# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:14:37 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-[4-(difluoromethoxy)-3-{[(3S)-oxolan-3-yl]oxy}phenyl]-3-methylbutan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(=O)c1ccc(OC(F)F)c(O[C@H]2CCOC2)c1
#
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
 AKJ  AKJ  1-[4-(difluoromethoxy)-3-{[(3S)-oxolan-3-yl]oxy}phenyl]-3-methylbutan-1-one  ligand  42  22  .  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_AKJ
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
 AKJ  C1   C  CH1   0   0.671   2.9446  -2.1444  -0.6427
 AKJ  O2   O  O2    0  -0.467   2.1131   0.7414   0.7644
 AKJ  C3   C  CR6   0   0.374   0.9564   0.0916   0.5883
 AKJ  C4   C  CR16  0  -0.411  -0.3008   0.6776   0.5718
 AKJ  C5   C  CR6   0   0.010  -1.4512  -0.0996   0.4186
 AKJ  C6   C  CR16  0  -0.323  -1.3398  -1.4784   0.2899
 AKJ  C7   C  CR16  0  -0.287  -0.0869  -2.0749   0.3027
 AKJ  C8   C  CR15  0  -0.083   2.1385   2.1646   0.7953
 AKJ  C10  C  CH2   0  -0.150   4.2185   2.4335  -0.2873
 AKJ  C11  C  CH2   0  -0.515   3.5739   2.5649   1.0849
 AKJ  C14  C  CH1   0  -0.231  -5.3221   0.5248   0.0774
 AKJ  C16  C  CH3   0  -0.655  -6.5013  -0.4296   0.2425
 AKJ  F1   F  F     0  -0.333   2.2544  -3.0247  -1.4076
 AKJ  F2   F  F     0  -0.326   3.0682  -1.0317  -1.3984
 AKJ  O1   O  O2    0  -0.501   2.2891  -1.8893   0.5177
 AKJ  C2   C  CR6   0   0.255   1.0464  -1.3009   0.4434
 AKJ  O3   O  O     0  -0.500   3.2028   2.7770  -1.2201
 AKJ  C9   C  CH2   0  -0.160   1.9349   2.7744  -0.5877
 AKJ  O4   O  O     0  -0.394  -2.8307   1.7956   0.5797
 AKJ  C13  C  CH2   0  -0.574  -4.0167  -0.2461   0.2517
 AKJ  C15  C  CH3   0  -0.655  -5.3944   1.2228  -1.2777
 AKJ  H1   H  HCH1  0   0.216   3.9253  -2.5501  -0.4068
 AKJ  H2   H  HCR6  0   0.290  -0.4130   1.7473   0.6821
 AKJ  H3   H  HCR6  0   0.268  -2.2107  -2.1084   0.1811
 AKJ  H4   H  HCR6  0   0.282   0.0028  -3.1497   0.2241
 AKJ  H5   H  HCR5  0   0.276   1.4335   2.5491   1.5375
 AKJ  H6   H  HCH2  0   0.226   5.0698   3.1049  -0.4142
 AKJ  H7   H  HCH2  0   0.211   4.5662   1.4102  -0.4642
 AKJ  H8   H  HCH2  0   0.260   3.5901   3.6011   1.4272
 AKJ  H9   H  HCH2  0   0.268   4.0426   1.9476   1.8505
 AKJ  H10  H  HCH1  0   0.227  -5.3876   1.2819   0.8643
 AKJ  H11  H  HCH3  0   0.215  -6.4818  -1.2146  -0.5173
 AKJ  H12  H  HCH3  0   0.227  -6.4935  -0.9147   1.2203
 AKJ  H13  H  HCH3  0   0.230  -7.4495   0.1012   0.1444
 AKJ  H14  H  HCH2  0   0.237   1.2164   2.2233  -1.2009
 AKJ  H15  H  HCH2  0   0.224   1.5575   3.7975  -0.4766
 AKJ  H16  H  HCH2  0   0.281  -4.0788  -0.8878   1.1398
 AKJ  H17  H  HCH2  0   0.262  -3.8790  -0.9375  -0.5865
 AKJ  H18  H  HCH3  0   0.213  -5.3283   0.4961  -2.0913
 AKJ  H19  H  HCH3  0   0.227  -6.3425   1.7525  -1.3875
 AKJ  H20  H  HCH3  0   0.232  -4.5952   1.9509  -1.4131
 AKJ  C12  C  C     0   0.381  -2.7763   0.5947   0.4191

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
 AKJ  C16  C14  single    1.526  0.020  1.526
 AKJ  C14  C15  single    1.526  0.020  1.526
 AKJ  C14  C13  single    1.526  0.020  1.526
 AKJ  C13  C12  single    1.508  0.020  1.508
 AKJ  O4   C12  double    1.213  0.020  1.213
