# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:44:21 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-(4-{[3-(piperidin-1-yl)propyl]amino}quinolin-2-yl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1ccccc1c2cc(NCCCN3CCCCC3)c4ccccc4n2
#
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
 6LJ  6LJ  2-(4-{[3-(piperidin-1-yl)propyl]amino}quinolin-2-yl)benzonitrile  ligand  54  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6LJ
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
 6LJ  C24  C  CH2   0  -0.439  -8.3448   0.3803  -0.0677
 6LJ  C23  C  CH2   0  -0.435  -7.4553  -0.8267  -0.3339
 6LJ  C22  C  CH2   0  -0.285  -6.0512  -0.3919  -0.7274
 6LJ  C12  C  CR6   0   0.135   3.2873   1.6732  -0.0922
 6LJ  C5   C  CR66  0   0.026   1.3822  -2.0926  -0.1818
 6LJ  C2   C  CR6   0   0.182   2.6005   0.3633  -0.1243
 6LJ  C1   C  CR16  0  -0.460   1.1995   0.3137  -0.1042
 6LJ  C4   C  CR66  0   0.184   2.7863  -1.9074  -0.1873
 6LJ  C6   C  CR6   0   0.479   0.5546  -0.9164  -0.1289
 6LJ  C7   C  CR16  0  -0.307   3.6245  -3.0448  -0.2271
 6LJ  C8   C  CR16  0  -0.259   3.0964  -4.3070  -0.2652
 6LJ  C25  C  CH2   0  -0.438  -7.6738   1.3003   0.9434
 6LJ  C26  C  CH2   0  -0.276  -6.2621   1.6519   0.5017
 6LJ  C9   C  CR16  0  -0.251   1.7021  -4.4904  -0.2689
 6LJ  C10  C  CR16  0  -0.318   0.8661  -3.4043  -0.2282
 6LJ  C13  C  CH2   0  -0.252  -1.6787   0.1169  -0.0375
 6LJ  C14  C  CH2   0  -0.504  -3.1222  -0.3563   0.0149
 6LJ  C17  C  CR6   0  -0.017   4.4896   1.8498   0.6089
 6LJ  C18  C  CR16  0  -0.237   5.1388   3.0848   0.6125
 6LJ  C19  C  CR16  0  -0.255   4.6037   4.1533  -0.0860
 6LJ  C20  C  CR16  0  -0.221   3.4146   3.9900  -0.7823
 6LJ  C21  C  CR16  0  -0.315   2.7657   2.7643  -0.7795
 6LJ  N28  N  NS    0  -0.255   5.6248   0.0705   2.0913
 6LJ  N11  N  NH1   0  -0.702  -0.7838  -1.0153  -0.1025
 6LJ  N16  N  NT    0  -0.419  -5.4554   0.4605   0.2890
 6LJ  N3   N  N     0  -0.489   3.3777  -0.6913  -0.1632
 6LJ  H1   H  HCH2  0   0.209  -8.5106   0.9232  -1.0045
 6LJ  H2   H  HCH2  0   0.230  -9.3279   0.0654   0.2895
 6LJ  H3   H  HCH2  0   0.214  -7.3994  -1.4488   0.5646
 6LJ  H4   H  HCH2  0   0.229  -7.8738  -1.4502  -1.1271
 6LJ  H5   H  HCH2  0   0.238  -5.4287  -1.2769  -0.8690
 6LJ  H6   H  HCH2  0   0.181  -6.0895   0.1268  -1.7037
 6LJ  H7   H  HCR6  0   0.280   0.6303   1.2300  -0.0366
 6LJ  H8   H  HCR6  0   0.258   4.6954  -2.8867  -0.2270
 6LJ  H9   H  HCR6  0   0.262   3.7521  -5.1673  -0.2956
 6LJ  H10  H  HCH2  0   0.229  -8.2488   2.2191   1.0775
 6LJ  H11  H  HCH2  0   0.214  -7.6291   0.8053   1.9183
 6LJ  H12  H  HCH2  0   0.181  -6.3096   2.2701  -0.4138
 6LJ  H13  H  HCH2  0   0.230  -5.7785   2.2660   1.2660
