# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 04:14:34 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]-5-fluoranyl-phenyl]-N,N'-dimethyl-ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCN(C)c1cc(F)cc(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
 S85  S85  N'-[3-[2-(6-azanyl-4-methyl-pyridin-2-yl)ethyl]-5-fluoranyl-phenyl]-N,N'-dimethyl-ethane-1,2-diamine  ligand  48  23  .  2022-07-22  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_S85
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
 S85  F17   F  F     0  -0.325   2.3683  -3.4944  -0.3543
 S85  C13   C  CR6   0   0.568   1.9262  -2.2284  -0.2265
 S85  C14   C  CR16  0  -0.544   2.8257  -1.2792   0.2045
 S85  C15   C  CR6   0   0.439   2.3950   0.0531   0.3577
 S85  N18   N  NT    0  -0.510   3.2301   1.0314   0.8232
 S85  C19   C  CH3   0  -0.548   2.7909   2.4085   0.8218
 S85  C20   C  CH2   0  -0.351   4.6362   0.7837   1.0490
 S85  C21   C  CH2   0  -0.264   5.4840   0.9143  -0.2130
 S85  N22   N  NH1   0  -0.594   6.8749   0.6496   0.0843
 S85  C23   C  CH3   0  -0.515   7.7246   0.7218  -1.0862
 S85  C12   C  CR16  0  -0.525   0.6092  -1.9584  -0.5382
 S85  C11   C  CR6   0   0.171   0.1798  -0.6405  -0.4097
 S85  C16   C  CR16  0  -0.441   1.0567   0.3433   0.0268
 S85  C09   C  CH2   0  -0.513  -1.2525  -0.2870  -0.6973
 S85  C08   C  CH2   0  -0.488  -2.1183  -0.3665   0.5667
 S85  C06   C  CR6   0   0.283  -3.5578  -0.0357   0.2913
 S85  N01   N  N     0  -0.487  -3.8005   1.1893  -0.1801
 S85  C02   C  CR6   0   0.441  -5.0541   1.5298  -0.4567
 S85  N02   N  NH2   0  -0.839  -5.2581   2.7695  -0.9914
 S85  C03   C  CR16  0  -0.449  -6.1332   0.6510  -0.2548
 S85  C04   C  CR6   0   0.207  -5.8853  -0.6140   0.2360
 S85  C07   C  CH3   0  -0.726  -6.9965  -1.5935   0.4573
 S85  C05   C  CR16  0  -0.438  -4.5580  -0.9655   0.5104
 S85  H14   H  HCR6  0   0.275   3.8408  -1.5879   0.4094
 S85  H12   H  HCR6  0   0.256  -0.0569  -2.7421  -0.8760
 S85  H16   H  HCR6  0   0.260   0.6812   1.3542   0.1124
 S85  H191  H  HCH3  0   0.241   1.9315   2.5618   1.4789
 S85  H192  H  HCH3  0   0.260   3.5986   3.0372   1.1884
 S85  H193  H  HCH3  0   0.233   2.5194   2.7666  -0.1758
 S85  H201  H  HCH2  0   0.257   4.9855   1.4981   1.7988
 S85  H202  H  HCH2  0   0.250   4.7836  -0.2010   1.4944
 S85  H211  H  HCH2  0   0.223   5.1428   0.1885  -0.9576
 S85  H212  H  HCH2  0   0.198   5.3187   1.9100  -0.6566
 S85  H22   H  HNH1  0   0.344   7.1993   1.3259   0.7648
 S85  H231  H  HCH3  0   0.222   7.4781  -0.0867  -1.7773
 S85  H232  H  HCH3  0   0.193   7.6442   1.6654  -1.6441
 S85  H233  H  HCH3  0   0.231   8.7669   0.5956  -0.7932
 S85  H091  H  HCH2  0   0.249  -1.3154   0.7229  -1.1065
 S85  H092  H  HCH2  0   0.248  -1.6577  -0.9635  -1.4537
 S85  H081  H  HCH2  0   0.248  -2.0464  -1.3666   0.9982
 S85  H082  H  HCH2  0   0.248  -1.7222   0.3283   1.3130
 S85  H05   H  HCR6  0   0.244  -4.3136  -1.9478   0.8952
 S85  H021  H  HNH2  0   0.379  -4.5215   3.4412  -0.8506
