# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:07:11 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4-[3-(methylsulfonyl)phenoxy]-N-[(1S,3S,5S)-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
 K5M  K5M  4-[3-(methylsulfonyl)phenoxy]-N-[(1S,3S,5S)-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_K5M
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
 K5M  C10   C  CR6   0   0.413   2.7728   0.5782  -0.1259
 K5M  C13   C  CR16  0  -0.263   5.3600   1.6306  -0.3949
 K5M  C21   C  CH2   0  -0.424  -6.7505   0.7576   1.2594
 K5M  C22   C  CR15  0  -0.262  -8.1088   0.3668   0.7056
 K5M  C24   C  CH2   0  -0.477  -8.3985  -1.0774   0.5818
 K5M  C02   C  CR5   0   0.448  -6.4543  -0.3455  -0.8673
 K5M  C03   C  CR15  0  -0.224  -5.7467  -0.0884   0.4710
 K5M  C05   C  C     0   0.569  -3.3195  -0.1987   0.1890
 K5M  C06   C  CH2   0  -0.602  -2.0884   0.6416  -0.0806
 K5M  C07   C  CH2   0  -0.456  -0.7917  -0.1306   0.1014
 K5M  C08   C  CH2   0  -0.177   0.3989   0.7664  -0.1605
 K5M  C11   C  CR16  0  -0.365   2.9606   1.9168  -0.4685
 K5M  C12   C  CR16  0  -0.228   4.2459   2.4270  -0.5990
 K5M  C14   C  CR6   0  -0.185   5.1512   0.3001  -0.0563
 K5M  C16   C  CH3   0  -0.790   6.7994  -0.6628   1.9855
 K5M  C19   C  CR16  0  -0.333   3.8853  -0.2400   0.0765
 K5M  C23   C  CR15  0  -0.401  -7.9090  -0.3136  -0.6352
 K5M  N04   N  NH1   0  -0.640  -4.4567   0.5133   0.3258
 K5M  O09   O  O2    0  -0.472   1.5762  -0.0078   0.0249
 K5M  O17   O  OS    0  -0.668   6.1819  -2.1228  -0.1178
 K5M  O18   O  OS    0  -0.668   7.7151  -0.1550  -0.4314
 K5M  O20   O  O     0  -0.492  -3.2840  -1.4151   0.2864
 K5M  S15   S  S     0   1.216   6.5553  -0.7524   0.2268
 K5M  H131  H  HCR6  0   0.281   6.3554   2.0368  -0.5042
 K5M  H212  H  HCH2  0   0.254  -6.5759   1.8188   1.0627
 K5M  H211  H  HCH2  0   0.260  -6.6715   0.6005   2.3354
 K5M  H221  H  HCR5  0   0.283  -8.9342   1.0555   0.8307
 K5M  H241  H  HCH2  0   0.268  -7.7475  -1.8079   1.0474
 K5M  H242  H  HCH2  0   0.285  -9.4364  -1.3793   0.5368
 K5M  H031  H  HCR5  0   0.297  -5.6108  -1.0603   0.9549
 K5M  H061  H  HCH2  0   0.279  -2.1611   1.0272  -1.1032
 K5M  H062  H  HCH2  0   0.267  -2.1066   1.5203   0.5707
 K5M  H071  H  HCH2  0   0.244  -0.7318  -0.5256   1.1178
 K5M  H072  H  HCH2  0   0.245  -0.7645  -0.9820  -0.5811
 K5M  H081  H  HCH2  0   0.229   0.3643   1.1642  -1.1813
 K5M  H082  H  HCH2  0   0.229   0.3966   1.6195   0.5277
 K5M  H111  H  HCR6  0   0.294   2.1200   2.5752  -0.6382
 K5M  H121  H  HCR6  0   0.277   4.3745   3.4670  -0.8675
 K5M  H161  H  HCH3  0   0.311   7.6450  -1.3051   2.2298
 K5M  H163  H  HCH3  0   0.296   7.0167   0.3650   2.2664
