# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:40:13 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 6-[2-[5-(3-methoxypropylamino)pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCNc1cncc(CCc2cc(C)cc(N)n2)c1
#
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
 D8H  D8H  6-[2-[5-(3-methoxypropylamino)pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine  ligand  46  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8H
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
 D8H  N02   N  NH2   0  -0.839   5.1393   3.1666   0.6502
 D8H  C02   C  CR6   0   0.442   5.0457   1.8842   0.1933
 D8H  C03   C  CR16  0  -0.448   6.2037   1.1456  -0.1094
 D8H  C04   C  CR6   0   0.205   6.0722  -0.1282  -0.6218
 D8H  C07   C  CH3   0  -0.726   7.2722  -0.9661  -0.9407
 D8H  C05   C  CR16  0  -0.431   4.7799  -0.6275  -0.8232
 D8H  N01   N  N     0  -0.484   3.8242   1.3959   0.0070
 D8H  C06   C  CR6   0   0.272   3.6956   0.1648  -0.4931
 D8H  C08   C  CH2   0  -0.488   2.2899  -0.3411  -0.6452
 D8H  C09   C  CH2   0  -0.512   1.6648  -0.6938   0.7130
 D8H  C13   C  CR6   0   0.057   0.2515  -1.1745   0.5613
 D8H  C12   C  CR16  0  -0.156  -0.0521  -2.5352   0.5804
 D8H  C14   C  CR16  0  -0.301  -0.7896  -0.2880   0.3496
 D8H  C15   C  CR6   0   0.317  -2.0941  -0.7588   0.1603
 D8H  C16   C  CR16  0  -0.173  -2.2748  -2.1492   0.2110
 D8H  N11   N  N     0  -0.384  -1.2798  -3.0014   0.4119
 D8H  N17   N  NH1   0  -0.694  -3.1198   0.1125  -0.0909
 D8H  C18   C  CH2   0  -0.268  -4.5047  -0.2905  -0.0047
 D8H  C19   C  CH2   0  -0.502  -5.4139   0.8887  -0.3121
 D8H  C20   C  CH2   0  -0.120  -6.8743   0.4920  -0.2261
 D8H  O21   O  O2    0  -0.486  -7.6733   1.6099  -0.5223
 D8H  C22   C  CH3   0  -0.398  -9.0461   1.3205  -0.4633
 D8H  H021  H  HNH2  0   0.388   6.0060   3.4501   1.0756
 D8H  H022  H  HNH2  0   0.379   4.3176   3.5453   1.0916
 D8H  H03   H  HCR6  0   0.255   7.1829   1.5772   0.0609
 D8H  H071  H  HCH3  0   0.253   7.3601  -1.7929  -0.2336
 D8H  H072  H  HCH3  0   0.250   7.1934  -1.4048  -1.9357
 D8H  H073  H  HCH3  0   0.246   8.1933  -0.3871  -0.8940
 D8H  H05   H  HCR6  0   0.243   4.6279  -1.6211  -1.2267
 D8H  H081  H  HCH2  0   0.248   1.6794   0.4250  -1.1304
 D8H  H082  H  HCH2  0   0.248   2.2740  -1.2219  -1.2902
 D8H  H091  H  HCH2  0   0.250   2.2680  -1.4656   1.1970
 D8H  H092  H  HCH2  0   0.252   1.6969   0.1865   1.3586
 D8H  H12   H  HCR6  0   0.243   0.7339  -3.2664   0.7432
 D8H  H14   H  HCR6  0   0.260  -0.5998   0.7810   0.3273
 D8H  H16   H  HCR6  0   0.259  -3.2593  -2.5843   0.0802
 D8H  H17   H  HNH1  0   0.381  -2.9381   1.0656   0.1842
 D8H  H181  H  HCH2  0   0.232  -4.6945  -1.0873  -0.7293
 D8H  H182  H  HCH2  0   0.219  -4.7479  -0.7005   0.9855
 D8H  H191  H  HCH2  0   0.236  -5.2143   1.6991   0.3958
