# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 19:07:15 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-{[(1R,2S)-1,2-dihydroxy-2-methyl-3-(4-nitrophenoxy)propyl]amino}-2-(trifluoromethyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(COc1ccc(cc1)[N+]([O-])=O)[C@@H](O)Nc2ccc(C#N)c(c2)C(F)(F)F
#
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
 B66  B66  4-{[(1R,2S)-1,2-dihydroxy-2-methyl-3-(4-nitrophenoxy)propyl]amino}-2-(trifluoromethyl)benzonitrile  ligand  45  29  .  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_B66
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
 B66  C17   C  CR16   0  -0.345  -5.4671  -1.4245  -0.6586
 B66  C18   C  CR16   0  -0.252  -6.8036  -1.1176  -0.5548
 B66  C21   C  CR6    0   0.227  -7.1840   0.0945   0.0167
 B66  N19   N  N      1   0.328  -8.5859   0.4195   0.1302
 B66  O20   O  O     -1  -0.390  -9.3948  -0.3904  -0.2653
 B66  O19   O  O      0  -0.390  -8.8909   1.4861   0.6155
 B66  C20   C  CR16   0  -0.252  -6.2329   0.9923   0.4781
 B66  C19   C  CR16   0  -0.376  -4.8889   0.6843   0.3748
 B66  C16   C  CR6    0   0.427  -4.4953  -0.5298  -0.1929
 B66  O14   O  O2     0  -0.457  -3.2285  -0.9179  -0.3300
 B66  C13   C  CH2    0  -0.186  -2.1887  -0.0784   0.1398
 B66  C11   C  CT     0   0.083  -0.8587  -0.7862  -0.1192
 B66  O11   O  OH1    0  -0.662  -0.7768  -1.9973   0.6040
 B66  C12   C  CH3    0  -0.665  -0.7037  -1.1349  -1.5944
 B66  C10   C  CH1    0   0.210   0.2775   0.1811   0.3002
 B66  O10   O  OH1    0  -0.657   0.0810   0.7533   1.5701
 B66  N9    N  NH1    0  -0.737   1.5287  -0.5017   0.1928
 B66  C6    C  CR6    0   0.469   2.7399   0.1068   0.1606
 B66  C5    C  CR16   0  -0.418   3.8981  -0.6966   0.1435
 B66  C1    C  CR16   0  -0.339   2.8966   1.4997   0.1221
 B66  C2    C  CR16   0  -0.231   4.1560   2.0547   0.0474
 B66  C3    C  CR6    0   0.001   5.3004   1.2591   0.0230
 B66  C8    C  CSP    0   0.006   6.5731   1.8874  -0.0488
 B66  N8    N  NS     0  -0.253   7.5901   2.4282  -0.1080
 B66  C4    C  CR6    0  -0.151   5.1498  -0.1361   0.0766
 B66  C7    C  CT     0   1.073   6.3705  -1.0089   0.0558
 B66  F2    F  F      0  -0.292   6.0780  -2.3068   0.1179
 B66  F3    F  F      0  -0.312   7.0849  -0.8157  -1.0599
 B66  F1    F  F      0  -0.312   7.1792  -0.7350   1.0873
 B66  H17   H  HCR6   0   0.285  -5.1581  -2.3630  -1.0992
 B66  H18   H  HCR6   0   0.298  -7.5401  -1.8203  -0.9162
 B66  H20   H  HCR6   0   0.301  -6.5228   1.9342   0.9205
 B66  H19   H  HCR6   0   0.301  -4.1657   1.4000   0.7390
 B66  H13   H  HCH2   0   0.250  -2.2042   0.8841  -0.3833
 B66  H13A  H  HCH2   0   0.255  -2.3219   0.1167   1.2089
 B66  HO11  H  HOH1   0   0.454  -1.0728  -1.8641   1.5114
 B66  H12   H  HCH3   0   0.236  -0.7486  -0.2340  -2.2063
 B66  H12A  H  HCH3   0   0.248   0.2534  -1.6189  -1.7857