 K5M  H162  H  HCH3  0   0.296   5.9048  -1.0141   2.4945
 K5M  H191  H  HCR6  0   0.290   3.7391  -1.2819   0.3327
 K5M  H231  H  HCR5  0   0.287  -8.5807  -0.1788  -1.4725
 K5M  H041  H  HNH1  0   0.402  -4.4214   1.5074   0.1607
 K5M  O01   O  O     0  -0.395  -5.8876  -0.4694  -1.9252

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
 K5M  O17  S15   double    1.462  0.020  1.462
 K5M  O18  S15   double    1.461  0.020  1.461
 K5M  S15  C16   single    1.778  0.020  1.778
 K5M  S15  C14   single    1.777  0.020  1.777
 K5M  C13  C14   aromatic  1.389  0.020  1.389
 K5M  C13  C12   aromatic  1.385  0.020  1.385
 K5M  C14  C19   aromatic  1.383  0.020  1.383
 K5M  C12  C11   aromatic  1.389  0.020  1.389
 K5M  C19  C10   aromatic  1.396  0.020  1.396
 K5M  O01  C02   double    1.206  0.020  1.206
 K5M  C23  C24   single    1.518  0.020  1.518
 K5M  C23  C02   single    1.473  0.020  1.473
 K5M  C23  C22   single    1.517  0.020  1.517
 K5M  C24  C22   single    1.478  0.020  1.478
 K5M  C11  C10   aromatic  1.394  0.020  1.394
 K5M  C10  O09   single    1.341  0.020  1.341
 K5M  C02  C03   single    1.536  0.020  1.536
 K5M  C22  C21   single    1.518  0.020  1.518
 K5M  C08  O09   single    1.421  0.020  1.421
 K5M  C08  C07   single    1.514  0.020  1.514
 K5M  C03  C21   single    1.531  0.020  1.531
 K5M  C03  N04   single    1.431  0.020  1.431
 K5M  O20  C05   double    1.221  0.020  1.221
 K5M  C07  C06   single    1.520  0.020  1.520
 K5M  N04  C05   single    1.349  0.020  1.349
 K5M  C05  C06   single    1.515  0.020  1.515
 K5M  C13  H131  single    0.930  0.020  1.080
 K5M  C21  H212  single    0.970  0.020  1.090
 K5M  C21  H211  single    0.970  0.020  1.090
 K5M  C22  H221  single    0.970  0.020  1.090
 K5M  C24  H241  single    0.970  0.020  1.090
 K5M  C24  H242  single    0.970  0.020  1.090
 K5M  C03  H031  single    0.970  0.020  1.090
 K5M  C06  H061  single    0.970  0.020  1.090
 K5M  C06  H062  single    0.970  0.020  1.090
 K5M  C07  H071  single    0.970  0.020  1.090
 K5M  C07  H072  single    0.970  0.020  1.090
 K5M  C08  H081  single    0.970  0.020  1.090
 K5M  C08  H082  single    0.970  0.020  1.090
 K5M  C11  H111  single    0.930  0.020  1.080
 K5M  C12  H121  single    0.930  0.020  1.080
 K5M  C16  H161  single    0.970  0.020  1.090
 K5M  C16  H163  single    0.970  0.020  1.090
 K5M  C16  H162  single    0.970  0.020  1.090
 K5M  C19  H191  single    0.930  0.020  1.080
 K5M  C23  H231  single    0.970  0.020  1.090
 K5M  N04  H041  single    0.860  0.020  1.020

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
 K5M  O09   C10  C19   116.02  3.000
 K5M  O09   C10  C11   124.57  3.000
 K5M  C19   C10  C11   119.41  3.000
