# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 00:09:50 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 2-(2-chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(O)c(Oc2ccc(cc2Cl)[N+]([O-])=O)cc1F
#
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
 9W7  9W7  2-(2-chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol  ligand  32  21  .  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_9W7
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
 9W7  C    C   CH3    0  -0.658   6.3483  -0.2297  -0.3812
 9W7  F    F   F      0  -0.315   4.1497  -0.5438   2.1451
 9W7  N    N   N      1   0.329  -4.6797  -1.5266  -0.0025
 9W7  O    O   OH1    0  -0.616   0.9969   0.4523  -2.1871
 9W7  CL   CL  CL     0  -0.079  -2.0916   2.8975   0.2412
 9W7  C1   C   CH2    0  -0.498   5.2414  -1.2830  -0.3645
 9W7  O1   O   O2     0  -0.477   0.1684   1.1626   0.2708
 9W7  C2   C   CR6    0  -0.063   3.8789  -0.6733  -0.1903
 9W7  O2   O   O      0  -0.379  -4.6790  -2.7346  -0.0489
 9W7  C3   C   CR16   0  -0.421   3.0656  -0.4099  -1.2889
 9W7  O3   O   O     -1  -0.380  -5.6830  -0.8517  -0.0060
 9W7  C4   C   CR6    0   0.332   1.8175   0.1866  -1.1572
 9W7  C5   C   CR6    0   0.234   1.3771   0.5240   0.1210
 9W7  C6   C   CR6    0   0.478  -0.9649   0.4511   0.1860
 9W7  C7   C   CR16   0  -0.345  -1.0153  -0.9377   0.1349
 9W7  C8   C   CR16   0  -0.253  -2.2313  -1.5901   0.0728
 9W7  C9   C   CR6    0   0.237  -3.4017  -0.8479   0.0612
 9W7  C10  C   CR16   0  -0.227  -3.3784   0.5393   0.1129
 9W7  C11  C   CR6    0  -0.139  -2.1599   1.1789   0.1745
 9W7  C12  C   CR16   0  -0.454   2.1572   0.2760   1.2344
 9W7  C13  C   CR6    0   0.499   3.3932  -0.3120   1.0562
 9W7  H    H   HCH3   0   0.230   6.3761   0.3353   0.5506
 9W7  HA   H   HCH3   0   0.236   7.3228  -0.7000  -0.5135
 9W7  HB   H   HCH3   0   0.229   6.2024   0.4768  -1.1986
 9W7  HO   H   HOH1   0   0.483   1.3937   0.1667  -3.0182
 9W7  H1   H   HCH2   0   0.250   5.2579  -1.8411  -1.3022
 9W7  H1A  H   HCH2   0   0.250   5.4340  -2.0090   0.4270
 9W7  H3   H   HCR6   0   0.284   3.4211  -0.6782  -2.2778
 9W7  H7   H   HCR6   0   0.307  -0.1076  -1.5251   0.1551
 9W7  H8   H   HCR6   0   0.309  -2.2495  -2.6691   0.0379
 9W7  H10  H   HCR6   0   0.319  -4.2888   1.1206   0.1036
 9W7  H12  H   HCR6   0   0.298   1.8042   0.5420   2.2227

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
 9W7  C    C1   single    1.528  0.020  1.528
 9W7  F    C13  single    1.346  0.020  1.346
 9W7  N    O2   double    1.209  0.020  1.209
 9W7  N    O3   single    1.209  0.020  1.209
 9W7  N    C9   single    1.448  0.020  1.448
 9W7  O    C4   single    1.343  0.020  1.343
 9W7  CL   C11  single    1.721  0.020  1.721
 9W7  C1   C2   single    1.503  0.020  1.503
 9W7  O1   C5   single    1.375  0.020  1.375
 9W7  O1   C6   single    1.341  0.020  1.341
