# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:04:10 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-(2,4-dinitrophenyl)-N-(4-fluorophenyl)hydrazinecarbothioamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(NNC(=S)Nc2ccc(F)cc2)c(c1)[N+]([O-])=O
#
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
 KOB  KOB  2-(2,4-dinitrophenyl)-N-(4-fluorophenyl)hydrazinecarbothioamide  ligand  34  24  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KOB
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
 KOB  C13  C  CR16   0  -0.278   7.1962  -13.7251  7.3564
 KOB  C12  C  CR16   0  -0.411   6.9839  -12.3660  7.5381
 KOB  C11  C  CR6    0   0.527   5.6863  -11.8954  7.5439
 KOB  F11  F  F      0  -0.314   5.4709  -10.5837  7.7283
 KOB  C10  C  CR16   0  -0.415   4.6013  -12.7320  7.3586
 KOB  C9   C  CR16   0  -0.232   4.8253  -14.0849  7.1618
 KOB  C8   C  CR6    0   0.322   6.1221  -14.5864  7.1725
 KOB  N8   N  NH1    0  -0.711   6.3827  -15.9534  6.9380
 KOB  C7   C  C      0   0.384   5.8688  -16.9805  7.6227
 KOB  S7   S  S1     0  -0.379   4.8086  -16.8646  8.9071
 KOB  N7   N  NH1    0  -0.467   6.2548  -18.2141  7.2058
 KOB  N6   N  NH1    0  -0.563   7.2229  -18.3951  6.2648
 KOB  C6   C  CR6    0   0.416   6.8930  -18.8473  5.0268
 KOB  C5   C  CR16   0  -0.336   5.5357  -18.9182  4.6549
 KOB  C4   C  CR16   0  -0.240   5.1460  -19.3338  3.4105
 KOB  C3   C  CR6    0   0.261   6.1093  -19.7053  2.4728
 KOB  N3   N  N      1   0.326   5.7053  -20.1445  1.1562
 KOB  O3B  O  O     -1  -0.379   6.5666  -20.4716  0.3731
 KOB  O3A  O  O      0  -0.376   4.5224  -20.1606  0.9070
 KOB  C2   C  CR16   0  -0.342   7.4458  -19.6615  2.7891
 KOB  C1   C  CR6    0   0.239   7.8418  -19.2382  4.0497
 KOB  N1   N  N      1   0.354   9.2642  -19.2239  4.3037
 KOB  O1B  O  O     -1  -0.403   9.6529  -18.8561  5.3945
 KOB  O1A  O  O      0  -0.366  10.0109  -19.5766  3.4248
 KOB  HE1  H  HCR6   0   0.285   3.5951  -12.3347  7.3540
 KOB  HE2  H  HCR6   0   0.286   7.8171  -11.6909  7.6807
 KOB  HD2  H  HCR6   0   0.282   8.2069  -14.1132  7.3587
 KOB  HD1  H  HCR6   0   0.279   3.9874  -14.7466  6.9970
 KOB  HAD  H  HNH1   0   0.425   7.1078  -16.1584  6.2622
 KOB  HAC  H  HNH1   0   0.428   5.9862  -19.0082  7.7714
 KOB  HAB  H  HNH1   0   0.437   8.1740  -18.4847  6.5922
 KOB  H5   H  HCR6   0   0.308   4.7776  -18.6408  5.3720
 KOB  H4   H  HCR6   0   0.316   4.0924  -19.3692  3.1753
 KOB  H2   H  HCR6   0   0.336   8.1927  -19.9530  2.0659

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
 KOB  O3B  N3   single    1.209  0.020  1.209
 KOB  O3A  N3   double    1.209  0.020  1.209
 KOB  N3   C3   single    1.445  0.020  1.445
 KOB  C3   C2   aromatic  1.374  0.020  1.374
 KOB  C3   C4   aromatic  1.395  0.020  1.395
 KOB  C2   C1   aromatic  1.388  0.020  1.388
 KOB  C4   C5   aromatic  1.369  0.020  1.369
 KOB  O1A  N1   double    1.206  0.020  1.206
 KOB  C1   N1   single    1.445  0.020  1.445
 KOB  C1   C6   aromatic  1.417  0.020  1.417
 KOB  C5   C6   aromatic  1.409  0.020  1.409
 KOB  N1   O1B  single    1.215  0.020  1.215
 KOB  C6   N6   single    1.359  0.020  1.359
 KOB  C13  C12  aromatic  1.388  0.020  1.388
