# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:12:00 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-{hydroxy[2-nitro-4-(trifluoromethyl)phenyl]methylidene}cyclohexane-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(c1ccc(cc1[N+]([O-])=O)C(F)(F)F)=C2C(=O)CCCC2=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
 NTD  NTD  2-{hydroxy[2-nitro-4-(trifluoromethyl)phenyl]methylidene}cyclohexane-1,3-dione  ligand  33  23  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NTD
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
 NTD  O1   O  O      0  -0.408   4.2102   1.4702  -0.8937
 NTD  C5   C  C      0   0.389   3.8544   0.6647  -0.0555
 NTD  C2   C  CH2    0  -0.564   4.8471   0.1066   0.9354
 NTD  C3   C  CH2    0  -0.471   4.5518  -1.3270   1.3404
 NTD  C4   C  CH2    0  -0.562   3.1366  -1.4353   1.8853
 NTD  C1   C  C      0   0.381   2.1111  -0.9673   0.8889
 NTD  O5   O  O      0  -0.416   1.0440  -1.5424   0.7725
 NTD  C6   C  C      0  -0.304   2.4533   0.2125   0.0716
 NTD  C7   C  C      0   0.442   1.4398   0.8714  -0.5693
 NTD  O7   O  OH1    0  -0.527   1.6649   1.9175  -1.3280
 NTD  C8   C  CR6    0  -0.075  -0.0062   0.6046  -0.3144
 NTD  C13  C  CR16   0  -0.235  -0.6080   1.3416   0.6924
 NTD  C12  C  CR16   0  -0.253  -1.9665   1.2196   0.9511
 NTD  C11  C  CR6    0  -0.187  -2.7387   0.3562   0.1933
 NTD  C14  C  CT     0   1.066  -4.2098   0.1972   0.4382
 NTD  F2   F  F      0  -0.296  -4.6633   1.0388   1.3665
 NTD  F3   F  F      0  -0.307  -4.9140   0.4148  -0.6782
 NTD  F1   F  F      0  -0.308  -4.5039  -1.0434   0.8447
 NTD  C10  C  CR16   0  -0.304  -2.1546  -0.3988  -0.8156
 NTD  C9   C  CR6    0   0.319  -0.8055  -0.2578  -1.0596
 NTD  N    N  N      1   0.336  -0.2045  -1.0641  -2.1071
 NTD  ON2  O  O      0  -0.360  -0.8121  -2.0255  -2.5062
 NTD  ON1  O  O     -1  -0.367   0.8771  -0.7177  -2.5196
 NTD  H21  H  HCH2   0   0.271   5.8496   0.2118   0.5198
 NTD  H22  H  HCH2   0   0.271   4.8020   0.7485   1.8236
 NTD  H31  H  HCH2   0   0.246   4.6764  -1.9950   0.4844
 NTD  H32  H  HCH2   0   0.262   5.2641  -1.6515   2.0988
 NTD  H41  H  HCH2   0   0.272   2.8949  -2.4534   2.1904
 NTD  H42  H  HCH2   0   0.270   3.0420  -0.7977   2.7727
 NTD  HO7  H  HOH1   0   0.500   0.8403   2.3189  -1.6362
 NTD  H13  H  HCR6   0   0.302  -0.0109   2.0116   1.2958
 NTD  H12  H  HCR6   0   0.298  -2.3983   1.8093   1.7472
 NTD  H10  H  HCR6   0   0.320  -2.7432  -1.0855  -1.4084

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
 NTD  O1   C5   double    1.216  0.020  1.216
 NTD  C5   C2   single    1.510  0.020  1.510
 NTD  C5   C6   single    1.478  0.020  1.478
 NTD  C2   C3   single    1.519  0.020  1.519
