# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 00:16:48 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (2~{R})-2-acetamido-2-(4-ethylsulfonylphenyl)-~{N}-[4-[1,1,1,3,3,3-hexakis(fluoranyl)-2-oxidanyl-propan-2-yl]phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[S](=O)(=O)c1ccc(cc1)[C@@H](NC(C)=O)C(=O)Nc2ccc(cc2)C(O)(C(F)(F)F)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
 JUN  JUN  (2~{R})-2-acetamido-2-(4-ethylsulfonylphenyl)-~{N}-[4-[1,1,1,3,3,3-hexakis(fluoranyl)-2-oxidanyl-propan-2-yl]phenyl]ethanamide  ligand  55  35  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JUN
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
 JUN  C1   C  CH3   0  -0.677  -5.0061   5.0928  -0.2027
 JUN  C2   C  CH2   0  -0.546  -4.3674   3.7197  -0.0838
 JUN  O4   O  OS    0  -0.690  -6.3280   2.6382   1.3248
 JUN  O5   O  OS    0  -0.582  -6.4053   2.4383  -1.1807
 JUN  C7   C  CR16  0  -0.157  -4.3086   0.4485   1.3794
 JUN  C8   C  CR16  0  -0.294  -3.5638  -0.7194   1.4296
 JUN  C9   C  CR6   0   0.127  -3.2045  -1.3798   0.2624
 JUN  C10  C  CR16  0  -0.246  -3.6093  -0.8718  -0.9681
 JUN  C11  C  CR16  0  -0.208  -4.3572   0.2900  -1.0339
 JUN  C12  C  CH1   0  -0.368  -2.3434  -2.6268   0.3177
 JUN  C16  C  CH3   0  -0.784  -4.3669  -5.4625  -1.1143
 JUN  C20  C  CR6   0   0.340   1.0861  -1.0656   0.5790
 JUN  C21  C  CR16  0  -0.309   1.7412  -0.6707   1.7433
 JUN  C22  C  CR16  0  -0.252   3.0131  -0.1347   1.6939
 JUN  C24  C  CR16  0  -0.192   3.0086  -0.3531  -0.6796
 JUN  C32  C  CT    0   1.025   6.0182  -0.0396  -0.5483
 JUN  S3   S  S     0   1.183  -5.6260   2.4517   0.0562
 JUN  C6   C  CR6   0  -0.219  -4.6945   0.9446   0.1433
 JUN  N13  N  NH1   0  -0.570  -2.8484  -3.6919  -0.4960
 JUN  O15  O  O     0  -0.416  -4.5525  -4.1631   0.8911
 JUN  C17  C  C     0   0.631  -0.9463  -2.2557  -0.1911
 JUN  O18  O  O     0  -0.489  -0.5992  -2.5147  -1.3246
 JUN  N19  N  NH1   0  -0.654  -0.1991  -1.5945   0.7207
 JUN  C23  C  CR6   0  -0.077   3.6797   0.0190   0.4812
 JUN  C25  C  CR16  0  -0.326   1.7337  -0.8938  -0.6419
 JUN  C26  C  CT    0  -0.134   5.0790   0.6224   0.4972
 JUN  O27  O  OH1   0  -0.655   5.6966   0.5021   1.7376
 JUN  C28  C  CT    0   1.093   4.9634   2.1471   0.2760
 JUN  F29  F  F     0  -0.233   4.3541   2.4314  -0.8734
 JUN  F30  F  F     0  -0.318   4.2475   2.6890   1.2581
 JUN  F31  F  F     0  -0.382   6.1510   2.7508   0.2665
 JUN  F33  F  F     0  -0.347   5.7000   0.2431  -1.8134
 JUN  F34  F  F     0  -0.321   7.2820   0.3327  -0.3725
 JUN  F35  F  F     0  -0.308   5.9703  -1.3651  -0.4016
 JUN  H1   H  HCH3  0   0.253  -4.2188   5.8392  -0.2902