 B66  H12B  H  HCH3   0   0.253  -1.4912  -1.8092  -1.9257
 B66  HN9   H  HNH1   0   0.400   1.5178  -1.4982   0.3556
 B66  H5    H  HCR6   0   0.289   3.7788  -1.7713   0.1802
 B66  H1    H  HCR6   0   0.292   2.0443   2.1624   0.1565
 B66  H2    H  HCR6   0   0.289   4.2572   3.1309   0.0155
 B66  H15   H  HCH1   0   0.254   0.2660   1.0258  -0.3939
 B66  H16   H  HOH1   0   0.447   0.2630   0.0969   2.2529

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
 B66  C17  C18   aromatic  1.375  0.020  1.375
 B66  C17  C16   aromatic  1.401  0.020  1.401
 B66  C17  H17   single    0.930  0.020  1.080
 B66  C18  C21   aromatic  1.393  0.020  1.393
 B66  C18  H18   single    0.930  0.020  1.080
 B66  C21  N19   single    1.444  0.020  1.444
 B66  C21  C20   aromatic  1.387  0.020  1.387
 B66  N19  O20   single    1.211  0.020  1.211
 B66  N19  O19   double    1.211  0.020  1.211
 B66  C20  C19   aromatic  1.383  0.020  1.383
 B66  C20  H20   single    0.930  0.020  1.080
 B66  C19  C16   aromatic  1.397  0.020  1.397
 B66  C19  H19   single    0.930  0.020  1.080
 B66  C16  O14   single    1.332  0.020  1.332
 B66  O14  C13   single    1.417  0.020  1.417
 B66  C13  C11   single    1.529  0.020  1.529
 B66  C13  H13   single    0.970  0.020  1.090
 B66  C13  H13A  single    0.970  0.020  1.090
 B66  C11  O11   single    1.413  0.020  1.413
 B66  C11  C12   single    1.524  0.020  1.524
 B66  C11  C10   single    1.550  0.020  1.550
 B66  O11  HO11  single    0.850  0.020  0.980
 B66  C12  H12   single    0.970  0.020  1.090
 B66  C12  H12A  single    0.970  0.020  1.090
 B66  C12  H12B  single    0.970  0.020  1.090
 B66  C10  O10   single    1.407  0.020  1.407
 B66  C10  N9    single    1.429  0.020  1.429
 B66  N9   C6    single    1.356  0.020  1.356
 B66  N9   HN9   single    0.860  0.020  1.020
 B66  C6   C5    aromatic  1.410  0.020  1.410
 B66  C6   C1    aromatic  1.402  0.020  1.402
 B66  C5   C4    aromatic  1.373  0.020  1.373
 B66  C5   H5    single    0.930  0.020  1.080
 B66  C1   C2    aromatic  1.378  0.020  1.378
 B66  C1   H1    single    0.930  0.020  1.080
 B66  C2   C3    aromatic  1.394  0.020  1.394
 B66  C2   H2    single    0.930  0.020  1.080
 B66  C3   C8    single    1.421  0.020  1.421
 B66  C3   C4    aromatic  1.404  0.020  1.404
 B66  C8   N8    triple    1.153  0.020  1.153
 B66  C4   C7    single    1.501  0.020  1.501
 B66  C7   F2    single    1.332  0.020  1.332
 B66  C7   F3    single    1.339  0.020  1.339
 B66  C7   F1    single    1.339  0.020  1.339
 B66  C10  H15   single    0.970  0.020  1.090
 B66  O10  H16   single    0.850  0.020  0.980

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
 B66  H17   C17  C16   119.43  3.000
 B66  H17   C17  C18   120.13  3.000
 B66  C16   C17  C18   120.44  3.000
 B66  H18   C18  C21   121.14  3.000