 KOB  C13  C8   aromatic  1.389  0.020  1.389
 KOB  N6   N7   single    1.362  0.020  1.362
 KOB  C12  C11  aromatic  1.380  0.020  1.380
 KOB  N8   C8   single    1.411  0.020  1.411
 KOB  N8   C7   single    1.337  0.020  1.337
 KOB  C8   C9   aromatic  1.390  0.020  1.390
 KOB  N7   C7   single    1.358  0.020  1.358
 KOB  C11  F11  single    1.342  0.020  1.342
 KOB  C11  C10  aromatic  1.383  0.020  1.383
 KOB  C7   S7   double    1.670  0.020  1.670
 KOB  C9   C10  aromatic  1.385  0.020  1.385
 KOB  C12  HE2  single    0.930  0.020  1.080
 KOB  C10  HE1  single    0.930  0.020  1.080
 KOB  C13  HD2  single    0.930  0.020  1.080
 KOB  C9   HD1  single    0.930  0.020  1.080
 KOB  N8   HAD  single    0.860  0.020  1.020
 KOB  N7   HAC  single    0.860  0.020  1.020
 KOB  N6   HAB  single    0.890  0.020  1.040
 KOB  C5   H5   single    0.930  0.020  1.080
 KOB  C4   H4   single    0.930  0.020  1.080
 KOB  C2   H2   single    0.930  0.020  1.080

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
 KOB  HD2  C13  C8   119.99  3.000
 KOB  HD2  C13  C12  119.58  3.000
 KOB  C8   C13  C12  120.42  3.000
 KOB  HE2  C12  C11  120.72  3.000
 KOB  HE2  C12  C13  120.70  3.000
 KOB  C11  C12  C13  118.58  3.000
 KOB  C10  C11  F11  118.94  3.000
 KOB  C10  C11  C12  122.07  3.000
 KOB  F11  C11  C12  119.00  3.000
 KOB  HE1  C10  C9   120.55  3.000
 KOB  HE1  C10  C11  120.55  3.000
 KOB  C9   C10  C11  118.89  3.000
 KOB  HD1  C9   C8   120.24  3.000
 KOB  HD1  C9   C10  119.63  3.000
 KOB  C8   C9   C10  120.12  3.000
 KOB  N8   C8   C9   121.35  3.000
 KOB  C9   C8   C13  119.91  3.000
 KOB  N8   C8   C13  118.67  3.000
 KOB  HAD  N8   C7   117.50  3.000
 KOB  HAD  N8   C8   116.06  3.000
 KOB  C7   N8   C8   126.02  3.000
 KOB  N7   C7   S7   118.67  3.000
 KOB  S7   C7   N8   125.78  3.000
 KOB  N7   C7   N8   115.55  3.000
 KOB  HAC  N7   N6   118.08  3.000
 KOB  HAC  N7   C7   117.78  3.000
 KOB  N6   N7   C7   122.33  3.000
 KOB  HAB  N6   C6   119.64  3.000
 KOB  HAB  N6   N7   117.20  3.000
 KOB  C6   N6   N7   120.08  3.000
 KOB  C1   C6   C5   116.69  3.000
 KOB  C5   C6   N6   119.41  3.000
 KOB  C1   C6   N6   123.89  3.000
 KOB  H5   C5   C4   118.82  3.000
 KOB  H5   C5   C6   119.21  3.000
 KOB  C4   C5   C6   121.97  3.000
 KOB  H4   C4   C3   121.24  3.000
 KOB  H4   C4   C5   119.05  3.000
 KOB  C3   C4   C5   119.71  3.000
 KOB  C2   C3   N3   119.42  3.000
 KOB  C2   C3   C4   120.56  3.000
 KOB  N3   C3   C4   120.02  3.000
 KOB  O3A  N3   O3B  124.04  3.000
 KOB  O3A  N3   C3   117.72  3.000
 KOB  O3B  N3   C3   118.23  3.000
 KOB  H2   C2   C1   119.57  3.000
 KOB  H2   C2   C3   120.66  3.000
 KOB  C1   C2   C3   119.77  3.000
 KOB  N1   C1   C2   116.34  3.000
 KOB  N1   C1   C6   122.36  3.000
 KOB  C2   C1   C6   121.30  3.000
 KOB  O1A  N1   O1B  123.01  3.000
 KOB  O1B  N1   C1   118.41  3.000
 KOB  O1A  N1   C1   118.58  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
 KOB  CONST_01  C10  C11  C12  C13    0.00  0.0  0
 KOB  CONST_02  C10  C9   C8   C13    0.00  0.0  0
 KOB  CONST_03  C9   C8   C13  C12    0.00  0.0  0
 KOB  CONST_04  C9   C10  C11  C12    0.00  0.0  0