 D8H  H192  H  HCH2  0   0.240  -5.1911   1.2657  -1.3136
 D8H  H201  H  HCH2  0   0.197  -7.0821  -0.3284  -0.9289
 D8H  H202  H  HCH2  0   0.197  -7.1008   0.1094   0.7803
 D8H  H221  H  HCH3  0   0.233  -9.5945   2.2288  -0.7111
 D8H  H222  H  HCH3  0   0.203  -9.3329   0.5381  -1.1766
 D8H  H223  H  HCH3  0   0.203  -9.3543   0.9907   0.5361

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
 D8H  N02  C02   single    1.365  0.020  1.365
 D8H  C02  C03   aromatic  1.406  0.020  1.406
 D8H  C02  N01   aromatic  1.329  0.020  1.329
 D8H  C03  C04   aromatic  1.379  0.020  1.379
 D8H  C04  C07   single    1.498  0.020  1.498
 D8H  C04  C05   aromatic  1.400  0.020  1.400
 D8H  C05  C06   aromatic  1.383  0.020  1.383
 D8H  N01  C06   aromatic  1.335  0.020  1.335
 D8H  C06  C08   single    1.502  0.020  1.502
 D8H  C08  C09   single    1.536  0.020  1.536
 D8H  C09  C13   single    1.500  0.020  1.500
 D8H  C13  C12   aromatic  1.394  0.020  1.394
 D8H  C13  C14   aromatic  1.384  0.020  1.384
 D8H  C12  N11   aromatic  1.324  0.020  1.324
 D8H  C14  C15   aromatic  1.400  0.020  1.400
 D8H  C15  C16   aromatic  1.403  0.020  1.403
 D8H  C15  N17   single    1.369  0.020  1.369
 D8H  C16  N11   aromatic  1.325  0.020  1.325
 D8H  N17  C18   single    1.445  0.020  1.445
 D8H  C18  C19   single    1.520  0.020  1.520
 D8H  C19  C20   single    1.516  0.020  1.516
 D8H  C20  O21   single    1.406  0.020  1.406
 D8H  O21  C22   single    1.404  0.020  1.404
 D8H  N02  H021  single    0.890  0.020  1.040
 D8H  N02  H022  single    0.890  0.020  1.040
 D8H  C03  H03   single    0.930  0.020  1.080
 D8H  C07  H071  single    0.970  0.020  1.090
 D8H  C07  H072  single    0.970  0.020  1.090
 D8H  C07  H073  single    0.970  0.020  1.090
 D8H  C05  H05   single    0.930  0.020  1.080
 D8H  C08  H081  single    0.970  0.020  1.090
 D8H  C08  H082  single    0.970  0.020  1.090
 D8H  C09  H091  single    0.970  0.020  1.090
 D8H  C09  H092  single    0.970  0.020  1.090
 D8H  C12  H12   single    0.930  0.020  1.080
 D8H  C14  H14   single    0.930  0.020  1.080
 D8H  C16  H16   single    0.930  0.020  1.080
 D8H  N17  H17   single    0.890  0.020  1.040
 D8H  C18  H181  single    0.970  0.020  1.090
 D8H  C18  H182  single    0.970  0.020  1.090
 D8H  C19  H191  single    0.970  0.020  1.090
 D8H  C19  H192  single    0.970  0.020  1.090
 D8H  C20  H201  single    0.970  0.020  1.090
 D8H  C20  H202  single    0.970  0.020  1.090
 D8H  C22  H221  single    0.970  0.020  1.090
 D8H  C22  H222  single    0.970  0.020  1.090
 D8H  C22  H223  single    0.970  0.020  1.090

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
 D8H  H022  N02  H021  114.31  3.000
 D8H  H022  N02  C02   116.38  3.000
 D8H  H021  N02  C02   117.74  3.000
 D8H  N01   C02  C03   122.26  3.000