 B66  H18   C18  C17   119.48  3.000
 B66  C21   C18  C17   119.38  3.000
 B66  C20   C21  N19   119.61  3.000
 B66  C20   C21  C18   120.83  3.000
 B66  N19   C21  C18   119.56  3.000
 B66  O19   N19  O20   123.48  3.000
 B66  O19   N19  C21   118.32  3.000
 B66  O20   N19  C21   118.19  3.000
 B66  H20   C20  C19   119.06  3.000
 B66  H20   C20  C21   121.10  3.000
 B66  C19   C20  C21   119.84  3.000
 B66  H19   C19  C16   121.60  3.000
 B66  H19   C19  C20   118.54  3.000
 B66  C16   C19  C20   119.86  3.000
 B66  O14   C16  C19   124.27  3.000
 B66  O14   C16  C17   116.07  3.000
 B66  C19   C16  C17   119.65  3.000
 B66  C13   O14  C16   119.42  3.000
 B66  H13A  C13  H13   107.93  3.000
 B66  H13A  C13  C11   110.71  3.000
 B66  H13   C13  C11   109.77  3.000
 B66  H13A  C13  O14   109.89  3.000
 B66  H13   C13  O14   110.61  3.000
 B66  C11   C13  O14   107.94  3.000
 B66  C10   C11  C12   109.28  3.000
 B66  C10   C11  O11   110.73  3.000
 B66  C12   C11  O11   107.07  3.000
 B66  C10   C11  C13   107.64  3.000
 B66  C12   C11  C13   111.01  3.000
 B66  O11   C11  C13   111.14  3.000
 B66  HO11  O11  C11   110.22  3.000
 B66  H12B  C12  H12A  107.88  3.000
 B66  H12B  C12  H12   108.15  3.000
 B66  H12A  C12  H12   107.75  3.000
 B66  H12B  C12  C11   111.28  3.000
 B66  H12A  C12  C11   111.16  3.000
 B66  H12   C12  C11   110.49  3.000
 B66  H15   C10  N9    109.30  3.000
 B66  H15   C10  O10   104.92  3.000
 B66  N9    C10  O10   112.61  3.000
 B66  H15   C10  C11   107.61  3.000
 B66  N9    C10  C11   108.86  3.000
 B66  O10   C10  C11   113.31  3.000
 B66  H16   O10  C10   109.63  3.000
 B66  HN9   N9   C6    117.15  3.000
 B66  HN9   N9   C10   116.73  3.000
 B66  C6    N9   C10   124.71  3.000
 B66  C1    C6   C5    118.29  3.000
 B66  C1    C6   N9    123.11  3.000
 B66  C5    C6   N9    118.59  3.000
 B66  H5    C5   C4    120.51  3.000
 B66  H5    C5   C6    118.36  3.000
 B66  C4    C5   C6    121.13  3.000
 B66  H1    C1   C2    118.41  3.000
 B66  H1    C1   C6    121.36  3.000
 B66  C2    C1   C6    120.23  3.000
 B66  H2    C2   C3    119.38  3.000
 B66  H2    C2   C1    119.19  3.000
 B66  C3    C2   C1    121.42  3.000
 B66  C4    C3   C8    122.49  3.000
 B66  C4    C3   C2    118.58  3.000
 B66  C8    C3   C2    118.93  3.000
 B66  N8    C8   C3    180.00  3.000
 B66  C7    C4   C3    119.34  3.000
 B66  C7    C4   C5    120.32  3.000
 B66  C3    C4   C5    120.34  3.000
 B66  F1    C7   F3    106.87  3.000
 B66  F1    C7   F2    107.22  3.000
 B66  F3    C7   F2    107.26  3.000
 B66  F1    C7   C4    111.20  3.000
 B66  F3    C7   C4    111.20  3.000
 B66  F2    C7   C4    112.79  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
 B66  CONST_01  C20  C21  C18  C17    0.00   0.0  0
 B66  CONST_02  C20  C19  C16  C17    0.00   0.0  0
 B66  CONST_03  C19  C16  C17  C18    0.00   0.0  0
