# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:18:34 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 6-[2-[5-[2-(dimethylamino)ethyl]pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCc1cncc(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
 7S9  7S9  6-[2-[5-[2-(dimethylamino)ethyl]pyridin-3-yl]ethyl]-4-methyl-pyridin-2-amine  ligand  45  21  .  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_7S9
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
 7S9  C07   C  CH3   0  -0.725  -4.8424   3.3523  -0.2714
 7S9  C06   C  CR6   0   0.280  -2.8242   0.1590  -0.3906
 7S9  C05   C  CR16  0  -0.439  -3.1337   1.5073  -0.4214
 7S9  C04   C  CR6   0   0.205  -4.4570   1.9060  -0.2028
 7S9  C03   C  CR16  0  -0.444  -5.3972   0.9273   0.0486
 7S9  C02   C  CR6   0   0.440  -4.9933  -0.4185   0.0686
 7S9  N02   N  NH2   0  -0.839  -5.8857  -1.4085   0.3638
 7S9  N01   N  N     0  -0.486  -3.7350  -0.7858  -0.1519
 7S9  C09   C  CH2   0  -0.513  -0.8264  -0.9927   0.6281
 7S9  C16   C  CR16  0  -0.121   3.0602  -2.4227  -0.1979
 7S9  C15   C  CR6   0   0.051   2.9645  -1.1842   0.4264
 7S9  C14   C  CR16  0  -0.245   1.6848  -0.7186   0.7114
 7S9  C13   C  CR6   0   0.049   0.5710  -1.4777   0.3788
 7S9  C12   C  CR16  0  -0.110   0.8037  -2.7037  -0.2400
 7S9  N11   N  N     0  -0.398   2.0118  -3.1698  -0.5226
 7S9  C18   C  CH2   0  -0.253   4.3462   0.7867  -0.2379
 7S9  N19   N  NT    0  -0.407   5.5738   1.5338  -0.0490
 7S9  C20   C  CH3   0  -0.520   5.8099   2.4220  -1.1674
 7S9  C21   C  CH3   0  -0.527   5.5926   2.2703   1.1972
 7S9  H071  H  HCH3  0   0.255  -5.0732   3.6339  -1.3007
 7S9  H072  H  HCH3  0   0.247  -5.7245   3.5649   0.3309
 7S9  H073  H  HCH3  0   0.247  -4.0315   3.9974   0.0653
 7S9  H05   H  HCR6  0   0.244  -2.3604   2.2409  -0.6122
 7S9  H081  H  HCH2  0   0.249  -1.4095  -1.0326  -1.4454
 7S9  H082  H  HCH2  0   0.250  -0.7858   0.5205  -0.9140
 7S9  H03   H  HCR6  0   0.254  -6.4334   1.1851   0.2336
 7S9  H021  H  HNH2  0   0.388  -6.8629  -1.2144   0.2240
 7S9  H022  H  HNH2  0   0.379  -5.6109  -2.3441   0.1139
 7S9  H091  H  HCH2  0   0.253  -0.8288  -0.2850   1.4605
 7S9  H092  H  HCH2  0   0.253  -1.4664  -1.8286   0.9191
 7S9  H16   H  HCR6  0   0.252   4.0383  -2.8287  -0.4393
 7S9  H14   H  HCR6  0   0.255   1.5545   0.2392   1.2053
 7S9  H171  H  HCH2  0   0.254   4.1197  -0.0069   1.7703
 7S9  H172  H  HCH2  0   0.246   5.0768  -1.0076   0.6895
 7S9  H12   H  HCR6  0   0.252  -0.0357  -3.3380  -0.5119
 7S9  H181  H  HCH2  0   0.236   4.3561   0.3743  -1.2509
 7S9  H182  H  HCH2  0   0.195   3.4569   1.4395  -0.1785
 7S9  H201  H  HCH3  0   0.191   5.0318   3.1935  -1.2819
 7S9  H202  H  HCH3  0   0.232   6.7654   2.9338  -1.0433
