# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 14:42:20 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-(2-{[(2-aminoquinolin-7-yl)methyl]amino}ethyl)-2-chlorobenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2ccc(CNCCc3ccc(C#N)c(Cl)c3)cc2n1
#
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
 9PM  9PM  4-(2-{[(2-aminoquinolin-7-yl)methyl]amino}ethyl)-2-chlorobenzonitrile  ligand  41  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_9PM
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
 9PM  N28  N   NS    0  -0.239   8.4736  -0.4705  -0.7699
 9PM  C27  C   CSP   0   0.051   7.3669  -0.4999  -0.4516
 9PM  C24  C   CR6   0   0.066   5.9980  -0.5672  -0.0653
 9PM  C23  C   CR6   0  -0.032   5.3298   0.5640   0.4063
 9PM  CL2  CL  CL    0  -0.088   6.1706   2.0629   0.5225
 9PM  C22  C   CR16  0  -0.251   4.0026   0.4905   0.7834
 9PM  C25  C   CR16  0  -0.237   5.3088  -1.7771  -0.1506
 9PM  C26  C   CR16  0  -0.288   3.9823  -1.8460   0.2275
 9PM  C21  C   CR6   0   0.130   3.3139  -0.7172   0.6987
 9PM  C14  C   CH2   0  -0.535   1.8606  -0.7854   1.0594
 9PM  C13  C   CH2   0  -0.248   0.9812  -0.4962  -0.1571
 9PM  N12  N   NH1   0  -0.593  -0.4198  -0.5742   0.2005
 9PM  C11  C   CH2   0  -0.329  -1.2995  -0.3283  -0.9270
 9PM  C08  C   CR6   0   0.094  -2.7409  -0.4783  -0.5255
 9PM  C09  C   CR16  0  -0.380  -3.6378   0.5448  -0.7099
 9PM  C07  C   CR16  0  -0.294  -3.1763  -1.6919   0.0535
 9PM  C06  C   CR16  0  -0.307  -4.4861  -1.8545   0.4166
 9PM  C05  C   CR66  0   0.044  -5.4181  -0.8139   0.2287
 9PM  C04  C   CR16  0  -0.180  -6.7855  -0.9178   0.5878
 9PM  C03  C   CR16  0  -0.378  -7.6228   0.1296   0.3797
 9PM  C02  C   CR6   0   0.434  -7.0959   1.3261  -0.1996
 9PM  N02  N   NH2   0  -0.835  -7.9360   2.3645  -0.4456
 9PM  N01  N   N     0  -0.507  -5.8346   1.4524  -0.5413
 9PM  C10  C   CR66  0   0.235  -4.9957   0.4088  -0.3416
 9PM  H1   H   HCR6  0   0.287   3.5008   1.3765   1.1503
 9PM  H2   H   HCR6  0   0.290   5.8221  -2.6580  -0.5110
 9PM  H3   H   HCR6  0   0.272   3.4588  -2.7912   0.1603
 9PM  H4   H   HCH2  0   0.258   1.6174  -1.7760   1.4480
 9PM  H5   H   HCH2  0   0.257   1.6395  -0.0607   1.8471
 9PM  H6   H   HCH2  0   0.205   1.2630   0.4796  -0.5829
 9PM  H7   H   HCH2  0   0.232   1.1806  -1.2420  -0.9324
 9PM  H8   H   HNH1  0   0.345  -0.6156   0.1101   0.9224
 9PM  H10  H   HCH2  0   0.218  -1.1463   0.6586  -1.3872
 9PM  H11  H   HCH2  0   0.240  -1.0642  -1.0669  -1.7006
 9PM  H12  H   HCR6  0   0.245  -3.3153   1.4852  -1.1428
 9PM  H13  H   HCR6  0   0.245  -2.4634  -2.4916   0.2062
 9PM  H14  H   HCR6  0   0.253  -4.8224  -2.7875   0.8539
 9PM  H15  H   HCR6  0   0.267  -7.1555  -1.8366   1.0267