 JUN  H2   H  HCH3  0   0.237  -5.6360   5.1677  -1.0872
 JUN  H3   H  HCH3  0   0.265  -5.6012   5.3365   0.6754
 JUN  H4   H  HCH2  0   0.307  -3.7631   3.4764  -0.9590
 JUN  H5   H  HCH2  0   0.248  -3.7354   3.6382   0.8014
 JUN  H6   H  HCR6  0   0.282  -4.5875   0.9487   2.2966
 JUN  H7   H  HCR6  0   0.263  -3.2779  -1.1211   2.3937
 JUN  H8   H  HCR6  0   0.264  -3.3504  -1.3827  -1.8863
 JUN  H9   H  HCR6  0   0.287  -4.6682   0.6751  -1.9952
 JUN  H10  H  HCH1  0   0.283  -2.2744  -2.9641   1.3571
 JUN  H11  H  HCH3  0   0.284  -4.4399  -6.4160  -0.5934
 JUN  H12  H  HCH3  0   0.217  -5.3566  -5.2272  -1.5051
 JUN  H13  H  HCH3  0   0.300  -3.6869  -5.5784  -1.9555
 JUN  H14  H  HCR6  0   0.280   1.2567  -0.7830   2.7053
 JUN  H15  H  HCR6  0   0.282   3.4681   0.1617   2.6282
 JUN  H16  H  HCR6  0   0.300   3.4516  -0.2323  -1.6560
 JUN  H17  H  HNH1  0   0.393  -2.3711  -3.8888  -1.3619
 JUN  H18  H  HNH1  0   0.417  -0.5826  -1.5212   1.6508
 JUN  H19  H  HCR6  0   0.281   1.2631  -1.1650  -1.5716
 JUN  H20  H  HOH1  0   0.481   5.6082  -0.4005   2.0662
 JUN  C14  C  C     0   0.430  -3.9471  -4.3903  -0.1437

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
 JUN  F29  C28  single    1.332  0.020  1.332
 JUN  F31  C28  single    1.332  0.020  1.332
 JUN  O4   S3   double    1.462  0.020  1.462
 JUN  F30  C28  single    1.331  0.020  1.331
 JUN  C1   C2   single    1.519  0.020  1.519
 JUN  C28  C26  single    1.545  0.020  1.545
 JUN  C2   S3   single    1.792  0.020  1.792
 JUN  S3   O5   double    1.462  0.020  1.462
 JUN  S3   C6   single    1.774  0.020  1.774
 JUN  F35  C32  single    1.334  0.020  1.334
 JUN  F34  C32  single    1.329  0.020  1.329
 JUN  C26  C32  single    1.554  0.020  1.554
 JUN  C26  C23  single    1.524  0.020  1.524
 JUN  C26  O27  single    1.391  0.020  1.391
 JUN  C7   C6   aromatic  1.387  0.020  1.387
 JUN  C7   C8   aromatic  1.386  0.020  1.386
 JUN  C22  C23  aromatic  1.392  0.020  1.392
 JUN  C22  C21  aromatic  1.381  0.020  1.381
 JUN  C32  F33  single    1.335  0.020  1.335
 JUN  C6   C11  aromatic  1.389  0.020  1.389
 JUN  C23  C24  aromatic  1.392  0.020  1.392
 JUN  C21  C20  aromatic  1.393  0.020  1.393
 JUN  C8   C9   aromatic  1.388  0.020  1.388
 JUN  C24  C25  aromatic  1.385  0.020  1.385
 JUN  C20  C25  aromatic  1.393  0.020  1.393
 JUN  C20  N19  single    1.397  0.020  1.397
 JUN  C11  C10  aromatic  1.383  0.020  1.383
 JUN  N19  C17  single    1.352  0.020  1.352
 JUN  C9   C10  aromatic  1.391  0.020  1.391
 JUN  C9   C12  single    1.516  0.020  1.516
 JUN  C17  O18  double    1.213  0.020  1.213
