# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 27 12:14:29 2020
#   Inital geometry file: a 171 line input string
#   Ligand name: 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1/C=C/C=C\CC/C=C/C(=O)O[C@H]1C(/C)=C/[C@H](C)C(=O)C[C@H](O)CC2CC(=O)NC(=O)C2
#
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
 3H3  3H3  4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione  ligand  68  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3H3
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
 3H3  C7   C  CH2   0  -0.480  19.3938  -42.9704  82.8399
 3H3  C8   C  C1    0  -0.140  20.3482  -43.8864  82.1622
 3H3  C2   C  C1    0  -0.234  23.5955  -44.8801  83.8992
 3H3  C3   C  C1    0  -0.244  22.7265  -43.8899  84.1182
 3H3  C4   C  C1    0  -0.227  21.6903  -43.9161  85.1395
 3H3  C5   C  C1    0  -0.223  20.5519  -43.2112  85.0951
 3H3  C6   C  CH2   0  -0.523  20.1271  -42.2644  84.0099
 3H3  C1   C  CH1   0  -0.272  24.4834  -44.9806  82.6903
 3H3  O1   O  O2    0  -0.479  22.4909  -45.4594  81.4222
 3H3  C23  C  C     0   0.551  30.2088  -40.9521  83.7389
 3H3  N    N  NH1   0  -0.677  31.0509  -41.7443  84.4900
 3H3  C22  C  C     0   0.556  31.4467  -43.0381  84.2264
 3H3  C21  C  CH2   0  -0.577  30.8792  -43.6691  82.9863
 3H3  C24  C  CH2   0  -0.562  29.6497  -41.5786  82.4947
 3H3  C20  C  CH1   0  -0.311  29.5254  -43.0937  82.5894
 3H3  C19  C  CH2   0  -0.419  29.0101  -43.6605  81.2713
 3H3  C18  C  CH1   0   0.046  28.7789  -45.1703  81.2625
 3H3  O5   O  OH1   0  -0.656  27.9136  -45.5862  82.2990
 3H3  C16  C  C     0   0.445  27.8473  -47.0679  79.8659
 3H3  O2   O  O     0  -0.402  28.6622  -47.8918  80.2110
 3H3  C14  C  CH1   0  -0.445  26.4789  -47.4558  79.3278
 3H3  C15  C  CH3   0  -0.648  26.3972  -48.9193  78.9163
 3H3  C13  C  C1    0  -0.219  25.4942  -47.1330  80.4179
 3H3  C12  C  C     0   0.086  24.5794  -46.1620  80.4177
 3H3  C25  C  CH3   0  -0.757  24.3312  -45.2491  79.2478
 3H3  C11  C  CH1   0  -0.030  23.8034  -45.9617  81.6983
 3H3  C    C  CH3   0  -0.690  24.8445  -43.6393  82.0664
 3H3  C10  C  C     0   0.577  21.4272  -46.0986  81.9121
 3H3  O    O  O     0  -0.457  21.4135  -47.2838  82.1538
 3H3  C9   C  C1    0  -0.376  20.2908  -45.2172  82.2171
 3H3  H1   H  HCH2  0   0.258  19.0406  -42.2000  82.1498
 3H3  H2   H  HCH2  0   0.247  18.5221  -43.5126  83.2112
 3H3  H3   H  H     0   0.271  21.2065  -43.4048  81.7053
 3H3  H4   H  H     0   0.244  23.5886  -45.7462  84.5581
 3H3  H6   H  H     0   0.242  22.7286  -43.0431  83.4411
 3H3  H8   H  H     0   0.241  21.8278  -44.6204  85.9547
 3H3  H9   H  H     0   0.241  19.8284  -43.3755  85.8869
 3H3  H10  H  HCH2  0   0.248  20.9800  -41.7162  83.6014
 3H3  H11  H  HCH2  0   0.259  19.4529  -41.5146  84.4272
 3H3  H12  H  HCH1  0   0.262  25.4170  -45.4735  82.9743
 3H3  H14  H  HCH2  0   0.288  31.6013  -43.5070  82.1766