 NTD  C2   H21  single    0.970  0.020  1.090
 NTD  C2   H22  single    0.970  0.020  1.090
 NTD  C3   C4   single    1.520  0.020  1.520
 NTD  C3   H31  single    0.970  0.020  1.090
 NTD  C3   H32  single    0.970  0.020  1.090
 NTD  C4   C1   single    1.504  0.020  1.504
 NTD  C4   H41  single    0.970  0.020  1.090
 NTD  C4   H42  single    0.970  0.020  1.090
 NTD  C1   O5   double    1.218  0.020  1.218
 NTD  C1   C6   single    1.475  0.020  1.475
 NTD  C6   C7   double    1.368  0.020  1.368
 NTD  C7   O7   single    1.312  0.020  1.312
 NTD  C7   C8   single    1.492  0.020  1.492
 NTD  O7   HO7  single    0.850  0.020  0.980
 NTD  C8   C13  aromatic  1.385  0.020  1.385
 NTD  C8   C9   aromatic  1.392  0.020  1.392
 NTD  C13  C12  aromatic  1.388  0.020  1.388
 NTD  C13  H13  single    0.930  0.020  1.080
 NTD  C12  C11  aromatic  1.384  0.020  1.384
 NTD  C12  H12  single    0.930  0.020  1.080
 NTD  C11  C14  single    1.500  0.020  1.500
 NTD  C11  C10  aromatic  1.389  0.020  1.389
 NTD  C14  F2   single    1.333  0.020  1.333
 NTD  C14  F3   single    1.338  0.020  1.338
 NTD  C14  F1   single    1.338  0.020  1.338
 NTD  C10  C9   aromatic  1.378  0.020  1.378
 NTD  C10  H10  single    0.930  0.020  1.080
 NTD  C9   N    single    1.452  0.020  1.452
 NTD  N    ON2  double    1.205  0.020  1.205
 NTD  N    ON1  single    1.208  0.020  1.208

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
 NTD  C6   C5   C2   116.99  3.000
 NTD  C6   C5   O1   122.66  3.000
 NTD  C2   C5   O1   120.34  3.000
 NTD  H22  C2   H21  106.85  3.000
 NTD  H22  C2   C3   109.18  3.000
 NTD  H21  C2   C3   111.81  3.000
 NTD  H22  C2   C5   106.75  3.000
 NTD  H21  C2   C5   108.59  3.000
 NTD  C3   C2   C5   113.34  3.000
 NTD  H32  C3   H31  106.77  3.000
 NTD  H32  C3   C4   109.74  3.000
 NTD  H31  C3   C4   110.08  3.000
 NTD  H32  C3   C2   109.85  3.000
 NTD  H31  C3   C2   110.24  3.000
 NTD  C4   C3   C2   110.11  3.000
 NTD  H42  C4   H41  107.30  3.000
 NTD  H42  C4   C1   107.24  3.000
 NTD  H41  C4   C1   108.95  3.000
 NTD  H42  C4   C3   109.20  3.000
 NTD  H41  C4   C3   111.92  3.000
 NTD  C1   C4   C3   112.02  3.000
 NTD  C6   C1   O5   121.87  3.000
 NTD  C6   C1   C4   117.23  3.000
 NTD  O5   C1   C4   120.91  3.000
 NTD  C7   C6   C1   118.21  3.000
 NTD  C7   C6   C5   120.97  3.000
 NTD  C1   C6   C5   120.81  3.000
 NTD  C8   C7   O7   114.05  3.000
 NTD  C8   C7   C6   123.48  3.000
 NTD  O7   C7   C6   121.86  3.000
 NTD  HO7  O7   C7   111.65  3.000
 NTD  C9   C8   C13  117.98  3.000
 NTD  C9   C8   C7   125.15  3.000
 NTD  C13  C8   C7   116.74  3.000
 NTD  H13  C13  C12  119.39  3.000
 NTD  H13  C13  C8   119.69  3.000
 NTD  C12  C13  C8   120.92  3.000