 JUN  C17  C12  single    1.532  0.020  1.532
 JUN  C12  N13  single    1.432  0.020  1.432
 JUN  N13  C14  single    1.349  0.020  1.349
 JUN  O15  C14  double    1.220  0.020  1.220
 JUN  C14  C16  single    1.506  0.020  1.506
 JUN  C1   H1   single    0.970  0.020  1.090
 JUN  C1   H2   single    0.970  0.020  1.090
 JUN  C1   H3   single    0.970  0.020  1.090
 JUN  C2   H4   single    0.970  0.020  1.090
 JUN  C2   H5   single    0.970  0.020  1.090
 JUN  C7   H6   single    0.930  0.020  1.080
 JUN  C8   H7   single    0.930  0.020  1.080
 JUN  C10  H8   single    0.930  0.020  1.080
 JUN  C11  H9   single    0.930  0.020  1.080
 JUN  C12  H10  single    0.970  0.020  1.090
 JUN  C16  H11  single    0.970  0.020  1.090
 JUN  C16  H12  single    0.970  0.020  1.090
 JUN  C16  H13  single    0.970  0.020  1.090
 JUN  C21  H14  single    0.930  0.020  1.080
 JUN  C22  H15  single    0.930  0.020  1.080
 JUN  C24  H16  single    0.930  0.020  1.080
 JUN  N13  H17  single    0.860  0.020  1.020
 JUN  N19  H18  single    0.860  0.020  1.020
 JUN  C25  H19  single    0.930  0.020  1.080
 JUN  O27  H20  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
 JUN  H3   C1   H2   108.89  3.000
 JUN  H3   C1   H1   107.87  3.000
 JUN  H2   C1   H1   107.82  3.000
 JUN  H3   C1   C2   111.67  3.000
 JUN  H2   C1   C2   111.66  3.000
 JUN  H1   C1   C2   108.79  3.000
 JUN  H5   C2   H4   108.27  3.000
 JUN  H5   C2   S3   106.90  3.000
 JUN  H4   C2   S3   107.08  3.000
 JUN  H5   C2   C1   112.01  3.000
 JUN  H4   C2   C1   111.83  3.000
 JUN  S3   C2   C1   110.51  3.000
 JUN  H6   C7   C6   121.26  3.000
 JUN  H6   C7   C8   119.84  3.000
 JUN  C6   C7   C8   118.90  3.000
 JUN  H7   C8   C9   120.25  3.000
 JUN  H7   C8   C7   119.12  3.000
 JUN  C9   C8   C7   120.62  3.000
 JUN  C12  C9   C10  119.85  3.000
 JUN  C12  C9   C8   120.49  3.000
 JUN  C10  C9   C8   119.64  3.000
 JUN  H8   C10  C11  119.04  3.000
 JUN  H8   C10  C9   120.56  3.000
 JUN  C11  C10  C9   120.40  3.000
 JUN  H9   C11  C6   121.06  3.000
 JUN  H9   C11  C10  119.80  3.000
 JUN  C6   C11  C10  119.14  3.000
 JUN  H10  C12  C17  109.41  3.000
 JUN  H10  C12  N13  109.42  3.000
 JUN  C17  C12  N13  108.23  3.000
 JUN  H10  C12  C9   108.89  3.000
 JUN  N13  C12  C9   112.99  3.000
 JUN  C17  C12  C9   107.84  3.000
 JUN  H13  C16  H12  108.27  3.000
 JUN  H13  C16  H11  108.57  3.000
 JUN  H12  C16  H11  107.44  3.000
 JUN  H13  C16  C14  113.57  3.000
 JUN  H12  C16  C14  109.30  3.000
 JUN  H11  C16  C14  109.50  3.000
 JUN  C25  C20  N19  124.29  3.000
 JUN  N19  C20  C21  117.08  3.000
 JUN  C25  C20  C21  118.62  3.000
