# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:49:44 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N'-[5-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]pyridin-3-yl]-N,N'-dimethyl-ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCN(C)c1cncc(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
 EXI  EXI  N'-[5-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]pyridin-3-yl]-N,N'-dimethyl-ethane-1,2-diamine  ligand  47  22  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EXI
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
 EXI  N01   N  N     0  -0.486  -3.6147  -1.1520  -0.0347
 EXI  C02   C  CR6   0   0.440  -4.8529  -1.5433   0.2425
 EXI  N02   N  NH2   0  -0.839  -5.0385  -2.8661   0.5274
 EXI  C03   C  CR16  0  -0.449  -5.9471  -0.6601   0.2029
 EXI  C04   C  CR6   0   0.205  -5.7314   0.6595  -0.1342
 EXI  C05   C  CR16  0  -0.434  -4.4211   1.0595  -0.4254
 EXI  C06   C  CR6   0   0.279  -3.4042   0.1250  -0.3628
 EXI  C07   C  CH3   0  -0.726  -6.8553   1.6488  -0.1817
 EXI  C08   C  CH2   0  -0.487  -1.9782   0.5099  -0.6357
 EXI  C09   C  CH2   0  -0.516  -1.1057   0.3922   0.6211
 EXI  N11   N  N     0  -0.382   2.0276   2.4295   0.3374
 EXI  C12   C  CR16  0  -0.164   0.7786   2.0590   0.5882
 EXI  C13   C  CR6   0   0.072   0.3204   0.7697   0.3484
 EXI  C14   C  CR16  0  -0.322   1.2125  -0.1510  -0.1820
 EXI  C15   C  CR6   0   0.330   2.5357   0.2171  -0.4686
 EXI  C16   C  CR16  0  -0.164   2.8774   1.5520  -0.1653
 EXI  C17   C  CH3   0  -0.550   3.0499  -2.0535  -1.1497
 EXI  N17   N  NT    0  -0.505   3.4282  -0.6648  -1.0192
 EXI  C18   C  CH2   0  -0.357   4.8417  -0.3571  -1.0661
 EXI  C19   C  CH2   0  -0.264   5.5473  -0.5342   0.2754
 EXI  N20   N  NH1   0  -0.593   6.9505  -0.2014   0.1553
 EXI  C21   C  CH3   0  -0.515   7.6622  -0.3155   1.4119
 EXI  HN02  H  HNH2  0   0.379  -4.2168  -3.3778   0.8047
 EXI  HN0A  H  HNH2  0   0.388  -5.8691  -3.1182   1.0364
 EXI  H03   H  HCR6  0   0.256  -6.9423  -1.0177   0.4385
 EXI  H05   H  HCR6  0   0.243  -4.2032   2.0866  -0.6902
 EXI  H07   H  HCH3  0   0.252  -6.7115   2.4305   0.5656
 EXI  H07A  H  HCH3  0   0.251  -6.8993   2.1417  -1.1538
 EXI  H07B  H  HCH3  0   0.247  -7.8190   1.1775   0.0044
 EXI  H08   H  HCH2  0   0.248  -1.5696  -0.1377  -1.4166
 EXI  H08A  H  HCH2  0   0.248  -1.9352   1.5325  -1.0156
 EXI  H09   H  HCH2  0   0.250  -1.5151   1.0359   1.4038
 EXI  H09A  H  HCH2  0   0.251  -1.1589  -0.6327   0.9936
 EXI  H12   H  HCR6  0   0.242   0.1162   2.8107   1.0059
 EXI  H14   H  HCR6  0   0.268   0.8634  -1.1597  -0.3640
 EXI  H16   H  HCR6  0   0.254   3.8820   1.9214  -0.3337
 EXI  H17   H  HCH3  0   0.243   2.1881  -2.1734  -1.8098
 EXI  H17A  H  HCH3  0   0.259   3.8762  -2.6056  -1.5901
 EXI  H17B  H  HCH3  0   0.230   2.8070  -2.5239  -0.1911
 EXI  H18   H  HCH2  0   0.256   5.2980  -1.0155  -1.8089
 EXI  H18A  H  HCH2  0   0.250   5.0011   0.6572  -1.4361
