# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:26:19 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 7-[(3-pyridin-3-ylpropylamino)methyl]quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2ccc(CNCCCc3cccnc3)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
 XH8  XH8  7-[(3-pyridin-3-ylpropylamino)methyl]quinolin-2-amine  ligand  42  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XH8
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
 XH8  N01   N  NH2   0  -0.835   5.6917   3.0671   0.2844
 XH8  C02   C  CR6   0   0.435   5.2957   1.7696   0.3386
 XH8  C03   C  CR16  0  -0.379   6.1626   0.8085   0.9507
 XH8  C04   C  CR16  0  -0.178   5.7524  -0.4811   1.0327
 XH8  C05   C  CR66  0   0.042   4.4820  -0.8538   0.5215
 XH8  C06   C  CR16  0  -0.302   3.9890  -2.1695   0.5631
 XH8  C07   C  CR16  0  -0.323   2.7522  -2.4660   0.0477
 XH8  C08   C  CR6   0   0.078   1.9561  -1.4580  -0.5320
 XH8  C09   C  CH2   0  -0.318   0.5998  -1.7973  -1.0928
 XH8  N10   N  NH1   0  -0.592  -0.4349  -0.9598  -0.5166
 XH8  C11   C  CH2   0  -0.255  -1.7575  -1.2749  -1.0208
 XH8  C12   C  CH2   0  -0.439  -2.8138  -0.3911  -0.3776
 XH8  C13   C  CH2   0  -0.512  -4.2233  -0.7320  -0.8636
 XH8  C14   C  CR6   0   0.040  -5.2596   0.1624  -0.2504
 XH8  C15   C  CR16  0  -0.194  -5.5443   1.4193  -0.7739
 XH8  C16   C  CR16  0  -0.318  -6.4809   2.2242  -0.1452
 XH8  C17   C  CR16  0  -0.077  -7.1059   1.7440   0.9963
 XH8  N18   N  N     0  -0.401  -6.8502   0.5475   1.5116
 XH8  C19   C  CR16  0  -0.108  -5.9513  -0.2129   0.8979
 XH8  C20   C  CR16  0  -0.349   2.4259  -0.1646  -0.5729
 XH8  C21   C  CR66  0   0.234   3.6948   0.1707  -0.0584
 XH8  N22   N  N     0  -0.508   4.1157   1.4570  -0.1413
 XH8  H011  H  HNH2  0   0.395   6.6709   3.2744   0.3830
 XH8  H012  H  HNH2  0   0.385   5.1882   3.6773  -0.3379
 XH8  H03   H  HCR6  0   0.273   7.1258   1.1176   1.3350
 XH8  H04   H  HCR6  0   0.267   6.3883  -1.2318   1.4865
 XH8  H06   H  HCR6  0   0.254   4.5959  -2.9479   1.0105
 XH8  H07   H  HCR6  0   0.249   2.3800  -3.4826   0.0858
 XH8  H091  H  HCH2  0   0.238   0.6018  -1.6315  -2.1752
 XH8  H092  H  HCH2  0   0.212   0.4107  -2.8729  -0.9526
 XH8  H20   H  HCR6  0   0.240   1.8224   0.6230  -1.0083
 XH8  H10   H  HNH1  0   0.340  -0.4285  -1.0846   0.4896
 XH8  H111  H  HCH2  0   0.219  -1.7593  -1.1112  -2.1038
 XH8  H112  H  HCH2  0   0.190  -2.0251  -2.3350  -0.8748
 XH8  H121  H  HCH2  0   0.228  -2.7719  -0.5016   0.7111
 XH8  H122  H  HCH2  0   0.231  -2.5916   0.6573  -0.5955
 XH8  H131  H  HCH2  0   0.246  -4.2622  -0.6411  -1.9527
 XH8  H132  H  HCH2  0   0.245  -4.4474  -1.7753  -0.6273
 XH8  H15   H  HCR6  0   0.264  -5.0385   1.7615  -1.6693
 XH8  H19   H  HCR6  0   0.253  -5.7672  -1.1892   1.3375