 K5M  H131  C13  C14   121.55  3.000
 K5M  H131  C13  C12   120.67  3.000
 K5M  C14   C13  C12   117.78  3.000
 K5M  H211  C21  H212  107.81  3.000
 K5M  H211  C21  C03   112.40  3.000
 K5M  H212  C21  C03   109.81  3.000
 K5M  H211  C21  C22   112.81  3.000
 K5M  H212  C21  C22   109.09  3.000
 K5M  C03   C21  C22   104.86  3.000
 K5M  H221  C22  C23   119.21  3.000
 K5M  H221  C22  C24   118.81  3.000
 K5M  C23   C22  C24    60.89  3.000
 K5M  H221  C22  C21   118.46  3.000
 K5M  C24   C22  C21   117.22  3.000
 K5M  C23   C22  C21   108.67  3.000
 K5M  H242  C24  H241  113.96  3.000
 K5M  H242  C24  C23   114.61  3.000
 K5M  H241  C24  C23   119.34  3.000
 K5M  H242  C24  C22   117.66  3.000
 K5M  H241  C24  C22   120.32  3.000
 K5M  C23   C24  C22    60.82  3.000
 K5M  O01   C02  C23   127.17  3.000
 K5M  C23   C02  C03   108.30  3.000
 K5M  O01   C02  C03   124.39  3.000
 K5M  H031  C03  N04   107.84  3.000
 K5M  H031  C03  C02   107.09  3.000
 K5M  N04   C03  C02   113.42  3.000
 K5M  H031  C03  C21   110.15  3.000
 K5M  N04   C03  C21   114.26  3.000
 K5M  C02   C03  C21   103.84  3.000
 K5M  O20   C05  N04   122.85  3.000
 K5M  N04   C05  C06   114.23  3.000
 K5M  O20   C05  C06   122.91  3.000
 K5M  H062  C06  H061  105.78  3.000
 K5M  H062  C06  C07   110.54  3.000
 K5M  H061  C06  C07   110.32  3.000
 K5M  H062  C06  C05   109.03  3.000
 K5M  H061  C06  C05   107.91  3.000
 K5M  C07   C06  C05   112.96  3.000
 K5M  H072  C07  H071  107.36  3.000
 K5M  H072  C07  C08   109.54  3.000
 K5M  H071  C07  C08   109.41  3.000
 K5M  H072  C07  C06   110.04  3.000
 K5M  H071  C07  C06   110.00  3.000
 K5M  C08   C07  C06   110.44  3.000
 K5M  H082  C08  H081  107.59  3.000
 K5M  H082  C08  O09   110.11  3.000
 K5M  H081  C08  O09   110.21  3.000
 K5M  H082  C08  C07   110.54  3.000
 K5M  H081  C08  C07   110.57  3.000
 K5M  O09   C08  C07   107.83  3.000
 K5M  H111  C11  C12   118.76  3.000
 K5M  H111  C11  C10   121.22  3.000
 K5M  C12   C11  C10   120.02  3.000
 K5M  H121  C12  C11   119.11  3.000
 K5M  H121  C12  C13   119.60  3.000
 K5M  C11   C12  C13   121.30  3.000
 K5M  S15   C14  C19   118.46  3.000
 K5M  C19   C14  C13   122.36  3.000
 K5M  S15   C14  C13   119.17  3.000
 K5M  H162  C16  H163  110.41  3.000
 K5M  H162  C16  H161  110.06  3.000
 K5M  H163  C16  H161  110.13  3.000
 K5M  H162  C16  S15   109.50  3.000
 K5M  H163  C16  S15   109.31  3.000
 K5M  H161  C16  S15   107.38  3.000
 K5M  H191  C19  C14   121.48  3.000
 K5M  H191  C19  C10   119.39  3.000
 K5M  C14   C19  C10   119.13  3.000
 K5M  H231  C23  C02   119.59  3.000
 K5M  H231  C23  C24   118.88  3.000
 K5M  C02   C23  C24   115.71  3.000
 K5M  H231  C23  C22   123.13  3.000
 K5M  C02   C23  C22   106.20  3.000