 EXI  H19   H  HCH2  0   0.222   5.0948   0.1335   1.0156
 EXI  H19A  H  HCH2  0   0.200   5.3758  -1.5593   0.6430
 EXI  HN20  H  HNH1  0   0.344   7.3782  -0.8242  -0.5192
 EXI  H21   H  HCH3  0   0.231   8.7227  -0.1167   1.2563
 EXI  H21A  H  HCH3  0   0.222   7.2885   0.4273   2.1194
 EXI  H21B  H  HCH3  0   0.194   7.5707  -1.2996   1.8928

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
 EXI  N01  C02   aromatic  1.328  0.020  1.328
 EXI  N01  C06   aromatic  1.335  0.020  1.335
 EXI  C02  N02   single    1.366  0.020  1.366
 EXI  C02  C03   aromatic  1.407  0.020  1.407
 EXI  C03  C04   aromatic  1.379  0.020  1.379
 EXI  C04  C05   aromatic  1.400  0.020  1.400
 EXI  C04  C07   single    1.498  0.020  1.498
 EXI  C05  C06   aromatic  1.382  0.020  1.382
 EXI  C06  C08   single    1.502  0.020  1.502
 EXI  C08  C09   single    1.534  0.020  1.534
 EXI  C09  C13   single    1.500  0.020  1.500
 EXI  N11  C12   aromatic  1.327  0.020  1.327
 EXI  N11  C16   aromatic  1.321  0.020  1.321
 EXI  C12  C13   aromatic  1.389  0.020  1.389
 EXI  C13  C14   aromatic  1.387  0.020  1.387
 EXI  C14  C15   aromatic  1.403  0.020  1.403
 EXI  C15  C16   aromatic  1.411  0.020  1.411
 EXI  C15  N17   single    1.370  0.020  1.370
 EXI  C17  N17   single    1.445  0.020  1.445
 EXI  N17  C18   single    1.447  0.020  1.447
 EXI  C18  C19   single    1.526  0.020  1.526
 EXI  C19  N20   single    1.447  0.020  1.447
 EXI  N20  C21   single    1.449  0.020  1.449
 EXI  N02  HN02  single    0.890  0.020  1.040
 EXI  N02  HN0A  single    0.890  0.020  1.040
 EXI  C03  H03   single    0.930  0.020  1.080
 EXI  C05  H05   single    0.930  0.020  1.080
 EXI  C07  H07   single    0.970  0.020  1.090
 EXI  C07  H07A  single    0.970  0.020  1.090
 EXI  C07  H07B  single    0.970  0.020  1.090
 EXI  C08  H08   single    0.970  0.020  1.090
 EXI  C08  H08A  single    0.970  0.020  1.090
 EXI  C09  H09   single    0.970  0.020  1.090
 EXI  C09  H09A  single    0.970  0.020  1.090
 EXI  C12  H12   single    0.930  0.020  1.080
 EXI  C14  H14   single    0.930  0.020  1.080
 EXI  C16  H16   single    0.930  0.020  1.080
 EXI  C17  H17   single    0.970  0.020  1.090
 EXI  C17  H17A  single    0.970  0.020  1.090
 EXI  C17  H17B  single    0.970  0.020  1.090
 EXI  C18  H18   single    0.970  0.020  1.090
 EXI  C18  H18A  single    0.970  0.020  1.090
 EXI  C19  H19   single    0.970  0.020  1.090
 EXI  C19  H19A  single    0.970  0.020  1.090
 EXI  N20  HN20  single    0.890  0.020  1.040
 EXI  C21  H21   single    0.970  0.020  1.090
 EXI  C21  H21A  single    0.970  0.020  1.090
 EXI  C21  H21B  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
 EXI  C06   N01  C02   118.70  3.000
 EXI  C03   C02  N02   120.55  3.000
 EXI  C03   C02  N01   122.30  3.000
 EXI  N02   C02  N01   117.11  3.000
 EXI  HN0A  N02  HN02  114.02  3.000
 EXI  HN0A  N02  C02   117.41  3.000