 3H3  H15  H  HCH2  0   0.287  30.8445  -44.7454  83.1578
 3H3  H16  H  HCH2  0   0.284  30.3196  -41.3109  81.6685
 3H3  H17  H  HCH2  0   0.288  28.6887  -41.1089  82.2824
 3H3  H18  H  HCH1  0   0.258  28.7988  -43.3206  83.3777
 3H3  H19  H  HCH2  0   0.232  29.7194  -43.4131  80.4739
 3H3  H20  H  HCH2  0   0.240  28.0700  -43.1574  81.0225
 3H3  H21  H  HCH1  0   0.223  29.7461  -45.6825  81.3466
 3H3  H22  H  HOH1  0   0.451  28.3996  -45.6081  83.1283
 3H3  H25  H  HCH1  0   0.275  26.2829  -46.8162  78.4611
 3H3  H26  H  HCH3  0   0.237  25.4152  -49.1310  78.4942
 3H3  H27  H  HCH3  0   0.236  27.1458  -49.1648  78.1627
 3H3  H28  H  HCH3  0   0.228  26.5438  -49.5842  79.7673
 3H3  H29  H  H     0   0.242  25.5784  -47.7626  81.3013
 3H3  H30  H  HCH3  0   0.259  23.3653  -44.7538  79.3162
 3H3  H31  H  HCH3  0   0.245  25.0831  -44.4612  79.1672
 3H3  H32  H  HCH3  0   0.254  24.3476  -45.8005  78.3075
 3H3  H33  H  HCH1  0   0.263  23.7210  -46.9282  82.2004
 3H3  H34  H  HCH3  0   0.239  25.2524  -42.9684  82.8228
 3H3  H35  H  HCH3  0   0.244  25.6126  -43.7669  81.3046
 3H3  H36  H  HCH3  0   0.226  23.9905  -43.1444  81.6025
 3H3  H37  H  H     0   0.262  19.4401  -45.7122  82.6712
 3H3  C17  C  CH2   0  -0.571  28.1319  -45.5861  79.9511
 3H3  H13  H  HNH1  0   0.414  31.4445  -41.3172  85.3214
 3H3  O3   O  O     0  -0.433  32.2249  -43.5985  84.9657
 3H3  O4   O  O     0  -0.434  29.9734  -39.8154  84.0837
 3H3  H23  H  HCH2  0   0.286  28.8009  -45.3362  79.1207
 3H3  H24  H  HCH2  0   0.255  27.2146  -45.0173  79.7873

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
 3H3  C15  C14  single  1.522  0.020  1.522
 3H3  C14  C16  single  1.521  0.020  1.521
 3H3  C14  C13  single  1.504  0.020  1.504
 3H3  O2   C16  double  1.209  0.020  1.209
 3H3  C16  C17  single  1.511  0.020  1.511
 3H3  C25  C12  single  1.505  0.020  1.505
 3H3  C13  C12  double  1.334  0.020  1.334
 3H3  C17  C18  single  1.520  0.020  1.520
 3H3  C12  C11  single  1.511  0.020  1.511
 3H3  C18  C19  single  1.527  0.020  1.527
 3H3  C18  O5   single  1.413  0.020  1.413
 3H3  C21  C22  single  1.503  0.020  1.503
 3H3  C21  C20  single  1.524  0.020  1.524
 3H3  C9   C8   double  1.333  0.020  1.333
 3H3  C9   C10  single  1.470  0.020  1.470
 3H3  C19  C20  single  1.524  0.020  1.524
 3H3  C7   C8   single  1.486  0.020  1.486
 3H3  C7   C6   single  1.551  0.020  1.551
 3H3  O    C10  double  1.210  0.020  1.210
 3H3  C10  O1   single  1.334  0.020  1.334
 3H3  O3   C22  double  1.211  0.020  1.211
 3H3  O1   C11  single  1.432  0.020  1.432
 3H3  C22  N    single  1.378  0.020  1.378
 3H3  C11  C1   single  1.552  0.020  1.552
 3H3  C6   C5   single  1.501  0.020  1.501
 3H3  C20  C24  single  1.523  0.020  1.523
 3H3  C24  C23  single  1.501  0.020  1.501
 3H3  C    C1   single  1.523  0.020  1.523
 3H3  N    C23  single  1.379  0.020  1.379
