# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:07:02 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4-[3-(methylsulfonyl)phenoxy]-N-[(1R,3R,5R)-2-oxobicyclo[3.1.0]hexan-3-yl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc(OCCCC(=O)N[C@@H]2C[C@H]3C[C@H]3C2=O)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
 K5J  K5J  4-[3-(methylsulfonyl)phenoxy]-N-[(1R,3R,5R)-2-oxobicyclo[3.1.0]hexan-3-yl]butanamide  ligand  45  24  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K5J
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
 K5J  C10   C  CR6   0   0.413  -2.7731  -0.6130  -0.0715
 K5J  C15   C  CH3   0  -0.790  -6.9626   1.0944  -1.5301
 K5J  C17   C  CR16  0  -0.261  -5.3875  -1.6189   0.1026
 K5J  C21   C  CH2   0  -0.423   6.8655  -1.0519  -0.8474
 K5J  C22   C  CR15  0  -0.263   8.1344  -0.6577  -0.1147
 K5J  C24   C  CH2   0  -0.477   8.4589   0.7828  -0.0455
 K5J  C02   C  CR5   0   0.447   6.2853   0.2200   1.1239
 K5J  C03   C  CR15  0  -0.226   5.7797  -0.1295  -0.2838
 K5J  N04   N  NH1   0  -0.638   4.4689  -0.7027  -0.2828
 K5J  C05   C  C     0   0.566   3.3377   0.0092  -0.4591
 K5J  C06   C  CH2   0  -0.601   2.0706  -0.8174  -0.3773
 K5J  C07   C  CH2   0  -0.457   0.8076   0.0231  -0.2846
 K5J  C08   C  CH2   0  -0.176  -0.4110  -0.8744  -0.2311
 K5J  O09   O  O2    0  -0.472  -1.5609  -0.0447  -0.1460
 K5J  C11   C  CR16  0  -0.334  -3.8559   0.2642   0.0136
 K5J  C12   C  CR6   0  -0.186  -5.1352  -0.2525   0.0960
 K5J  S13   S  S     0   1.216  -6.5054   0.8766   0.1743
 K5J  O14   O  OS    0  -0.667  -6.0250   2.1577   0.6881
 K5J  O16   O  OS    0  -0.668  -7.6091   0.2134   0.8654
 K5J  C18   C  CR16  0  -0.228  -4.3033  -2.4748   0.0161
 K5J  C19   C  CR16  0  -0.365  -3.0050  -1.9878  -0.0709
 K5J  O20   O  O     0  -0.492   3.3359   1.2054  -0.7024
 K5J  C23   C  CR15  0  -0.402   7.7559   0.1249   1.1279
 K5J  H151  H  HCH3  0   0.296  -6.1210   1.5100  -2.0794
 K5J  H152  H  HCH3  0   0.296  -7.2541   0.1358  -1.9524
 K5J  H153  H  HCH3  0   0.311  -7.8048   1.7856  -1.5545
 K5J  H171  H  HCR6  0   0.281  -6.3933  -2.0079   0.1760
 K5J  H212  H  HCH2  0   0.254   6.6256  -2.0925  -0.6140
 K5J  H221  H  HCR5  0   0.283   8.9420  -1.3758  -0.0621
 K5J  H241  H  HCH2  0   0.285   9.4885   1.0561   0.1430
 K5J  H242  H  HCH2  0   0.268   7.9191   1.4970  -0.6562
 K5J  H031  H  HCR5  0   0.300   5.7421   0.8005  -0.8583
 K5J  H041  H  HNH1  0   0.402   4.3874  -1.6713  -0.0148
 K5J  H062  H  HCH2  0   0.280   2.0341  -1.4582  -1.2652
 K5J  H061  H  HCH2  0   0.267   2.1404  -1.4979   0.4764
 K5J  H071  H  HCH2  0   0.245   0.8376   0.6503   0.6094
 K5J  H072  H  HCH2  0   0.245   0.7334   0.6877  -1.1471
 K5J  H081  H  HCH2  0   0.229  -0.4614  -1.5026  -1.1280
