# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:15:53 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: ethyl (4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}-2,6-dioxopiperidin-1-yl)acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CN1C(=O)CC(C[C@@H](O)[C@@H]2C[C@@H](C)C[C@H](C)C2=O)CC1=O
#
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
 JZF  JZF  'ethyl (4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}-2,6-dioxopiperidin-1-yl)acetate'  ligand  55  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JZF
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
 JZF  N1    N  NT    0  -0.537  -2.9260  -0.0047  -0.6116
 JZF  O1    O  O     0  -0.401   4.4656   2.0438  -0.8556
 JZF  C2    C  C     0   0.578  -2.4340  -1.2871  -0.8125
 JZF  O2    O  O     0  -0.437  -3.1464  -2.1474  -1.2786
 JZF  C3    C  CH2   0  -0.567  -1.0091  -1.5453  -0.4201
 JZF  O3    O  O     0  -0.438  -2.8399   1.9954   0.4173
 JZF  C4    C  CH1   0  -0.277  -0.1384  -0.2987  -0.3965
 JZF  O4    O  O     0  -0.442  -4.8442  -0.5455   1.2470
 JZF  C5    C  CH2   0  -0.569  -0.8323   0.7191   0.4946
 JZF  O5    O  O2    0  -0.453  -6.4645   0.2524  -0.0744
 JZF  C6    C  C     0   0.581  -2.2608   0.9767   0.1127
 JZF  C7    C  CH2   0  -0.457   1.2749  -0.6606   0.0556
 JZF  C8    C  CH1   0   0.052   2.3071   0.4592  -0.0751
 JZF  C9    C  CH1   0  -0.395   3.7385  -0.0912  -0.0398
 JZF  OH    O  OH1   0  -0.663   2.1177   1.4867   0.8762
 JZF  C10   C  C     0   0.449   4.7673   0.9309  -0.4876
 JZF  C11   C  CH1   0  -0.370   6.2021   0.4482  -0.4733
 JZF  C12   C  CH2   0  -0.415   6.5359  -0.1351   0.9082
 JZF  C13   C  CH1   0  -0.248   5.5622  -1.2220   1.3573
 JZF  C14   C  CH2   0  -0.447   4.1346  -0.6757   1.3273
 JZF  C15   C  CH2   0  -0.468  -4.3049   0.2518  -0.9570
 JZF  C16   C  CH2   0  -0.181  -7.4685   0.0181   0.9311
 JZF  C17   C  CH3   0  -0.690  -8.7903   0.4970   0.3847
 JZF  C18   C  CH3   0  -0.653   7.1965   1.5205  -0.8858
 JZF  C19   C  CH3   0  -0.665   5.7135  -2.5141   0.5589
 JZF  C21   C  C     0   0.602  -5.2165  -0.0645   0.2089
 JZF  H13   H  HCH2  0   0.284  -1.0291  -1.9988   0.5787
 JZF  H23   H  HCH2  0   0.291  -0.6153  -2.3053  -1.0961
 JZF  H4    H  HCH1  0   0.258  -0.0773   0.1039  -1.4139
 JZF  H15   H  HCH2  0   0.279  -0.8371   0.3572   1.5303
 JZF  H25   H  HCH2  0   0.298  -0.3244   1.6812   0.5073
 JZF  H17   H  HCH2  0   0.235   1.2401  -1.0340   1.0864
 JZF  H27   H  HCH2  0   0.248   1.6118  -1.5041  -0.5549
 JZF  H8    H  HCH1  0   0.238   2.1585   0.9322  -1.0510
 JZF  H9    H  HCH1  0   0.273   3.7918  -0.9011  -0.7796
 JZF  H1OH  H  HOH1  0   0.444   2.0334   1.0887   1.7484
 JZF  H11   H  HCH1  0   0.264   6.2472  -0.3692  -1.2051
 JZF  H112  H  HCH2  0   0.240   7.5581  -0.5227   0.8886
 JZF  H212  H  HCH2  0   0.232   6.5303   0.6801   1.6401
 JZF  H13A  H  HCH1  0   0.241   5.7954  -1.4583   2.4003
 JZF  H114  H  HCH2  0   0.233   4.0446   0.1020   2.0922
 JZF  H214  H  HCH2  0   0.253   3.4322  -1.4671   1.6026
 JZF  H115  H  HCH2  0   0.315  -4.4279   1.2922  -1.2535
 JZF  H215  H  HCH2  0   0.319  -4.5893  -0.3575  -1.8140
 JZF  H116  H  HCH2  0   0.240  -7.5038  -1.0468   1.1673
 JZF  H216  H  HCH2  0   0.240  -7.2014   0.5575   1.8415
 JZF  H117  H  HCH3  0   0.238  -8.7654   1.5604   0.1473
 JZF  H217  H  HCH3  0   0.238  -9.0806  -0.0548  -0.5092
 JZF  H317  H  HCH3  0   0.242  -9.5623   0.3408   1.1376
 JZF  H118  H  HCH3  0   0.222   7.2073   2.3502  -0.1771