 B66  CONST_04  C19  C20  C21  C18    0.00   0.0  0
 B66  CONST_05  C16  C17  C18  C21    0.00   0.0  0
 B66  CONST_06  C16  C19  C20  C21    0.00   0.0  0
 B66  CONST_07  C3   C4   C5   C6     0.00   0.0  0
 B66  CONST_08  C3   C2   C1   C6     0.00   0.0  0
 B66  CONST_09  C2   C1   C6   C5     0.00   0.0  0
 B66  CONST_10  C2   C3   C4   C5     0.00   0.0  0
 B66  CONST_11  C4   C5   C6   C1     0.00   0.0  0
 B66  CONST_12  C4   C3   C2   C1     0.00   0.0  0
 B66  CONST_13  N19  C21  C18  C17  180.00   0.0  0
 B66  CONST_14  O14  C16  C17  C18  180.00   0.0  0
 B66  CONST_15  C19  C20  C21  N19  180.00   0.0  0
 B66  CONST_16  O14  C16  C19  C20  180.00   0.0  0
 B66  CONST_17  C4   C5   C6   N9   180.00   0.0  0
 B66  CONST_18  C2   C1   C6   N9   180.00   0.0  0
 B66  CONST_19  C7   C4   C5   C6   180.00   0.0  0
 B66  CONST_20  C8   C3   C4   C5   180.00   0.0  0
 B66  CONST_21  C8   C3   C2   C1   180.00   0.0  0
 B66  CONST_22  C7   C4   C3   C2   180.00   0.0  0
 B66  CONST_23  H19  C19  C16  C17  180.00   0.0  0
 B66  CONST_24  H20  C20  C21  C18  180.00   0.0  0
 B66  CONST_25  H17  C17  C18  C21  180.00   0.0  0
 B66  CONST_26  H18  C18  C21  C20  180.00   0.0  0
 B66  CONST_27  H2   C2   C1   C6   180.00   0.0  0
 B66  CONST_28  H1   C1   C6   C5   180.00   0.0  0
 B66  CONST_29  H5   C5   C6   C1   180.00   0.0  0
 B66  CONST_30  O20  N19  C21  C18    0.00   0.0  0
 B66  CONST_31  O19  N19  C21  C18  180.00   0.0  0
 B66  CONST_32  C20  C21  N19  O20  180.00   0.0  0
 B66  CONST_33  C20  C21  N19  O19    0.00   0.0  0
 B66  CONST_34  C5   C6   N9   C10  180.00   0.0  0
 B66  CONST_35  C1   C6   N9   C10    0.00   0.0  0
 B66  CONST_36  HN9  N9   C6   C5     0.00   0.0  0
 B66  Var_01    F2   C7   C4   C5    -0.46  30.0  2
 B66  Var_02    C11  C13  O14  C16  178.73  30.0  3

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
 B66  chir_01  C11  O11  C12  C10  positiv
 B66  chir_02  C10  O10  N9   C11  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
 B66  plan-1  C17  0.020
 B66  plan-1  C18  0.020
 B66  plan-1  C21  0.020
 B66  plan-1  N19  0.020
 B66  plan-1  C20  0.020
 B66  plan-1  C19  0.020
 B66  plan-1  C16  0.020
 B66  plan-1  O14  0.020
 B66  plan-1  H17  0.020
 B66  plan-1  H18  0.020
 B66  plan-1  H20  0.020
 B66  plan-1  H19  0.020
 B66  plan-2  N9   0.020
 B66  plan-2  C6   0.020
 B66  plan-2  C5   0.020
 B66  plan-2  C1   0.020
 B66  plan-2  C2   0.020
 B66  plan-2  C3   0.020
 B66  plan-2  C8   0.020
 B66  plan-2  N8   0.020
 B66  plan-2  C4   0.020
 B66  plan-2  C7   0.020
 B66  plan-2  H5   0.020
 B66  plan-2  H1   0.020
 B66  plan-2  H2   0.020
 B66  plan-3  C21  0.020
 B66  plan-3  N19  0.020
 B66  plan-3  O20  0.020
 B66  plan-3  O19  0.020
 B66  plan-4  C10  0.020
 B66  plan-4  N9   0.020
 B66  plan-4  C6   0.020
 B66  plan-4  HN9  0.020

