# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:22:06 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(Oc2ccc(cc2Cl)C(F)(F)F)ccc1[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
 ACJ  ACJ  '5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoic acid'  ligand  31  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ACJ
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
 ACJ  O3   O   O      0  -0.410   4.5064   1.0974  -2.0108
 ACJ  C11  C   C      0   0.492   4.1998  -0.0112  -1.6652
 ACJ  O2   O   OH1    0  -0.571   4.4994  -1.1248  -2.3023
 ACJ  C9   C   CR16   0  -0.308   2.0648  -0.8068  -0.7027
 ACJ  C14  C   CR6    0   0.254   3.6636   0.1044   0.8160
 ACJ  C8   C   CR6    0   0.345   1.1751  -0.9358   0.3532
 ACJ  N1   N   N      1   0.333   5.0056   0.5814   1.1004
 ACJ  C13  C   CR16   0  -0.261   2.7745  -0.0206   1.8699
 ACJ  O5   O   O     -1  -0.360   5.1580   1.3060   2.0520
 ACJ  C12  C   CR16   0  -0.293   1.5156  -0.5437   1.6378
 ACJ  O1   O   O2     0  -0.490  -0.0390  -1.5105   0.1102
 ACJ  C7   C   CR6    0   0.448  -1.1489  -0.7394   0.0671
 ACJ  O4   O   O      0  -0.371   5.8946   0.2033   0.3743
 ACJ  C6   C   CR16   0  -0.331  -1.1319   0.6467   0.0048
 ACJ  C10  C   CR6    0  -0.020   3.3260  -0.2776  -0.4776
 ACJ  C4   C   CR6    0  -0.120  -2.3723  -1.4089   0.0602
 ACJ  C5   C   CR16   0  -0.260  -2.3220   1.3520  -0.0624
 ACJ  C2   C   CR6    0  -0.218  -3.5364   0.6813  -0.0683
 ACJ  CL1  CL  CL     0  -0.085  -2.3900  -3.1292   0.1390
 ACJ  C3   C   CR16   0  -0.230  -3.5594  -0.7069  -0.0106
 ACJ  C1   C   CT     0   1.056  -4.8173   1.4408  -0.2038
 ACJ  F1   F   F      0  -0.312  -5.1482   1.6221  -1.4915
 ACJ  F2   F   F      0  -0.305  -5.8448   0.8068   0.3709
 ACJ  F3   F   F      0  -0.305  -4.7435   2.6569   0.3479
 ACJ  H2   H   HOH1   0   0.497   5.0058  -0.9286  -3.1071
 ACJ  H9   H   HCR6   0   0.310   1.7584  -1.1039  -1.6973
 ACJ  H13  H   HCR6   0   0.315   3.0616   0.2596   2.8731
 ACJ  H12  H   HCR6   0   0.310   0.8172  -0.6605   2.4557
 ACJ  H6   H   HCR6   0   0.303  -0.1983   1.1928  -0.0007
 ACJ  H5   H   HCR6   0   0.289  -2.2762   2.4310  -0.1134
 ACJ  H3   H   HCR6   0   0.298  -4.4908  -1.2567  -0.0152

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
 ACJ  O3   C11  double    1.201  0.020  1.201
 ACJ  C11  O2   single    1.317  0.020  1.317
 ACJ  C11  C10  single    1.498  0.020  1.498
 ACJ  O2   H2   single    0.850  0.020  0.980
 ACJ  C9   C8   aromatic  1.387  0.020  1.387
 ACJ  C9   C10  aromatic  1.386  0.020  1.386
 ACJ  C9   H9   single    0.930  0.020  1.080
 ACJ  C14  N1   single    1.452  0.020  1.452
 ACJ  C14  C13  aromatic  1.385  0.020  1.385
 ACJ  C14  C10  aromatic  1.390  0.020  1.390
