# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 17:53:22 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2S)-2-hydroxy-2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-3-(pentafluorophenoxy)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(COc1c(F)c(F)c(F)c(F)c1F)C(=O)Nc2ccc(c(c2)C(F)(F)F)[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
 B67  B67  (2S)-2-hydroxy-2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-3-(pentafluorophenoxy)propanamide  ligand  42  32  .  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_B67
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
 B67  F1    F  F      0  -0.296  -5.2850   2.6219  -0.6287
 B67  C7    C  CT     0   1.073  -5.9367   1.4951  -0.3259
 B67  F2    F  F      0  -0.305  -6.6748   1.7634   0.7543
 B67  F3    F  F      0  -0.301  -6.7603   1.2482  -1.3445
 B67  C4    C  CR6    0  -0.163  -4.9710   0.3607  -0.0779
 B67  C5    C  CR16   0  -0.413  -3.6755   0.5068  -0.5304
 B67  C3    C  CR6    0   0.227  -5.2914  -0.8007   0.6321
 B67  N8    N  N      1   0.318  -6.6342  -1.0891   1.1038
 B67  O2    O  O      0  -0.365  -6.7439  -1.6500   2.1675
 B67  O1    O  O     -1  -0.370  -7.5610  -0.7835   0.3928
 B67  C2    C  CR16   0  -0.248  -4.3269  -1.7593   0.8834
 B67  C1    C  CR16   0  -0.313  -3.0368  -1.6154   0.4083
 B67  C6    C  CR6    0   0.457  -2.6998  -0.4737  -0.3150
 B67  N9    N  NH1    0  -0.748  -1.4444  -0.2132  -0.8366
 B67  C10   C  C      0   0.532  -0.3202  -0.9693  -0.7756
 B67  O10   O  O      0  -0.444  -0.2381  -2.0519  -0.2310
 B67  C11   C  CT     0   0.054   0.8843  -0.3493  -1.5086
 B67  O11   O  OH1    0  -0.654   0.6636   1.0034  -1.8237
 B67  C12   C  CH3    0  -0.660   1.0552  -1.0986  -2.8283
 B67  C13   C  CH2    0  -0.185   2.0981  -0.5139  -0.5947
 B67  O14   O  O2     0  -0.484   3.2193   0.0577  -1.2657
 B67  C16   C  CR6    0   0.050   4.3346   0.1606  -0.5194
 B67  C17   C  CR6    0   0.372   5.2817  -0.8545  -0.5014
 B67  F17   F  F      0  -0.285   5.0660  -1.9628  -1.1996
 B67  C18   C  CR6    0   0.273   6.4490  -0.7274   0.2276
 B67  F18   F  F      0  -0.289   7.3487  -1.7035   0.2289
 B67  C19   C  CR6    0   0.279   6.6809   0.4230   0.9588
 B67  F19   F  F      0  -0.286   7.7999   0.5503   1.6594
 B67  C20   C  CR6    0   0.274   5.7470   1.4425   0.9581
 B67  F20   F  F      0  -0.288   5.9722   2.5469   1.6595
 B67  C21   C  CR6    0   0.373   4.5840   1.3060   0.2251
 B67  F21   F  F      0  -0.286   3.6899   2.2879   0.2294
 B67  H5    H  HCR6   0   0.306  -3.3884   1.4041  -1.0609
 B67  H2    H  HCR6   0   0.309  -4.5812  -2.6511   1.4382
 B67  H1    H  HCR6   0   0.308  -2.3163  -2.3902   0.6075
 B67  HN9   H  HNH1   0   0.428  -1.3427   0.6615  -1.3359
 B67  HO11  H  HOH1   0   0.463   0.8012   1.5545  -1.0437
 B67  H12   H  HCH3   0   0.254   0.1627  -0.9967  -3.4465
 B67  H12A  H  HCH3   0   0.260   1.9011  -0.7013  -3.3872
 B67  H12B  H  HCH3   0   0.248   1.2275  -2.1592  -2.6530
 B67  H13   H  HCH2   0   0.262   1.9217  -0.0012   0.3592
 B67  H13A  H  HCH2   0   0.262   2.2755  -1.5689  -0.3792

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
 B67  F1   C7    single    1.336  0.020  1.336
 B67  C7   F2    single    1.336  0.020  1.336
 B67  C7   F3    single    1.333  0.020  1.333
 B67  C7   C4    single    1.510  0.020  1.510
 B67  C4   C5    aromatic  1.380  0.020  1.380
 B67  C4   C3    aromatic  1.398  0.020  1.398
 B67  C5   C6    aromatic  1.400  0.020  1.400
 B67  C5   H5    single    0.930  0.020  1.080
 B67  C3   N8    single    1.452  0.020  1.452
 B67  C3   C2    aromatic  1.383  0.020  1.383
 B67  N8   O2    double    1.208  0.020  1.208
 B67  O1   N8    single    1.207  0.020  1.207
