# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:34:00 2021
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-[(Z)-(2,3-difluorophenyl)diazenyl]pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(N=Nc2cccc(F)c2F)c(N)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
 U8M  U8M  3-[(Z)-(2,3-difluorophenyl)diazenyl]pyridine-2,6-diamine  ligand  27  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U8M
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
 U8M  N1   N  N     0  -0.513  15.6590  36.9292   5.3122
 U8M  N3   N  N     0  -0.272  11.5793  34.6615   6.1619
 U8M  C4   C  CR6   0   0.461  14.5819  36.1936   5.0477
 U8M  C5   C  CR6   0   0.023  13.6363  35.8129   6.0519
 U8M  C6   C  CR6   0  -0.034  11.1440  35.2456   7.3725
 U8M  C7   C  CR16  0  -0.261  10.7344  36.5777   7.4442
 U8M  C8   C  CR16  0  -0.250  10.1710  37.0727   8.6073
 U8M  C10  C  CR6   0   0.398  10.3947  34.9388   9.6392
 U8M  C1   C  CR16  0  -0.144  13.9280  36.2223   7.3706
 U8M  C2   C  CR16  0  -0.407  15.0418  36.9587   7.6437
 U8M  C3   C  CR6   0   0.497  15.8937  37.3109   6.5631
 U8M  N2   N  N     0  -0.262  12.6342  34.9951   5.5890
 U8M  C9   C  CR16  0  -0.415  10.0006  36.2576   9.7206
 U8M  C11  C  CR6   0   0.398  10.9505  34.4322   8.4775
 U8M  N4   N  NH2   0  -0.819  16.9931  38.0378   6.7849
 U8M  N5   N  NH2   0  -0.808  14.3933  35.8444   3.7693
 U8M  F1   F  F     0  -0.299  11.3306  33.1511   8.4324
 U8M  F2   F  F     0  -0.305  10.2477  34.1217  10.6868
 U8M  H3   H  HCR6  0   0.282  10.8569  37.2201   6.5821
 U8M  H4   H  HCR6  0   0.276   9.8562  38.1062   8.6526
 U8M  H1   H  HCR6  0   0.281  13.2999  35.9305   8.1977
 U8M  H2   H  HCR6  0   0.272  15.2872  37.2525   8.6548
 U8M  H5   H  HCR6  0   0.292   9.5656  36.6359  10.6357
 U8M  H6   H  HNH2  0   0.400  17.5843  38.3085   6.0180
 U8M  H7   H  HNH2  0   0.411  17.2082  38.3981   7.6976
 U8M  H9   H  HNH2  0   0.395  15.1245  36.0145   3.1011
 U8M  H8   H  HNH2  0   0.403  13.6565  35.2045   3.5289

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
 U8M  N5   C4   single    1.339  0.020  1.339
 U8M  C4   N1   aromatic  1.331  0.020  1.331
 U8M  C4   C5   aromatic  1.431  0.020  1.431
 U8M  N1   C3   aromatic  1.329  0.020  1.329
 U8M  N2   N3   double    1.246  0.020  1.246
 U8M  N2   C5   single    1.374  0.020  1.374
 U8M  N3   C6   single    1.413  0.020  1.413
 U8M  C5   C1   aromatic  1.411  0.020  1.411
 U8M  C3   N4   single    1.337  0.020  1.337
 U8M  C3   C2   aromatic  1.420  0.020  1.420
 U8M  C6   C7   aromatic  1.396  0.020  1.396
 U8M  C6   C11  aromatic  1.386  0.020  1.386
 U8M  C1   C2   aromatic  1.363  0.020  1.363
 U8M  C7   C8   aromatic  1.384  0.020  1.384
 U8M  F1   C11  single    1.337  0.020  1.337
 U8M  C11  C10  aromatic  1.384  0.020  1.384
 U8M  C8   C9   aromatic  1.390  0.020  1.390
 U8M  C10  C9   aromatic  1.379  0.020  1.379
 U8M  C10  F2   single    1.337  0.020  1.337
 U8M  C7   H3   single    0.930  0.020  1.080
 U8M  C8   H4   single    0.930  0.020  1.080
 U8M  C1   H1   single    0.930  0.020  1.080
 U8M  C2   H2   single    0.930  0.020  1.080
 U8M  C9   H5   single    0.930  0.020  1.080
 U8M  N4   H6   single    0.860  0.020  1.020
 U8M  N4   H7   single    0.860  0.020  1.020
 U8M  N5   H9   single    0.860  0.020  1.020
 U8M  N5   H8   single    0.860  0.020  1.020

