# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 22:42:05 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: 1-[4-oxidanyl-2-(1,3-thiazolidin-3-ylcarbonyl)pyrrolidin-1-yl]-4-[2-[(~{E})-2-phenylethenyl]phenoxy]butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@H](N(C1)C(=O)CCCOc2ccccc2\C=C\c3ccccc3)C(=O)N4CCSC4
#
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
 BKO  BKO  1-[4-oxidanyl-2-(1,3-thiazolidin-3-ylcarbonyl)pyrrolidin-1-yl]-4-[2-[(~{E})-2-phenylethenyl]phenoxy]butan-1-one  ligand  63  33  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BKO
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
 BKO  C10  C  CH2   0  -0.608   0.8949  -2.1199   0.1077
 BKO  C13  C  CH2   0  -0.404   5.0801   1.7343   1.2111
 BKO  C15  C  CH2   0  -0.450  -0.4377  -1.3984   0.2341
 BKO  C20  C  CR6   0   0.363  -3.9684  -2.3024   0.1165
 BKO  C21  C  CR6   0   0.014  -5.1242  -1.4947   0.1060
 BKO  C22  C  CR16  0  -0.381  -4.0770  -3.6881   0.0332
 BKO  C24  C  CR16  0  -0.314  -6.3647  -2.1290   0.0303
 BKO  C26  C  C1    0  -0.294  -5.9245   0.8338  -0.2396
 BKO  C28  C  CR6   0   0.166  -5.8346   2.2920  -0.1739
 BKO  C01  C  CR15  0  -0.171   4.4716  -0.8795   0.0890
 BKO  C03  C  C     0   0.574   4.3347   0.3933  -0.7388
 BKO  C04  C  CH2   0  -0.490   5.5778  -1.7796  -0.4790
 BKO  C05  C  CH2   0  -0.292   3.5820  -3.0508  -0.4916
 BKO  C06  C  C     0   0.587   2.0812  -1.1981   0.2791
 BKO  C09  C  CR15  0  -0.009   5.0732  -3.1855  -0.1962
 BKO  C12  C  CH2   0  -0.249   4.7717   2.7590  -1.0134
 BKO  C16  C  CH2   0  -0.595   5.5222   3.8101  -0.2196
 BKO  C18  C  CH2   0  -0.170  -1.5814  -2.3873   0.1449
 BKO  C23  C  C1    0  -0.283  -4.9970  -0.0388   0.1773
 BKO  C25  C  CR16  0  -0.252  -5.3284  -4.2837  -0.0543
 BKO  C27  C  CR16  0  -0.267  -6.4773  -3.5077  -0.0550
 BKO  C29  C  CR16  0  -0.333  -4.7245   2.9755   0.3361
 BKO  C30  C  CR16  0  -0.319  -6.9081   3.0496  -0.6517
 BKO  C31  C  CR16  0  -0.232  -4.6942   4.3593   0.3628
 BKO  C32  C  CR16  0  -0.240  -6.8798   4.4364  -0.6227
 BKO  C33  C  CR16  0  -0.271  -5.7712   5.0989  -0.1154
 BKO  N02  N  NR5   0  -0.478   3.2837  -1.7028  -0.0368
 BKO  N07  N  NR5   0  -0.474   4.7687   1.5476  -0.1996
 BKO  O08  O  O     0  -0.494   3.9220   0.3319  -1.8872
 BKO  O11  O  O     0  -0.501   1.9718  -0.0474   0.6883
 BKO  O14  O  OH1   0  -0.667   5.3210  -3.4669   1.1617
 BKO  O19  O  O2    0  -0.470  -2.7931  -1.6530   0.1975
 BKO  S17  S  S2    0  -0.009   5.0076   3.5229   1.4942
 BKO  H1   H  HCH2  0   0.277   0.9690  -2.9170   0.8568
 BKO  H2   H  HCH2  0   0.271   0.9589  -2.6229  -0.8620
 BKO  H3   H  HCH2  0   0.290   4.3430   1.2604   1.8567
 BKO  H4   H  HCH2  0   0.243  -0.4911  -0.8645   1.1843
 BKO  H5   H  HCH2  0   0.243  -0.5362  -0.6570  -0.5618
 BKO  H6   H  HCR6  0   0.282  -3.1979  -4.3176   0.0339
 BKO  H7   H  HCR6  0   0.253  -7.2649  -1.5277   0.0539
 BKO  H8   H  H     0   0.247  -6.8398   0.4605  -0.6895
 BKO  H9   H  HCH2  0   0.264   5.6625  -1.6444  -1.5583