 K5J  H082  H  HCH2  0   0.229  -0.3572  -1.5391   0.6382
 K5J  H111  H  HCR6  0   0.289  -3.6790   1.3324   0.0158
 K5J  H181  H  HCR6  0   0.277  -4.4635  -3.5445   0.0197
 K5J  H191  H  HCR6  0   0.294  -2.1897  -2.6948  -0.1336
 K5J  H231  H  HCR5  0   0.287   8.2820   0.0321   2.0689
 K5J  H211  H  HCH2  0   0.260   6.9594  -0.9672  -1.9304
 K5J  O01   O  O     0  -0.395   5.5687   0.4515   2.0663

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
 K5J  C21  C22   single    1.517  0.020  1.517
 K5J  C21  C03   single    1.532  0.020  1.532
 K5J  C22  C24   single    1.478  0.020  1.478
 K5J  C22  C23   single    1.517  0.020  1.517
 K5J  C24  C23   single    1.518  0.020  1.518
 K5J  C03  N04   single    1.431  0.020  1.431
 K5J  C03  C02   single    1.536  0.020  1.536
 K5J  C23  C02   single    1.474  0.020  1.474
 K5J  N04  C05   single    1.348  0.020  1.348
 K5J  O20  C05   double    1.221  0.020  1.221
 K5J  C15  S13   single    1.778  0.020  1.778
 K5J  O16  S13   double    1.461  0.020  1.461
 K5J  C05  C06   single    1.515  0.020  1.515
 K5J  C02  O01   double    1.206  0.020  1.206
 K5J  C06  C07   single    1.520  0.020  1.520
 K5J  S13  O14   double    1.462  0.020  1.462
 K5J  S13  C12   single    1.777  0.020  1.777
 K5J  C11  C12   aromatic  1.382  0.020  1.382
 K5J  C11  C10   aromatic  1.396  0.020  1.396
 K5J  C12  C17   aromatic  1.389  0.020  1.389
 K5J  C07  C08   single    1.514  0.020  1.514
 K5J  O09  C08   single    1.421  0.020  1.421
 K5J  O09  C10   single    1.341  0.020  1.341
 K5J  C10  C19   aromatic  1.394  0.020  1.394
 K5J  C17  C18   aromatic  1.384  0.020  1.384
 K5J  C19  C18   aromatic  1.389  0.020  1.389
 K5J  C15  H151  single    0.970  0.020  1.090
 K5J  C15  H152  single    0.970  0.020  1.090
 K5J  C15  H153  single    0.970  0.020  1.090
 K5J  C17  H171  single    0.930  0.020  1.080
 K5J  C21  H211  single    0.970  0.020  1.090
 K5J  C21  H212  single    0.970  0.020  1.090
 K5J  C22  H221  single    0.970  0.020  1.090
 K5J  C24  H241  single    0.970  0.020  1.090
 K5J  C24  H242  single    0.970  0.020  1.090
 K5J  C03  H031  single    0.970  0.020  1.090
 K5J  N04  H041  single    0.860  0.020  1.020
 K5J  C06  H062  single    0.970  0.020  1.090
 K5J  C06  H061  single    0.970  0.020  1.090
 K5J  C07  H071  single    0.970  0.020  1.090
 K5J  C07  H072  single    0.970  0.020  1.090
 K5J  C08  H081  single    0.970  0.020  1.090
 K5J  C08  H082  single    0.970  0.020  1.090
 K5J  C11  H111  single    0.930  0.020  1.080
 K5J  C18  H181  single    0.930  0.020  1.080
 K5J  C19  H191  single    0.930  0.020  1.080
 K5J  C23  H231  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
 K5J  C19   C10  C11   119.37  3.000