 ACJ  C8   C12  aromatic  1.386  0.020  1.386
 ACJ  C8   O1   single    1.365  0.020  1.365
 ACJ  N1   O5   single    1.206  0.020  1.206
 ACJ  N1   O4   double    1.208  0.020  1.208
 ACJ  C13  C12  aromatic  1.383  0.020  1.383
 ACJ  C13  H13  single    0.930  0.020  1.080
 ACJ  C12  H12  single    0.930  0.020  1.080
 ACJ  O1   C7   single    1.352  0.020  1.352
 ACJ  C7   C6   aromatic  1.388  0.020  1.388
 ACJ  C7   C4   aromatic  1.395  0.020  1.395
 ACJ  C6   C5   aromatic  1.385  0.020  1.385
 ACJ  C6   H6   single    0.930  0.020  1.080
 ACJ  C4   CL1  single    1.722  0.020  1.722
 ACJ  C4   C3   aromatic  1.381  0.020  1.381
 ACJ  C5   C2   aromatic  1.387  0.020  1.387
 ACJ  C5   H5   single    0.930  0.020  1.080
 ACJ  C2   C3   aromatic  1.390  0.020  1.390
 ACJ  C2   C1   single    1.495  0.020  1.495
 ACJ  C3   H3   single    0.930  0.020  1.080
 ACJ  C1   F1   single    1.342  0.020  1.342
 ACJ  C1   F2   single    1.337  0.020  1.337
 ACJ  C1   F3   single    1.337  0.020  1.337

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
 ACJ  C10  C11  O2   111.45  3.000
 ACJ  C10  C11  O3   122.75  3.000
 ACJ  O2   C11  O3   125.66  3.000
 ACJ  H2   O2   C11  110.41  3.000
 ACJ  H9   C9   C10  120.77  3.000
 ACJ  H9   C9   C8   119.51  3.000
 ACJ  C10  C9   C8   119.71  3.000
 ACJ  C10  C14  C13  121.83  3.000
 ACJ  C10  C14  N1   119.79  3.000
 ACJ  C13  C14  N1   118.29  3.000
 ACJ  O1   C8   C12  120.18  3.000
 ACJ  O1   C8   C9   118.31  3.000
 ACJ  C12  C8   C9   121.46  3.000
 ACJ  O4   N1   O5   124.69  3.000
 ACJ  O4   N1   C14  117.34  3.000
 ACJ  O5   N1   C14  117.95  3.000
 ACJ  H13  C13  C12  119.73  3.000
 ACJ  H13  C13  C14  120.85  3.000
 ACJ  C12  C13  C14  119.40  3.000
 ACJ  H12  C12  C13  120.11  3.000
 ACJ  H12  C12  C8   120.78  3.000
 ACJ  C13  C12  C8   119.10  3.000
 ACJ  C7   O1   C8   119.71  3.000
 ACJ  C4   C7   C6   119.35  3.000
 ACJ  C4   C7   O1   116.51  3.000
 ACJ  C6   C7   O1   124.13  3.000
 ACJ  H6   C6   C5   118.97  3.000
 ACJ  H6   C6   C7   121.01  3.000
 ACJ  C5   C6   C7   120.02  3.000
 ACJ  C14  C10  C9   118.48  3.000
 ACJ  C14  C10  C11  123.16  3.000
 ACJ  C9   C10  C11  118.02  3.000
 ACJ  C3   C4   CL1  120.09  3.000
 ACJ  C3   C4   C7   120.68  3.000
 ACJ  CL1  C4   C7   119.23  3.000
 ACJ  H5   C5   C2   121.29  3.000
 ACJ  H5   C5   C6   118.30  3.000
 ACJ  C2   C5   C6   120.41  3.000
 ACJ  C1   C2   C3   119.80  3.000
 ACJ  C1   C2   C5   120.31  3.000
 ACJ  C3   C2   C5   119.82  3.000
 ACJ  H3   C3   C2   121.46  3.000
 ACJ  H3   C3   C4   118.82  3.000
 ACJ  C2   C3   C4   119.72  3.000
 ACJ  F3   C1   F2   107.23  3.000
 ACJ  F3   C1   F1   106.65  3.000
 ACJ  F2   C1   F1   106.68  3.000
 ACJ  F3   C1   C2   112.16  3.000