 KOB  CONST_05  C8   C13  C12  C11    0.00  0.0  0
 KOB  CONST_06  C8   C9   C10  C11    0.00  0.0  0
 KOB  CONST_07  C3   C2   C1   C6     0.00  0.0  0
 KOB  CONST_08  C3   C4   C5   C6     0.00  0.0  0
 KOB  CONST_09  C2   C3   C4   C5     0.00  0.0  0
 KOB  CONST_10  C2   C1   C6   C5     0.00  0.0  0
 KOB  CONST_11  C1   C2   C3   C4     0.00  0.0  0
 KOB  CONST_12  C1   C6   C5   C4     0.00  0.0  0
 KOB  CONST_13  F11  C11  C12  C13  180.00  0.0  0
 KOB  CONST_14  N8   C8   C13  C12  180.00  0.0  0
 KOB  CONST_15  C9   C10  C11  F11  180.00  0.0  0
 KOB  CONST_16  N8   C8   C9   C10  180.00  0.0  0
 KOB  CONST_17  C2   C1   C6   N6   180.00  0.0  0
 KOB  CONST_18  C4   C5   C6   N6   180.00  0.0  0
 KOB  CONST_19  N3   C3   C4   C5   180.00  0.0  0
 KOB  CONST_20  N1   C1   C6   C5   180.00  0.0  0
 KOB  CONST_21  N1   C1   C2   C3   180.00  0.0  0
 KOB  CONST_22  C1   C2   C3   N3   180.00  0.0  0
 KOB  CONST_23  HD1  C9   C8   C13  180.00  0.0  0
 KOB  CONST_24  HE1  C10  C11  C12  180.00  0.0  0
 KOB  CONST_25  HD2  C13  C12  C11  180.00  0.0  0
 KOB  CONST_26  HE2  C12  C11  C10  180.00  0.0  0
 KOB  CONST_27  H2   C2   C1   C6   180.00  0.0  0
 KOB  CONST_28  H4   C4   C5   C6   180.00  0.0  0
 KOB  CONST_29  H5   C5   C4   C3   180.00  0.0  0
 KOB  CONST_32  C1   C6   N6   N7   180.00  0.0  0
 KOB  CONST_33  C5   C6   N6   N7     0.00  0.0  0
 KOB  CONST_34  O1A  N1   C1   C6   180.00  0.0  0
 KOB  CONST_35  O1B  N1   C1   C6     0.00  0.0  0
 KOB  CONST_36  O3B  N3   C3   C4   180.00  0.0  0
 KOB  CONST_37  O3A  N3   C3   C4     0.00  0.0  0
 KOB  CONST_38  C2   C3   N3   O3B    0.00  0.0  0
 KOB  CONST_39  C2   C3   N3   O3A  180.00  0.0  0
 KOB  CONST_40  O1A  N1   C1   C2     0.00  0.0  0
 KOB  CONST_41  O1B  N1   C1   C2   180.00  0.0  0
 KOB  CONST_43  HAB  N6   C6   C5   180.00  0.0  0
 KOB  CONST_44  N7   C7   N8   C8   180.00  0.0  0
 KOB  CONST_45  S7   C7   N8   C8     0.00  0.0  0
 KOB  CONST_48  N6   N7   C7   N8     0.00  0.0  0
 KOB  CONST_49  N6   N7   C7   S7   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
 KOB  plan-1  C13  0.020
 KOB  plan-1  C12  0.020
 KOB  plan-1  C11  0.020
 KOB  plan-1  F11  0.020
 KOB  plan-1  C10  0.020
 KOB  plan-1  C9   0.020
 KOB  plan-1  C8   0.020
 KOB  plan-1  N8   0.020
 KOB  plan-1  HE1  0.020
 KOB  plan-1  HE2  0.020
 KOB  plan-1  HD2  0.020
 KOB  plan-1  HD1  0.020
 KOB  plan-2  N6   0.020
 KOB  plan-2  C6   0.020
 KOB  plan-2  C5   0.020
 KOB  plan-2  C4   0.020
 KOB  plan-2  C3   0.020
 KOB  plan-2  N3   0.020
 KOB  plan-2  C2   0.020
 KOB  plan-2  C1   0.020
 KOB  plan-2  N1   0.020
 KOB  plan-2  H5   0.020
 KOB  plan-2  H4   0.020
 KOB  plan-2  H2   0.020
 KOB  plan-3  C8   0.020
 KOB  plan-3  N8   0.020
 KOB  plan-3  C7   0.020
 KOB  plan-3  S7   0.020
 KOB  plan-3  N7   0.020
 KOB  plan-3  N6   0.020
 KOB  plan-3  HAD  0.020
 KOB  plan-3  HAC  0.020
 KOB  plan-4  N7   0.020
 KOB  plan-4  N6   0.020
 KOB  plan-4  C6   0.020
 KOB  plan-4  HAB  0.020
 KOB  plan-5  C3   0.020
 KOB  plan-5  N3   0.020
 KOB  plan-5  O3B  0.020
 KOB  plan-5  O3A  0.020
 KOB  plan-6  C1   0.020
 KOB  plan-6  N1   0.020
 KOB  plan-6  O1B  0.020
 KOB  plan-6  O1A  0.020