 JUN  H14  C21  C22  118.94  3.000
 JUN  H14  C21  C20  120.18  3.000
 JUN  C22  C21  C20  120.88  3.000
 JUN  H15  C22  C23  121.41  3.000
 JUN  H15  C22  C21  117.60  3.000
 JUN  C23  C22  C21  120.99  3.000
 JUN  H16  C24  C25  116.50  3.000
 JUN  H16  C24  C23  121.80  3.000
 JUN  C25  C24  C23  121.70  3.000
 JUN  F35  C32  F34  107.33  3.000
 JUN  F34  C32  F33  107.02  3.000
 JUN  F35  C32  F33  107.82  3.000
 JUN  F33  C32  C26  113.79  3.000
 JUN  F34  C32  C26  111.50  3.000
 JUN  F35  C32  C26  109.12  3.000
 JUN  C6   S3   O5   108.28  3.000
 JUN  C6   S3   O4   108.54  3.000
 JUN  O5   S3   O4   118.65  3.000
 JUN  C6   S3   C2   103.66  3.000
 JUN  O5   S3   C2   108.35  3.000
 JUN  O4   S3   C2   108.35  3.000
 JUN  S3   C6   C11  119.11  3.000
 JUN  C11  C6   C7   121.29  3.000
 JUN  S3   C6   C7   119.59  3.000
 JUN  H17  N13  C14  120.59  3.000
 JUN  H17  N13  C12  117.80  3.000
 JUN  C14  N13  C12  121.59  3.000
 JUN  N19  C17  O18  125.20  3.000
 JUN  O18  C17  C12  121.28  3.000
 JUN  N19  C17  C12  113.48  3.000
 JUN  H18  N19  C17  116.58  3.000
 JUN  H18  N19  C20  114.57  3.000
 JUN  C17  N19  C20  128.71  3.000
 JUN  C26  C23  C24  123.88  3.000
 JUN  C24  C23  C22  117.79  3.000
 JUN  C26  C23  C22  118.31  3.000
 JUN  H19  C25  C24  118.50  3.000
 JUN  H19  C25  C20  121.51  3.000
 JUN  C24  C25  C20  119.99  3.000
 JUN  C28  C26  O27  104.26  3.000
 JUN  O27  C26  C23  112.51  3.000
 JUN  C28  C26  C23  108.70  3.000
 JUN  O27  C26  C32  107.15  3.000
 JUN  C23  C26  C32  112.30  3.000
 JUN  C28  C26  C32  111.68  3.000
 JUN  H20  O27  C26  110.13  3.000
 JUN  F31  C28  F30  107.48  3.000
 JUN  F30  C28  F29  107.69  3.000
 JUN  F31  C28  F29  107.76  3.000
 JUN  F30  C28  C26  109.66  3.000
 JUN  F31  C28  C26  112.43  3.000
 JUN  F29  C28  C26  111.62  3.000
 JUN  O15  C14  N13  121.96  3.000
 JUN  O15  C14  C16  122.74  3.000
 JUN  N13  C14  C16  115.30  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
 JUN  CONST_01  C10  C11  C6   C7      0.00   0.0  0
 JUN  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 JUN  CONST_03  C11  C6   C7   C8      0.00   0.0  0
 JUN  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 JUN  CONST_05  C6   C7   C8   C9      0.00   0.0  0
 JUN  CONST_06  C6   C11  C10  C9      0.00   0.0  0
 JUN  CONST_07  C23  C22  C21  C20     0.00   0.0  0
 JUN  CONST_08  C23  C24  C25  C20     0.00   0.0  0
 JUN  CONST_09  C24  C23  C22  C21     0.00   0.0  0
 JUN  CONST_10  C24  C25  C20  C21     0.00   0.0  0
 JUN  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 JUN  CONST_12  C25  C20  C21  C22     0.00   0.0  0
 JUN  CONST_13  C12  C9   C8   C7    180.00   0.0  0