 3H3  C1   C2   single  1.503  0.020  1.503
 3H3  C3   C2   double  1.336  0.020  1.336
 3H3  C3   C4   single  1.455  0.020  1.455
 3H3  C23  O4   double  1.211  0.020  1.211
 3H3  C5   C4   double  1.340  0.020  1.340
 3H3  C7   H1   single  0.970  0.020  1.090
 3H3  C7   H2   single  0.970  0.020  1.090
 3H3  C8   H3   single  0.930  0.020  1.080
 3H3  C2   H4   single  0.930  0.020  1.080
 3H3  C3   H6   single  0.930  0.020  1.080
 3H3  C4   H8   single  0.930  0.020  1.080
 3H3  C5   H9   single  0.930  0.020  1.080
 3H3  C6   H10  single  0.970  0.020  1.090
 3H3  C6   H11  single  0.970  0.020  1.090
 3H3  C1   H12  single  0.970  0.020  1.090
 3H3  N    H13  single  0.860  0.020  1.020
 3H3  C21  H14  single  0.970  0.020  1.090
 3H3  C21  H15  single  0.970  0.020  1.090
 3H3  C24  H16  single  0.970  0.020  1.090
 3H3  C24  H17  single  0.970  0.020  1.090
 3H3  C20  H18  single  0.970  0.020  1.090
 3H3  C19  H19  single  0.970  0.020  1.090
 3H3  C19  H20  single  0.970  0.020  1.090
 3H3  C18  H21  single  0.970  0.020  1.090
 3H3  O5   H22  single  0.850  0.020  0.980
 3H3  C17  H23  single  0.970  0.020  1.090
 3H3  C17  H24  single  0.970  0.020  1.090
 3H3  C14  H25  single  0.970  0.020  1.090
 3H3  C15  H26  single  0.970  0.020  1.090
 3H3  C15  H27  single  0.970  0.020  1.090
 3H3  C15  H28  single  0.970  0.020  1.090
 3H3  C13  H29  single  0.930  0.020  1.080
 3H3  C25  H30  single  0.970  0.020  1.090
 3H3  C25  H31  single  0.970  0.020  1.090
 3H3  C25  H32  single  0.970  0.020  1.090
 3H3  C11  H33  single  0.970  0.020  1.090
 3H3  C    H34  single  0.970  0.020  1.090
 3H3  C    H35  single  0.970  0.020  1.090
 3H3  C    H36  single  0.970  0.020  1.090
 3H3  C9   H37  single  0.930  0.020  1.080

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
 3H3  H2   C7   H1   107.86  3.000
 3H3  H2   C7   C6   110.31  3.000
 3H3  H1   C7   C6   107.96  3.000
 3H3  H2   C7   C8   111.21  3.000
 3H3  H1   C7   C8   110.73  3.000
 3H3  C6   C7   C8   108.72  3.000
 3H3  H3   C8   C9   119.63  3.000
 3H3  H3   C8   C7   115.24  3.000
 3H3  C9   C8   C7   124.66  3.000
 3H3  H4   C2   C1   115.94  3.000
 3H3  H4   C2   C3   119.12  3.000
 3H3  C1   C2   C3   124.46  3.000
 3H3  H6   C3   C4   116.99  3.000
 3H3  H6   C3   C2   118.38  3.000
 3H3  C4   C3   C2   124.41  3.000
 3H3  H8   C4   C5   118.27  3.000
 3H3  H8   C4   C3   116.64  3.000
 3H3  C5   C4   C3   124.92  3.000
 3H3  H9   C5   C6   115.73  3.000
 3H3  H9   C5   C4   117.57  3.000
 3H3  C6   C5   C4   126.59  3.000
 3H3  H11  C6   H10  106.29  3.000
 3H3  H11  C6   C5   109.37  3.000
 3H3  H10  C6   C5   111.44  3.000
 3H3  H11  C6   C7   108.00  3.000
 3H3  H10  C6   C7   108.38  3.000
 3H3  C5   C6   C7   113.08  3.000
 3H3  H12  C1   C    107.52  3.000
 3H3  H12  C1   C11  104.78  3.000
 3H3  C    C1   C11  113.50  3.000