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
 U8M  C3   N1   C4   119.26  3.000
 U8M  N2   N3   C6   122.97  3.000
 U8M  N5   C4   C5   120.51  3.000
 U8M  C5   C4   N1   122.85  3.000
 U8M  N5   C4   N1   116.61  3.000
 U8M  N2   C5   C1   129.66  3.000
 U8M  C1   C5   C4   116.23  3.000
 U8M  N2   C5   C4   113.83  3.000
 U8M  C11  C6   C7   118.58  3.000
 U8M  C11  C6   N3   118.92  3.000
 U8M  C7   C6   N3   121.94  3.000
 U8M  H3   C7   C8   120.22  3.000
 U8M  H3   C7   C6   119.51  3.000
 U8M  C8   C7   C6   120.27  3.000
 U8M  H4   C8   C9   119.42  3.000
 U8M  H4   C8   C7   119.70  3.000
 U8M  C9   C8   C7   120.87  3.000
 U8M  F2   C10  C11  118.57  3.000
 U8M  F2   C10  C9   120.46  3.000
 U8M  C11  C10  C9   120.96  3.000
 U8M  H1   C1   C2   117.93  3.000
 U8M  H1   C1   C5   121.17  3.000
 U8M  C2   C1   C5   120.86  3.000
 U8M  H2   C2   C3   120.53  3.000
 U8M  H2   C2   C1   121.31  3.000
 U8M  C3   C2   C1   118.15  3.000
 U8M  N4   C3   C2   120.13  3.000
 U8M  C2   C3   N1   122.62  3.000
 U8M  N4   C3   N1   117.24  3.000
 U8M  C5   N2   N3   128.47  3.000
 U8M  H5   C9   C10  119.96  3.000
 U8M  H5   C9   C8   121.45  3.000
 U8M  C10  C9   C8   118.59  3.000
 U8M  F1   C11  C10  119.56  3.000
 U8M  C10  C11  C6   120.70  3.000
 U8M  F1   C11  C6   119.73  3.000
 U8M  H7   N4   H6   118.07  3.000
 U8M  H7   N4   C3   121.47  3.000
 U8M  H6   N4   C3   120.23  3.000
 U8M  H8   N5   H9   118.82  3.000
 U8M  H8   N5   C4   119.86  3.000
 U8M  H9   N5   C4   119.23  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
 U8M  CONST_01  C1   C5   C4   N1    0.00  0.0  0
 U8M  CONST_02  C1   C2   C3   N1    0.00  0.0  0
 U8M  CONST_03  C2   C3   N1   C4    0.00  0.0  0
 U8M  CONST_04  C2   C1   C5   C4    0.00  0.0  0
 U8M  CONST_05  C3   N1   C4   C5    0.00  0.0  0
 U8M  CONST_06  C3   C2   C1   C5    0.00  0.0  0
 U8M  CONST_07  C9   C8   C7   C6    0.00  0.0  0
 U8M  CONST_08  C9   C10  C11  C6    0.00  0.0  0
 U8M  CONST_09  C10  C11  C6   C7    0.00  0.0  0
 U8M  CONST_10  C10  C9   C8   C7    0.00  0.0  0
 U8M  CONST_11  C11  C6   C7   C8    0.00  0.0  0
 U8M  CONST_12  C11  C10  C9   C8    0.00  0.0  0
 U8M  CONST_13  N2   C5   C4   N1  180.00  0.0  0
 U8M  CONST_14  C8   C7   C6   N3  180.00  0.0  0
 U8M  CONST_15  C10  C11  C6   N3  180.00  0.0  0
 U8M  CONST_16  N4   C3   N1   C4  180.00  0.0  0
 U8M  CONST_17  F2   C10  C11  C6  180.00  0.0  0
 U8M  CONST_18  F1   C11  C6   C7  180.00  0.0  0
 U8M  CONST_19  F2   C10  C9   C8  180.00  0.0  0
 U8M  CONST_20  N5   C4   C5   C1  180.00  0.0  0
 U8M  CONST_21  N4   C3   C2   C1  180.00  0.0  0
 U8M  CONST_22  N2   C5   C1   C2  180.00  0.0  0
 U8M  CONST_23  N5   C4   N1   C3  180.00  0.0  0
 U8M  CONST_24  F1   C11  C10  C9  180.00  0.0  0
 U8M  CONST_25  H2   C2   C3   N1  180.00  0.0  0
 U8M  CONST_26  H1   C1   C5   C4  180.00  0.0  0
 U8M  CONST_27  H4   C8   C7   C6  180.00  0.0  0
 U8M  CONST_28  H5   C9   C8   C7  180.00  0.0  0
 U8M  CONST_29  H3   C7   C8   C9  180.00  0.0  0
 U8M  CONST_30  C4   C5   N2   N3  180.00  0.0  0
 U8M  CONST_34  H9   N5   C4   N1    0.00  0.0  0
 U8M  CONST_35  H8   N5   C4   N1  180.00  0.0  0
 U8M  CONST_36  H6   N4   C3   N1    0.00  0.0  0
 U8M  CONST_37  H7   N4   C3   N1  180.00  0.0  0

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
 U8M  plan-1  N1   0.020
 U8M  plan-1  N3   0.020
 U8M  plan-1  C4   0.020
 U8M  plan-1  C5   0.020
 U8M  plan-1  C6   0.020
 U8M  plan-1  C1   0.020
 U8M  plan-1  C2   0.020
 U8M  plan-1  C3   0.020
 U8M  plan-1  N2   0.020
 U8M  plan-1  N4   0.020
 U8M  plan-1  N5   0.020
 U8M  plan-1  H1   0.020
 U8M  plan-1  H2   0.020
 U8M  plan-2  N3   0.020
 U8M  plan-2  C6   0.020
 U8M  plan-2  C7   0.020
 U8M  plan-2  C8   0.020
 U8M  plan-2  C10  0.020
 U8M  plan-2  N2   0.020
 U8M  plan-2  C9   0.020
 U8M  plan-2  C11  0.020
 U8M  plan-2  F1   0.020
 U8M  plan-2  F2   0.020
 U8M  plan-2  H3   0.020
 U8M  plan-2  H4   0.020
 U8M  plan-2  H5   0.020
 U8M  plan-3  C3   0.020
 U8M  plan-3  N4   0.020
 U8M  plan-3  H6   0.020
 U8M  plan-3  H7   0.020
 U8M  plan-4  C4   0.020
 U8M  plan-4  N5   0.020
 U8M  plan-4  H9   0.020
 U8M  plan-4  H8   0.020