 7S9  H203  H  HCH3  0   0.233   5.8547   1.8540  -2.0977
 7S9  H211  H  HCH3  0   0.236   5.5213   1.6000   2.0532
 7S9  H212  H  HCH3  0   0.235   6.5352   2.8117   1.2894
 7S9  H213  H  HCH3  0   0.191   4.7758   3.0058   1.2764
 7S9  C08   C  CH2   0  -0.489  -1.4176  -0.3191  -0.6162
 7S9  C17   C  CH2   0  -0.537   4.1876  -0.3755   0.7440

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
 7S9  C07  C04   single    1.498  0.020  1.498
 7S9  C06  C05   aromatic  1.384  0.020  1.384
 7S9  C06  N01   aromatic  1.334  0.020  1.334
 7S9  C06  C08   single    1.503  0.020  1.503
 7S9  C05  C04   aromatic  1.399  0.020  1.399
 7S9  C04  C03   aromatic  1.380  0.020  1.380
 7S9  C03  C02   aromatic  1.405  0.020  1.405
 7S9  C02  N02   single    1.365  0.020  1.365
 7S9  C02  N01   aromatic  1.329  0.020  1.329
 7S9  C08  C09   single    1.534  0.020  1.534
 7S9  C09  C13   single    1.500  0.020  1.500
 7S9  C16  C15   aromatic  1.390  0.020  1.390
 7S9  C16  N11   aromatic  1.328  0.020  1.328
 7S9  C15  C14   aromatic  1.391  0.020  1.391
 7S9  C15  C17   single    1.500  0.020  1.500
 7S9  C14  C13   aromatic  1.388  0.020  1.388
 7S9  C13  C12   aromatic  1.393  0.020  1.393
 7S9  C12  N11   aromatic  1.325  0.020  1.325
 7S9  C17  C18   single    1.530  0.020  1.530
 7S9  C18  N19   single    1.449  0.020  1.449
 7S9  N19  C20   single    1.448  0.020  1.448
 7S9  N19  C21   single    1.448  0.020  1.448
 7S9  C07  H071  single    0.970  0.020  1.090
 7S9  C07  H072  single    0.970  0.020  1.090
 7S9  C07  H073  single    0.970  0.020  1.090
 7S9  C05  H05   single    0.930  0.020  1.080
 7S9  C08  H081  single    0.970  0.020  1.090
 7S9  C08  H082  single    0.970  0.020  1.090
 7S9  C03  H03   single    0.930  0.020  1.080
 7S9  N02  H021  single    0.890  0.020  1.040
 7S9  N02  H022  single    0.890  0.020  1.040
 7S9  C09  H091  single    0.970  0.020  1.090
 7S9  C09  H092  single    0.970  0.020  1.090
 7S9  C16  H16   single    0.930  0.020  1.080
 7S9  C14  H14   single    0.930  0.020  1.080
 7S9  C17  H171  single    0.970  0.020  1.090
 7S9  C17  H172  single    0.970  0.020  1.090
 7S9  C12  H12   single    0.930  0.020  1.080
 7S9  C18  H181  single    0.970  0.020  1.090
 7S9  C18  H182  single    0.970  0.020  1.090
 7S9  C20  H201  single    0.970  0.020  1.090
 7S9  C20  H202  single    0.970  0.020  1.090
 7S9  C20  H203  single    0.970  0.020  1.090
 7S9  C21  H211  single    0.970  0.020  1.090
 7S9  C21  H212  single    0.970  0.020  1.090
 7S9  C21  H213  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
 7S9  H073  C07  H072  108.44  3.000
 7S9  H073  C07  H071  107.22  3.000
 7S9  H072  C07  H071  107.44  3.000
 7S9  H073  C07  C04   111.47  3.000
 7S9  H072  C07  C04   111.80  3.000