 6LJ  H14  H  HCR6  0   0.263   1.2883  -5.4893  -0.3063
 6LJ  H15  H  HCR6  0   0.251  -0.2019  -3.5811  -0.2401
 6LJ  H16  H  HCH2  0   0.235  -1.5259   0.7625  -0.9097
 6LJ  H17  H  HCH2  0   0.235  -1.4594   0.7278   0.8457
 6LJ  H18  H  HCH2  0   0.243  -3.3000  -1.0373  -0.8214
 6LJ  H19  H  HCH2  0   0.239  -3.2864  -0.9249   0.9346
 6LJ  H20  H  HCH2  0   0.227  -3.7625   1.5595   0.7142
 6LJ  H21  H  HCH2  0   0.190  -4.0129   1.3201  -1.0081
 6LJ  H22  H  HCR6  0   0.284   6.0589   3.2037   1.1685
 6LJ  H23  H  HCR6  0   0.276   5.1118   5.1077  -0.0814
 6LJ  H24  H  HCR6  0   0.276   2.9918   4.8172  -1.3363
 6LJ  H25  H  HCR6  0   0.269   1.8491   2.6491  -1.3429
 6LJ  H26  H  HNH1  0   0.406  -1.2029  -1.9259  -0.0305
 6LJ  C15  C  CH2   0  -0.248  -4.0865   0.8210  -0.0255
 6LJ  C27  C  CSP   0   0.027   5.0801   0.8114   1.3965

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
 6LJ  N28  C27  triple    1.153  0.020  1.153
 6LJ  C18  C19  aromatic  1.384  0.020  1.384
 6LJ  C18  C17  aromatic  1.395  0.020  1.395
 6LJ  C27  C17  single    1.431  0.020  1.431
 6LJ  C19  C20  aromatic  1.388  0.020  1.388
 6LJ  C17  C12  aromatic  1.403  0.020  1.403
 6LJ  C20  C21  aromatic  1.387  0.020  1.387
 6LJ  C12  C21  aromatic  1.391  0.020  1.391
 6LJ  C12  C2   single    1.479  0.020  1.479
 6LJ  C1   C2   aromatic  1.402  0.020  1.402
 6LJ  C1   C6   aromatic  1.389  0.020  1.389
 6LJ  C2   N3   aromatic  1.311  0.020  1.311
 6LJ  C26  C25  single    1.520  0.020  1.520
 6LJ  C26  N16  single    1.454  0.020  1.454
 6LJ  N11  C6   single    1.342  0.020  1.342
 6LJ  N11  C13  single    1.445  0.020  1.445
 6LJ  C6   C5   aromatic  1.439  0.020  1.439
 6LJ  C13  C14  single    1.520  0.020  1.520
 6LJ  C25  C24  single    1.523  0.020  1.523
 6LJ  N3   C4   aromatic  1.352  0.020  1.352
 6LJ  C24  C23  single    1.523  0.020  1.523
 6LJ  C15  N16  single    1.450  0.020  1.450
 6LJ  C15  C14  single    1.522  0.020  1.522
 6LJ  N16  C22  single    1.454  0.020  1.454
 6LJ  C22  C23  single    1.522  0.020  1.522
 6LJ  C5   C4   aromatic  1.416  0.020  1.416
 6LJ  C5   C10  aromatic  1.410  0.020  1.410
 6LJ  C4   C7   aromatic  1.413  0.020  1.413
 6LJ  C10  C9   aromatic  1.371  0.020  1.371
 6LJ  C7   C8   aromatic  1.369  0.020  1.369
 6LJ  C9   C8   aromatic  1.406  0.020  1.406
 6LJ  C24  H1   single    0.970  0.020  1.090
 6LJ  C24  H2   single    0.970  0.020  1.090
 6LJ  C23  H3   single    0.970  0.020  1.090
 6LJ  C23  H4   single    0.970  0.020  1.090
 6LJ  C22  H5   single    0.970  0.020  1.090
 6LJ  C22  H6   single    0.970  0.020  1.090
 6LJ  C1   H7   single    0.930  0.020  1.080
 6LJ  C7   H8   single    0.930  0.020  1.080
 6LJ  C8   H9   single    0.930  0.020  1.080
 6LJ  C25  H10  single    0.970  0.020  1.090