 9PM  H16  H   HCR6  0   0.273  -8.6713   0.0724   0.6423
 9PM  H17  H   HNH2  0   0.395  -8.8088   2.4032   0.0522
 9PM  H18  H   HNH2  0   0.385  -7.5158   3.2590  -0.6365

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
 9PM  C04  C03  aromatic  1.357  0.020  1.357
 9PM  C04  C05  aromatic  1.418  0.020  1.418
 9PM  C03  C02  aromatic  1.430  0.020  1.430
 9PM  C06  C05  aromatic  1.410  0.020  1.410
 9PM  C06  C07  aromatic  1.369  0.020  1.369
 9PM  C05  C10  aromatic  1.414  0.020  1.414
 9PM  C02  N02  single    1.358  0.020  1.358
 9PM  C02  N01  aromatic  1.313  0.020  1.313
 9PM  C07  C08  aromatic  1.413  0.020  1.413
 9PM  C10  N01  aromatic  1.354  0.020  1.354
 9PM  C10  C09  aromatic  1.413  0.020  1.413
 9PM  C08  C09  aromatic  1.373  0.020  1.373
 9PM  C08  C11  single    1.504  0.020  1.504
 9PM  N12  C11  single    1.451  0.020  1.451
 9PM  N12  C13  single    1.448  0.020  1.448
 9PM  C13  C14  single    1.529  0.020  1.529
 9PM  C14  C21  single    1.499  0.020  1.499
 9PM  C22  C21  aromatic  1.393  0.020  1.393
 9PM  C22  C23  aromatic  1.382  0.020  1.382
 9PM  C21  C26  aromatic  1.394  0.020  1.394
 9PM  CL2  C23  single    1.723  0.020  1.723
 9PM  C23  C24  aromatic  1.396  0.020  1.396
 9PM  C26  C25  aromatic  1.381  0.020  1.381
 9PM  C24  C25  aromatic  1.395  0.020  1.395
 9PM  C24  C27  single    1.424  0.020  1.424
 9PM  C27  N28  triple    1.152  0.020  1.152
 9PM  C22  H1   single    0.930  0.020  1.080
 9PM  C25  H2   single    0.930  0.020  1.080
 9PM  C26  H3   single    0.930  0.020  1.080
 9PM  C14  H4   single    0.970  0.020  1.090
 9PM  C14  H5   single    0.970  0.020  1.090
 9PM  C13  H6   single    0.970  0.020  1.090
 9PM  C13  H7   single    0.970  0.020  1.090
 9PM  N12  H8   single    0.890  0.020  1.040
 9PM  C11  H10  single    0.970  0.020  1.090
 9PM  C11  H11  single    0.970  0.020  1.090
 9PM  C09  H12  single    0.930  0.020  1.080
 9PM  C07  H13  single    0.930  0.020  1.080
 9PM  C06  H14  single    0.930  0.020  1.080
 9PM  C04  H15  single    0.930  0.020  1.080
 9PM  C03  H16  single    0.930  0.020  1.080
 9PM  N02  H17  single    0.890  0.020  1.040
 9PM  N02  H18  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
 9PM  C24  C27  N28  180.00  3.000
 9PM  C25  C24  C23  119.15  3.000
 9PM  C25  C24  C27  119.95  3.000
 9PM  C23  C24  C27  120.90  3.000
 9PM  C22  C23  CL2  119.78  3.000
 9PM  CL2  C23  C24  119.63  3.000
 9PM  C22  C23  C24  120.59  3.000
 9PM  H1   C22  C21  120.08  3.000
 9PM  H1   C22  C23  119.62  3.000
 9PM  C21  C22  C23  120.30  3.000
 9PM  H2   C25  C26  120.43  3.000
 9PM  H2   C25  C24  119.50  3.000
 9PM  C26  C25  C24  120.07  3.000
 9PM  H3   C26  C21  119.75  3.000