 AKJ  C12  C5   single    1.496  0.020  1.496
 AKJ  C5   C4   aromatic  1.397  0.020  1.397
 AKJ  C5   C6   aromatic  1.389  0.020  1.389
 AKJ  C4   C3   aromatic  1.387  0.020  1.387
 AKJ  C6   C7   aromatic  1.388  0.020  1.388
 AKJ  C11  C8   single    1.518  0.020  1.518
 AKJ  C11  C10  single    1.522  0.020  1.522
 AKJ  C8   O2   single    1.424  0.020  1.424
 AKJ  C8   C9   single    1.525  0.020  1.525
 AKJ  C3   O2   single    1.338  0.020  1.338
 AKJ  C3   C2   aromatic  1.403  0.020  1.403
 AKJ  C10  O3   single    1.421  0.020  1.421
 AKJ  C7   C2   aromatic  1.380  0.020  1.380
 AKJ  C9   O3   single    1.417  0.020  1.417
 AKJ  C2   O1   single    1.377  0.020  1.377
 AKJ  O1   C1   single    1.357  0.020  1.357
 AKJ  F2   C1   single    1.351  0.020  1.351
 AKJ  C1   F1   single    1.355  0.020  1.355
 AKJ  C1   H1   single    0.970  0.020  1.090
 AKJ  C4   H2   single    0.930  0.020  1.080
 AKJ  C6   H3   single    0.930  0.020  1.080
 AKJ  C7   H4   single    0.930  0.020  1.080
 AKJ  C8   H5   single    0.970  0.020  1.090
 AKJ  C10  H6   single    0.970  0.020  1.090
 AKJ  C10  H7   single    0.970  0.020  1.090
 AKJ  C11  H8   single    0.970  0.020  1.090
 AKJ  C11  H9   single    0.970  0.020  1.090
 AKJ  C14  H10  single    0.970  0.020  1.090
 AKJ  C16  H11  single    0.970  0.020  1.090
 AKJ  C16  H12  single    0.970  0.020  1.090
 AKJ  C16  H13  single    0.970  0.020  1.090
 AKJ  C9   H14  single    0.970  0.020  1.090
 AKJ  C9   H15  single    0.970  0.020  1.090
 AKJ  C13  H16  single    0.970  0.020  1.090
 AKJ  C13  H17  single    0.970  0.020  1.090
 AKJ  C15  H18  single    0.970  0.020  1.090
 AKJ  C15  H19  single    0.970  0.020  1.090
 AKJ  C15  H20  single    0.970  0.020  1.090

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
 AKJ  H1   C1   O1   108.69  3.000
 AKJ  H1   C1   F2   110.26  3.000
 AKJ  O1   C1   F2   111.58  3.000
 AKJ  H1   C1   F1   109.85  3.000
 AKJ  F2   C1   F1   105.42  3.000
 AKJ  O1   C1   F1   111.03  3.000
 AKJ  C8   O2   C3   120.24  3.000
 AKJ  C2   C3   C4   118.43  3.000
 AKJ  C2   C3   O2   116.11  3.000
 AKJ  C4   C3   O2   125.44  3.000
 AKJ  H2   C4   C5   118.44  3.000
 AKJ  H2   C4   C3   120.71  3.000
 AKJ  C5   C4   C3   120.85  3.000
 AKJ  C12  C5   C6   122.12  3.000
 AKJ  C6   C5   C4   119.76  3.000
 AKJ  C12  C5   C4   118.11  3.000
 AKJ  H3   C6   C7   118.56  3.000
 AKJ  H3   C6   C5   121.56  3.000
 AKJ  C7   C6   C5   119.88  3.000
 AKJ  H4   C7   C2   119.79  3.000
 AKJ  H4   C7   C6   120.10  3.000
 AKJ  C2   C7   C6   120.10  3.000
 AKJ  H5   C8   C9   112.88  3.000
 AKJ  H5   C8   C11  112.80  3.000
 AKJ  C9   C8   C11  101.17  3.000
 AKJ  H5   C8   O2   110.78  3.000
 AKJ  C9   C8   O2   112.18  3.000
 AKJ  C11  C8   O2   106.53  3.000
 AKJ  H7   C10  H6   107.96  3.000
 AKJ  H7   C10  O3   110.29  3.000
 AKJ  H6   C10  O3   109.41  3.000
 AKJ  H7   C10  C11  111.15  3.000
 AKJ  H6   C10  C11  112.46  3.000
 AKJ  O3   C10  C11  105.56  3.000
 AKJ  H9   C11  H8   108.12  3.000
 AKJ  H9   C11  C10  113.73  3.000
 AKJ  H8   C11  C10  111.01  3.000
 AKJ  H9   C11  C8   113.04  3.000
 AKJ  H8   C11  C8   108.92  3.000
 AKJ  C10  C11  C8   101.88  3.000
 AKJ  H10  C14  C15  108.62  3.000
