# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 20:27:14 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N'-[6-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]pyridin-2-yl]-N,N'-dimethyl-ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCN(C)c1cccc(CCc2cc(C)cc(N)n2)n1
#
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
 SKO  SKO  N'-[6-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]pyridin-2-yl]-N,N'-dimethyl-ethane-1,2-diamine  ligand  47  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SKO
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
 SKO  N02   N  NH2   0  -0.839   4.1596  -1.2780  -2.3768
 SKO  C02   C  CR6   0   0.439   3.9105  -0.7871  -1.1264
 SKO  C03   C  CR16  0  -0.448   4.9386  -0.7056  -0.1706
 SKO  C04   C  CR6   0   0.206   4.6405  -0.2529   1.0979
 SKO  C07   C  CH3   0  -0.726   5.6931  -0.1667   2.1603
 SKO  C05   C  CR16  0  -0.438   3.3168   0.1103   1.3733
 SKO  N01   N  N     0  -0.485   2.6584  -0.4394  -0.8531
 SKO  C06   C  CR6   0   0.281   2.3676   0.0002   0.3732
 SKO  C08   C  CH2   0  -0.496   0.9372   0.3880   0.6146
 SKO  C09   C  CH2   0  -0.485   0.4941   1.5653  -0.2620
 SKO  C12   C  CR6   0   0.259  -0.9549   1.8954  -0.0418
 SKO  C13   C  CR16  0  -0.400  -1.3452   3.0916   0.5417
 SKO  C14   C  CR16  0  -0.146  -2.7062   3.2929   0.7530
 SKO  C15   C  CR16  0  -0.414  -3.6178   2.3248   0.3928
 SKO  N11   N  N     0  -0.484  -1.8251   0.9567  -0.4009
 SKO  C16   C  CR6   0   0.518  -3.1300   1.1397  -0.1995
 SKO  N17   N  NT    0  -0.491  -3.9672   0.1402  -0.5970
 SKO  C17   C  CH3   0  -0.540  -5.3686   0.1974  -0.2495
 SKO  C18   C  CH2   0  -0.318  -3.4232  -1.1157  -1.0709
 SKO  C19   C  CH2   0  -0.273  -2.9462  -2.0323   0.0508
 SKO  N20   N  NH1   0  -0.595  -2.4848  -3.2930  -0.4919
 SKO  C21   C  CH3   0  -0.516  -1.8524  -4.1364   0.5012
 SKO  H021  H  HNH2  0   0.387   5.1131  -1.2659  -2.6978
 SKO  H022  H  HNH2  0   0.379   3.4871  -1.0375  -3.0867
 SKO  H03   H  HCR6  0   0.255   5.9496  -0.9916  -0.4348
 SKO  H071  H  HCH3  0   0.249   5.6560   0.7924   2.6774
 SKO  H072  H  HCH3  0   0.254   5.5397  -0.9421   2.9129
 SKO  H073  H  HCH3  0   0.246   6.6932  -0.2948   1.7492
 SKO  H05   H  HCR6  0   0.244   3.0354   0.4745   2.3535
 SKO  H081  H  HCH2  0   0.250   0.2888  -0.4667   0.4029
 SKO  H082  H  HCH2  0   0.244   0.7961   0.6411   1.6674
 SKO  H091  H  HCH2  0   0.244   1.1129   2.4389  -0.0473
 SKO  H092  H  HCH2  0   0.245   0.6563   1.3049  -1.3107
 SKO  H13   H  HCR6  0   0.248  -0.6145   3.8359   0.8271
 SKO  H14   H  HCR6  0   0.260  -3.0573   4.2110   1.2072
 SKO  H15   H  HCR6  0   0.266  -4.6717   2.4846   0.5664
 SKO  H171  H  HCH3  0   0.241  -5.8571   1.0722  -0.6841
 SKO  H172  H  HCH3  0   0.258  -5.8691  -0.6829  -0.6449
 SKO  H173  H  HCH3  0   0.232  -5.5365   0.2201   0.8315
 SKO  H181  H  HCH2  0   0.239  -4.2027  -1.6152  -1.6517
