1.357  0.020  1.357
 9P7  C02  N01  aromatic  1.313  0.020  1.313
 9P7  C07  C08  aromatic  1.413  0.020  1.413
 9P7  C10  N01  aromatic  1.354  0.020  1.354
 9P7  C10  C09  aromatic  1.413  0.020  1.413
 9P7  C08  C09  aromatic  1.373  0.020  1.373
 9P7  C08  C11  single    1.504  0.020  1.504
 9P7  C11  N12  single    1.450  0.020  1.450
 9P7  N12  C13  single    1.448  0.020  1.448
 9P7  C13  C14  single    1.528  0.020  1.528
 9P7  C14  C21  single    1.500  0.020  1.500
 9P7  C22  C21  aromatic  1.393  0.020  1.393
 9P7  C22  C23  aromatic  1.388  0.020  1.388
 9P7  C27  C23  single    1.498  0.020  1.498
 9P7  C21  C26  aromatic  1.393  0.020  1.393
 9P7  C23  C24  aromatic  1.402  0.020  1.402
 9P7  C26  C25  aromatic  1.382  0.020  1.382
 9P7  C24  C25  aromatic  1.395  0.020  1.395
 9P7  C24  C28  single    1.426  0.020  1.426
 9P7  C28  N29  triple    1.153  0.020  1.153
 9P7  C11  H1   single    0.970  0.020  1.090
 9P7  C11  H2   single    0.970  0.020  1.090
 9P7  C13  H3   single    0.970  0.020  1.090
 9P7  C13  H4   single    0.970  0.020  1.090
 9P7  C14  H5   single    0.970  0.020  1.090
 9P7  C14  H6   single    0.970  0.020  1.090
 9P7  C25  H7   single    0.930  0.020  1.080
 9P7  C27  H8   single    0.970  0.020  1.090
 9P7  C27  H9   single    0.970  0.020  1.090
 9P7  C27  H10  single    0.970  0.020  1.090
 9P7  C22  H11  single    0.930  0.020  1.080
 9P7  C26  H12  single    0.930  0.020  1.080
 9P7  N12  H13  single    0.890  0.020  1.040
 9P7  C09  H15  single    0.930  0.020  1.080
 9P7  C07  H16  single    0.930  0.020  1.080
 9P7  C06  H17  single    0.930  0.020  1.080
 9P7  C04  H18  single    0.930  0.020  1.080
 9P7  C03  H19  single    0.930  0.020  1.080
 9P7  N02  H20  single    0.890  0.020  1.040
 9P7  N02  H21  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
 9P7  N01  C10  C05  122.76  3.000
 9P7  N01  C10  C09  118.86  3.000
 9P7  C05  C10  C09  118.38  3.000
 9P7  H2   C11  H1   106.10  3.000
 9P7  H2   C11  C08  108.94  3.000
 9P7  H1   C11  C08  109.40  3.000
 9P7  H2   C11  N12  107.77  3.000
 9P7  H1   C11  N12  113.25  3.000
 9P7  C08  C11  N12  111.17  3.000
 9P7  H4   C13  H3   106.41  3.000
 9P7  H4   C13  N12  108.32  3.000
 9P7  H3   C13  N12  113.01  3.000
 9P7  H4   C13  C14  109.24  3.000
 9P7  H3   C13  C14  109.10  3.000
 9P7  N12  C13  C14  110.62  3.000
 9P7  H6   C14  H5   107.35  3.000
 9P7  H6   C14  C21  110.23  3.000
 9P7  H5   C14  C21  109.84  3.000
 9P7  H6   C14  C13  108.96  3.000
 9P7  H5   C14  C13  109.29  3.000
 9P7  C21  C14  C13  111.08  3.000
 9P7  C23  C24  C25  121.20  3.000
 9P7  C25  C24  C28  119.21  3.000
 9P7  C23  C24  C28  119.59  3.000