 3H3  H12  C1   C2   109.01  3.000
 3H3  C    C1   C2   114.25  3.000
 3H3  C11  C1   C2   107.31  3.000
 3H3  C10  O1   C11  119.46  3.000
 3H3  C24  C23  N    116.06  3.000
 3H3  N    C23  O4   120.19  3.000
 3H3  C24  C23  O4   123.74  3.000
 3H3  H13  N    C22  116.14  3.000
 3H3  H13  N    C23  116.21  3.000
 3H3  C22  N    C23  127.62  3.000
 3H3  C21  C22  N    116.33  3.000
 3H3  N    C22  O3   120.14  3.000
 3H3  C21  C22  O3   123.52  3.000
 3H3  H15  C21  H14  106.43  3.000
 3H3  H15  C21  C20  112.67  3.000
 3H3  H14  C21  C20  109.69  3.000
 3H3  H15  C21  C22  107.26  3.000
 3H3  H14  C21  C22  107.37  3.000
 3H3  C20  C21  C22  113.08  3.000
 3H3  H17  C24  H16  106.65  3.000
 3H3  H17  C24  C20  111.63  3.000
 3H3  H16  C24  C20  109.84  3.000
 3H3  H17  C24  C23  108.05  3.000
 3H3  H16  C24  C23  107.16  3.000
 3H3  C20  C24  C23  113.21  3.000
 3H3  H18  C20  C19  108.72  3.000
 3H3  H18  C20  C24  107.75  3.000
 3H3  C19  C20  C24  110.10  3.000
 3H3  H18  C20  C21  108.88  3.000
 3H3  C24  C20  C21  108.62  3.000
 3H3  C19  C20  C21  112.66  3.000
 3H3  H20  C19  H19  106.67  3.000
 3H3  H20  C19  C18  108.84  3.000
 3H3  H19  C19  C18  108.48  3.000
 3H3  H20  C19  C20  108.41  3.000
 3H3  H19  C19  C20  109.06  3.000
 3H3  C18  C19  C20  115.06  3.000
 3H3  H21  C18  C17  108.27  3.000
 3H3  H21  C18  O5   110.25  3.000
 3H3  C17  C18  O5   106.95  3.000
 3H3  H21  C18  C19  109.11  3.000
 3H3  O5   C18  C19  112.30  3.000
 3H3  C17  C18  C19  109.86  3.000
 3H3  H22  O5   C18  109.26  3.000
 3H3  C14  C16  O2   122.25  3.000
 3H3  O2   C16  C17  121.68  3.000
 3H3  C14  C16  C17  116.07  3.000
 3H3  H25  C14  C13  109.34  3.000
 3H3  H25  C14  C15  109.76  3.000
 3H3  C13  C14  C15  111.54  3.000
 3H3  H25  C14  C16  106.99  3.000
 3H3  C13  C14  C16  106.14  3.000
 3H3  C15  C14  C16  112.90  3.000
 3H3  H28  C15  H27  108.06  3.000
 3H3  H28  C15  H26  107.77  3.000
 3H3  H27  C15  H26  107.90  3.000
 3H3  H28  C15  C14  111.60  3.000
 3H3  H27  C15  C14  111.50  3.000
 3H3  H26  C15  C14  109.87  3.000
 3H3  H29  C13  C12  118.31  3.000
 3H3  H29  C13  C14  114.44  3.000
 3H3  C12  C13  C14  127.23  3.000
 3H3  C11  C12  C25  119.60  3.000
 3H3  C11  C12  C13  116.65  3.000
 3H3  C25  C12  C13  123.70  3.000
 3H3  H32  C25  H31  106.91  3.000
 3H3  H32  C25  H30  107.33  3.000
 3H3  H31  C25  H30  106.71  3.000
 3H3  H32  C25  C12  111.18  3.000
 3H3  H31  C25  C12  112.43  3.000
 3H3  H30  C25  C12  111.96  3.000
 3H3  H33  C11  C12  108.13  3.000
 3H3  H33  C11  O1   109.26  3.000
 3H3  C12  C11  O1   110.72  3.000
 3H3  H33  C11  C1   107.37  3.000
 3H3  O1   C11  C1   107.64  3.000
 3H3  C12  C11  C1   113.61  3.000
 3H3  H36  C    H35  107.94  3.000
 3H3  H36  C    H34  107.99  3.000
 3H3  H35  C    H34  107.07  3.000
 3H3  H36  C    C1   112.84  3.000
 3H3  H35  C    C1   110.52  3.000
 3H3  H34  C    C1   110.27  3.000