 JZF  H218  H  HCH3  0   0.231   8.2022   1.0998  -0.9157
 JZF  H318  H  HCH3  0   0.234   6.9779   1.9253  -1.8734
 JZF  H119  H  HCH3  0   0.231   6.7345  -2.8927   0.6273
 JZF  H219  H  HCH3  0   0.231   5.0488  -3.2880   0.9459
 JZF  H319  H  HCH3  0   0.220   5.4837  -2.3907  -0.5008

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
 JZF  N1   C2    single  1.388  0.020  1.388
 JZF  N1   C6    single  1.389  0.020  1.389
 JZF  N1   C15   single  1.444  0.020  1.444
 JZF  O1   C10   double  1.210  0.020  1.210
 JZF  C2   O2    double  1.210  0.020  1.210
 JZF  C2   C3    single  1.500  0.020  1.500
 JZF  C3   C4    single  1.521  0.020  1.521
 JZF  C3   H13   single  0.970  0.020  1.090
 JZF  C3   H23   single  0.970  0.020  1.090
 JZF  O3   C6    double  1.211  0.020  1.211
 JZF  C4   C5    single  1.520  0.020  1.520
 JZF  C4   C7    single  1.527  0.020  1.527
 JZF  C4   H4    single  0.970  0.020  1.090
 JZF  O4   C21   double  1.203  0.020  1.203
 JZF  C5   C6    single  1.501  0.020  1.501
 JZF  C5   H15   single  0.970  0.020  1.090
 JZF  C5   H25   single  0.970  0.020  1.090
 JZF  O5   C16   single  1.440  0.020  1.440
 JZF  O5   C21   single  1.318  0.020  1.318
 JZF  C7   C8    single  1.529  0.020  1.529
 JZF  C7   H17   single  0.970  0.020  1.090
 JZF  C7   H27   single  0.970  0.020  1.090
 JZF  C8   C9    single  1.534  0.020  1.534
 JZF  C8   OH    single  1.413  0.020  1.413
 JZF  C8   H8    single  0.970  0.020  1.090
 JZF  C9   C10   single  1.518  0.020  1.518
 JZF  C9   C14   single  1.539  0.020  1.539
 JZF  C9   H9    single  0.970  0.020  1.090
 JZF  OH   H1OH  single  0.850  0.020  0.980
 JZF  C10  C11   single  1.514  0.020  1.514
 JZF  C11  C12   single  1.536  0.020  1.536
 JZF  C11  C18   single  1.519  0.020  1.519
 JZF  C11  H11   single  0.970  0.020  1.090
 JZF  C12  C13   single  1.527  0.020  1.527
 JZF  C12  H112  single  0.970  0.020  1.090
 JZF  C12  H212  single  0.970  0.020  1.090
 JZF  C13  C14   single  1.529  0.020  1.529
 JZF  C13  C19   single  1.526  0.020  1.526
 JZF  C13  H13A  single  0.970  0.020  1.090
 JZF  C14  H114  single  0.970  0.020  1.090
 JZF  C14  H214  single  0.970  0.020  1.090
 JZF  C15  C21   single  1.513  0.020  1.513
 JZF  C15  H115  single  0.970  0.020  1.090
 JZF  C15  H215  single  0.970  0.020  1.090
 JZF  C16  C17   single  1.508  0.020  1.508
 JZF  C16  H116  single  0.970  0.020  1.090
 JZF  C16  H216  single  0.970  0.020  1.090
 JZF  C17  H117  single  0.970  0.020  1.090
 JZF  C17  H217  single  0.970  0.020  1.090
 JZF  C17  H317  single  0.970  0.020  1.090
 JZF  C18  H118  single  0.970  0.020  1.090
 JZF  C18  H218  single  0.970  0.020  1.090
 JZF  C18  H318  single  0.970  0.020  1.090
 JZF  C19  H119  single  0.970  0.020  1.090
 JZF  C19  H219  single  0.970  0.020  1.090
 JZF  C19  H319  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
 JZF  C15   N1   C6    117.15  3.000
 JZF  C15   N1   C2    117.89  3.000
 JZF  C6    N1   C2    123.94  3.000
 JZF  C3    C2   O2    122.50  3.000
 JZF  C3    C2   N1    117.24  3.000
 JZF  O2    C2   N1    120.25  3.000
 JZF  H23   C3   H13   106.43  3.000
 JZF  H23   C3   C4    111.97  3.000
 JZF  H13   C3   C4    109.58  3.000
 JZF  H23   C3   C2    107.50  3.000
 JZF  H13   C3   C2    106.97  3.000
 JZF  C4    C3   C2    114.00  3.000
 JZF  H4    C4   C7    108.08  3.000
 JZF  H4    C4   C5    108.88  3.000
 JZF  C7    C4   C5    114.05  3.000
 JZF  H4    C4   C3    108.58  3.000