 D8H  N01   C02  N02   117.09  3.000
 D8H  C03   C02  N02   120.60  3.000
 D8H  H03   C03  C04   120.82  3.000
 D8H  H03   C03  C02   120.07  3.000
 D8H  C04   C03  C02   119.11  3.000
 D8H  C05   C04  C07   120.62  3.000
 D8H  C05   C04  C03   118.09  3.000
 D8H  C07   C04  C03   121.29  3.000
 D8H  H073  C07  H072  108.31  3.000
 D8H  H073  C07  H071  107.87  3.000
 D8H  H072  C07  H071  106.99  3.000
 D8H  H073  C07  C04   111.78  3.000
 D8H  H072  C07  C04   111.19  3.000
 D8H  H071  C07  C04   110.51  3.000
 D8H  H05   C05  C06   120.29  3.000
 D8H  H05   C05  C04   120.69  3.000
 D8H  C06   C05  C04   119.02  3.000
 D8H  C06   N01  C02   118.68  3.000
 D8H  C08   C06  N01   116.02  3.000
 D8H  C08   C06  C05   121.12  3.000
 D8H  N01   C06  C05   122.84  3.000
 D8H  H082  C08  H081  107.16  3.000
 D8H  H082  C08  C09   109.34  3.000
 D8H  H081  C08  C09   109.03  3.000
 D8H  H082  C08  C06   110.19  3.000
 D8H  H081  C08  C06   109.37  3.000
 D8H  C09   C08  C06   111.63  3.000
 D8H  H092  C09  H091  106.93  3.000
 D8H  H092  C09  C13   110.22  3.000
 D8H  H091  C09  C13   109.78  3.000
 D8H  H092  C09  C08   109.00  3.000
 D8H  H091  C09  C08   109.22  3.000
 D8H  C13   C09  C08   111.56  3.000
 D8H  C14   C13  C12   117.62  3.000
 D8H  C14   C13  C09   121.26  3.000
 D8H  C12   C13  C09   121.09  3.000
 D8H  H12   C12  N11   116.95  3.000
 D8H  H12   C12  C13   120.11  3.000
 D8H  N11   C12  C13   122.94  3.000
 D8H  H14   C14  C15   119.43  3.000
 D8H  H14   C14  C13   120.15  3.000
 D8H  C15   C14  C13   120.42  3.000
 D8H  N17   C15  C16   122.74  3.000
 D8H  N17   C15  C14   120.59  3.000
 D8H  C16   C15  C14   116.65  3.000
 D8H  H16   C16  N11   116.22  3.000
 D8H  H16   C16  C15   120.68  3.000
 D8H  N11   C16  C15   123.09  3.000
 D8H  C16   N11  C12   119.28  3.000
 D8H  H17   N17  C18   114.83  3.000
 D8H  H17   N17  C15   114.61  3.000
 D8H  C18   N17  C15   121.98  3.000
 D8H  H182  C18  H181  106.66  3.000
 D8H  H182  C18  C19   109.82  3.000
 D8H  H181  C18  C19   109.11  3.000
 D8H  H182  C18  N17   111.71  3.000
 D8H  H181  C18  N17   109.28  3.000
 D8H  C19   C18  N17   110.17  3.000
 D8H  H192  C19  H191  107.46  3.000
 D8H  H192  C19  C20   109.80  3.000
 D8H  H191  C19  C20   109.44  3.000
 D8H  H192  C19  C18   109.32  3.000
 D8H  H191  C19  C18   109.54  3.000
 D8H  C20   C19  C18   111.21  3.000
 D8H  H202  C20  H201  106.62  3.000
 D8H  H202  C20  O21   110.63  3.000
 D8H  H201  C20  O21   110.56  3.000
 D8H  H202  C20  C19   109.95  3.000
 D8H  H201  C20  C19   109.93  3.000
 D8H  O21   C20  C19   109.12  3.000
 D8H  C22   O21  C20   112.52  3.000
 D8H  H223  C22  H222  107.74  3.000
 D8H  H223  C22  H221  108.45  3.000
 D8H  H222  C22  H221  108.37  3.000
 D8H  H223  C22  O21   112.02  3.000
 D8H  H222  C22  O21   112.04  3.000