 7S9  H071  C07  C04   110.27  3.000
 7S9  C08   C06  N01   116.15  3.000
 7S9  C08   C06  C05   121.07  3.000
 7S9  N01   C06  C05   122.78  3.000
 7S9  H05   C05  C04   120.65  3.000
 7S9  H05   C05  C06   120.28  3.000
 7S9  C04   C05  C06   119.06  3.000
 7S9  C03   C04  C05   118.07  3.000
 7S9  C03   C04  C07   121.17  3.000
 7S9  C05   C04  C07   120.74  3.000
 7S9  H03   C03  C02   120.01  3.000
 7S9  H03   C03  C04   120.91  3.000
 7S9  C02   C03  C04   119.08  3.000
 7S9  N01   C02  N02   117.02  3.000
 7S9  N01   C02  C03   122.30  3.000
 7S9  N02   C02  C03   120.65  3.000
 7S9  H022  N02  H021  114.20  3.000
 7S9  H022  N02  C02   116.22  3.000
 7S9  H021  N02  C02   117.71  3.000
 7S9  C02   N01  C06   118.71  3.000
 7S9  H092  C09  H091  106.95  3.000
 7S9  H092  C09  C13   110.04  3.000
 7S9  H091  C09  C13   109.76  3.000
 7S9  H092  C09  C08   109.05  3.000
 7S9  H091  C09  C08   109.44  3.000
 7S9  C13   C09  C08   111.49  3.000
 7S9  H16   C16  N11   116.51  3.000
 7S9  H16   C16  C15   119.66  3.000
 7S9  N11   C16  C15   123.83  3.000
 7S9  C17   C15  C14   121.74  3.000
 7S9  C17   C15  C16   121.28  3.000
 7S9  C14   C15  C16   116.96  3.000
 7S9  H14   C14  C13   119.68  3.000
 7S9  H14   C14  C15   119.93  3.000
 7S9  C13   C14  C15   120.39  3.000
 7S9  C12   C13  C14   116.98  3.000
 7S9  C12   C13  C09   120.94  3.000
 7S9  C14   C13  C09   122.06  3.000
 7S9  H12   C12  N11   116.46  3.000
 7S9  H12   C12  C13   119.72  3.000
 7S9  N11   C12  C13   123.82  3.000
 7S9  C12   N11  C16   118.02  3.000
 7S9  H182  C18  H181  106.25  3.000
 7S9  H182  C18  N19   111.72  3.000
 7S9  H181  C18  N19   107.90  3.000
 7S9  H182  C18  C17   109.33  3.000
 7S9  H181  C18  C17   108.00  3.000
 7S9  N19   C18  C17   113.32  3.000
 7S9  C21   N19  C20   110.54  3.000
 7S9  C21   N19  C18   112.67  3.000
 7S9  C20   N19  C18   110.72  3.000
 7S9  H203  C20  H202  107.78  3.000
 7S9  H203  C20  H201  107.76  3.000
 7S9  H202  C20  H201  107.57  3.000
 7S9  H203  C20  N19   110.24  3.000
 7S9  H202  C20  N19   110.05  3.000
 7S9  H201  C20  N19   113.25  3.000
 7S9  H213  C21  H212  107.65  3.000
 7S9  H213  C21  H211  107.80  3.000
 7S9  H212  C21  H211  107.19  3.000
 7S9  H213  C21  N19   113.06  3.000
 7S9  H212  C21  N19   109.66  3.000
 7S9  H211  C21  N19   111.25  3.000
 7S9  H082  C08  H081  106.88  3.000
 7S9  H082  C08  C09   109.63  3.000
 7S9  H081  C08  C09   109.00  3.000
 7S9  H082  C08  C06   109.75  3.000
 7S9  H081  C08  C06   109.16  3.000
 7S9  C09   C08  C06   112.26  3.000
 7S9  H172  C17  H171  107.02  3.000
 7S9  H172  C17  C18   108.85  3.000
 7S9  H171  C17  C18   110.67  3.000
 7S9  H172  C17  C15   109.95  3.000
 7S9  H171  C17  C15   109.27  3.000