 S85  H022  H  HNH2  0   0.388  -6.1851   3.1563  -0.9308
 S85  H03   H  HCR6  0   0.255  -7.1432   0.9705  -0.4817
 S85  H071  H  HCH3  0   0.253  -6.9480  -2.4010  -0.2754
 S85  H072  H  HCH3  0   0.249  -6.9265  -2.0531   1.4437
 S85  H073  H  HCH3  0   0.246  -7.9740  -1.1217   0.3692

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
 S85  F17  C13   single    1.347  0.020  1.347
 S85  C13  C14   aromatic  1.377  0.020  1.377
 S85  C13  C12   aromatic  1.380  0.020  1.380
 S85  C14  C15   aromatic  1.408  0.020  1.408
 S85  C15  N18   single    1.368  0.020  1.368
 S85  C15  C16   aromatic  1.409  0.020  1.409
 S85  N18  C19   single    1.445  0.020  1.445
 S85  N18  C20   single    1.445  0.020  1.445
 S85  C20  C21   single    1.526  0.020  1.526
 S85  C21  N22   single    1.447  0.020  1.447
 S85  N22  C23   single    1.448  0.020  1.448
 S85  C12  C11   aromatic  1.392  0.020  1.392
 S85  C11  C16   aromatic  1.388  0.020  1.388
 S85  C11  C09   single    1.503  0.020  1.503
 S85  C09  C08   single    1.534  0.020  1.534
 S85  C08  C06   single    1.502  0.020  1.502
 S85  C06  N01   aromatic  1.335  0.020  1.335
 S85  C06  C05   aromatic  1.383  0.020  1.383
 S85  N01  C02   aromatic  1.328  0.020  1.328
 S85  C02  N02   single    1.365  0.020  1.365
 S85  C02  C03   aromatic  1.406  0.020  1.406
 S85  C03  C04   aromatic  1.379  0.020  1.379
 S85  C04  C07   single    1.498  0.020  1.498
 S85  C04  C05   aromatic  1.400  0.020  1.400
 S85  C14  H14   single    0.930  0.020  1.080
 S85  C12  H12   single    0.930  0.020  1.080
 S85  C16  H16   single    0.930  0.020  1.080
 S85  C19  H191  single    0.970  0.020  1.090
 S85  C19  H192  single    0.970  0.020  1.090
 S85  C19  H193  single    0.970  0.020  1.090
 S85  C20  H201  single    0.970  0.020  1.090
 S85  C20  H202  single    0.970  0.020  1.090
 S85  C21  H211  single    0.970  0.020  1.090
 S85  C21  H212  single    0.970  0.020  1.090
 S85  N22  H22   single    0.890  0.020  1.040
 S85  C23  H231  single    0.970  0.020  1.090
 S85  C23  H232  single    0.970  0.020  1.090
 S85  C23  H233  single    0.970  0.020  1.090
 S85  C09  H091  single    0.970  0.020  1.090
 S85  C09  H092  single    0.970  0.020  1.090
 S85  C08  H081  single    0.970  0.020  1.090
 S85  C08  H082  single    0.970  0.020  1.090
 S85  C05  H05   single    0.930  0.020  1.080
 S85  N02  H021  single    0.890  0.020  1.040
 S85  N02  H022  single    0.890  0.020  1.040
 S85  C03  H03   single    0.930  0.020  1.080
 S85  C07  H071  single    0.970  0.020  1.090
 S85  C07  H072  single    0.970  0.020  1.090
 S85  C07  H073  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
 S85  C12   C13  C14   124.00  3.000
 S85  C12   C13  F17   118.40  3.000
 S85  C14   C13  F17   117.60  3.000
 S85  H14   C14  C15   122.47  3.000
 S85  H14   C14  C13   118.43  3.000
 S85  C15   C14  C13   119.11  3.000
 S85  C16   C15  N18   120.83  3.000
 S85  C16   C15  C14   117.37  3.000