 EXI  HN02  N02  C02   116.02  3.000
 EXI  H03   C03  C04   120.85  3.000
 EXI  H03   C03  C02   120.07  3.000
 EXI  C04   C03  C02   119.08  3.000
 EXI  C07   C04  C05   120.45  3.000
 EXI  C07   C04  C03   121.49  3.000
 EXI  C05   C04  C03   118.06  3.000
 EXI  H05   C05  C06   120.27  3.000
 EXI  H05   C05  C04   120.66  3.000
 EXI  C06   C05  C04   119.06  3.000
 EXI  C08   C06  C05   121.13  3.000
 EXI  C08   C06  N01   116.06  3.000
 EXI  C05   C06  N01   122.79  3.000
 EXI  H07B  C07  H07A  108.19  3.000
 EXI  H07B  C07  H07   108.04  3.000
 EXI  H07A  C07  H07   106.98  3.000
 EXI  H07B  C07  C04   111.89  3.000
 EXI  H07A  C07  C04   110.91  3.000
 EXI  H07   C07  C04   110.65  3.000
 EXI  H08A  C08  H08   106.95  3.000
 EXI  H08A  C08  C09   109.54  3.000
 EXI  H08   C08  C09   109.09  3.000
 EXI  H08A  C08  C06   109.91  3.000
 EXI  H08   C08  C06   109.42  3.000
 EXI  C09   C08  C06   111.80  3.000
 EXI  H09A  C09  H09   106.88  3.000
 EXI  H09A  C09  C13   110.15  3.000
 EXI  H09   C09  C13   109.76  3.000
 EXI  H09A  C09  C08   108.89  3.000
 EXI  H09   C09  C08   109.17  3.000
 EXI  C13   C09  C08   111.85  3.000
 EXI  C16   N11  C12   119.48  3.000
 EXI  H12   C12  C13   120.53  3.000
 EXI  H12   C12  N11   116.99  3.000
 EXI  C13   C12  N11   122.48  3.000
 EXI  C14   C13  C12   118.03  3.000
 EXI  C14   C13  C09   120.91  3.000
 EXI  C12   C13  C09   121.04  3.000
 EXI  H14   C14  C15   120.94  3.000
 EXI  H14   C14  C13   118.37  3.000
 EXI  C15   C14  C13   120.69  3.000
 EXI  N17   C15  C16   122.52  3.000
 EXI  N17   C15  C14   121.84  3.000
 EXI  C16   C15  C14   115.64  3.000
 EXI  H16   C16  C15   120.91  3.000
 EXI  H16   C16  N11   115.41  3.000
 EXI  C15   C16  N11   123.68  3.000
 EXI  H17B  C17  H17A  107.77  3.000
 EXI  H17B  C17  H17   107.87  3.000
 EXI  H17A  C17  H17   107.41  3.000
 EXI  H17B  C17  N17   113.07  3.000
 EXI  H17A  C17  N17   109.01  3.000
 EXI  H17   C17  N17   111.50  3.000
 EXI  C18   N17  C17   117.19  3.000
 EXI  C18   N17  C15   120.82  3.000
 EXI  C17   N17  C15   118.96  3.000
 EXI  H18A  C18  H18   105.57  3.000
 EXI  H18A  C18  C19   109.77  3.000
 EXI  H18   C18  C19   109.55  3.000
 EXI  H18A  C18  N17   110.57  3.000
 EXI  H18   C18  N17   107.57  3.000
 EXI  C19   C18  N17   113.48  3.000
 EXI  H19A  C19  H19   106.10  3.000
 EXI  H19A  C19  N20   113.10  3.000
 EXI  H19   C19  N20   108.46  3.000
 EXI  H19A  C19  C18   109.21  3.000
 EXI  H19   C19  C18   109.42  3.000
 EXI  N20   C19  C18   110.41  3.000
 EXI  HN20  N20  C21   108.77  3.000
 EXI  HN20  N20  C19   108.87  3.000
 EXI  C21   N20  C19   112.72  3.000
 EXI  H21B  C21  H21A  107.29  3.000
 EXI  H21B  C21  H21   107.86  3.000
 EXI  H21A  C21  H21   107.54  3.000
 EXI  H21B  C21  N20   114.15  3.000
 EXI  H21A  C21  N20   109.90  3.000
 EXI  H21   C21  N20   109.86  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
 EXI  CONST_01  C04  C03  C02  N01     0.00   0.0  0