 9P7  H7   C25  C26  120.33  3.000
 9P7  H7   C25  C24  119.93  3.000
 9P7  C26  C25  C24  119.74  3.000
 9P7  C22  C23  C27  121.34  3.000
 9P7  C27  C23  C24  121.14  3.000
 9P7  C22  C23  C24  117.51  3.000
 9P7  H10  C27  H9   107.87  3.000
 9P7  H10  C27  H8   107.20  3.000
 9P7  H9   C27  H8   107.93  3.000
 9P7  H10  C27  C23  111.28  3.000
 9P7  H9   C27  C23  111.04  3.000
 9P7  H8   C27  C23  111.35  3.000
 9P7  H11  C22  C21  119.13  3.000
 9P7  H11  C22  C23  118.64  3.000
 9P7  C21  C22  C23  122.22  3.000
 9P7  C26  C21  C22  118.88  3.000
 9P7  C26  C21  C14  120.53  3.000
 9P7  C22  C21  C14  120.55  3.000
 9P7  H12  C26  C21  119.92  3.000
 9P7  H12  C26  C25  119.64  3.000
 9P7  C21  C26  C25  120.44  3.000
 9P7  H13  N12  C13  109.05  3.000
 9P7  H13  N12  C11  108.88  3.000
 9P7  C13  N12  C11  112.86  3.000
 9P7  C07  C08  C09  119.58  3.000
 9P7  C09  C08  C11  120.90  3.000
 9P7  C07  C08  C11  119.52  3.000
 9P7  H15  C09  C08  120.33  3.000
 9P7  H15  C09  C10  118.29  3.000
 9P7  C08  C09  C10  121.39  3.000
 9P7  H16  C07  C06  120.37  3.000
 9P7  H16  C07  C08  119.28  3.000
 9P7  C06  C07  C08  120.36  3.000
 9P7  H17  C06  C05  118.94  3.000
 9P7  H17  C06  C07  120.42  3.000
 9P7  C05  C06  C07  120.64  3.000
 9P7  C04  C05  C06  123.35  3.000
 9P7  C06  C05  C10  119.65  3.000
 9P7  C04  C05  C10  116.99  3.000
 9P7  H18  C04  C03  120.38  3.000
 9P7  H18  C04  C05  119.64  3.000
 9P7  C03  C04  C05  119.97  3.000
 9P7  H19  C03  C02  119.95  3.000
 9P7  H19  C03  C04  121.31  3.000
 9P7  C02  C03  C04  118.74  3.000
 9P7  N01  C02  N02  118.29  3.000
 9P7  N01  C02  C03  122.67  3.000
 9P7  N02  C02  C03  119.01  3.000
 9P7  H21  N02  H20  115.32  3.000
 9P7  H21  N02  C02  117.45  3.000
 9P7  H20  N02  C02  118.75  3.000
 9P7  C02  N01  C10  118.86  3.000
 9P7  C24  C28  N29  180.00  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
 9P7  CONST_01  C03  C04  C05  C10     0.00   0.0  0
 9P7  CONST_02  C07  C06  C05  C10     0.00   0.0  0
 9P7  CONST_03  C03  C02  N01  C10     0.00   0.0  0
 9P7  CONST_04  C07  C08  C09  C10     0.00   0.0  0
 9P7  CONST_05  C21  C22  C23  C24     0.00   0.0  0
 9P7  CONST_06  C21  C26  C25  C24     0.00   0.0  0
 9P7  CONST_07  C22  C21  C26  C25     0.00   0.0  0
 9P7  CONST_08  C22  C23  C24  C25     0.00   0.0  0
 9P7  CONST_09  C26  C21  C22  C23     0.00   0.0  0
 9P7  CONST_10  C26  C25  C24  C23     0.00   0.0  0
 9P7  CONST_11  C05  C06  C07  C08     0.00   0.0  0
 9P7  CONST_12  C05  C10  C09  C08     0.00   0.0  0
 9P7  CONST_13  N01  C10  C09  C08   180.00   0.0  0
 9P7  CONST_14  C04  C05  C10  C09   180.00   0.0  0
 9P7  CONST_15  C06  C05  C10  C09     0.00   0.0  0