 SKO  H182  H  HCH2  0   0.245  -2.5948  -0.9236  -1.7519
 SKO  H191  H  HCH2  0   0.228  -2.1093  -1.5507   0.5642
 SKO  H192  H  HCH2  0   0.195  -3.7449  -2.1524   0.8009
 SKO  H20   H  HNH1  0   0.342  -3.2734  -3.7890  -0.8885
 SKO  H211  H  HCH3  0   0.220  -0.9239  -3.6735   0.8417
 SKO  H212  H  HCH3  0   0.192  -2.4671  -4.3283   1.3919
 SKO  H213  H  HCH3  0   0.231  -1.5961  -5.0996   0.0598

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
 SKO  N02  C02   single    1.366  0.020  1.366
 SKO  C02  C03   aromatic  1.406  0.020  1.406
 SKO  C02  N01   aromatic  1.328  0.020  1.328
 SKO  C03  C04   aromatic  1.380  0.020  1.380
 SKO  C04  C07   single    1.498  0.020  1.498
 SKO  C04  C05   aromatic  1.400  0.020  1.400
 SKO  C05  C06   aromatic  1.383  0.020  1.383
 SKO  N01  C06   aromatic  1.335  0.020  1.335
 SKO  C06  C08   single    1.502  0.020  1.502
 SKO  C08  C09   single    1.533  0.020  1.533
 SKO  C09  C12   single    1.502  0.020  1.502
 SKO  C12  C13   aromatic  1.387  0.020  1.387
 SKO  C12  N11   aromatic  1.329  0.020  1.329
 SKO  C13  C14   aromatic  1.392  0.020  1.392
 SKO  C14  C15   aromatic  1.378  0.020  1.378
 SKO  C15  C16   aromatic  1.412  0.020  1.412
 SKO  N11  C16   aromatic  1.333  0.020  1.333
 SKO  C16  N17   single    1.363  0.020  1.363
 SKO  N17  C17   single    1.445  0.020  1.445
 SKO  N17  C18   single    1.448  0.020  1.448
 SKO  C18  C19   single    1.525  0.020  1.525
 SKO  C19  N20   single    1.448  0.020  1.448
 SKO  N20  C21   single    1.448  0.020  1.448
 SKO  N02  H021  single    0.890  0.020  1.040
 SKO  N02  H022  single    0.890  0.020  1.040
 SKO  C03  H03   single    0.930  0.020  1.080
 SKO  C07  H071  single    0.970  0.020  1.090
 SKO  C07  H072  single    0.970  0.020  1.090
 SKO  C07  H073  single    0.970  0.020  1.090
 SKO  C05  H05   single    0.930  0.020  1.080
 SKO  C08  H081  single    0.970  0.020  1.090
 SKO  C08  H082  single    0.970  0.020  1.090
 SKO  C09  H091  single    0.970  0.020  1.090
 SKO  C09  H092  single    0.970  0.020  1.090
 SKO  C13  H13   single    0.930  0.020  1.080
 SKO  C14  H14   single    0.930  0.020  1.080
 SKO  C15  H15   single    0.930  0.020  1.080
 SKO  C17  H171  single    0.970  0.020  1.090
 SKO  C17  H172  single    0.970  0.020  1.090
 SKO  C17  H173  single    0.970  0.020  1.090
 SKO  C18  H181  single    0.970  0.020  1.090
 SKO  C18  H182  single    0.970  0.020  1.090
 SKO  C19  H191  single    0.970  0.020  1.090
 SKO  C19  H192  single    0.970  0.020  1.090
 SKO  N20  H20   single    0.890  0.020  1.040
 SKO  C21  H211  single    0.970  0.020  1.090
 SKO  C21  H212  single    0.970  0.020  1.090
 SKO  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
 SKO  H022  N02  H021  113.89  3.000
 SKO  H022  N02  C02   115.96  3.000
 SKO  H021  N02  C02   117.42  3.000
 SKO  N01   C02  C03   122.30  3.000
 SKO  N01   C02  N02   117.02  3.000
 SKO  C03   C02  N02   120.64  3.000