 XH8  H16   H  HCR6  0   0.269  -6.7260   3.2048  -0.5298
 XH8  H17   H  HCR6  0   0.260  -7.8446   2.3483   1.5113

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
 XH8  N01  C02   single    1.358  0.020  1.358
 XH8  C02  C03   aromatic  1.432  0.020  1.432
 XH8  C02  N22   aromatic  1.312  0.020  1.312
 XH8  C03  C04   aromatic  1.356  0.020  1.356
 XH8  C04  C05   aromatic  1.419  0.020  1.419
 XH8  C05  C06   aromatic  1.406  0.020  1.406
 XH8  C05  C21   aromatic  1.416  0.020  1.416
 XH8  C06  C07   aromatic  1.372  0.020  1.372
 XH8  C07  C08   aromatic  1.409  0.020  1.409
 XH8  C08  C09   single    1.506  0.020  1.506
 XH8  C08  C20   aromatic  1.377  0.020  1.377
 XH8  C09  N10   single    1.451  0.020  1.451
 XH8  N10  C11   single    1.450  0.020  1.450
 XH8  C11  C12   single    1.520  0.020  1.520
 XH8  C12  C13   single    1.529  0.020  1.529
 XH8  C13  C14   single    1.500  0.020  1.500
 XH8  C14  C15   aromatic  1.391  0.020  1.391
 XH8  C14  C19   aromatic  1.392  0.020  1.392
 XH8  C15  C16   aromatic  1.386  0.020  1.386
 XH8  C16  C17   aromatic  1.387  0.020  1.387
 XH8  C17  N18   aromatic  1.328  0.020  1.328
 XH8  N18  C19   aromatic  1.328  0.020  1.328
 XH8  C20  C21   aromatic  1.410  0.020  1.410
 XH8  C21  N22   aromatic  1.356  0.020  1.356
 XH8  N01  H011  single    0.890  0.020  1.040
 XH8  N01  H012  single    0.890  0.020  1.040
 XH8  C03  H03   single    0.930  0.020  1.080
 XH8  C04  H04   single    0.930  0.020  1.080
 XH8  C06  H06   single    0.930  0.020  1.080
 XH8  C07  H07   single    0.930  0.020  1.080
 XH8  C09  H091  single    0.970  0.020  1.090
 XH8  C09  H092  single    0.970  0.020  1.090
 XH8  C20  H20   single    0.930  0.020  1.080
 XH8  N10  H10   single    0.890  0.020  1.040
 XH8  C11  H111  single    0.970  0.020  1.090
 XH8  C11  H112  single    0.970  0.020  1.090
 XH8  C12  H121  single    0.970  0.020  1.090
 XH8  C12  H122  single    0.970  0.020  1.090
 XH8  C13  H131  single    0.970  0.020  1.090
 XH8  C13  H132  single    0.970  0.020  1.090
 XH8  C15  H15   single    0.930  0.020  1.080
 XH8  C19  H19   single    0.930  0.020  1.080
 XH8  C16  H16   single    0.930  0.020  1.080
 XH8  C17  H17   single    0.930  0.020  1.080

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
 XH8  H012  N01  H011  115.00  3.000
 XH8  H012  N01  C02   117.27  3.000
 XH8  H011  N01  C02   118.49  3.000
 XH8  N22   C02  C03   122.76  3.000
 XH8  N22   C02  N01   118.39  3.000
 XH8  C03   C02  N01   118.82  3.000
 XH8  H03   C03  C04   121.30  3.000
 XH8  H03   C03  C02   119.94  3.000
 XH8  C04   C03  C02   118.76  3.000
 XH8  H04   C04  C05   119.62  3.000
 XH8  H04   C04  C03   120.45  3.000
 XH8  C05   C04  C03   119.92  3.000
 XH8  C21   C05  C06   119.62  3.000
 XH8  C21   C05  C04   117.07  3.000