 9P7  CONST_16  C02  N01  C10  C09   180.00   0.0  0
 9P7  CONST_17  C06  C07  C08  C09     0.00   0.0  0
 9P7  CONST_18  C04  C05  C06  C07   180.00   0.0  0
 9P7  CONST_19  C03  C04  C05  C06   180.00   0.0  0
 9P7  CONST_20  N01  C10  C05  C06   180.00   0.0  0
 9P7  CONST_21  C02  C03  C04  C05     0.00   0.0  0
 9P7  CONST_22  C02  N01  C10  C05     0.00   0.0  0
 9P7  CONST_23  N01  C02  C03  C04     0.00   0.0  0
 9P7  CONST_24  N01  C10  C05  C04     0.00   0.0  0
 9P7  CONST_25  N02  C02  N01  C10   180.00   0.0  0
 9P7  CONST_26  C11  C08  C09  C10   180.00   0.0  0
 9P7  CONST_27  C06  C07  C08  C11   180.00   0.0  0
 9P7  CONST_28  C23  C22  C21  C14   180.00   0.0  0
 9P7  CONST_29  C25  C26  C21  C14   180.00   0.0  0
 9P7  CONST_30  C22  C23  C24  C28   180.00   0.0  0
 9P7  CONST_31  C26  C25  C24  C28   180.00   0.0  0
 9P7  CONST_32  C27  C23  C24  C25   180.00   0.0  0
 9P7  CONST_33  C21  C22  C23  C27   180.00   0.0  0
 9P7  CONST_34  N02  C02  C03  C04   180.00   0.0  0
 9P7  CONST_35  H18  C04  C05  C10   180.00   0.0  0
 9P7  CONST_36  H17  C06  C05  C10   180.00   0.0  0
 9P7  CONST_37  H11  C22  C23  C24   180.00   0.0  0
 9P7  CONST_38  H12  C26  C25  C24   180.00   0.0  0
 9P7  CONST_39  H7   C25  C24  C23   180.00   0.0  0
 9P7  CONST_40  H16  C07  C08  C09   180.00   0.0  0
 9P7  CONST_41  H15  C09  C08  C07   180.00   0.0  0
 9P7  CONST_42  H19  C03  C04  C05   180.00   0.0  0
 9P7  CONST_44  H21  N02  C02  C03   180.00   0.0  0
 9P7  Var_01    C22  C21  C14  C13    88.07  30.0  2
 9P7  Var_02    C07  C08  C11  N12   -53.02  30.0  3
 9P7  Var_03    H8   C27  C23  C24    59.11  30.0  2
 9P7  Var_04    C08  C11  N12  C13   177.13  30.0  1
 9P7  Var_05    N12  C13  C14  C21   179.25  30.0  1
 9P7  Var_06    C14  C13  N12  C11  -178.54  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
 9P7  plan-1  C14  0.020
 9P7  plan-1  N29  0.020
 9P7  plan-1  C24  0.020
 9P7  plan-1  C25  0.020
 9P7  plan-1  C23  0.020
 9P7  plan-1  C27  0.020
 9P7  plan-1  C22  0.020
 9P7  plan-1  C21  0.020
 9P7  plan-1  C26  0.020
 9P7  plan-1  H7   0.020
 9P7  plan-1  H11  0.020
 9P7  plan-1  H12  0.020
 9P7  plan-1  C28  0.020
 9P7  plan-2  C10  0.020
 9P7  plan-2  C11  0.020
 9P7  plan-2  C08  0.020
 9P7  plan-2  C09  0.020
 9P7  plan-2  C07  0.020
 9P7  plan-2  C06  0.020
 9P7  plan-2  C05  0.020
 9P7  plan-2  C04  0.020
 9P7  plan-2  C03  0.020
 9P7  plan-2  C02  0.020
 9P7  plan-2  N02  0.020
 9P7  plan-2  N01  0.020
 9P7  plan-2  H15  0.020
 9P7  plan-2  H16  0.020
 9P7  plan-2  H17  0.020
 9P7  plan-2  H18  0.020
 9P7  plan-2  H19  0.020
 9P7  plan-3  C02  0.020
 9P7  plan-3  N02  0.020
 9P7  plan-3  H20  0.020
 9P7  plan-3  H21  0.020