 JUN  CONST_14  S3   C6   C7   C8    180.00   0.0  0
 JUN  CONST_15  S3   C6   C11  C10   180.00   0.0  0
 JUN  CONST_16  C12  C9   C10  C11   180.00   0.0  0
 JUN  CONST_17  C26  C23  C22  C21   180.00   0.0  0
 JUN  CONST_18  N19  C20  C21  C22   180.00   0.0  0
 JUN  CONST_19  N19  C20  C25  C24   180.00   0.0  0
 JUN  CONST_20  C26  C23  C24  C25   180.00   0.0  0
 JUN  CONST_21  H9   C11  C6   C7    180.00   0.0  0
 JUN  CONST_22  H8   C10  C9   C8    180.00   0.0  0
 JUN  CONST_23  H6   C7   C8   C9    180.00   0.0  0
 JUN  CONST_24  H7   C8   C9   C10   180.00   0.0  0
 JUN  CONST_25  H15  C22  C21  C20   180.00   0.0  0
 JUN  CONST_26  H16  C24  C25  C20   180.00   0.0  0
 JUN  CONST_27  H19  C25  C20  C21   180.00   0.0  0
 JUN  CONST_28  H14  C21  C22  C23   180.00   0.0  0
 JUN  CONST_29  C17  N19  C20  C21   180.00   0.0  0
 JUN  CONST_30  C25  C20  N19  C17     0.00   0.0  0
 JUN  CONST_31  H18  N19  C20  C21     0.00   0.0  0
 JUN  CONST_32  C20  N19  C17  C12   180.00   0.0  0
 JUN  CONST_33  O18  C17  N19  C20     0.00   0.0  0
 JUN  CONST_34  O15  C14  N13  C12     0.00   0.0  0
 JUN  CONST_35  C16  C14  N13  C12   180.00   0.0  0
 JUN  CONST_36  H17  N13  C14  C16     0.00   0.0  0
 JUN  Var_01    C7   C6   S3   C2     90.72  30.0  2
 JUN  Var_02    C28  C26  C23  C22   -93.15  30.0  2
 JUN  Var_03    C6   S3   C2   C1    178.69  30.0  3
 JUN  Var_04    F29  C28  C26  C23   -58.30  30.0  3
 JUN  Var_05    F35  C32  C26  C23   -51.06  30.0  3
 JUN  Var_06    H1   C1   C2   S3   -179.76  30.0  3
 JUN  Var_07    H11  C16  C14  N13   125.13  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
 JUN  chir_01  C12  C9  C17  N13  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
 JUN  plan-1  C7   0.020
 JUN  plan-1  C8   0.020
 JUN  plan-1  C9   0.020
 JUN  plan-1  C10  0.020
 JUN  plan-1  C11  0.020
 JUN  plan-1  C12  0.020
 JUN  plan-1  S3   0.020
 JUN  plan-1  C6   0.020
 JUN  plan-1  H6   0.020
 JUN  plan-1  H7   0.020
 JUN  plan-1  H8   0.020
 JUN  plan-1  H9   0.020
 JUN  plan-2  C20  0.020
 JUN  plan-2  C21  0.020
 JUN  plan-2  C22  0.020
 JUN  plan-2  C24  0.020
 JUN  plan-2  N19  0.020
 JUN  plan-2  C23  0.020
 JUN  plan-2  C25  0.020
 JUN  plan-2  C26  0.020
 JUN  plan-2  H14  0.020
 JUN  plan-2  H15  0.020
 JUN  plan-2  H16  0.020
 JUN  plan-2  H19  0.020
 JUN  plan-3  C12  0.020
 JUN  plan-3  C20  0.020
 JUN  plan-3  C17  0.020
 JUN  plan-3  O18  0.020
 JUN  plan-3  N19  0.020
 JUN  plan-3  H18  0.020
 JUN  plan-4  C12  0.020
 JUN  plan-4  C16  0.020
 JUN  plan-4  N13  0.020
 JUN  plan-4  O15  0.020
 JUN  plan-4  H17  0.020
 JUN  plan-4  C14  0.020