 XH8  C06   C05  C04   123.31  3.000
 XH8  H06   C06  C07   120.30  3.000
 XH8  H06   C06  C05   119.21  3.000
 XH8  C07   C06  C05   120.48  3.000
 XH8  H07   C07  C08   119.45  3.000
 XH8  H07   C07  C06   119.95  3.000
 XH8  C08   C07  C06   120.60  3.000
 XH8  C20   C08  C09   120.52  3.000
 XH8  C20   C08  C07   119.44  3.000
 XH8  C09   C08  C07   120.04  3.000
 XH8  H092  C09  H091  105.91  3.000
 XH8  H092  C09  N10   113.02  3.000
 XH8  H091  C09  N10   107.85  3.000
 XH8  H092  C09  C08   109.10  3.000
 XH8  H091  C09  C08   109.40  3.000
 XH8  N10   C09  C08   111.36  3.000
 XH8  H10   N10  C11   108.91  3.000
 XH8  H10   N10  C09   108.58  3.000
 XH8  C11   N10  C09   112.77  3.000
 XH8  H112  C11  H111  105.91  3.000
 XH8  H112  C11  C12   109.52  3.000
 XH8  H111  C11  C12   109.29  3.000
 XH8  H112  C11  N10   112.59  3.000
 XH8  H111  C11  N10   108.23  3.000
 XH8  C12   C11  N10   111.12  3.000
 XH8  H122  C12  H121  106.68  3.000
 XH8  H122  C12  C13   109.74  3.000
 XH8  H121  C12  C13   109.19  3.000
 XH8  H122  C12  C11   109.38  3.000
 XH8  H121  C12  C11   109.59  3.000
 XH8  C13   C12  C11   112.11  3.000
 XH8  H132  C13  H131  106.70  3.000
 XH8  H132  C13  C14   109.82  3.000
 XH8  H131  C13  C14   109.45  3.000
 XH8  H132  C13  C12   109.45  3.000
 XH8  H131  C13  C12   109.31  3.000
 XH8  C14   C13  C12   111.95  3.000
 XH8  C19   C14  C15   116.89  3.000
 XH8  C19   C14  C13   121.32  3.000
 XH8  C15   C14  C13   121.76  3.000
 XH8  H15   C15  C16   120.46  3.000
 XH8  H15   C15  C14   120.04  3.000
 XH8  C16   C15  C14   119.50  3.000
 XH8  H16   C16  C17   120.29  3.000
 XH8  H16   C16  C15   121.23  3.000
 XH8  C17   C16  C15   118.48  3.000
 XH8  H17   C17  N18   116.69  3.000
 XH8  H17   C17  C16   120.32  3.000
 XH8  N18   C17  C16   122.99  3.000
 XH8  C19   N18  C17   117.85  3.000
 XH8  H19   C19  N18   116.25  3.000
 XH8  H19   C19  C14   119.46  3.000
 XH8  N18   C19  C14   124.29  3.000
 XH8  H20   C20  C21   118.37  3.000
 XH8  H20   C20  C08   120.31  3.000
 XH8  C21   C20  C08   121.32  3.000
 XH8  N22   C21  C20   118.86  3.000
 XH8  N22   C21  C05   122.59  3.000
 XH8  C20   C21  C05   118.54  3.000
 XH8  C21   N22  C02   118.88  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
 XH8  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 XH8  CONST_02  C05   C21  N22  C02     0.00   0.0  0
 XH8  CONST_03  C20   C21  N22  C02   180.00   0.0  0
 XH8  CONST_04  C21   N22  C02  C03     0.00   0.0  0
 XH8  CONST_05  C06   C05  C04  C03   180.00   0.0  0
 XH8  CONST_06  C21   C05  C04  C03     0.00   0.0  0
 XH8  CONST_07  N22   C02  C03  C04     0.00   0.0  0
 XH8  CONST_08  C07   C06  C05  C04   180.00   0.0  0
 XH8  CONST_09  C20   C21  C05  C04   180.00   0.0  0
 XH8  CONST_10  N22   C21  C05  C04     0.00   0.0  0