 S85  N18   C15  C14   121.80  3.000
 S85  C20   N18  C19   117.32  3.000
 S85  C20   N18  C15   121.63  3.000
 S85  C19   N18  C15   119.71  3.000
 S85  H193  C19  H192  107.61  3.000
 S85  H193  C19  H191  107.89  3.000
 S85  H192  C19  H191  107.48  3.000
 S85  H193  C19  N18   112.83  3.000
 S85  H192  C19  N18   108.96  3.000
 S85  H191  C19  N18   111.84  3.000
 S85  H202  C20  H201  105.47  3.000
 S85  H202  C20  C21   109.87  3.000
 S85  H201  C20  C21   109.50  3.000
 S85  H202  C20  N18   110.49  3.000
 S85  H201  C20  N18   107.82  3.000
 S85  C21   C20  N18   113.37  3.000
 S85  H212  C21  H211  106.17  3.000
 S85  H212  C21  N22   113.08  3.000
 S85  H211  C21  N22   108.56  3.000
 S85  H212  C21  C20   109.07  3.000
 S85  H211  C21  C20   109.43  3.000
 S85  N22   C21  C20   110.40  3.000
 S85  H22   N22  C23   108.77  3.000
 S85  H22   N22  C21   108.90  3.000
 S85  C23   N22  C21   112.88  3.000
 S85  H233  C23  H232  107.80  3.000
 S85  H233  C23  H231  107.47  3.000
 S85  H232  C23  H231  107.34  3.000
 S85  H233  C23  N22   109.75  3.000
 S85  H232  C23  N22   114.22  3.000
 S85  H231  C23  N22   110.01  3.000
 S85  H12   C12  C11   121.63  3.000
 S85  H12   C12  C13   121.06  3.000
 S85  C11   C12  C13   117.30  3.000
 S85  C09   C11  C16   119.70  3.000
 S85  C09   C11  C12   119.93  3.000
 S85  C16   C11  C12   120.34  3.000
 S85  H16   C16  C11   117.89  3.000
 S85  H16   C16  C15   120.25  3.000
 S85  C11   C16  C15   121.86  3.000
 S85  H092  C09  H091  106.97  3.000
 S85  H092  C09  C08   109.21  3.000
 S85  H091  C09  C08   108.92  3.000
 S85  H092  C09  C11   109.89  3.000
 S85  H091  C09  C11   110.14  3.000
 S85  C08   C09  C11   111.59  3.000
 S85  H082  C08  H081  106.76  3.000
 S85  H082  C08  C06   109.40  3.000
 S85  H081  C08  C06   109.71  3.000
 S85  H082  C08  C09   108.95  3.000
 S85  H081  C08  C09   109.63  3.000
 S85  C06   C08  C09   112.23  3.000
 S85  C05   C06  N01   122.78  3.000
 S85  C05   C06  C08   121.05  3.000
 S85  N01   C06  C08   116.16  3.000
 S85  C02   N01  C06   118.71  3.000
 S85  C03   C02  N02   120.59  3.000
 S85  C03   C02  N01   122.29  3.000
 S85  N02   C02  N01   117.09  3.000
 S85  H022  N02  H021  114.15  3.000
 S85  H022  N02  C02   117.59  3.000
 S85  H021  N02  C02   116.21  3.000
 S85  H03   C03  C04   120.83  3.000
 S85  H03   C03  C02   120.07  3.000
 S85  C04   C03  C02   119.10  3.000
 S85  C05   C04  C07   120.67  3.000
 S85  C05   C04  C03   118.06  3.000
 S85  C07   C04  C03   121.27  3.000
 S85  H073  C07  H072  108.27  3.000
 S85  H073  C07  H071  107.82  3.000
 S85  H072  C07  H071  107.02  3.000
 S85  H073  C07  C04   111.75  3.000
 S85  H072  C07  C04   111.20  3.000
 S85  H071  C07  C04   110.59  3.000
 S85  H05   C05  C04   120.75  3.000
 S85  H05   C05  C06   120.19  3.000
 S85  C04   C05  C06   119.06  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
 S85  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 S85  CONST_02  C16   C11  C12  C13     0.00   0.0  0