 6LJ  C25  H11  single    0.970  0.020  1.090
 6LJ  C26  H12  single    0.970  0.020  1.090
 6LJ  C26  H13  single    0.970  0.020  1.090
 6LJ  C9   H14  single    0.930  0.020  1.080
 6LJ  C10  H15  single    0.930  0.020  1.080
 6LJ  C13  H16  single    0.970  0.020  1.090
 6LJ  C13  H17  single    0.970  0.020  1.090
 6LJ  C14  H18  single    0.970  0.020  1.090
 6LJ  C14  H19  single    0.970  0.020  1.090
 6LJ  C15  H20  single    0.970  0.020  1.090
 6LJ  C15  H21  single    0.970  0.020  1.090
 6LJ  C18  H22  single    0.930  0.020  1.080
 6LJ  C19  H23  single    0.930  0.020  1.080
 6LJ  C20  H24  single    0.930  0.020  1.080
 6LJ  C21  H25  single    0.930  0.020  1.080
 6LJ  N11  H26  single    0.860  0.020  1.020

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
 6LJ  H2   C24  H1   106.63  3.000
 6LJ  H2   C24  C25  110.71  3.000
 6LJ  H1   C24  C25  109.58  3.000
 6LJ  H2   C24  C23  110.76  3.000
 6LJ  H1   C24  C23  109.38  3.000
 6LJ  C25  C24  C23  109.73  3.000
 6LJ  H4   C23  H3   106.94  3.000
 6LJ  H4   C23  C22  109.20  3.000
 6LJ  H3   C23  C22  109.13  3.000
 6LJ  H4   C23  C24  110.83  3.000
 6LJ  H3   C23  C24  109.69  3.000
 6LJ  C22  C23  C24  110.96  3.000
 6LJ  H6   C22  H5   106.58  3.000
 6LJ  H6   C22  N16  110.87  3.000
 6LJ  H5   C22  N16  109.41  3.000
 6LJ  H6   C22  C23  109.28  3.000
 6LJ  H5   C22  C23  109.16  3.000
 6LJ  N16  C22  C23  111.40  3.000
 6LJ  C21  C12  C17  118.00  3.000
 6LJ  C21  C12  C2   120.65  3.000
 6LJ  C17  C12  C2   121.34  3.000
 6LJ  C10  C5   C6   123.44  3.000
 6LJ  C10  C5   C4   118.97  3.000
 6LJ  C6   C5   C4   117.60  3.000
 6LJ  N3   C2   C1   124.37  3.000
 6LJ  N3   C2   C12  115.96  3.000
 6LJ  C1   C2   C12  119.67  3.000
 6LJ  H7   C1   C6   120.49  3.000
 6LJ  H7   C1   C2   119.81  3.000
 6LJ  C6   C1   C2   119.67  3.000
 6LJ  N3   C4   C7   117.69  3.000
 6LJ  C7   C4   C5   118.87  3.000
 6LJ  N3   C4   C5   123.44  3.000
 6LJ  N11  C6   C1   121.86  3.000
 6LJ  N11  C6   C5   120.92  3.000
 6LJ  C1   C6   C5   117.23  3.000
 6LJ  H8   C7   C8   121.09  3.000
 6LJ  H8   C7   C4   117.98  3.000
 6LJ  C8   C7   C4   120.93  3.000
 6LJ  H9   C8   C9   119.80  3.000
 6LJ  H9   C8   C7   120.01  3.000
 6LJ  C9   C8   C7   120.19  3.000
 6LJ  H11  C25  H10  107.02  3.000
 6LJ  H11  C25  C26  109.00  3.000
 6LJ  H10  C25  C26  109.26  3.000
 6LJ  H11  C25  C24  109.64  3.000
 6LJ  H10  C25  C24  110.96  3.000
 6LJ  C26  C25  C24  110.85  3.000
 6LJ  H13  C26  H12  106.49  3.000
 6LJ  H13  C26  N16  108.48  3.000
 6LJ  H12  C26  N16  111.15  3.000
 6LJ  H13  C26  C25  109.73  3.000
 6LJ  H12  C26  C25  109.27  3.000
 6LJ  N16  C26  C25  111.59  3.000
 6LJ  H14  C9   C10  119.94  3.000
 6LJ  H14  C9   C8   119.99  3.000