 ACJ  F2   C1   C2   112.24  3.000
 ACJ  F1   C1   C2   111.52  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
 ACJ  CONST_01  C13  C12  C8   C9     0.00   0.0  0
 ACJ  CONST_02  C13  C14  C10  C9     0.00   0.0  0
 ACJ  CONST_03  C8   C12  C13  C14    0.00   0.0  0
 ACJ  CONST_04  C8   C9   C10  C14    0.00   0.0  0
 ACJ  CONST_05  C10  C9   C8   C12    0.00   0.0  0
 ACJ  CONST_06  C10  C14  C13  C12    0.00   0.0  0
 ACJ  CONST_07  C2   C5   C6   C7     0.00   0.0  0
 ACJ  CONST_08  C2   C3   C4   C7     0.00   0.0  0
 ACJ  CONST_09  C3   C4   C7   C6     0.00   0.0  0
 ACJ  CONST_10  C3   C2   C5   C6     0.00   0.0  0
 ACJ  CONST_11  C5   C6   C7   C4     0.00   0.0  0
 ACJ  CONST_12  C5   C2   C3   C4     0.00   0.0  0
 ACJ  CONST_13  C8   C9   C10  C11  180.00   0.0  0
 ACJ  CONST_14  C13  C14  C10  C11  180.00   0.0  0
 ACJ  CONST_15  N1   C14  C10  C9   180.00   0.0  0
 ACJ  CONST_16  C12  C13  C14  N1   180.00   0.0  0
 ACJ  CONST_17  O1   C8   C12  C13  180.00   0.0  0
 ACJ  CONST_18  C10  C9   C8   O1   180.00   0.0  0
 ACJ  CONST_19  C5   C6   C7   O1   180.00   0.0  0
 ACJ  CONST_20  C3   C4   C7   O1   180.00   0.0  0
 ACJ  CONST_21  CL1  C4   C7   C6   180.00   0.0  0
 ACJ  CONST_22  C1   C2   C5   C6   180.00   0.0  0
 ACJ  CONST_23  C1   C2   C3   C4   180.00   0.0  0
 ACJ  CONST_24  CL1  C4   C3   C2   180.00   0.0  0
 ACJ  CONST_25  H12  C12  C8   C9   180.00   0.0  0
 ACJ  CONST_26  H9   C9   C10  C14  180.00   0.0  0
 ACJ  CONST_27  H13  C13  C12  C8   180.00   0.0  0
 ACJ  CONST_28  H5   C5   C6   C7   180.00   0.0  0
 ACJ  CONST_29  H3   C3   C4   C7   180.00   0.0  0
 ACJ  CONST_30  H6   C6   C7   C4   180.00   0.0  0
 ACJ  CONST_35  H2   O2   C11  C10  180.00   0.0  0
 ACJ  Var_01    C6   C7   O1   C8    12.64  30.0  2
 ACJ  Var_02    C9   C10  C11  O3   112.47  30.0  2
 ACJ  Var_03    F1   C1   C2   C5    87.82  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
 ACJ  plan-1  C11  0.020
 ACJ  plan-1  C9   0.020
 ACJ  plan-1  C14  0.020
 ACJ  plan-1  C8   0.020
 ACJ  plan-1  N1   0.020
 ACJ  plan-1  C13  0.020
 ACJ  plan-1  C12  0.020
 ACJ  plan-1  O1   0.020
 ACJ  plan-1  C10  0.020
 ACJ  plan-1  H9   0.020
 ACJ  plan-1  H13  0.020
 ACJ  plan-1  H12  0.020
 ACJ  plan-2  O1   0.020
 ACJ  plan-2  C7   0.020
 ACJ  plan-2  C6   0.020
 ACJ  plan-2  C4   0.020
 ACJ  plan-2  C5   0.020
 ACJ  plan-2  C2   0.020
 ACJ  plan-2  CL1  0.020
 ACJ  plan-2  C3   0.020
 ACJ  plan-2  C1   0.020
 ACJ  plan-2  H6   0.020
 ACJ  plan-2  H5   0.020
 ACJ  plan-2  H3   0.020
 ACJ  plan-3  C14  0.020
 ACJ  plan-3  N1   0.020
 ACJ  plan-3  O5   0.020
 ACJ  plan-3  O4   0.020
 ACJ  plan-4  O3   0.020
 ACJ  plan-4  C11  0.020
 ACJ  plan-4  O2   0.020
 ACJ  plan-4  C10  0.020
 ACJ  plan-4  H2   0.020