 BKO  H10  H  HCH2  0   0.250   3.3921  -3.1625  -1.5633
 BKO  H11  H  HCH2  0   0.252   3.7497   3.0886  -1.2146
 BKO  H12  H  HCH2  0   0.283   6.6021   3.6957  -0.3163
 BKO  H13  H  HCH2  0   0.223  -1.5264  -2.9585  -0.7890
 BKO  H14  H  HCH2  0   0.224  -1.5287  -3.1028   0.9735
 BKO  H15  H  H     0   0.252  -4.0690   0.3387   0.5906
 BKO  H16  H  HCR6  0   0.260  -5.3966  -5.3620  -0.1157
 BKO  H17  H  HCR6  0   0.254  -7.4535  -3.9699  -0.1108
 BKO  H18  H  HCR6  0   0.249  -3.8710   2.4284   0.7154
 BKO  H19  H  HCR6  0   0.253  -7.7777   2.5419  -1.0520
 BKO  H20  H  HCR6  0   0.259  -3.8239   4.8655   0.7601
 BKO  H21  H  HCR6  0   0.257  -7.7257   4.9977  -0.9983
 BKO  H22  H  HCR6  0   0.257  -5.7434   6.1805  -0.0912
 BKO  H23  H  HOH1  0   0.453   4.9637  -4.3369   1.3655
 BKO  H26  H  HCH2  0   0.299   5.2460   4.8190  -0.5187
 BKO  H25  H  HCH2  0   0.264   5.2617   2.5718  -1.9691
 BKO  H24  H  HCH2  0   0.284   6.0721   1.3512   1.4567
 BKO  H28  H  HCH2  0   0.273   6.5507  -1.5754  -0.0335
 BKO  H29  H  HCH2  0   0.265   2.9890  -3.7999   0.0346
 BKO  H27  H  HCR5  0   0.283   4.6661  -0.6698   1.1423
 BKO  H30  H  HCR5  0   0.246   5.5371  -3.9289  -0.8535

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
 BKO  C16  S17  single    1.812  0.020  1.812
 BKO  C16  C12  single    1.516  0.020  1.516
 BKO  S17  C13  single    1.812  0.020  1.812
 BKO  C12  N07  single    1.459  0.020  1.459
 BKO  N07  C13  single    1.457  0.020  1.457
 BKO  N07  C03  single    1.346  0.020  1.346
 BKO  O08  C03  double    1.222  0.020  1.222
 BKO  C03  C01  single    1.524  0.020  1.524
 BKO  C04  C01  single    1.535  0.020  1.535
 BKO  C04  C09  single    1.520  0.020  1.520
 BKO  C01  N02  single    1.451  0.020  1.451
 BKO  O14  C09  single    1.409  0.020  1.409
 BKO  C09  C05  single    1.526  0.020  1.526
 BKO  N02  C05  single    1.454  0.020  1.454
 BKO  N02  C06  single    1.342  0.020  1.342
 BKO  O11  C06  double    1.226  0.020  1.226
 BKO  C06  C10  single    1.512  0.020  1.512
 BKO  C10  C15  single    1.521  0.020  1.521
 BKO  C15  C18  single    1.515  0.020  1.515
 BKO  C31  C29  aromatic  1.384  0.020  1.384
 BKO  C31  C33  aromatic  1.391  0.020  1.391
 BKO  C29  C28  aromatic  1.400  0.020  1.400
 BKO  C33  C32  aromatic  1.388  0.020  1.388
 BKO  C18  O19  single    1.418  0.020  1.418
 BKO  O19  C20  single    1.345  0.020  1.345
 BKO  C28  C26  single    1.462  0.020  1.462
 BKO  C28  C30  aromatic  1.398  0.020  1.398
 BKO  C32  C30  aromatic  1.387  0.020  1.387
 BKO  C20  C22  aromatic  1.392  0.020  1.392
 BKO  C20  C21  aromatic  1.410  0.020  1.410
 BKO  C23  C26  double    1.340  0.020  1.340
 BKO  C23  C21  single    1.463  0.020  1.463
 BKO  C22  C25  aromatic  1.389  0.020  1.389
 BKO  C21  C24  aromatic  1.395  0.020  1.395
 BKO  C25  C27  aromatic  1.386  0.020  1.386
 BKO  C24  C27  aromatic  1.386  0.020  1.386
 BKO  C10  H1   single    0.970  0.020  1.090
 BKO  C10  H2   single    0.970  0.020  1.090
 BKO  C13  H3   single    0.970  0.020  1.090
 BKO  C15  H4   single    0.970  0.020  1.090