 D8H  H221  C22  O21   108.10  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
 D8H  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 D8H  CONST_02  C05   C06  N01  C02     0.00   0.0  0
 D8H  CONST_03  C06   N01  C02  C03     0.00   0.0  0
 D8H  CONST_04  C06   C05  C04  C03     0.00   0.0  0
 D8H  CONST_05  N01   C02  C03  C04     0.00   0.0  0
 D8H  CONST_06  N01   C06  C05  C04     0.00   0.0  0
 D8H  CONST_07  C16   N11  C12  C13     0.00   0.0  0
 D8H  CONST_08  C16   C15  C14  C13     0.00   0.0  0
 D8H  CONST_09  C15   C14  C13  C12     0.00   0.0  0
 D8H  CONST_10  C15   C16  N11  C12     0.00   0.0  0
 D8H  CONST_11  N11   C12  C13  C14     0.00   0.0  0
 D8H  CONST_12  N11   C16  C15  C14     0.00   0.0  0
 D8H  CONST_13  C04   C03  C02  N02   180.00   0.0  0
 D8H  CONST_14  C06   N01  C02  N02   180.00   0.0  0
 D8H  CONST_15  C07   C04  C03  C02   180.00   0.0  0
 D8H  CONST_16  C08   C06  N01  C02   180.00   0.0  0
 D8H  CONST_17  C08   C06  C05  C04   180.00   0.0  0
 D8H  CONST_18  C06   C05  C04  C07   180.00   0.0  0
 D8H  CONST_19  N11   C12  C13  C09   180.00   0.0  0
 D8H  CONST_20  C15   C14  C13  C09   180.00   0.0  0
 D8H  CONST_21  N17   C15  C14  C13   180.00   0.0  0
 D8H  CONST_22  N17   C15  C16  N11   180.00   0.0  0
 D8H  CONST_23  H05   C05  C04  C03   180.00   0.0  0
 D8H  CONST_24  H03   C03  C04  C05   180.00   0.0  0
 D8H  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 D8H  CONST_26  H16   C16  N11  C12   180.00   0.0  0
 D8H  CONST_27  H12   C12  C13  C14   180.00   0.0  0
 D8H  CONST_28  C18   N17  C15  C14   180.00   0.0  0
 D8H  Var_01    C09   C08  C06  C05   105.15  30.0  2
 D8H  Var_02    C13   C09  C08  C06   178.93  30.0  3
 D8H  Var_03    C12   C13  C09  C08    99.76  30.0  2
 D8H  Var_04    H071  C07  C04  C03   109.66  30.0  2
 D8H  Var_05    C19   C18  N17  C15   179.04  30.0  3
 D8H  Var_06    C20   C19  C18  N17  -179.91  30.0  3
 D8H  Var_07    O21   C20  C19  C18  -179.78  30.0  3
 D8H  Var_08    H221  C22  O21  C20  -179.55  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
 D8H  plan-1  N02   0.020
 D8H  plan-1  C02   0.020
 D8H  plan-1  C03   0.020
 D8H  plan-1  C04   0.020
 D8H  plan-1  C07   0.020
 D8H  plan-1  C05   0.020
 D8H  plan-1  N01   0.020
 D8H  plan-1  C06   0.020
 D8H  plan-1  C08   0.020
 D8H  plan-1  H03   0.020
 D8H  plan-1  H05   0.020
 D8H  plan-2  C09   0.020
 D8H  plan-2  C13   0.020
 D8H  plan-2  C12   0.020
 D8H  plan-2  C14   0.020
 D8H  plan-2  C15   0.020
 D8H  plan-2  C16   0.020
 D8H  plan-2  N11   0.020
 D8H  plan-2  N17   0.020
 D8H  plan-2  H12   0.020
 D8H  plan-2  H14   0.020
 D8H  plan-2  H16   0.020
 D8H  plan-3  N02   0.020
 D8H  plan-3  C02   0.020
 D8H  plan-3  H021  0.020
 D8H  plan-3  H022  0.020
 D8H  plan-4  C15   0.020
 D8H  plan-4  N17   0.020
 D8H  plan-4  C18   0.020
 D8H  plan-4  H17   0.020

