# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 14:41:15 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2S)-3-(4-chloro-3-fluorophenoxy)-N-[4-cyano-3-(trifluoromethyl)phenyl]-2-hydroxy-2-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(COc1ccc(Cl)c(F)c1)C(=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
 B5R  B5R  (2S)-3-(4-chloro-3-fluorophenoxy)-N-[4-cyano-3-(trifluoromethyl)phenyl]-2-hydroxy-2-methylpropanamide  ligand  41  28  .  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_B5R
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
 B5R  C21   C   CR16  0  -0.508  -5.4128  -1.2826   0.1737
 B5R  C20   C   CR6   0   0.625  -6.6828  -0.7958   0.3728
 B5R  F20   F   F     0  -0.294  -7.6777  -1.6514   0.6130
 B5R  C19   C   CR6   0  -0.252  -6.9599   0.5632   0.3317
 B5R  CL19  CL  CL    0  -0.099  -8.5714   1.1173   0.5916
 B5R  C18   C   CR16  0  -0.192  -5.9235   1.4431   0.0812
 B5R  C17   C   CR16  0  -0.394  -4.6307   0.9798  -0.1239
 B5R  C16   C   CR6   0   0.421  -4.3709  -0.3879  -0.0768
 B5R  O14   O   O2    0  -0.469  -3.1616  -0.9409  -0.2567
 B5R  C13   C   CH2   0  -0.192  -2.0567  -0.1022  -0.5163
 B5R  C11   C   CT    0   0.046  -0.8256  -1.0014  -0.6386
 B5R  O11   O   OH1   0  -0.653  -0.6175  -1.7471   0.5357
 B5R  C12   C   CH3   0  -0.661  -0.9555  -2.0006  -1.7871
 B5R  C10   C   C     0   0.540   0.3813  -0.1000  -0.9598
 B5R  O10   O   O     0  -0.444   0.2920   0.8318  -1.7336
 B5R  N9    N   NH1   0  -0.748   1.5264  -0.4867  -0.3416
 B5R  C6    C   CR6   0   0.446   2.8032   0.0331  -0.4701
 B5R  C5    C   CR16  0  -0.417   3.8222  -0.6520   0.2055
 B5R  C1    C   CR16  0  -0.300   3.1231   1.1707  -1.2104
 B5R  C2    C   CR16  0  -0.230   4.4364   1.5997  -1.2695
 B5R  C3    C   CR6   0   0.028   5.4494   0.9191  -0.6037
 B5R  C8    C   CSP   0   0.016   6.7845   1.4064  -0.7063
 B5R  N8    N   NS    0  -0.238   7.8542   1.8256  -0.7913
 B5R  C4    C   CR6   0  -0.151   5.1272  -0.2220   0.1431
 B5R  C7    C   CT    0   1.079   6.2113  -0.9714   0.8622
 B5R  F2    F   F     0  -0.291   5.7443  -2.0173   1.5406
 B5R  F1    F   F     0  -0.310   7.1304  -1.4289   0.0041
 B5R  F3    F   F     0  -0.310   6.8496  -0.1818   1.7332
 B5R  H21   H   HCR6  0   0.298  -5.2275  -2.3487   0.2111
 B5R  H18   H   HCR6  0   0.294  -6.1191   2.5061   0.0455
 B5R  H17   H   HCR6  0   0.296  -3.8505   1.7028  -0.3151
 B5R  H13   H   HCH2  0   0.255  -2.2039   0.4662  -1.4378
 B5R  H13A  H   HCH2  0   0.257  -1.9147   0.6139   0.3035
 B5R  HO11  H   HOH1  0   0.464  -0.7292  -1.1810   1.3092
 B5R  H12   H   HCH3  0   0.248  -1.0915  -1.4850  -2.7364
 B5R  H12A  H   HCH3  0   0.254  -0.0581  -2.6160  -1.8605
 B5R  H12B  H   HCH3  0   0.260  -1.8068  -2.6609  -1.6294
 B5R  HN9   H   HNH1  0   0.427   1.4320  -1.2857   0.2721
 B5R  H5    H   HCR6  0   0.301   3.5648  -1.5339   0.7768
 B5R  H1    H   HCR6  0   0.306   2.3675   1.7253  -1.7398
 B5R  H2    H   HCR6  0   0.296   4.6764   2.4832  -1.8445

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
 B5R  C21  C20   aromatic  1.375  0.020  1.375
 B5R  C21  C16   aromatic  1.396  0.020  1.396
 B5R  C20  F20   single    1.334  0.020  1.334
 B5R  C20  C19   aromatic  1.388  0.020  1.388
 B5R  C19  CL19  single    1.724  0.020  1.724
 B5R  C19  C18   aromatic  1.382  0.020  1.382
 B5R  C18  C17   aromatic  1.389  0.020  1.389
 B5R  C17  C16   aromatic  1.393  0.020  1.393
 B5R  C16  O14   single    1.342  0.020  1.342
 B5R  O14  C13   single    1.411  0.020  1.411