 S85  CONST_03  C11   C12  C13  C14     0.00   0.0  0
 S85  CONST_04  C11   C16  C15  C14     0.00   0.0  0
 S85  CONST_05  C12   C13  C14  C15     0.00   0.0  0
 S85  CONST_06  C12   C11  C16  C15     0.00   0.0  0
 S85  CONST_07  C03   C02  N01  C06     0.00   0.0  0
 S85  CONST_08  C03   C04  C05  C06     0.00   0.0  0
 S85  CONST_09  C04   C05  C06  N01     0.00   0.0  0
 S85  CONST_10  C04   C03  C02  N01     0.00   0.0  0
 S85  CONST_11  C05   C06  N01  C02     0.00   0.0  0
 S85  CONST_12  C05   C04  C03  C02     0.00   0.0  0
 S85  CONST_13  C15   C14  C13  F17   180.00   0.0  0
 S85  CONST_14  C11   C12  C13  F17   180.00   0.0  0
 S85  CONST_15  N18   C15  C14  C13   180.00   0.0  0
 S85  CONST_16  C09   C11  C12  C13   180.00   0.0  0
 S85  CONST_17  C09   C11  C16  C15   180.00   0.0  0
 S85  CONST_18  C11   C16  C15  N18   180.00   0.0  0
 S85  CONST_19  C02   N01  C06  C08   180.00   0.0  0
 S85  CONST_20  C04   C05  C06  C08   180.00   0.0  0
 S85  CONST_21  N02   C02  N01  C06   180.00   0.0  0
 S85  CONST_22  C07   C04  C05  C06   180.00   0.0  0
 S85  CONST_23  C07   C04  C03  C02   180.00   0.0  0
 S85  CONST_24  C04   C03  C02  N02   180.00   0.0  0
 S85  CONST_25  H12   C12  C13  C14   180.00   0.0  0
 S85  CONST_26  H16   C16  C15  C14   180.00   0.0  0
 S85  CONST_27  H14   C14  C13  C12   180.00   0.0  0
 S85  CONST_28  H05   C05  C06  N01   180.00   0.0  0
 S85  CONST_29  H03   C03  C02  N01   180.00   0.0  0
 S85  CONST_30  C19   N18  C15  C14   180.00   0.0  0
 S85  CONST_31  C20   N18  C15  C14     0.00   0.0  0
 S85  CONST_32  C16   C15  N18  C19     0.00   0.0  0
 S85  CONST_33  C16   C15  N18  C20   180.00   0.0  0
 S85  Var_01    C08   C09  C11  C12    91.24  30.0  2
 S85  Var_02    C06   C08  C09  C11  -179.14  30.0  3
 S85  Var_03    N01   C06  C08  C09   -61.01  30.0  2
 S85  Var_04    H071  C07  C04  C03   109.35  30.0  2
 S85  Var_05    C21   C20  N18  C15    83.46  30.0  3
 S85  Var_06    H191  C19  N18  C15    63.51  30.0  3
 S85  Var_07    N22   C21  C20  N18  -179.80  30.0  3
 S85  Var_08    C23   N22  C21  C20   178.35  30.0  3
 S85  Var_09    H231  C23  N22  C21   -66.54  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
 S85  plan-1  F17   0.020
 S85  plan-1  C13   0.020
 S85  plan-1  C14   0.020
 S85  plan-1  C15   0.020
 S85  plan-1  N18   0.020
 S85  plan-1  C12   0.020
 S85  plan-1  C11   0.020
 S85  plan-1  C16   0.020
 S85  plan-1  C09   0.020
 S85  plan-1  H14   0.020
 S85  plan-1  H12   0.020
 S85  plan-1  H16   0.020
 S85  plan-2  C08   0.020
 S85  plan-2  C06   0.020
 S85  plan-2  N01   0.020
 S85  plan-2  C02   0.020
 S85  plan-2  N02   0.020
 S85  plan-2  C03   0.020
 S85  plan-2  C04   0.020
 S85  plan-2  C07   0.020
 S85  plan-2  C05   0.020
 S85  plan-2  H05   0.020
 S85  plan-2  H03   0.020
 S85  plan-3  C15   0.020
 S85  plan-3  N18   0.020
 S85  plan-3  C19   0.020
 S85  plan-3  C20   0.020
 S85  plan-4  C02   0.020
 S85  plan-4  N02   0.020
 S85  plan-4  H021  0.020
 S85  plan-4  H022  0.020