 BKO  C15  H5   single    0.970  0.020  1.090
 BKO  C22  H6   single    0.930  0.020  1.080
 BKO  C24  H7   single    0.930  0.020  1.080
 BKO  C26  H8   single    0.930  0.020  1.080
 BKO  C04  H9   single    0.970  0.020  1.090
 BKO  C05  H10  single    0.970  0.020  1.090
 BKO  C12  H11  single    0.970  0.020  1.090
 BKO  C16  H12  single    0.970  0.020  1.090
 BKO  C18  H13  single    0.970  0.020  1.090
 BKO  C18  H14  single    0.970  0.020  1.090
 BKO  C23  H15  single    0.930  0.020  1.080
 BKO  C25  H16  single    0.930  0.020  1.080
 BKO  C27  H17  single    0.930  0.020  1.080
 BKO  C29  H18  single    0.930  0.020  1.080
 BKO  C30  H19  single    0.930  0.020  1.080
 BKO  C31  H20  single    0.930  0.020  1.080
 BKO  C32  H21  single    0.930  0.020  1.080
 BKO  C33  H22  single    0.930  0.020  1.080
 BKO  O14  H23  single    0.850  0.020  0.980
 BKO  C16  H26  single    0.970  0.020  1.090
 BKO  C12  H25  single    0.970  0.020  1.090
 BKO  C13  H24  single    0.970  0.020  1.090
 BKO  C04  H28  single    0.970  0.020  1.090
 BKO  C05  H29  single    0.970  0.020  1.090
 BKO  C01  H27  single    0.970  0.020  1.090
 BKO  C09  H30  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
 BKO  H2   C10  H1   105.51  3.000
 BKO  H2   C10  C06  109.56  3.000
 BKO  H1   C10  C06  108.22  3.000
 BKO  H2   C10  C15  110.06  3.000
 BKO  H1   C10  C15  110.33  3.000
 BKO  C06  C10  C15  112.88  3.000
 BKO  H24  C13  H3   109.22  3.000
 BKO  H24  C13  S17  110.34  3.000
 BKO  H3   C13  S17  108.06  3.000
 BKO  H24  C13  N07  111.55  3.000
 BKO  H3   C13  N07  111.95  3.000
 BKO  S17  C13  N07  105.62  3.000
 BKO  H5   C15  H4   107.33  3.000
 BKO  H5   C15  C18  109.40  3.000
 BKO  H4   C15  C18  109.50  3.000
 BKO  H5   C15  C10  109.91  3.000
 BKO  H4   C15  C10  110.33  3.000
 BKO  C18  C15  C10  110.31  3.000
 BKO  O19  C20  C22  123.52  3.000
 BKO  C22  C20  C21  120.37  3.000
 BKO  O19  C20  C21  116.11  3.000
 BKO  C23  C21  C24  122.16  3.000
 BKO  C24  C21  C20  117.95  3.000
 BKO  C23  C21  C20  119.89  3.000
 BKO  H6   C22  C25  118.88  3.000
 BKO  H6   C22  C20  121.05  3.000
 BKO  C25  C22  C20  120.06  3.000
 BKO  H7   C24  C27  119.09  3.000
 BKO  H7   C24  C21  119.04  3.000
 BKO  C27  C24  C21  121.86  3.000
 BKO  H8   C26  C23  119.24  3.000
 BKO  H8   C26  C28  114.40  3.000
 BKO  C23  C26  C28  126.35  3.000
 BKO  C30  C28  C29  117.96  3.000
 BKO  C30  C28  C26  118.54  3.000
 BKO  C29  C28  C26  123.50  3.000
 BKO  H27  C01  N02  109.79  3.000
 BKO  H27  C01  C04  109.96  3.000
 BKO  N02  C01  C04  103.01  3.000
 BKO  H27  C01  C03  112.32  3.000
 BKO  N02  C01  C03  110.68  3.000
 BKO  C04  C01  C03  110.69  3.000
 BKO  O08  C03  N07  121.91  3.000
 BKO  O08  C03  C01  119.92  3.000
 BKO  N07  C03  C01  118.01  3.000
 BKO  H28  C04  H9   108.18  3.000
 BKO  H28  C04  C09  113.19  3.000
 BKO  H9   C04  C09  108.93  3.000
 BKO  H28  C04  C01  112.48  3.000
 BKO  H9   C04  C01  110.45  3.000
 BKO  C09  C04  C01  103.55  3.000
 BKO  H29  C05  H10  107.94  3.000