 K5M  C24   C23  C22    58.30  3.000
 K5M  H041  N04  C05   118.32  3.000
 K5M  H041  N04  C03   117.57  3.000
 K5M  C05   N04  C03   123.26  3.000
 K5M  C08   O09  C10   119.10  3.000
 K5M  O18   S15  O17   118.68  3.000
 K5M  O18   S15  C16   108.42  3.000
 K5M  O17   S15  C16   108.39  3.000
 K5M  C16   S15  C14   103.66  3.000
 K5M  O18   S15  C14   108.25  3.000
 K5M  O17   S15  C14   108.42  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
 K5M  CONST_01  C13   C14  C19  C10     0.00   0.0  0
 K5M  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 K5M  CONST_03  C14   C13  C12  C11     0.00   0.0  0
 K5M  CONST_04  C14   C19  C10  C11     0.00   0.0  0
 K5M  CONST_05  C19   C14  C13  C12     0.00   0.0  0
 K5M  CONST_06  C19   C10  C11  C12     0.00   0.0  0
 K5M  CONST_07  S15   C14  C19  C10   180.00   0.0  0
 K5M  CONST_08  S15   C14  C13  C12   180.00   0.0  0
 K5M  CONST_09  O09   C10  C11  C12   180.00   0.0  0
 K5M  CONST_10  O09   C10  C19  C14   180.00   0.0  0
 K5M  CONST_11  H121  C12  C11  C10   180.00   0.0  0
 K5M  CONST_12  H191  C19  C14  C13   180.00   0.0  0
 K5M  CONST_13  H111  C11  C12  C13   180.00   0.0  0
 K5M  CONST_14  H131  C13  C12  C11   180.00   0.0  0
 K5M  CONST_15  O20   C05  N04  C03     0.00   0.0  0
 K5M  CONST_16  C06   C05  N04  C03   180.00   0.0  0
 K5M  CONST_17  H041  N04  C05  C06     0.00   0.0  0
 K5M  Var_01    C24   C23  C22  C21   111.38  30.0  1
 K5M  Var_02    C03   C02  C23  C22    16.87  30.0  1
 K5M  Var_03    C03   C21  C22  C24    48.30  30.0  1
 K5M  Var_04    O17   S15  C14  C13  -151.10  30.0  2
 K5M  Var_05    C19   C10  O09  C08   179.74  30.0  2
 K5M  Var_06    C07   C08  O09  C10  -178.68  30.0  1
 K5M  Var_07    H161  C16  S15  C14   179.14  30.0  3
 K5M  Var_08    C08   C07  C06  C05  -179.12  30.0  1
 K5M  Var_09    O09   C08  C07  C06   179.97  30.0  1
 K5M  Var_10    O20   C05  C06  C07   -13.22  30.0  2

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
 K5M  chir_02  C03  C02  C21  N04  positiv
 K5M  chir_03  C22  C23  C24  C21  both
 K5M  chir_04  C23  C22  C02  C24  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
 K5M  plan-1  C10   0.020
 K5M  plan-1  C13   0.020
 K5M  plan-1  C11   0.020
 K5M  plan-1  C12   0.020
 K5M  plan-1  C14   0.020
 K5M  plan-1  C19   0.020
 K5M  plan-1  O09   0.020
 K5M  plan-1  S15   0.020
 K5M  plan-1  H131  0.020
 K5M  plan-1  H111  0.020
 K5M  plan-1  H121  0.020
 K5M  plan-1  H191  0.020
 K5M  plan-2  C03   0.020
 K5M  plan-2  C05   0.020
 K5M  plan-2  C06   0.020
 K5M  plan-2  N04   0.020
 K5M  plan-2  O20   0.020
 K5M  plan-2  H041  0.020
 K5M  plan-3  C02   0.020
 K5M  plan-3  C03   0.020
 K5M  plan-3  C23   0.020
 K5M  plan-3  O01   0.020