 6LJ  C10  C9   C8   120.07  3.000
 6LJ  H15  C10  C9   118.15  3.000
 6LJ  H15  C10  C5   120.88  3.000
 6LJ  C9   C10  C5   120.97  3.000
 6LJ  H17  C13  H16  106.56  3.000
 6LJ  H17  C13  N11  110.43  3.000
 6LJ  H16  C13  N11  109.85  3.000
 6LJ  H17  C13  C14  109.61  3.000
 6LJ  H16  C13  C14  110.08  3.000
 6LJ  N11  C13  C14  110.24  3.000
 6LJ  H19  C14  H18  107.16  3.000
 6LJ  H19  C14  C15  109.23  3.000
 6LJ  H18  C14  C15  111.00  3.000
 6LJ  H19  C14  C13  109.48  3.000
 6LJ  H18  C14  C13  108.79  3.000
 6LJ  C15  C14  C13  111.09  3.000
 6LJ  C18  C17  C27  116.68  3.000
 6LJ  C27  C17  C12  122.50  3.000
 6LJ  C18  C17  C12  120.76  3.000
 6LJ  H22  C18  C19  120.23  3.000
 6LJ  H22  C18  C17  119.63  3.000
 6LJ  C19  C18  C17  120.14  3.000
 6LJ  H23  C19  C20  120.57  3.000
 6LJ  H23  C19  C18  119.84  3.000
 6LJ  C20  C19  C18  119.58  3.000
 6LJ  H24  C20  C21  119.61  3.000
 6LJ  H24  C20  C19  120.13  3.000
 6LJ  C21  C20  C19  120.26  3.000
 6LJ  H25  C21  C20  119.30  3.000
 6LJ  H25  C21  C12  119.43  3.000
 6LJ  C20  C21  C12  121.25  3.000
 6LJ  H26  N11  C13  116.65  3.000
 6LJ  H26  N11  C6   118.95  3.000
 6LJ  C13  N11  C6   124.11  3.000
 6LJ  C15  N16  C26  110.58  3.000
 6LJ  C15  N16  C22  112.39  3.000
 6LJ  C26  N16  C22  110.80  3.000
 6LJ  C4   N3   C2   117.69  3.000
 6LJ  H21  C15  H20  106.06  3.000
 6LJ  H21  C15  N16  111.60  3.000
 6LJ  H20  C15  N16  107.50  3.000
 6LJ  H21  C15  C14  109.32  3.000
 6LJ  H20  C15  C14  108.45  3.000
 6LJ  N16  C15  C14  113.57  3.000
 6LJ  N28  C27  C17  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
 6LJ  CONST_01  C19  C18  C17  C12     0.00   0.0  0
 6LJ  CONST_02  C19  C20  C21  C12     0.00   0.0  0
 6LJ  CONST_03  C6   C1   C2   C12   180.00   0.0  0
 6LJ  CONST_04  C4   N3   C2   C12   180.00   0.0  0
 6LJ  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 6LJ  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 6LJ  CONST_07  C8   C7   C4   C5      0.00   0.0  0
 6LJ  CONST_08  C8   C9   C10  C5      0.00   0.0  0
 6LJ  CONST_09  C18  C17  C12  C2    180.00   0.0  0
 6LJ  CONST_10  C20  C21  C12  C2    180.00   0.0  0
 6LJ  CONST_11  C7   C4   N3   C2    180.00   0.0  0
 6LJ  CONST_14  C4   N3   C2   C1      0.00   0.0  0
 6LJ  CONST_15  C4   C5   C6   C1      0.00   0.0  0
 6LJ  CONST_16  C10  C5   C6   C1    180.00   0.0  0
 6LJ  CONST_17  C9   C10  C5   C4      0.00   0.0  0
 6LJ  CONST_18  C9   C8   C7   C4      0.00   0.0  0
 6LJ  CONST_19  N3   C2   C1   C6      0.00   0.0  0
 6LJ  CONST_20  N3   C4   C5   C6      0.00   0.0  0
 6LJ  CONST_21  C7   C4   C5   C6    180.00   0.0  0
 6LJ  CONST_22  C9   C10  C5   C6    180.00   0.0  0
 6LJ  CONST_23  C10  C5   C4   C7      0.00   0.0  0