 9W7  C2   C3   aromatic  1.392  0.020  1.392
 9W7  C2   C13  aromatic  1.386  0.020  1.386
 9W7  C3   C4   aromatic  1.390  0.020  1.390
 9W7  C4   C5   aromatic  1.393  0.020  1.393
 9W7  C5   C12  aromatic  1.382  0.020  1.382
 9W7  C6   C7   aromatic  1.391  0.020  1.391
 9W7  C6   C11  aromatic  1.399  0.020  1.399
 9W7  C7   C8   aromatic  1.381  0.020  1.381
 9W7  C8   C9   aromatic  1.386  0.020  1.386
 9W7  C9   C10  aromatic  1.388  0.020  1.388
 9W7  C10  C11  aromatic  1.378  0.020  1.378
 9W7  C12  C13  aromatic  1.380  0.020  1.380
 9W7  C    H    single    0.970  0.020  1.090
 9W7  C    HA   single    0.970  0.020  1.090
 9W7  C    HB   single    0.970  0.020  1.090
 9W7  O    HO   single    0.850  0.020  0.980
 9W7  C1   H1   single    0.970  0.020  1.090
 9W7  C1   H1A  single    0.970  0.020  1.090
 9W7  C3   H3   single    0.930  0.020  1.080
 9W7  C7   H7   single    0.930  0.020  1.080
 9W7  C8   H8   single    0.930  0.020  1.080
 9W7  C10  H10  single    0.930  0.020  1.080
 9W7  C12  H12  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
 9W7  HB   C    HA   107.95  3.000
 9W7  HB   C    H    107.97  3.000
 9W7  HA   C    H    107.74  3.000
 9W7  HB   C    C1   110.97  3.000
 9W7  HA   C    C1   110.58  3.000
 9W7  H    C    C1   111.50  3.000
 9W7  C9   N    O3   118.08  3.000
 9W7  C9   N    O2   117.99  3.000
 9W7  O3   N    O2   123.93  3.000
 9W7  HO   O    C4   110.53  3.000
 9W7  H1A  C1   H1   106.28  3.000
 9W7  H1A  C1   C2   110.23  3.000
 9W7  H1   C1   C2   108.71  3.000
 9W7  H1A  C1   C    109.79  3.000
 9W7  H1   C1   C    109.41  3.000
 9W7  C2   C1   C    112.23  3.000
 9W7  C6   O1   C5   119.31  3.000
 9W7  C13  C2   C3   117.12  3.000
 9W7  C13  C2   C1   121.86  3.000
 9W7  C3   C2   C1   120.99  3.000
 9W7  H3   C3   C4   119.14  3.000
 9W7  H3   C3   C2   118.77  3.000
 9W7  C4   C3   C2   122.09  3.000
 9W7  C5   C4   C3   118.34  3.000
 9W7  C5   C4   O    117.53  3.000
 9W7  C3   C4   O    124.12  3.000
 9W7  C12  C5   C4   121.14  3.000
 9W7  C12  C5   O1   119.46  3.000
 9W7  C4   C5   O1   119.35  3.000
 9W7  C11  C6   C7   119.22  3.000
 9W7  C11  C6   O1   116.51  3.000
 9W7  C7   C6   O1   124.26  3.000
 9W7  H7   C7   C8   118.90  3.000
 9W7  H7   C7   C6   120.75  3.000
 9W7  C8   C7   C6   120.35  3.000
 9W7  H8   C8   C9   121.38  3.000
 9W7  H8   C8   C7   119.22  3.000
 9W7  C9   C8   C7   119.40  3.000
 9W7  C10  C9   C8   121.37  3.000
 9W7  C10  C9   N    118.99  3.000
 9W7  C8   C9   N    119.64  3.000
 9W7  H10  C10  C11  119.74  3.000
 9W7  H10  C10  C9   121.54  3.000
 9W7  C11  C10  C9   118.72  3.000
 9W7  C10  C11  C6   120.95  3.000
 9W7  C10  C11  CL   120.03  3.000
 9W7  C6   C11  CL   119.02  3.000
 9W7  H12  C12  C13  120.96  3.000
 9W7  H12  C12  C5   120.48  3.000
 9W7  C13  C12  C5   118.55  3.000
 9W7  C12  C13  C2   122.75  3.000
 9W7  C12  C13  F    118.18  3.000