 SKO  H03   C03  C04   120.83  3.000
 SKO  H03   C03  C02   120.08  3.000
 SKO  C04   C03  C02   119.08  3.000
 SKO  C05   C04  C07   120.66  3.000
 SKO  C05   C04  C03   118.06  3.000
 SKO  C07   C04  C03   121.28  3.000
 SKO  H073  C07  H072  107.81  3.000
 SKO  H073  C07  H071  108.29  3.000
 SKO  H072  C07  H071  107.05  3.000
 SKO  H073  C07  C04   111.77  3.000
 SKO  H072  C07  C04   110.45  3.000
 SKO  H071  C07  C04   111.29  3.000
 SKO  H05   C05  C06   120.19  3.000
 SKO  H05   C05  C04   120.73  3.000
 SKO  C06   C05  C04   119.08  3.000
 SKO  C06   N01  C02   118.74  3.000
 SKO  C08   C06  N01   116.12  3.000
 SKO  C08   C06  C05   121.13  3.000
 SKO  N01   C06  C05   122.75  3.000
 SKO  H082  C08  H081  106.93  3.000
 SKO  H082  C08  C09   109.63  3.000
 SKO  H081  C08  C09   108.55  3.000
 SKO  H082  C08  C06   109.75  3.000
 SKO  H081  C08  C06   109.38  3.000
 SKO  C09   C08  C06   112.44  3.000
 SKO  H092  C09  H091  107.18  3.000
 SKO  H092  C09  C12   109.65  3.000
 SKO  H091  C09  C12   109.99  3.000
 SKO  H092  C09  C08   108.84  3.000
 SKO  H091  C09  C08   109.76  3.000
 SKO  C12   C09  C08   111.32  3.000
 SKO  N11   C12  C13   122.58  3.000
 SKO  N11   C12  C09   115.89  3.000
 SKO  C13   C12  C09   121.51  3.000
 SKO  H13   C13  C14   121.40  3.000
 SKO  H13   C13  C12   120.96  3.000
 SKO  C14   C13  C12   117.63  3.000
 SKO  H14   C14  C15   119.41  3.000
 SKO  H14   C14  C13   120.22  3.000
 SKO  C15   C14  C13   120.37  3.000
 SKO  H15   C15  C16   121.92  3.000
 SKO  H15   C15  C14   119.98  3.000
 SKO  C16   C15  C14   118.10  3.000
 SKO  C16   N11  C12   120.20  3.000
 SKO  N17   C16  N11   117.17  3.000
 SKO  N17   C16  C15   121.71  3.000
 SKO  N11   C16  C15   121.12  3.000
 SKO  C18   N17  C17   118.51  3.000
 SKO  C18   N17  C16   120.03  3.000
 SKO  C17   N17  C16   119.77  3.000
 SKO  H173  C17  H172  107.79  3.000
 SKO  H173  C17  H171  107.94  3.000
 SKO  H172  C17  H171  107.34  3.000
 SKO  H173  C17  N17   112.78  3.000
 SKO  H172  C17  N17   109.08  3.000
 SKO  H171  C17  N17   111.71  3.000
 SKO  H182  C18  H181  106.90  3.000
 SKO  H182  C18  C19   109.15  3.000
 SKO  H181  C18  C19   109.83  3.000
 SKO  H182  C18  N17   109.71  3.000
 SKO  H181  C18  N17   107.59  3.000
 SKO  C19   C18  N17   113.45  3.000
 SKO  H192  C19  H191  106.44  3.000
 SKO  H192  C19  N20   113.02  3.000
 SKO  H191  C19  N20   108.40  3.000
 SKO  H192  C19  C18   109.84  3.000
 SKO  H191  C19  C18   108.66  3.000
 SKO  N20   C19  C18   110.32  3.000
 SKO  H20   N20  C21   108.87  3.000
 SKO  H20   N20  C19   108.98  3.000
 SKO  C21   N20  C19   112.90  3.000
 SKO  H213  C21  H212  107.78  3.000
 SKO  H213  C21  H211  107.51  3.000
 SKO  H212  C21  H211  107.27  3.000
 SKO  H213  C21  N20   109.85  3.000
 SKO  H212  C21  N20   114.40  3.000
 SKO  H211  C21  N20   109.78  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