 BKO  H29  C05  N02  111.99  3.000
 BKO  H10  C05  N02  111.43  3.000
 BKO  H29  C05  C09  112.17  3.000
 BKO  H10  C05  C09  110.50  3.000
 BKO  N02  C05  C09  102.82  3.000
 BKO  O11  C06  N02  120.76  3.000
 BKO  O11  C06  C10  122.68  3.000
 BKO  N02  C06  C10  116.56  3.000
 BKO  H30  C09  O14  111.61  3.000
 BKO  H30  C09  C05  110.95  3.000
 BKO  O14  C09  C05  112.09  3.000
 BKO  H30  C09  C04  112.05  3.000
 BKO  C05  C09  C04  101.93  3.000
 BKO  O14  C09  C04  107.80  3.000
 BKO  H25  C12  H11  108.10  3.000
 BKO  H25  C12  N07  110.32  3.000
 BKO  H11  C12  N07  110.56  3.000
 BKO  H25  C12  C16  110.83  3.000
 BKO  H11  C12  C16  110.51  3.000
 BKO  N07  C12  C16  106.54  3.000
 BKO  H26  C16  H12  108.93  3.000
 BKO  H26  C16  S17  109.56  3.000
 BKO  H12  C16  S17  110.39  3.000
 BKO  H26  C16  C12  111.92  3.000
 BKO  H12  C16  C12  111.79  3.000
 BKO  S17  C16  C12  104.16  3.000
 BKO  H14  C18  H13  107.55  3.000
 BKO  H14  C18  O19  110.56  3.000
 BKO  H13  C18  O19  110.14  3.000
 BKO  H14  C18  C15  110.21  3.000
 BKO  H13  C18  C15  110.65  3.000
 BKO  O19  C18  C15  107.76  3.000
 BKO  H15  C23  C26  118.98  3.000
 BKO  H15  C23  C21  116.08  3.000
 BKO  C26  C23  C21  124.93  3.000
 BKO  H16  C25  C27  120.36  3.000
 BKO  H16  C25  C22  119.19  3.000
 BKO  C27  C25  C22  120.45  3.000
 BKO  H17  C27  C25  120.58  3.000
 BKO  H17  C27  C24  120.11  3.000
 BKO  C25  C27  C24  119.30  3.000
 BKO  H18  C29  C31  118.76  3.000
 BKO  H18  C29  C28  120.42  3.000
 BKO  C31  C29  C28  120.82  3.000
 BKO  H19  C30  C32  119.50  3.000
 BKO  H19  C30  C28  119.24  3.000
 BKO  C32  C30  C28  121.26  3.000
 BKO  H20  C31  C33  120.00  3.000
 BKO  H20  C31  C29  119.48  3.000
 BKO  C33  C31  C29  120.52  3.000
 BKO  H21  C32  C33  120.24  3.000
 BKO  H21  C32  C30  119.68  3.000
 BKO  C33  C32  C30  120.07  3.000
 BKO  H22  C33  C32  120.38  3.000
 BKO  H22  C33  C31  120.25  3.000
 BKO  C32  C33  C31  119.36  3.000
 BKO  C06  N02  C05  127.32  3.000
 BKO  C06  N02  C01  120.00  3.000
 BKO  C05  N02  C01  112.67  3.000
 BKO  C12  N07  C03  119.29  3.000
 BKO  C03  N07  C13  124.53  3.000
 BKO  C12  N07  C13  115.67  3.000
 BKO  H23  O14  C09  108.63  3.000
 BKO  C18  O19  C20  119.63  3.000
 BKO  C16  S17  C13   89.84  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
 BKO  CONST_01  C27  C25  C22  C20     0.00   0.0  0
 BKO  CONST_02  C27  C24  C21  C20     0.00   0.0  0
 BKO  CONST_03  C25  C22  C20  C21     0.00   0.0  0
 BKO  CONST_04  C25  C27  C24  C21     0.00   0.0  0
 BKO  CONST_05  C24  C21  C20  C22     0.00   0.0  0
 BKO  CONST_06  C24  C27  C25  C22     0.00   0.0  0
 BKO  CONST_07  C33  C31  C29  C28     0.00   0.0  0
 BKO  CONST_08  C33  C32  C30  C28     0.00   0.0  0
 BKO  CONST_09  C32  C33  C31  C29     0.00   0.0  0
 BKO  CONST_10  C32  C30  C28  C29     0.00   0.0  0
 BKO  CONST_11  C31  C29  C28  C30     0.00   0.0  0
 BKO  CONST_12  C31  C33  C32  C30     0.00   0.0  0
 BKO  CONST_13  C23  C21  C20  C22   180.00   0.0  0
 BKO  CONST_14  O19  C20  C21  C24   180.00   0.0  0