 3H3  C9   C10  O    122.50  3.000
 3H3  O    C10  O1   123.49  3.000
 3H3  C9   C10  O1   113.90  3.000
 3H3  H37  C9   C10  114.82  3.000
 3H3  H37  C9   C8   120.46  3.000
 3H3  C10  C9   C8   123.82  3.000
 3H3  H24  C17  H23  106.29  3.000
 3H3  H24  C17  C16  110.13  3.000
 3H3  H23  C17  C16  107.22  3.000
 3H3  H24  C17  C18  110.16  3.000
 3H3  H23  C17  C18  109.37  3.000
 3H3  C16  C17  C18  113.39  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
 3H3  CONST_01  C24  C23  N    C22     0.00   0.0  0
 3H3  CONST_02  C22  N    C23  O4    180.00   0.0  0
 3H3  CONST_03  H13  N    C23  C24   180.00   0.0  0
 3H3  Var_01    C10  C9   C8   C7   -160.43   0.0  0
 3H3  Var_02    C6   C5   C4   C3     -0.42   0.0  0
 3H3  Var_03    C1   C2   C3   C4    167.47   0.0  0
 3H3  Var_04    C4   C5   C6   C7     86.40  30.0  1
 3H3  Var_05    O1   C10  C9   C8     -7.33  30.0  1
 3H3  Var_06    C5   C4   C3   C2   -155.20  30.0  1
 3H3  Var_07    C9   C8   C7   C6    109.59  30.0  1
 3H3  Var_08    C21  C22  N    C23    -1.00  30.0  1
 3H3  Var_09    C20  C21  C22  N     -27.16  30.0  1
 3H3  Var_10    C20  C24  C23  N      28.06  30.0  1
 3H3  Var_11    C9   C10  O1   C11   148.59  30.0  1
 3H3  Var_12    H9   C5   C4   C3    175.65   0.0  0
 3H3  Var_13    H6   C3   C2   C1     -6.95   0.0  0
 3H3  Var_14    H3   C8   C9   C10    11.35   0.0  0
 3H3  Var_15    C11  C12  C13  C14  -174.02   0.0  2
 3H3  Var_16    H30  C25  C12  C11   -20.66  30.0  3
 3H3  Var_17    C14  C16  C17  C18   135.05  30.0  1

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
 3H3  chir_01  C1   C11  C    C2   negativ
 3H3  chir_02  C20  C21  C19  C24  positiv
 3H3  chir_03  C18  O5   C19  C17  positiv
 3H3  chir_04  C14  C13  C16  C15  negativ
 3H3  chir_05  C11  O1   C12  C1   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
 3H3  plan-1  O1   0.020
 3H3  plan-1  C10  0.020
 3H3  plan-1  O    0.020
 3H3  plan-1  C9   0.020
 3H3  plan-2  C2   0.020
 3H3  plan-2  C3   0.020
 3H3  plan-2  C4   0.020
 3H3  plan-2  C1   0.020
 3H3  plan-2  H4   0.020
 3H3  plan-2  H6   0.020
 3H3  plan-3  C3   0.020
 3H3  plan-3  C4   0.020
 3H3  plan-3  C5   0.020
 3H3  plan-3  C6   0.020
 3H3  plan-3  H8   0.020
 3H3  plan-3  H9   0.020
 3H3  plan-4  N    0.020
 3H3  plan-4  C22  0.020
 3H3  plan-4  C21  0.020
 3H3  plan-4  O3   0.020
 3H3  plan-5  C16  0.020
 3H3  plan-5  O2   0.020
 3H3  plan-5  C14  0.020
 3H3  plan-5  C17  0.020
 3H3  plan-6  C23  0.020
 3H3  plan-6  N    0.020
 3H3  plan-6  C22  0.020
 3H3  plan-6  C24  0.020
 3H3  plan-6  H13  0.020
 3H3  plan-6  O4   0.020
 3H3  plan-7  C14  0.020
 3H3  plan-7  C13  0.020
 3H3  plan-7  C12  0.020
 3H3  plan-7  C25  0.020
 3H3  plan-7  C11  0.020
 3H3  plan-7  H29  0.020
 3H3  plan-8  C7   0.020
 3H3  plan-8  C8   0.020
 3H3  plan-8  C10  0.020
 3H3  plan-8  C9   0.020
 3H3  plan-8  H3   0.020
 3H3  plan-8  H37  0.020