 XH8  CONST_11  C08   C07  C06  C05     0.00   0.0  0
 XH8  CONST_12  C08   C20  C21  C05     0.00   0.0  0
 XH8  CONST_13  C20   C21  C05  C06     0.00   0.0  0
 XH8  CONST_14  N22   C21  C05  C06   180.00   0.0  0
 XH8  CONST_15  C20   C08  C07  C06     0.00   0.0  0
 XH8  CONST_16  C21   C05  C06  C07     0.00   0.0  0
 XH8  CONST_17  C21   C20  C08  C07     0.00   0.0  0
 XH8  CONST_18  N22   C21  C20  C08   180.00   0.0  0
 XH8  CONST_19  C17   C16  C15  C14     0.00   0.0  0
 XH8  CONST_20  C17   N18  C19  C14     0.00   0.0  0
 XH8  CONST_21  N18   C19  C14  C15     0.00   0.0  0
 XH8  CONST_22  N18   C17  C16  C15     0.00   0.0  0
 XH8  CONST_23  C19   C14  C15  C16     0.00   0.0  0
 XH8  CONST_24  C19   N18  C17  C16     0.00   0.0  0
 XH8  CONST_25  C04   C03  C02  N01   180.00   0.0  0
 XH8  CONST_26  C21   N22  C02  N01   180.00   0.0  0
 XH8  CONST_27  C09   C08  C07  C06   180.00   0.0  0
 XH8  CONST_28  C21   C20  C08  C09   180.00   0.0  0
 XH8  CONST_29  C16   C15  C14  C13   180.00   0.0  0
 XH8  CONST_30  N18   C19  C14  C13   180.00   0.0  0
 XH8  CONST_31  H04   C04  C03  C02   180.00   0.0  0
 XH8  CONST_32  H06   C06  C05  C04     0.00   0.0  0
 XH8  CONST_33  H03   C03  C04  C05   180.00   0.0  0
 XH8  CONST_34  H07   C07  C06  C05   180.00   0.0  0
 XH8  CONST_35  H20   C20  C21  C05   180.00   0.0  0
 XH8  CONST_36  H16   C16  C15  C14   180.00   0.0  0
 XH8  CONST_37  H19   C19  C14  C15   180.00   0.0  0
 XH8  CONST_38  H17   C17  C16  C15   180.00   0.0  0
 XH8  CONST_39  H15   C15  C16  C17   180.00   0.0  0
 XH8  CONST_41  H012  N01  C02  C03   180.00   0.0  0
 XH8  Var_01    N10   C09  C08  C07   125.68  30.0  2
 XH8  Var_02    C15   C14  C13  C12    83.45  30.0  2
 XH8  Var_03    C11   N10  C09  C08  -179.12  30.0  3
 XH8  Var_04    C14   C13  C12  C11  -178.71  30.0  3
 XH8  Var_05    C12   C11  N10  C09   179.12  30.0  3
 XH8  Var_06    C13   C12  C11  N10  -178.34  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
 XH8  plan-1  C13   0.020
 XH8  plan-1  C14   0.020
 XH8  plan-1  C15   0.020
 XH8  plan-1  C16   0.020
 XH8  plan-1  C17   0.020
 XH8  plan-1  N18   0.020
 XH8  plan-1  C19   0.020
 XH8  plan-1  H15   0.020
 XH8  plan-1  H19   0.020
 XH8  plan-1  H16   0.020
 XH8  plan-1  H17   0.020
 XH8  plan-2  N01   0.020
 XH8  plan-2  C02   0.020
 XH8  plan-2  C03   0.020
 XH8  plan-2  C04   0.020
 XH8  plan-2  C05   0.020
 XH8  plan-2  C06   0.020
 XH8  plan-2  C07   0.020
 XH8  plan-2  C08   0.020
 XH8  plan-2  C09   0.020
 XH8  plan-2  C20   0.020
 XH8  plan-2  C21   0.020
 XH8  plan-2  N22   0.020
 XH8  plan-2  H03   0.020
 XH8  plan-2  H04   0.020
 XH8  plan-2  H06   0.020
 XH8  plan-2  H07   0.020
 XH8  plan-2  H20   0.020
 XH8  plan-3  N01   0.020
 XH8  plan-3  C02   0.020
 XH8  plan-3  H011  0.020
 XH8  plan-3  H012  0.020