 B5R  C13  C11   single    1.529  0.020  1.529
 B5R  C11  O11   single    1.407  0.020  1.407
 B5R  C11  C12   single    1.528  0.020  1.528
 B5R  C11  C10   single    1.540  0.020  1.540
 B5R  C10  O10   double    1.215  0.020  1.215
 B5R  C10  N9    single    1.358  0.020  1.358
 B5R  N9   C6    single    1.385  0.020  1.385
 B5R  C6   C5    aromatic  1.402  0.020  1.402
 B5R  C6   C1    aromatic  1.394  0.020  1.394
 B5R  C5   C4    aromatic  1.375  0.020  1.375
 B5R  C1   C2    aromatic  1.383  0.020  1.383
 B5R  C2   C3    aromatic  1.390  0.020  1.390
 B5R  C3   C8    single    1.425  0.020  1.425
 B5R  C3   C4    aromatic  1.401  0.020  1.401
 B5R  C8   N8    triple    1.152  0.020  1.152
 B5R  C4   C7    single    1.501  0.020  1.501
 B5R  C7   F2    single    1.331  0.020  1.331
 B5R  C7   F1    single    1.338  0.020  1.338
 B5R  C7   F3    single    1.338  0.020  1.338
 B5R  C21  H21   single    0.930  0.020  1.080
 B5R  C18  H18   single    0.930  0.020  1.080
 B5R  C17  H17   single    0.930  0.020  1.080
 B5R  C13  H13   single    0.970  0.020  1.090
 B5R  C13  H13A  single    0.970  0.020  1.090
 B5R  O11  HO11  single    0.850  0.020  0.980
 B5R  C12  H12   single    0.970  0.020  1.090
 B5R  C12  H12A  single    0.970  0.020  1.090
 B5R  C12  H12B  single    0.970  0.020  1.090
 B5R  N9   HN9   single    0.860  0.020  1.020
 B5R  C5   H5    single    0.930  0.020  1.080
 B5R  C1   H1    single    0.930  0.020  1.080
 B5R  C2   H2    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
 B5R  H21   C21  C16   120.63  3.000
 B5R  H21   C21  C20   120.12  3.000
 B5R  C16   C21  C20   119.25  3.000
 B5R  C19   C20  F20   118.98  3.000
 B5R  C19   C20  C21   121.81  3.000
 B5R  F20   C20  C21   119.21  3.000
 B5R  C18   C19  CL19  121.57  3.000
 B5R  C18   C19  C20   118.62  3.000
 B5R  CL19  C19  C20   119.81  3.000
 B5R  H18   C18  C17   119.44  3.000
 B5R  H18   C18  C19   119.74  3.000
 B5R  C17   C18  C19   120.82  3.000
 B5R  H17   C17  C16   121.88  3.000
 B5R  H17   C17  C18   118.37  3.000
 B5R  C16   C17  C18   119.76  3.000
 B5R  O14   C16  C17   124.63  3.000
 B5R  O14   C16  C21   115.63  3.000
 B5R  C17   C16  C21   119.74  3.000
 B5R  C13   O14  C16   119.03  3.000
 B5R  H13A  C13  H13   107.94  3.000
 B5R  H13A  C13  C11   109.83  3.000
 B5R  H13   C13  C11   110.29  3.000
 B5R  H13A  C13  O14   110.59  3.000
 B5R  H13   C13  O14   111.02  3.000
 B5R  C11   C13  O14   107.19  3.000
 B5R  C10   C11  C12   107.01  3.000
 B5R  C10   C11  O11   111.62  3.000
 B5R  C12   C11  O11   107.06  3.000
 B5R  C10   C11  C13   107.66  3.000
 B5R  C12   C11  C13   112.10  3.000
 B5R  O11   C11  C13   111.35  3.000
 B5R  HO11  O11  C11   109.94  3.000
 B5R  H12B  C12  H12A  108.11  3.000
 B5R  H12B  C12  H12   108.41  3.000
 B5R  H12A  C12  H12   108.14  3.000
 B5R  H12B  C12  C11   110.74  3.000
 B5R  H12A  C12  C11   110.47  3.000
 B5R  H12   C12  C11   110.87  3.000
 B5R  N9    C10  O10   124.80  3.000
 B5R  N9    C10  C11   113.53  3.000
 B5R  O10   C10  C11   121.62  3.000
 B5R  HN9   N9   C6    116.02  3.000
 B5R  HN9   N9   C10   114.99  3.000
 B5R  C6    N9   C10   128.95  3.000
 B5R  C1    C6   C5    119.20  3.000
 B5R  C1    C6   N9    124.55  3.000
 B5R  C5    C6   N9    116.24  3.000
 B5R  H5    C5   C4    120.30  3.000
 B5R  H5    C5   C6    118.69  3.000
 B5R  C4    C5   C6    121.01  3.000
 B5R  H1    C1   C2    119.06  3.000
 B5R  H1    C1   C6    121.36  3.000
 B5R  C2    C1   C6    119.58  3.000
 B5R  H2    C2   C3    119.54  3.000
 B5R  H2    C2   C1    119.15  3.000