 7S9  C18   C17  C15   110.99  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
 7S9  CONST_01  C03   C04  C05  C06     0.00   0.0  0
 7S9  CONST_02  C03   C02  N01  C06     0.00   0.0  0
 7S9  CONST_03  C02   N01  C06  C05     0.00   0.0  0
 7S9  CONST_04  C02   C03  C04  C05     0.00   0.0  0
 7S9  CONST_05  N01   C06  C05  C04     0.00   0.0  0
 7S9  CONST_06  N01   C02  C03  C04     0.00   0.0  0
 7S9  CONST_07  C13   C14  C15  C16     0.00   0.0  0
 7S9  CONST_08  C13   C12  N11  C16     0.00   0.0  0
 7S9  CONST_09  C12   N11  C16  C15     0.00   0.0  0
 7S9  CONST_10  C12   C13  C14  C15     0.00   0.0  0
 7S9  CONST_11  N11   C16  C15  C14     0.00   0.0  0
 7S9  CONST_12  N11   C12  C13  C14     0.00   0.0  0
 7S9  CONST_13  C06   C05  C04  C07   180.00   0.0  0
 7S9  CONST_14  C02   C03  C04  C07   180.00   0.0  0
 7S9  CONST_15  N02   C02  N01  C06   180.00   0.0  0
 7S9  CONST_16  C08   C06  C05  C04   180.00   0.0  0
 7S9  CONST_17  N02   C02  C03  C04   180.00   0.0  0
 7S9  CONST_18  C08   C06  N01  C02   180.00   0.0  0
 7S9  CONST_19  C15   C14  C13  C09   180.00   0.0  0
 7S9  CONST_20  N11   C12  C13  C09   180.00   0.0  0
 7S9  CONST_21  C17   C15  C14  C13   180.00   0.0  0
 7S9  CONST_22  C17   C15  C16  N11   180.00   0.0  0
 7S9  CONST_23  H03   C03  C04  C05   180.00   0.0  0
 7S9  CONST_24  H05   C05  C04  C03   180.00   0.0  0
 7S9  CONST_25  H14   C14  C15  C16   180.00   0.0  0
 7S9  CONST_26  H12   C12  N11  C16   180.00   0.0  0
 7S9  CONST_27  H16   C16  C15  C14   180.00   0.0  0
 7S9  Var_01    C13   C09  C08  C06   179.31  30.0  3
 7S9  Var_02    C09   C08  C06  C05   115.15  30.0  2
 7S9  Var_03    C14   C13  C09  C08    95.03  30.0  2
 7S9  Var_04    C18   C17  C15  C16   104.17  30.0  2
 7S9  Var_05    H071  C07  C04  C05    86.38  30.0  2
 7S9  Var_06    N19   C18  C17  C15  -175.00  30.0  3
 7S9  Var_07    C20   N19  C18  C17   167.63  30.0  3
 7S9  Var_08    H201  C20  N19  C18    62.98  30.0  3
 7S9  Var_09    H211  C21  N19  C18    61.53  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
 7S9  plan-1  C07   0.020
 7S9  plan-1  C06   0.020
 7S9  plan-1  C05   0.020
 7S9  plan-1  C04   0.020
 7S9  plan-1  C03   0.020
 7S9  plan-1  C02   0.020
 7S9  plan-1  N02   0.020
 7S9  plan-1  N01   0.020
 7S9  plan-1  H05   0.020
 7S9  plan-1  H03   0.020
 7S9  plan-1  C08   0.020
 7S9  plan-2  C09   0.020
 7S9  plan-2  C16   0.020
 7S9  plan-2  C15   0.020
 7S9  plan-2  C14   0.020
 7S9  plan-2  C13   0.020
 7S9  plan-2  C12   0.020
 7S9  plan-2  N11   0.020
 7S9  plan-2  H16   0.020
 7S9  plan-2  H14   0.020
 7S9  plan-2  H12   0.020
 7S9  plan-2  C17   0.020
 7S9  plan-3  C02   0.020
 7S9  plan-3  N02   0.020
 7S9  plan-3  H021  0.020
 7S9  plan-3  H022  0.020