 K5J  C19   C10  O09   124.64  3.000
 K5J  C11   C10  O09   115.99  3.000
 K5J  H153  C15  H152  110.07  3.000
 K5J  H153  C15  H151  110.15  3.000
 K5J  H152  C15  H151  110.38  3.000
 K5J  H153  C15  S13   107.33  3.000
 K5J  H152  C15  S13   109.46  3.000
 K5J  H151  C15  S13   109.39  3.000
 K5J  H171  C17  C18   120.70  3.000
 K5J  H171  C17  C12   121.55  3.000
 K5J  C18   C17  C12   117.75  3.000
 K5J  H212  C21  H211  107.76  3.000
 K5J  H212  C21  C03   109.81  3.000
 K5J  H211  C21  C03   112.31  3.000
 K5J  H212  C21  C22   109.13  3.000
 K5J  H211  C21  C22   112.79  3.000
 K5J  C03   C21  C22   104.99  3.000
 K5J  H221  C22  C23   119.27  3.000
 K5J  H221  C22  C24   118.73  3.000
 K5J  C23   C22  C24    60.89  3.000
 K5J  H221  C22  C21   118.37  3.000
 K5J  C23   C22  C21   108.72  3.000
 K5J  C24   C22  C21   117.35  3.000
 K5J  H242  C24  H241  113.94  3.000
 K5J  H242  C24  C23   119.38  3.000
 K5J  H241  C24  C23   114.56  3.000
 K5J  H242  C24  C22   120.43  3.000
 K5J  H241  C24  C22   117.60  3.000
 K5J  C23   C24  C22    60.80  3.000
 K5J  C23   C02  C03   108.44  3.000
 K5J  C23   C02  O01   127.09  3.000
 K5J  C03   C02  O01   124.34  3.000
 K5J  H031  C03  N04   108.03  3.000
 K5J  H031  C03  C02   107.41  3.000
 K5J  N04   C03  C02   113.08  3.000
 K5J  H031  C03  C21   110.06  3.000
 K5J  C02   C03  C21   103.94  3.000
 K5J  N04   C03  C21   114.10  3.000
 K5J  H041  N04  C05   118.31  3.000
 K5J  H041  N04  C03   117.33  3.000
 K5J  C05   N04  C03   123.86  3.000
 K5J  O20   C05  C06   122.97  3.000
 K5J  C06   C05  N04   113.99  3.000
 K5J  O20   C05  N04   123.01  3.000
 K5J  H061  C06  H062  105.71  3.000
 K5J  H061  C06  C07   110.45  3.000
 K5J  H062  C06  C07   110.19  3.000
 K5J  H061  C06  C05   109.16  3.000
 K5J  H062  C06  C05   107.65  3.000
 K5J  C07   C06  C05   113.36  3.000
 K5J  H072  C07  H071  107.40  3.000
 K5J  H072  C07  C08   109.52  3.000
 K5J  H071  C07  C08   109.48  3.000
 K5J  H072  C07  C06   110.18  3.000
 K5J  H071  C07  C06   110.16  3.000
 K5J  C08   C07  C06   110.07  3.000
 K5J  H082  C08  H081  107.68  3.000
 K5J  H082  C08  O09   110.28  3.000
 K5J  H081  C08  O09   110.28  3.000
 K5J  H082  C08  C07   110.37  3.000
 K5J  H081  C08  C07   110.35  3.000
 K5J  O09   C08  C07   107.90  3.000
 K5J  C08   O09  C10   119.18  3.000
 K5J  H111  C11  C12   121.33  3.000
 K5J  H111  C11  C10   119.56  3.000
 K5J  C12   C11  C10   119.12  3.000
 K5J  S13   C12  C11   118.60  3.000
 K5J  C11   C12  C17   122.41  3.000
 K5J  S13   C12  C17   118.98  3.000
 K5J  O16   S13  O14   118.67  3.000
 K5J  O14   S13  C12   108.60  3.000
 K5J  O16   S13  C12   108.35  3.000
 K5J  C12   S13  C15   103.53  3.000
 K5J  O14   S13  C15   108.31  3.000
 K5J  O16   S13  C15   108.34  3.000