 NTD  H12  C12  C11  121.38  3.000
 NTD  H12  C12  C13  118.71  3.000
 NTD  C11  C12  C13  119.92  3.000
 NTD  C10  C11  C14  118.26  3.000
 NTD  C10  C11  C12  120.14  3.000
 NTD  C14  C11  C12  121.60  3.000
 NTD  F1   C14  F3   106.78  3.000
 NTD  F1   C14  F2   107.40  3.000
 NTD  F3   C14  F2   107.43  3.000
 NTD  F1   C14  C11  111.31  3.000
 NTD  F3   C14  C11  111.27  3.000
 NTD  F2   C14  C11  112.37  3.000
 NTD  H10  C10  C9   120.04  3.000
 NTD  H10  C10  C11  120.96  3.000
 NTD  C9   C10  C11  118.99  3.000
 NTD  N    C9   C10  118.43  3.000
 NTD  N    C9   C8   119.50  3.000
 NTD  C10  C9   C8   122.05  3.000
 NTD  ON1  N    ON2  124.53  3.000
 NTD  ON1  N    C9   117.23  3.000
 NTD  ON2  N    C9   118.24  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
 NTD  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 NTD  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 NTD  CONST_03  C10  C9   C8   C13     0.00   0.0  0
 NTD  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 NTD  CONST_05  C9   C8   C13  C12     0.00   0.0  0
 NTD  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 NTD  CONST_07  C12  C13  C8   C7    180.00   0.0  0
 NTD  CONST_08  C10  C9   C8   C7    180.00   0.0  0
 NTD  CONST_09  N    C9   C8   C13   180.00   0.0  0
 NTD  CONST_10  C14  C11  C12  C13   180.00   0.0  0
 NTD  CONST_11  N    C9   C10  C11   180.00   0.0  0
 NTD  CONST_12  C9   C10  C11  C14   180.00   0.0  0
 NTD  CONST_13  H12  C12  C13  C8    180.00   0.0  0
 NTD  CONST_14  H10  C10  C9   C8    180.00   0.0  0
 NTD  CONST_15  H13  C13  C12  C11   180.00   0.0  0
 NTD  Var_01    C4   C3   C2   C5    -55.63  30.0  1
 NTD  Var_02    C4   C1   C6   C5     17.48  30.0  1
 NTD  Var_03    C1   C6   C5   C2    -15.00  30.0  1
 NTD  Var_04    C1   C4   C3   C2     57.59  30.0  1
 NTD  Var_05    C6   C5   C2   C3     34.28  30.0  1
 NTD  Var_06    C6   C1   C4   C3    -38.75  30.0  1
 NTD  Var_07    C8   C7   C6   C5   -169.96  30.0  2
 NTD  Var_08    C13  C8   C7   C6     89.18  30.0  2
 NTD  Var_09    F2   C14  C11  C12     4.81  30.0  2

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
 NTD  plan-1  C7   0.020
 NTD  plan-1  C8   0.020
 NTD  plan-1  C13  0.020
 NTD  plan-1  C12  0.020
 NTD  plan-1  C11  0.020
 NTD  plan-1  C14  0.020
 NTD  plan-1  C10  0.020
 NTD  plan-1  C9   0.020
 NTD  plan-1  N    0.020
 NTD  plan-1  H13  0.020
 NTD  plan-1  H12  0.020
 NTD  plan-1  H10  0.020
 NTD  plan-2  C9   0.020
 NTD  plan-2  N    0.020
 NTD  plan-2  ON2  0.020
 NTD  plan-2  ON1  0.020
 NTD  plan-3  O1   0.020
 NTD  plan-3  C5   0.020
 NTD  plan-3  C2   0.020
 NTD  plan-3  C6   0.020
 NTD  plan-4  C4   0.020
 NTD  plan-4  C1   0.020
 NTD  plan-4  O5   0.020
 NTD  plan-4  C6   0.020