 B67  C2   C1    aromatic  1.382  0.020  1.382
 B67  C2   H2    single    0.930  0.020  1.080
 B67  C1   C6    aromatic  1.393  0.020  1.393
 B67  C1   H1    single    0.930  0.020  1.080
 B67  C6   N9    single    1.384  0.020  1.384
 B67  N9   C10   single    1.356  0.020  1.356
 B67  N9   HN9   single    0.860  0.020  1.020
 B67  C10  O10   double    1.215  0.020  1.215
 B67  C10  C11   single    1.540  0.020  1.540
 B67  C11  O11   single    1.406  0.020  1.406
 B67  C11  C12   single    1.527  0.020  1.527
 B67  C11  C13   single    1.528  0.020  1.528
 B67  O11  HO11  single    0.850  0.020  0.980
 B67  C12  H12   single    0.970  0.020  1.090
 B67  C12  H12A  single    0.970  0.020  1.090
 B67  C12  H12B  single    0.970  0.020  1.090
 B67  C13  O14   single    1.426  0.020  1.426
 B67  C13  H13   single    0.970  0.020  1.090
 B67  C13  H13A  single    0.970  0.020  1.090
 B67  O14  C16   single    1.346  0.020  1.346
 B67  C16  C17   aromatic  1.388  0.020  1.388
 B67  C16  C21   aromatic  1.389  0.020  1.389
 B67  C17  F17   single    1.327  0.020  1.327
 B67  C17  C18   aromatic  1.382  0.020  1.382
 B67  C18  F18   single    1.328  0.020  1.328
 B67  C18  C19   aromatic  1.383  0.020  1.383
 B67  C19  F19   single    1.326  0.020  1.326
 B67  C19  C20   aromatic  1.383  0.020  1.383
 B67  C20  F20   single    1.327  0.020  1.327
 B67  C20  C21   aromatic  1.382  0.020  1.382
 B67  C21  F21   single    1.328  0.020  1.328

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
 B67  C4    C7   F3    112.42  3.000
 B67  C4    C7   F2    111.81  3.000
 B67  F3    C7   F2    108.29  3.000
 B67  C4    C7   F1    111.02  3.000
 B67  F3    C7   F1    106.52  3.000
 B67  F2    C7   F1    106.46  3.000
 B67  C3    C4   C5    118.00  3.000
 B67  C3    C4   C7    124.11  3.000
 B67  C5    C4   C7    117.83  3.000
 B67  H5    C5   C6    118.14  3.000
 B67  H5    C5   C4    119.87  3.000
 B67  C6    C5   C4    121.98  3.000
 B67  C2    C3   N8    116.63  3.000
 B67  C2    C3   C4    120.54  3.000
 B67  N8    C3   C4    122.80  3.000
 B67  O1    N8   O2    124.51  3.000
 B67  O1    N8   C3    117.92  3.000
 B67  O2    N8   C3    117.54  3.000
 B67  H2    C2   C1    118.82  3.000
 B67  H2    C2   C3    120.08  3.000
 B67  C1    C2   C3    121.08  3.000
 B67  H1    C1   C6    121.60  3.000
 B67  H1    C1   C2    119.08  3.000
 B67  C6    C1   C2    119.31  3.000
 B67  N9    C6   C1    124.71  3.000
 B67  N9    C6   C5    116.25  3.000
 B67  C1    C6   C5    119.03  3.000
 B67  HN9   N9   C10   114.87  3.000
 B67  HN9   N9   C6    116.08  3.000
 B67  C10   N9   C6    129.05  3.000
 B67  C11   C10  O10   121.28  3.000
 B67  C11   C10  N9    113.73  3.000
 B67  O10   C10  N9    124.97  3.000
 B67  C13   C11  C12   112.03  3.000
 B67  C13   C11  O11   111.24  3.000
 B67  C12   C11  O11   107.21  3.000
 B67  C13   C11  C10   107.05  3.000
 B67  C12   C11  C10   107.53  3.000
 B67  O11   C11  C10   111.78  3.000
 B67  HO11  O11  C11   110.24  3.000
 B67  H12B  C12  H12A  108.37  3.000
 B67  H12B  C12  H12   108.17  3.000
 B67  H12A  C12  H12   108.10  3.000
 B67  H12B  C12  C11   110.89  3.000
 B67  H12A  C12  C11   110.58  3.000
 B67  H12   C12  C11   110.64  3.000
 B67  H13A  C13  H13   107.83  3.000
 B67  H13A  C13  O14   110.65  3.000
 B67  H13   C13  O14   110.37  3.000
 B67  H13A  C13  C11   110.57  3.000
 B67  H13   C13  C11   109.99  3.000
 B67  O14   C13  C11   107.45  3.000
 B67  C16   O14  C13   114.91  3.000
 B67  C21   C16  C17   118.27  3.000
 B67  C21   C16  O14   120.61  3.000
 B67  C17   C16  O14   121.10  3.000
 B67  C18   C17  F17   119.43  3.000
 B67  C18   C17  C16   121.04  3.000