 EXI  CONST_02  C04  C05  C06  N01     0.00   0.0  0
 EXI  CONST_03  C05  C06  N01  C02     0.00   0.0  0
 EXI  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 EXI  CONST_05  C06  N01  C02  C03     0.00   0.0  0
 EXI  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 EXI  CONST_07  C14  C13  C12  N11     0.00   0.0  0
 EXI  CONST_08  C14  C15  C16  N11     0.00   0.0  0
 EXI  CONST_09  C15  C16  N11  C12     0.00   0.0  0
 EXI  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 EXI  CONST_11  C16  N11  C12  C13     0.00   0.0  0
 EXI  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 EXI  CONST_13  C08  C06  N01  C02   180.00   0.0  0
 EXI  CONST_14  C07  C04  C03  C02   180.00   0.0  0
 EXI  CONST_15  C06  N01  C02  N02   180.00   0.0  0
 EXI  CONST_16  C04  C03  C02  N02   180.00   0.0  0
 EXI  CONST_17  C08  C06  C05  C04   180.00   0.0  0
 EXI  CONST_18  C07  C04  C05  C06   180.00   0.0  0
 EXI  CONST_19  N11  C12  C13  C09   180.00   0.0  0
 EXI  CONST_20  C15  C14  C13  C09   180.00   0.0  0
 EXI  CONST_21  N17  C15  C16  N11   180.00   0.0  0
 EXI  CONST_22  N17  C15  C14  C13   180.00   0.0  0
 EXI  CONST_23  H03  C03  C02  N01   180.00   0.0  0
 EXI  CONST_24  H05  C05  C06  N01   180.00   0.0  0
 EXI  CONST_25  H16  C16  N11  C12   180.00   0.0  0
 EXI  CONST_26  H14  C14  C13  C12   180.00   0.0  0
 EXI  CONST_27  H12  C12  C13  C14   180.00   0.0  0
 EXI  CONST_28  C17  N17  C15  C14     0.00   0.0  0
 EXI  CONST_29  C18  N17  C15  C14   180.00   0.0  0
 EXI  CONST_30  C17  N17  C15  C16   180.00   0.0  0
 EXI  CONST_31  C18  N17  C15  C16     0.00   0.0  0
 EXI  Var_01    C09  C08  C06  N01   -65.33  30.0  2
 EXI  Var_02    C13  C09  C08  C06   179.71  30.0  3
 EXI  Var_03    C12  C13  C09  C08    94.74  30.0  2
 EXI  Var_04    H07  C07  C04  C03   116.39  30.0  2
 EXI  Var_05    C19  C18  N17  C15    76.68  30.0  3
 EXI  Var_06    H17  C17  N17  C15    62.34  30.0  3
 EXI  Var_07    N20  C19  C18  N17  -179.62  30.0  3
 EXI  Var_08    C21  N20  C19  C18   178.34  30.0  3
 EXI  Var_09    H21  C21  N20  C19   176.44  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
 EXI  plan-1  N01   0.020
 EXI  plan-1  C02   0.020
 EXI  plan-1  N02   0.020
 EXI  plan-1  C03   0.020
 EXI  plan-1  C04   0.020
 EXI  plan-1  C05   0.020
 EXI  plan-1  C06   0.020
 EXI  plan-1  C07   0.020
 EXI  plan-1  C08   0.020
 EXI  plan-1  H03   0.020
 EXI  plan-1  H05   0.020
 EXI  plan-2  C09   0.020
 EXI  plan-2  N11   0.020
 EXI  plan-2  C12   0.020
 EXI  plan-2  C13   0.020
 EXI  plan-2  C14   0.020
 EXI  plan-2  C15   0.020
 EXI  plan-2  C16   0.020
 EXI  plan-2  N17   0.020
 EXI  plan-2  H12   0.020
 EXI  plan-2  H14   0.020
 EXI  plan-2  H16   0.020
 EXI  plan-3  C02   0.020
 EXI  plan-3  N02   0.020
 EXI  plan-3  HN02  0.020
 EXI  plan-3  HN0A  0.020
 EXI  plan-4  C15   0.020
 EXI  plan-4  C17   0.020
 EXI  plan-4  N17   0.020
 EXI  plan-4  C18   0.020