 SKO  CONST_01  C05   C04  C03  C02    0.00   0.0  0
 SKO  CONST_02  C05   C06  N01  C02    0.00   0.0  0
 SKO  CONST_03  C06   N01  C02  C03    0.00   0.0  0
 SKO  CONST_04  C06   C05  C04  C03    0.00   0.0  0
 SKO  CONST_05  N01   C02  C03  C04    0.00   0.0  0
 SKO  CONST_06  N01   C06  C05  C04    0.00   0.0  0
 SKO  CONST_07  C15   C14  C13  C12    0.00   0.0  0
 SKO  CONST_08  C15   C16  N11  C12    0.00   0.0  0
 SKO  CONST_09  C16   N11  C12  C13    0.00   0.0  0
 SKO  CONST_10  C16   C15  C14  C13    0.00   0.0  0
 SKO  CONST_11  N11   C12  C13  C14    0.00   0.0  0
 SKO  CONST_12  N11   C16  C15  C14    0.00   0.0  0
 SKO  CONST_13  C04   C03  C02  N02  180.00   0.0  0
 SKO  CONST_14  C06   N01  C02  N02  180.00   0.0  0
 SKO  CONST_15  C07   C04  C03  C02  180.00   0.0  0
 SKO  CONST_16  C08   C06  N01  C02  180.00   0.0  0
 SKO  CONST_17  C08   C06  C05  C04  180.00   0.0  0
 SKO  CONST_18  C06   C05  C04  C07  180.00   0.0  0
 SKO  CONST_19  C14   C13  C12  C09  180.00   0.0  0
 SKO  CONST_20  C16   N11  C12  C09  180.00   0.0  0
 SKO  CONST_21  N17   C16  N11  C12  180.00   0.0  0
 SKO  CONST_22  N17   C16  C15  C14  180.00   0.0  0
 SKO  CONST_23  H05   C05  C04  C03  180.00   0.0  0
 SKO  CONST_24  H03   C03  C04  C05  180.00   0.0  0
 SKO  CONST_25  H14   C14  C13  C12  180.00   0.0  0
 SKO  CONST_26  H15   C15  C14  C13  180.00   0.0  0
 SKO  CONST_27  H13   C13  C14  C15  180.00   0.0  0
 SKO  CONST_28  C17   N17  C16  C15    0.00   0.0  0
 SKO  CONST_29  C18   N17  C16  C15  180.00   0.0  0
 SKO  CONST_30  C17   N17  C16  N11  180.00   0.0  0
 SKO  CONST_31  C18   N17  C16  N11    0.00   0.0  0
 SKO  Var_01    C09   C08  C06  C05  116.52  30.0  2
 SKO  Var_02    C12   C09  C08  C06  177.65  30.0  3
 SKO  Var_03    C13   C12  C09  C08  113.21  30.0  2
 SKO  Var_04    H071  C07  C04  C03  133.05  30.0  2
 SKO  Var_05    C19   C18  N17  C16   78.01  30.0  3
 SKO  Var_06    H171  C17  N17  C16   61.87  30.0  3
 SKO  Var_07    N20   C19  C18  N17  176.88  30.0  3
 SKO  Var_08    C21   N20  C19  C18  172.16  30.0  3
 SKO  Var_09    H211  C21  N20  C19  -66.43  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
 SKO  plan-1  N02   0.020
 SKO  plan-1  C02   0.020
 SKO  plan-1  C03   0.020
 SKO  plan-1  C04   0.020
 SKO  plan-1  C07   0.020
 SKO  plan-1  C05   0.020
 SKO  plan-1  N01   0.020
 SKO  plan-1  C06   0.020
 SKO  plan-1  C08   0.020
 SKO  plan-1  H03   0.020
 SKO  plan-1  H05   0.020
 SKO  plan-2  C09   0.020
 SKO  plan-2  C12   0.020
 SKO  plan-2  C13   0.020
 SKO  plan-2  C14   0.020
 SKO  plan-2  C15   0.020
 SKO  plan-2  N11   0.020
 SKO  plan-2  C16   0.020
 SKO  plan-2  N17   0.020
 SKO  plan-2  H13   0.020
 SKO  plan-2  H14   0.020
 SKO  plan-2  H15   0.020
 SKO  plan-3  N02   0.020
 SKO  plan-3  C02   0.020
 SKO  plan-3  H021  0.020
 SKO  plan-3  H022  0.020
 SKO  plan-4  C16   0.020
 SKO  plan-4  N17   0.020
 SKO  plan-4  C17   0.020
 SKO  plan-4  C18   0.020