 9PM  H3   C26  C25  119.41  3.000
 9PM  C21  C26  C25  120.84  3.000
 9PM  C14  C21  C26  120.62  3.000
 9PM  C26  C21  C22  119.06  3.000
 9PM  C14  C21  C22  120.28  3.000
 9PM  H5   C14  H4   107.47  3.000
 9PM  H5   C14  C13  109.37  3.000
 9PM  H4   C14  C13  109.07  3.000
 9PM  H5   C14  C21  109.84  3.000
 9PM  H4   C14  C21  110.06  3.000
 9PM  C13  C14  C21  110.96  3.000
 9PM  H7   C13  H6   106.46  3.000
 9PM  H7   C13  N12  108.33  3.000
 9PM  H6   C13  N12  113.00  3.000
 9PM  H7   C13  C14  109.28  3.000
 9PM  H6   C13  C14  109.16  3.000
 9PM  N12  C13  C14  110.48  3.000
 9PM  H8   N12  C11  108.78  3.000
 9PM  H8   N12  C13  109.04  3.000
 9PM  C11  N12  C13  112.68  3.000
 9PM  H11  C11  H10  106.24  3.000
 9PM  H11  C11  C08  109.11  3.000
 9PM  H10  C11  C08  109.57  3.000
 9PM  H11  C11  N12  107.72  3.000
 9PM  H10  C11  N12  113.13  3.000
 9PM  C08  C11  N12  110.90  3.000
 9PM  C07  C08  C09  119.58  3.000
 9PM  C09  C08  C11  121.06  3.000
 9PM  C07  C08  C11  119.36  3.000
 9PM  H12  C09  C10  118.25  3.000
 9PM  H12  C09  C08  120.37  3.000
 9PM  C10  C09  C08  121.38  3.000
 9PM  H13  C07  C06  120.34  3.000
 9PM  H13  C07  C08  119.30  3.000
 9PM  C06  C07  C08  120.36  3.000
 9PM  H14  C06  C05  118.95  3.000
 9PM  H14  C06  C07  120.41  3.000
 9PM  C05  C06  C07  120.64  3.000
 9PM  C10  C05  C04  116.99  3.000
 9PM  C10  C05  C06  119.65  3.000
 9PM  C04  C05  C06  123.36  3.000
 9PM  H15  C04  C03  120.40  3.000
 9PM  H15  C04  C05  119.62  3.000
 9PM  C03  C04  C05  119.98  3.000
 9PM  H16  C03  C02  119.97  3.000
 9PM  H16  C03  C04  121.31  3.000
 9PM  C02  C03  C04  118.72  3.000
 9PM  N01  C02  N02  118.27  3.000
 9PM  N01  C02  C03  122.68  3.000
 9PM  N02  C02  C03  119.02  3.000
 9PM  H18  N02  H17  114.97  3.000
 9PM  H18  N02  C02  117.10  3.000
 9PM  H17  N02  C02  118.47  3.000
 9PM  C10  N01  C02  118.87  3.000
 9PM  N01  C10  C05  122.75  3.000
 9PM  N01  C10  C09  118.86  3.000
 9PM  C05  C10  C09  118.39  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
 9PM  CONST_01  C21  C22  C23  C24     0.00   0.0  0
 9PM  CONST_02  C21  C26  C25  C24     0.00   0.0  0
 9PM  CONST_03  C26  C21  C22  C23     0.00   0.0  0
 9PM  CONST_04  C26  C25  C24  C23     0.00   0.0  0
 9PM  CONST_05  C25  C26  C21  C22     0.00   0.0  0
 9PM  CONST_06  C25  C24  C23  C22     0.00   0.0  0
 9PM  CONST_07  C05  C06  C07  C08     0.00   0.0  0
 9PM  CONST_08  C05  C10  C09  C08     0.00   0.0  0
 9PM  CONST_09  N01  C10  C09  C08   180.00   0.0  0
 9PM  CONST_10  C04  C05  C10  C09   180.00   0.0  0
 9PM  CONST_11  C06  C05  C10  C09     0.00   0.0  0
 9PM  CONST_12  C02  N01  C10  C09   180.00   0.0  0
 9PM  CONST_13  C06  C07  C08  C09     0.00   0.0  0