 6LJ  CONST_24  C10  C9   C8   C7      0.00   0.0  0
 6LJ  CONST_25  N3   C4   C7   C8    180.00   0.0  0
 6LJ  CONST_26  N3   C4   C5   C10   180.00   0.0  0
 6LJ  CONST_27  C20  C19  C18  C17     0.00   0.0  0
 6LJ  CONST_28  C20  C21  C12  C17     0.00   0.0  0
 6LJ  CONST_30  C21  C20  C19  C18     0.00   0.0  0
 6LJ  CONST_31  C21  C12  C17  C18     0.00   0.0  0
 6LJ  CONST_33  C27  C17  C12  C2      0.00   0.0  0
 6LJ  CONST_34  N11  C6   C1   C2    180.00   0.0  0
 6LJ  CONST_35  N11  C6   C5   C4    180.00   0.0  0
 6LJ  CONST_36  C19  C18  C17  C27   180.00   0.0  0
 6LJ  CONST_37  C21  C12  C17  C27   180.00   0.0  0
 6LJ  CONST_38  N11  C6   C5   C10     0.00   0.0  0
 6LJ  CONST_39  H22  C18  C17  C12   180.00   0.0  0
 6LJ  CONST_40  H24  C20  C21  C12   180.00   0.0  0
 6LJ  CONST_41  H7   C1   C2   C12     0.00   0.0  0
 6LJ  CONST_42  H8   C7   C4   C5    180.00   0.0  0
 6LJ  CONST_43  H14  C9   C10  C5    180.00   0.0  0
 6LJ  CONST_44  H25  C21  C12  C2      0.00   0.0  0
 6LJ  CONST_45  H15  C10  C5   C4    180.00   0.0  0
 6LJ  CONST_46  H9   C8   C7   C4    180.00   0.0  0
 6LJ  CONST_47  H23  C19  C18  C17   180.00   0.0  0
 6LJ  CONST_48  C13  N11  C6   C5    180.00   0.0  0
 6LJ  CONST_49  C13  N11  C6   C1      0.00   0.0  0
 6LJ  CONST_50  H26  N11  C6   C5      0.00   0.0  0
 6LJ  Var_01    N16  C26  C25  C24   -56.58  30.0  1
 6LJ  Var_02    N16  C22  C23  C24    56.65  30.0  1
 6LJ  Var_03    C26  C25  C24  C23    52.95  30.0  1
 6LJ  Var_04    C26  N16  C22  C23   -59.25  30.0  1
 6LJ  Var_05    C25  C26  N16  C22    59.32  30.0  1
 6LJ  Var_06    C25  C24  C23  C22   -53.06  30.0  1
 6LJ  Var_07    C14  C15  N16  C22   -67.26  30.0  1
 6LJ  Var_08    C14  C13  N11  C6   -178.45  30.0  3
 6LJ  Var_09    N16  C15  C14  C13  -168.33  30.0  1
 6LJ  Var_10    N11  C13  C14  C15  -175.58  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
 6LJ  plan-1  C12  0.020
 6LJ  plan-1  C2   0.020
 6LJ  plan-1  C17  0.020
 6LJ  plan-1  C18  0.020
 6LJ  plan-1  C19  0.020
 6LJ  plan-1  C20  0.020
 6LJ  plan-1  C21  0.020
 6LJ  plan-1  N28  0.020
 6LJ  plan-1  H22  0.020
 6LJ  plan-1  H23  0.020
 6LJ  plan-1  H24  0.020
 6LJ  plan-1  H25  0.020
 6LJ  plan-1  C27  0.020
 6LJ  plan-2  C12  0.020
 6LJ  plan-2  C5   0.020
 6LJ  plan-2  C2   0.020
 6LJ  plan-2  C1   0.020
 6LJ  plan-2  C4   0.020
 6LJ  plan-2  C6   0.020
 6LJ  plan-2  C7   0.020
 6LJ  plan-2  C8   0.020
 6LJ  plan-2  C9   0.020
 6LJ  plan-2  C10  0.020
 6LJ  plan-2  N11  0.020
 6LJ  plan-2  N3   0.020
 6LJ  plan-2  H7   0.020
 6LJ  plan-2  H8   0.020
 6LJ  plan-2  H9   0.020
 6LJ  plan-2  H14  0.020
 6LJ  plan-2  H15  0.020
 6LJ  plan-3  C6   0.020
 6LJ  plan-3  C13  0.020
 6LJ  plan-3  N11  0.020
 6LJ  plan-3  H26  0.020