 K5J  H181  C18  C19   119.02  3.000
 K5J  H181  C18  C17   119.70  3.000
 K5J  C19   C18  C17   121.28  3.000
 K5J  H191  C19  C18   118.63  3.000
 K5J  H191  C19  C10   121.29  3.000
 K5J  C18   C19  C10   120.07  3.000
 K5J  H231  C23  C02   119.54  3.000
 K5J  H231  C23  C24   118.96  3.000
 K5J  C02   C23  C24   115.60  3.000
 K5J  H231  C23  C22   123.16  3.000
 K5J  C02   C23  C22   106.27  3.000
 K5J  C24   C23  C22    58.30  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
 K5J  CONST_01  C17   C12  C11  C10     0.00   0.0  0
 K5J  CONST_02  C17   C18  C19  C10     0.00   0.0  0
 K5J  CONST_03  C18   C17  C12  C11     0.00   0.0  0
 K5J  CONST_04  C18   C19  C10  C11     0.00   0.0  0
 K5J  CONST_05  C19   C10  C11  C12     0.00   0.0  0
 K5J  CONST_06  C19   C18  C17  C12     0.00   0.0  0
 K5J  CONST_07  S13   C12  C11  C10   180.00   0.0  0
 K5J  CONST_08  C12   C11  C10  O09   180.00   0.0  0
 K5J  CONST_09  C18   C19  C10  O09   180.00   0.0  0
 K5J  CONST_10  C18   C17  C12  S13   180.00   0.0  0
 K5J  CONST_11  H181  C18  C19  C10   180.00   0.0  0
 K5J  CONST_12  H111  C11  C12  C17   180.00   0.0  0
 K5J  CONST_13  H191  C19  C18  C17   180.00   0.0  0
 K5J  CONST_14  H171  C17  C12  C11   180.00   0.0  0
 K5J  CONST_15  O20   C05  N04  C03     0.00   0.0  0
 K5J  CONST_16  C06   C05  N04  C03   180.00   0.0  0
 K5J  CONST_17  H041  N04  C05  C06     0.00   0.0  0
 K5J  Var_01    C23   C24  C22  C21    97.22  30.0  1
 K5J  Var_02    C03   C02  C23  C22   -16.14  30.0  1
 K5J  Var_03    C03   C21  C22  C24   -48.63  30.0  1
 K5J  Var_04    C11   C12  S13  C15    91.55  30.0  2
 K5J  Var_05    C11   C10  O09  C08   179.82  30.0  2
 K5J  Var_06    C07   C08  O09  C10  -179.28  30.0  3
 K5J  Var_07    H151  C15  S13  C12   -60.35  30.0  3
 K5J  Var_08    C07   C06  C05  N04   167.88  30.0  3
 K5J  Var_09    C08   C07  C06  C05   179.01  30.0  3
 K5J  Var_10    O09   C08  C07  C06  -179.97  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
 K5J  chir_02  C03  C21  N04  C02  negativ
 K5J  chir_03  C22  C21  C24  C23  both
 K5J  chir_04  C23  C02  C24  C22  both

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
 K5J  plan-1  C10   0.020
 K5J  plan-1  C17   0.020
 K5J  plan-1  O09   0.020
 K5J  plan-1  C11   0.020
 K5J  plan-1  C12   0.020
 K5J  plan-1  S13   0.020
 K5J  plan-1  C18   0.020
 K5J  plan-1  C19   0.020
 K5J  plan-1  H171  0.020
 K5J  plan-1  H111  0.020
 K5J  plan-1  H181  0.020
 K5J  plan-1  H191  0.020
 K5J  plan-2  C03   0.020
 K5J  plan-2  N04   0.020
 K5J  plan-2  C05   0.020
 K5J  plan-2  C06   0.020
 K5J  plan-2  O20   0.020
 K5J  plan-2  H041  0.020
 K5J  plan-3  C02   0.020
 K5J  plan-3  C03   0.020
 K5J  plan-3  C23   0.020
 K5J  plan-3  O01   0.020