 9PM  CONST_14  C04  C05  C06  C07   180.00   0.0  0
 9PM  CONST_15  C10  C05  C06  C07     0.00   0.0  0
 9PM  CONST_16  C10  C09  C08  C07     0.00   0.0  0
 9PM  CONST_17  C03  C04  C05  C06   180.00   0.0  0
 9PM  CONST_18  N01  C10  C05  C06   180.00   0.0  0
 9PM  CONST_19  C02  C03  C04  C05     0.00   0.0  0
 9PM  CONST_20  C02  N01  C10  C05     0.00   0.0  0
 9PM  CONST_21  N01  C02  C03  C04     0.00   0.0  0
 9PM  CONST_22  N01  C10  C05  C04     0.00   0.0  0
 9PM  CONST_23  C10  C05  C04  C03     0.00   0.0  0
 9PM  CONST_24  C10  N01  C02  C03     0.00   0.0  0
 9PM  CONST_25  C22  C23  C24  C27   180.00   0.0  0
 9PM  CONST_26  C26  C25  C24  C27   180.00   0.0  0
 9PM  CONST_27  C14  C21  C22  C23   180.00   0.0  0
 9PM  CONST_28  C21  C22  C23  CL2   180.00   0.0  0
 9PM  CONST_29  C25  C24  C23  CL2   180.00   0.0  0
 9PM  CONST_30  C14  C21  C26  C25   180.00   0.0  0
 9PM  CONST_31  C06  C07  C08  C11   180.00   0.0  0
 9PM  CONST_32  C10  C09  C08  C11   180.00   0.0  0
 9PM  CONST_33  N02  C02  C03  C04   180.00   0.0  0
 9PM  CONST_34  C10  N01  C02  N02   180.00   0.0  0
 9PM  CONST_35  H1   C22  C23  C24   180.00   0.0  0
 9PM  CONST_36  H3   C26  C25  C24   180.00   0.0  0
 9PM  CONST_37  H2   C25  C24  C23   180.00   0.0  0
 9PM  CONST_38  H14  C06  C07  C08   180.00   0.0  0
 9PM  CONST_39  H13  C07  C08  C09   180.00   0.0  0
 9PM  CONST_40  H12  C09  C08  C07   180.00   0.0  0
 9PM  CONST_41  H15  C04  C05  C06     0.00   0.0  0
 9PM  CONST_42  H16  C03  C04  C05   180.00   0.0  0
 9PM  CONST_44  H18  N02  C02  C03   180.00   0.0  0
 9PM  Var_01    C13  C14  C21  C22    89.18  30.0  2
 9PM  Var_02    C07  C08  C11  N12   -56.28  30.0  3
 9PM  Var_03    N12  C13  C14  C21   179.59  30.0  1
 9PM  Var_04    C08  C11  N12  C13   177.51  30.0  3
 9PM  Var_05    C11  N12  C13  C14  -179.06  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
 9PM  plan-1  N28  0.020
 9PM  plan-1  C27  0.020
 9PM  plan-1  C24  0.020
 9PM  plan-1  C23  0.020
 9PM  plan-1  CL2  0.020
 9PM  plan-1  C22  0.020
 9PM  plan-1  C25  0.020
 9PM  plan-1  C26  0.020
 9PM  plan-1  C21  0.020
 9PM  plan-1  C14  0.020
 9PM  plan-1  H1   0.020
 9PM  plan-1  H2   0.020
 9PM  plan-1  H3   0.020
 9PM  plan-2  C11  0.020
 9PM  plan-2  C08  0.020
 9PM  plan-2  C09  0.020
 9PM  plan-2  C07  0.020
 9PM  plan-2  C06  0.020
 9PM  plan-2  C05  0.020
 9PM  plan-2  C04  0.020
 9PM  plan-2  C03  0.020
 9PM  plan-2  C02  0.020
 9PM  plan-2  N02  0.020
 9PM  plan-2  N01  0.020
 9PM  plan-2  C10  0.020
 9PM  plan-2  H12  0.020
 9PM  plan-2  H13  0.020
 9PM  plan-2  H14  0.020
 9PM  plan-2  H15  0.020
 9PM  plan-2  H16  0.020
 9PM  plan-3  C02  0.020
 9PM  plan-3  N02  0.020
 9PM  plan-3  H17  0.020
 9PM  plan-3  H18  0.020