 B5R  C3    C2   C1    121.31  3.000
 B5R  C4    C3   C8    122.16  3.000
 B5R  C4    C3   C2    119.10  3.000
 B5R  C8    C3   C2    118.74  3.000
 B5R  N8    C8   C3    180.00  3.000
 B5R  C7    C4   C3    119.72  3.000
 B5R  C7    C4   C5    120.49  3.000
 B5R  C3    C4   C5    119.80  3.000
 B5R  F3    C7   F1    106.95  3.000
 B5R  F3    C7   F2    107.42  3.000
 B5R  F1    C7   F2    107.41  3.000
 B5R  F3    C7   C4    111.21  3.000
 B5R  F1    C7   C4    111.07  3.000
 B5R  F2    C7   C4    112.52  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
 B5R  CONST_01  C18   C19  C20  C21     0.00   0.0  0
 B5R  CONST_02  C18   C17  C16  C21     0.00   0.0  0
 B5R  CONST_03  C17   C16  C21  C20     0.00   0.0  0
 B5R  CONST_04  C17   C18  C19  C20     0.00   0.0  0
 B5R  CONST_05  C16   C21  C20  C19     0.00   0.0  0
 B5R  CONST_06  C16   C17  C18  C19     0.00   0.0  0
 B5R  CONST_07  C3    C4   C5   C6      0.00   0.0  0
 B5R  CONST_08  C3    C2   C1   C6      0.00   0.0  0
 B5R  CONST_09  C2    C1   C6   C5      0.00   0.0  0
 B5R  CONST_10  C2    C3   C4   C5      0.00   0.0  0
 B5R  CONST_11  C4    C5   C6   C1      0.00   0.0  0
 B5R  CONST_12  C4    C3   C2   C1      0.00   0.0  0
 B5R  CONST_13  CL19  C19  C20  C21   180.00   0.0  0
 B5R  CONST_14  O14   C16  C21  C20   180.00   0.0  0
 B5R  CONST_15  C16   C21  C20  F20   180.00   0.0  0
 B5R  CONST_16  C18   C19  C20  F20   180.00   0.0  0
 B5R  CONST_17  C17   C18  C19  CL19  180.00   0.0  0
 B5R  CONST_18  O14   C16  C17  C18   180.00   0.0  0
 B5R  CONST_19  C4    C5   C6   N9    180.00   0.0  0
 B5R  CONST_20  C2    C1   C6   N9    180.00   0.0  0
 B5R  CONST_21  C7    C4   C5   C6    180.00   0.0  0
 B5R  CONST_22  C8    C3   C4   C5    180.00   0.0  0
 B5R  CONST_23  C8    C3   C2   C1    180.00   0.0  0
 B5R  CONST_24  C7    C4   C3   C2    180.00   0.0  0
 B5R  CONST_25  H17   C17  C16  C21   180.00   0.0  0
 B5R  CONST_26  H18   C18  C19  C20   180.00   0.0  0
 B5R  CONST_27  H21   C21  C20  C19   180.00   0.0  0
 B5R  CONST_28  H2    C2   C1   C6    180.00   0.0  0
 B5R  CONST_29  H1    C1   C6   C5    180.00   0.0  0
 B5R  CONST_30  H5    C5   C6   C1    180.00   0.0  0
 B5R  CONST_31  C5    C6   N9   C10   180.00   0.0  0
 B5R  CONST_32  C1    C6   N9   C10     0.00   0.0  0
 B5R  CONST_33  HN9   N9   C6   C5      0.00   0.0  0
 B5R  CONST_34  C6    N9   C10  C11   180.00   0.0  0
 B5R  CONST_35  C6    N9   C10  O10     0.00   0.0  0
 B5R  Var_01    F2    C7   C4   C5     -1.31  30.0  2
 B5R  Var_02    C11   C13  O14  C16   178.58  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
 B5R  chir_01  C11  O11  C12  C10  positiv

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
 B5R  plan-1  C21   0.020
 B5R  plan-1  C20   0.020
 B5R  plan-1  F20   0.020
 B5R  plan-1  C19   0.020
 B5R  plan-1  CL19  0.020
 B5R  plan-1  C18   0.020
 B5R  plan-1  C17   0.020
 B5R  plan-1  C16   0.020
 B5R  plan-1  O14   0.020
 B5R  plan-1  H21   0.020
 B5R  plan-1  H18   0.020
 B5R  plan-1  H17   0.020
 B5R  plan-2  N9    0.020
 B5R  plan-2  C6    0.020
 B5R  plan-2  C5    0.020
 B5R  plan-2  C1    0.020
 B5R  plan-2  C2    0.020
 B5R  plan-2  C3    0.020
 B5R  plan-2  C8    0.020
 B5R  plan-2  N8    0.020
 B5R  plan-2  C4    0.020
 B5R  plan-2  C7    0.020
 B5R  plan-2  H5    0.020
 B5R  plan-2  H1    0.020
 B5R  plan-2  H2    0.020
 B5R  plan-3  C11   0.020
 B5R  plan-3  C10   0.020
 B5R  plan-3  O10   0.020
 B5R  plan-3  N9    0.020
 B5R  plan-3  C6    0.020
 B5R  plan-3  HN9   0.020