 AKJ  H10  C14  C13  108.59  3.000
 AKJ  C15  C14  C13  111.90  3.000
 AKJ  H10  C14  C16  107.99  3.000
 AKJ  C13  C14  C16  109.44  3.000
 AKJ  C15  C14  C16  110.21  3.000
 AKJ  H13  C16  H12  107.64  3.000
 AKJ  H13  C16  H11  107.61  3.000
 AKJ  H12  C16  H11  107.66  3.000
 AKJ  H13  C16  C14  110.95  3.000
 AKJ  H12  C16  C14  111.67  3.000
 AKJ  H11  C16  C14  111.12  3.000
 AKJ  C2   O1   C1   118.04  3.000
 AKJ  O1   C2   C7   120.47  3.000
 AKJ  O1   C2   C3   118.45  3.000
 AKJ  C7   C2   C3   120.98  3.000
 AKJ  C9   O3   C10  110.25  3.000
 AKJ  H15  C9   H14  107.51  3.000
 AKJ  H15  C9   O3   110.59  3.000
 AKJ  H14  C9   O3   109.79  3.000
 AKJ  H15  C9   C8   109.10  3.000
 AKJ  H14  C9   C8   113.25  3.000
 AKJ  O3   C9   C8   106.62  3.000
 AKJ  H17  C13  H16  104.91  3.000
 AKJ  H17  C13  C12  109.48  3.000
 AKJ  H16  C13  C12  106.43  3.000
 AKJ  H17  C13  C14  109.82  3.000
 AKJ  H16  C13  C14  109.84  3.000
 AKJ  C12  C13  C14  115.77  3.000
 AKJ  H20  C15  H19  107.48  3.000
 AKJ  H20  C15  H18  107.90  3.000
 AKJ  H19  C15  H18  107.48  3.000
 AKJ  H20  C15  C14  112.41  3.000
 AKJ  H19  C15  C14  110.64  3.000
 AKJ  H18  C15  C14  110.74  3.000
 AKJ  C13  C12  O4   122.00  3.000
 AKJ  O4   C12  C5   119.96  3.000
 AKJ  C13  C12  C5   118.02  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
 AKJ  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 AKJ  CONST_02  C6   C7   C2   C3      0.00   0.0  0
 AKJ  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 AKJ  CONST_04  C7   C2   C3   C4      0.00   0.0  0
 AKJ  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 AKJ  CONST_06  C2   C7   C6   C5      0.00   0.0  0
 AKJ  CONST_07  C5   C4   C3   O2    180.00   0.0  0
 AKJ  CONST_08  C7   C2   C3   O2    180.00   0.0  0
 AKJ  CONST_09  C12  C5   C4   C3    180.00   0.0  0
 AKJ  CONST_10  O1   C2   C3   C4    180.00   0.0  0
 AKJ  CONST_11  O1   C2   C7   C6    180.00   0.0  0
 AKJ  CONST_12  C12  C5   C6   C7    180.00   0.0  0
 AKJ  CONST_13  H4   C7   C2   C3    180.00   0.0  0
 AKJ  CONST_14  H3   C6   C5   C4    180.00   0.0  0
 AKJ  CONST_15  H2   C4   C5   C6    180.00   0.0  0
 AKJ  Var_01    O3   C10  C11  C8     32.80  30.0  1
 AKJ  Var_02    C2   C3   O2   C8    174.10  30.0  2
 AKJ  Var_03    H14  C9   O3   C10  -132.69  30.0  1
 AKJ  Var_04    C3   C2   O1   C1    -96.06  30.0  1
 AKJ  Var_05    C13  C12  C5   C4    179.92  30.0  2
 AKJ  Var_06    C14  C13  C12  C5   -172.35  30.0  1
 AKJ  Var_07    H1   C1   O1   C2    176.63  30.0  3
 AKJ  Var_08    C12  C13  C14  C16  -167.09  30.0  3
 AKJ  Var_09    H18  C15  C14  C16   -62.09  30.0  3
 AKJ  Var_10    H11  C16  C14  C13   -61.58  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
 AKJ  chir_01  C8  C11  O2  C9  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
 AKJ  plan-1  O2   0.020
 AKJ  plan-1  C3   0.020
 AKJ  plan-1  C4   0.020
 AKJ  plan-1  C5   0.020
 AKJ  plan-1  C6   0.020
 AKJ  plan-1  C7   0.020
 AKJ  plan-1  O1   0.020
 AKJ  plan-1  C2   0.020
 AKJ  plan-1  H2   0.020
 AKJ  plan-1  H3   0.020
 AKJ  plan-1  H4   0.020
 AKJ  plan-1  C12  0.020
 AKJ  plan-2  C5   0.020
 AKJ  plan-2  O4   0.020
 AKJ  plan-2  C13  0.020
 AKJ  plan-2  C12  0.020