 9W7  C2   C13  F    119.07  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
 9W7  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 9W7  CONST_02  C5   C12  C13  C2     0.00   0.0  0
 9W7  CONST_03  C12  C13  C2   C3     0.00   0.0  0
 9W7  CONST_04  C12  C5   C4   C3     0.00   0.0  0
 9W7  CONST_05  C13  C2   C3   C4     0.00   0.0  0
 9W7  CONST_06  C13  C12  C5   C4     0.00   0.0  0
 9W7  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 9W7  CONST_08  C9   C10  C11  C6     0.00   0.0  0
 9W7  CONST_09  C10  C11  C6   C7     0.00   0.0  0
 9W7  CONST_10  C10  C9   C8   C7     0.00   0.0  0
 9W7  CONST_11  C11  C6   C7   C8     0.00   0.0  0
 9W7  CONST_12  C11  C10  C9   C8     0.00   0.0  0
 9W7  CONST_13  C3   C2   C13  F    180.00   0.0  0
 9W7  CONST_14  C5   C12  C13  F    180.00   0.0  0
 9W7  CONST_15  C7   C8   C9   N    180.00   0.0  0
 9W7  CONST_16  C11  C10  C9   N    180.00   0.0  0
 9W7  CONST_17  C2   C3   C4   O    180.00   0.0  0
 9W7  CONST_18  C12  C5   C4   O    180.00   0.0  0
 9W7  CONST_19  C7   C6   C11  CL   180.00   0.0  0
 9W7  CONST_20  C9   C10  C11  CL   180.00   0.0  0
 9W7  CONST_21  C4   C3   C2   C1   180.00   0.0  0
 9W7  CONST_22  C12  C13  C2   C1   180.00   0.0  0
 9W7  CONST_23  C3   C4   C5   O1   180.00   0.0  0
 9W7  CONST_24  C13  C12  C5   O1   180.00   0.0  0
 9W7  CONST_25  C8   C7   C6   O1   180.00   0.0  0
 9W7  CONST_26  C10  C11  C6   O1   180.00   0.0  0
 9W7  CONST_27  H12  C12  C13  C2   180.00   0.0  0
 9W7  CONST_28  H3   C3   C4   C5   180.00   0.0  0
 9W7  CONST_29  H8   C8   C7   C6   180.00   0.0  0
 9W7  CONST_30  H10  C10  C11  C6   180.00   0.0  0
 9W7  CONST_31  H7   C7   C8   C9   180.00   0.0  0
 9W7  CONST_32  C8   C9   N    O2     0.00   0.0  0
 9W7  CONST_33  C10  C9   N    O2   180.00   0.0  0
 9W7  CONST_34  C8   C9   N    O3   180.00   0.0  0
 9W7  CONST_35  C10  C9   N    O3     0.00   0.0  0
 9W7  Var_01    C7   C6   O1   C5     9.17  30.0  2
 9W7  Var_02    C12  C5   O1   C6  -104.66  30.0  2
 9W7  Var_03    C3   C2   C1   C     96.46  30.0  2
 9W7  Var_04    H    C    C1   C2    60.44  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
 9W7  plan-1  F    0.020
 9W7  plan-1  O    0.020
 9W7  plan-1  C1   0.020
 9W7  plan-1  O1   0.020
 9W7  plan-1  C2   0.020
 9W7  plan-1  C3   0.020
 9W7  plan-1  C4   0.020
 9W7  plan-1  C5   0.020
 9W7  plan-1  C12  0.020
 9W7  plan-1  C13  0.020
 9W7  plan-1  H3   0.020
 9W7  plan-1  H12  0.020
 9W7  plan-2  N    0.020
 9W7  plan-2  CL   0.020
 9W7  plan-2  O1   0.020
 9W7  plan-2  C6   0.020
 9W7  plan-2  C7   0.020
 9W7  plan-2  C8   0.020
 9W7  plan-2  C9   0.020
 9W7  plan-2  C10  0.020
 9W7  plan-2  C11  0.020
 9W7  plan-2  H7   0.020
 9W7  plan-2  H8   0.020
 9W7  plan-2  H10  0.020
 9W7  plan-3  N    0.020
 9W7  plan-3  O2   0.020
 9W7  plan-3  O3   0.020
 9W7  plan-3  C9   0.020