 BKO  CONST_15  C31  C29  C28  C26   180.00   0.0  0
 BKO  CONST_16  C32  C30  C28  C26   180.00   0.0  0
 BKO  CONST_17  C27  C24  C21  C23   180.00   0.0  0
 BKO  CONST_18  O19  C20  C22  C25   180.00   0.0  0
 BKO  CONST_19  C01  C03  N07  C13     0.00   0.0  0
 BKO  CONST_20  C12  N07  C03  C01   180.00   0.0  0
 BKO  CONST_21  H16  C25  C22  C20   180.00   0.0  0
 BKO  CONST_22  H7   C24  C21  C20   180.00   0.0  0
 BKO  CONST_23  H6   C22  C20  C21   180.00   0.0  0
 BKO  CONST_24  H17  C27  C24  C21   180.00   0.0  0
 BKO  CONST_25  H20  C31  C29  C28   180.00   0.0  0
 BKO  CONST_26  H21  C32  C30  C28   180.00   0.0  0
 BKO  CONST_27  H22  C33  C31  C29   180.00   0.0  0
 BKO  CONST_28  H19  C30  C28  C29   180.00   0.0  0
 BKO  CONST_29  H18  C29  C28  C30   180.00   0.0  0
 BKO  CONST_30  C01  N02  C06  C10   180.00   0.0  0
 BKO  CONST_31  C05  N02  C06  C10     0.00   0.0  0
 BKO  CONST_32  O08  C03  N07  C13   180.00   0.0  0
 BKO  CONST_33  O11  C06  N02  C01     0.00   0.0  0
 BKO  CONST_34  O11  C06  N02  C05   180.00   0.0  0
 BKO  CONST_35  O08  C03  N07  C12     0.00   0.0  0
 BKO  Var_01    C12  C16  S17  C13    39.73  30.0  1
 BKO  Var_02    C16  C12  N07  C13    17.27  30.0  1
 BKO  Var_03    C09  C05  N02  C01    18.70  30.0  1
 BKO  Var_04    S17  C13  N07  C12    12.13  30.0  1
 BKO  Var_05    N07  C13  S17  C16   -30.00  30.0  1
 BKO  Var_06    S17  C16  C12  N07   -38.33  30.0  1
 BKO  Var_07    C28  C26  C23  C21   179.50   0.0  2
 BKO  Var_08    C26  C23  C21  C20   157.64  30.0  2
 BKO  Var_09    C29  C28  C26  C23     0.77  30.0  2
 BKO  Var_10    N02  C06  C10  C15  -169.21  30.0  2
 BKO  Var_11    H13  C18  O19  C20    58.26  30.0  2
 BKO  Var_12    O19  C18  C15  C10  -176.97  30.0  3
 BKO  Var_13    C18  C15  C10  C06  -176.26  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
 BKO  chir_01  C01  C03  C04  N02  positiv
 BKO  chir_02  C09  O14  C05  C04  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
 BKO  plan-1  C20  0.020
 BKO  plan-1  C21  0.020
 BKO  plan-1  C22  0.020
 BKO  plan-1  C24  0.020
 BKO  plan-1  C23  0.020
 BKO  plan-1  C25  0.020
 BKO  plan-1  C27  0.020
 BKO  plan-1  O19  0.020
 BKO  plan-1  H6   0.020
 BKO  plan-1  H7   0.020
 BKO  plan-1  H16  0.020
 BKO  plan-1  H17  0.020
 BKO  plan-2  C26  0.020
 BKO  plan-2  C28  0.020
 BKO  plan-2  C29  0.020
 BKO  plan-2  C30  0.020
 BKO  plan-2  C31  0.020
 BKO  plan-2  C32  0.020
 BKO  plan-2  C33  0.020
 BKO  plan-2  H18  0.020
 BKO  plan-2  H19  0.020
 BKO  plan-2  H20  0.020
 BKO  plan-2  H21  0.020
 BKO  plan-2  H22  0.020
 BKO  plan-3  C13  0.020
 BKO  plan-3  C01  0.020
 BKO  plan-3  C03  0.020
 BKO  plan-3  C12  0.020
 BKO  plan-3  N07  0.020
 BKO  plan-3  O08  0.020
 BKO  plan-4  C10  0.020
 BKO  plan-4  C01  0.020
 BKO  plan-4  C05  0.020
 BKO  plan-4  C06  0.020
 BKO  plan-4  N02  0.020
 BKO  plan-4  O11  0.020
 BKO  plan-5  C21  0.020
 BKO  plan-5  C26  0.020
 BKO  plan-5  C28  0.020
 BKO  plan-5  C23  0.020
 BKO  plan-5  H8   0.020
 BKO  plan-5  H15  0.020