 B67  F17   C17  C16   119.53  3.000
 B67  C19   C18  F18   119.84  3.000
 B67  C19   C18  C17   119.81  3.000
 B67  F18   C18  C17   120.35  3.000
 B67  C20   C19  F19   119.96  3.000
 B67  C20   C19  C18   120.00  3.000
 B67  F19   C19  C18   120.05  3.000
 B67  C21   C20  F20   120.35  3.000
 B67  C21   C20  C19   119.74  3.000
 B67  F20   C20  C19   119.91  3.000
 B67  F21   C21  C20   119.47  3.000
 B67  F21   C21  C16   119.39  3.000
 B67  C20   C21  C16   121.14  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
 B67  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 B67  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 B67  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 B67  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 B67  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 B67  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 B67  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 B67  CONST_08  C19  C20  C21  C16    0.00   0.0  0
 B67  CONST_09  C20  C21  C16  C17    0.00   0.0  0
 B67  CONST_10  C20  C19  C18  C17    0.00   0.0  0
 B67  CONST_11  C21  C16  C17  C18    0.00   0.0  0
 B67  CONST_12  C21  C20  C19  C18    0.00   0.0  0
 B67  CONST_13  C6   C5   C4   C7   180.00   0.0  0
 B67  CONST_14  C2   C3   C4   C7   180.00   0.0  0
 B67  CONST_15  N9   C6   C5   C4   180.00   0.0  0
 B67  CONST_16  N8   C3   C4   C5   180.00   0.0  0
 B67  CONST_17  C1   C2   C3   N8   180.00   0.0  0
 B67  CONST_18  N9   C6   C1   C2   180.00   0.0  0
 B67  CONST_19  C18  C17  C16  O14  180.00   0.0  0
 B67  CONST_20  C20  C21  C16  O14  180.00   0.0  0
 B67  CONST_21  F18  C18  C17  C16  180.00   0.0  0
 B67  CONST_22  F20  C20  C21  C16  180.00   0.0  0
 B67  CONST_23  F21  C21  C16  C17  180.00   0.0  0
 B67  CONST_24  F19  C19  C18  C17  180.00   0.0  0
 B67  CONST_25  C21  C16  C17  F17  180.00   0.0  0
 B67  CONST_26  C19  C18  C17  F17  180.00   0.0  0
 B67  CONST_27  F20  C20  C19  C18  180.00   0.0  0
 B67  CONST_28  C20  C19  C18  F18  180.00   0.0  0
 B67  CONST_29  F21  C21  C20  C19  180.00   0.0  0
 B67  CONST_30  C21  C20  C19  F19  180.00   0.0  0
 B67  CONST_31  H2   C2   C3   C4   180.00   0.0  0
 B67  CONST_32  H1   C1   C6   C5   180.00   0.0  0
 B67  CONST_33  H5   C5   C4   C3   180.00   0.0  0
 B67  CONST_36  C10  N9   C6   C5   180.00   0.0  0
 B67  CONST_39  C10  N9   C6   C1     0.00   0.0  0
 B67  CONST_40  HN9  N9   C6   C5     0.00   0.0  0
 B67  CONST_41  O10  C10  N9   C6     0.00   0.0  0
 B67  CONST_42  C11  C10  N9   C6   180.00   0.0  0
 B67  Var_01    C5   C4   C7   F1   -17.14  30.0  2
 B67  Var_02    C17  C16  O14  C13   91.44  30.0  2
 B67  Var_03    H13  C13  O14  C16   51.33  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 B67  chir_01  C11  O11  C12  C13  negativ

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
 B67  plan-1  C7   0.020
 B67  plan-1  C4   0.020
 B67  plan-1  C5   0.020
 B67  plan-1  C3   0.020
 B67  plan-1  N8   0.020
 B67  plan-1  C2   0.020
 B67  plan-1  C1   0.020
 B67  plan-1  C6   0.020
 B67  plan-1  N9   0.020
 B67  plan-1  H5   0.020
 B67  plan-1  H2   0.020
 B67  plan-1  H1   0.020
 B67  plan-2  O14  0.020
 B67  plan-2  C16  0.020
 B67  plan-2  C17  0.020
 B67  plan-2  F17  0.020
 B67  plan-2  C18  0.020
 B67  plan-2  F18  0.020
 B67  plan-2  C19  0.020
 B67  plan-2  F19  0.020
 B67  plan-2  C20  0.020
 B67  plan-2  F20  0.020
 B67  plan-2  C21  0.020
 B67  plan-2  F21  0.020
 B67  plan-3  C6   0.020
 B67  plan-3  N9   0.020
 B67  plan-3  C10  0.020
 B67  plan-3  O10  0.020
 B67  plan-3  C11  0.020
 B67  plan-3  HN9  0.020
 B67  plan-4  C3   0.020
 B67  plan-4  N8   0.020
 B67  plan-4  O2   0.020
 B67  plan-4  O1   0.020