 JZF  C7    C4   C3    109.88  3.000
 JZF  C5    C4   C3    107.25  3.000
 JZF  H25   C5   H15   106.42  3.000
 JZF  H25   C5   C6    107.19  3.000
 JZF  H15   C5   C6    107.02  3.000
 JZF  H25   C5   C4    112.69  3.000
 JZF  H15   C5   C4    109.53  3.000
 JZF  C6    C5   C4    113.59  3.000
 JZF  C21   O5   C16   118.09  3.000
 JZF  C5    C6   O3    122.38  3.000
 JZF  C5    C6   N1    117.85  3.000
 JZF  O3    C6   N1    119.77  3.000
 JZF  H27   C7   H17   105.76  3.000
 JZF  H27   C7   C8    108.00  3.000
 JZF  H17   C7   C8    110.56  3.000
 JZF  H27   C7   C4    107.61  3.000
 JZF  H17   C7   C4    109.24  3.000
 JZF  C8    C7   C4    115.21  3.000
 JZF  H8    C8   OH    105.53  3.000
 JZF  H8    C8   C9    107.59  3.000
 JZF  OH    C8   C9    111.75  3.000
 JZF  H8    C8   C7    107.52  3.000
 JZF  OH    C8   C7    112.62  3.000
 JZF  C9    C8   C7    111.43  3.000
 JZF  H9    C9   C14   107.81  3.000
 JZF  H9    C9   C10   105.37  3.000
 JZF  C14   C9   C10   110.09  3.000
 JZF  H9    C9   C8    107.12  3.000
 JZF  C14   C9   C8    113.39  3.000
 JZF  C10   C9   C8    112.59  3.000
 JZF  H1OH  OH   C8    108.73  3.000
 JZF  C11   C10  C9    115.14  3.000
 JZF  C11   C10  O1    122.16  3.000
 JZF  C9    C10  O1    122.68  3.000
 JZF  H11   C11  C18   108.51  3.000
 JZF  H11   C11  C12   107.92  3.000
 JZF  C18   C11  C12   111.71  3.000
 JZF  H11   C11  C10   105.66  3.000
 JZF  C18   C11  C10   113.12  3.000
 JZF  C12   C11  C10   109.60  3.000
 JZF  H212  C12  H112  106.29  3.000
 JZF  H212  C12  C13   109.26  3.000
 JZF  H112  C12  C13   110.43  3.000
 JZF  H212  C12  C11   108.49  3.000
 JZF  H112  C12  C11   108.76  3.000
 JZF  C13   C12  C11   113.34  3.000
 JZF  H13A  C13  C19   107.13  3.000
 JZF  H13A  C13  C14   107.15  3.000
 JZF  C19   C13  C14   112.63  3.000
 JZF  H13A  C13  C12   107.35  3.000
 JZF  C19   C13  C12   112.68  3.000
 JZF  C14   C13  C12   109.59  3.000
 JZF  H214  C14  H114  106.58  3.000
 JZF  H214  C14  C13   109.65  3.000
 JZF  H114  C14  C13   108.48  3.000
 JZF  H214  C14  C9    109.47  3.000
 JZF  H114  C14  C9    109.26  3.000
 JZF  C13   C14  C9    113.18  3.000
 JZF  H215  C15  H115  106.90  3.000
 JZF  H215  C15  C21   109.39  3.000
 JZF  H115  C15  C21   109.97  3.000
 JZF  H215  C15  N1    109.76  3.000
 JZF  H115  C15  N1    110.04  3.000
 JZF  C21   C15  N1    110.71  3.000
 JZF  H216  C16  H116  108.04  3.000
 JZF  H216  C16  C17   111.08  3.000
 JZF  H116  C16  C17   111.09  3.000
 JZF  H216  C16  O5    109.35  3.000
 JZF  H116  C16  O5    109.41  3.000
 JZF  C17   C16  O5    107.84  3.000
 JZF  H317  C17  H217  107.79  3.000
 JZF  H317  C17  H117  107.86  3.000
 JZF  H217  C17  H117  108.75  3.000
 JZF  H317  C17  C16   108.97  3.000
 JZF  H217  C17  C16   111.70  3.000
 JZF  H117  C17  C16   111.63  3.000
 JZF  H318  C18  H218  107.67  3.000
 JZF  H318  C18  H118  107.95  3.000
 JZF  H218  C18  H118  107.58  3.000
 JZF  H318  C18  C11   112.14  3.000
 JZF  H218  C18  C11   109.80  3.000
 JZF  H118  C18  C11   111.51  3.000
 JZF  H319  C19  H219  107.24  3.000
 JZF  H319  C19  H119  107.29  3.000
 JZF  H219  C19  H119  107.56  3.000
 JZF  H319  C19  C13   113.04  3.000
 JZF  H219  C19  C13   110.76  3.000
 JZF  H119  C19  C13   110.71  3.000
 JZF  C15   C21  O5    110.76  3.000
 JZF  C15   C21  O4    124.18  3.000
 JZF  O5    C21  O4    125.06  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
 JZF  CONST_01  C6    N1   C2   C3     0.00   0.0  0
 JZF  CONST_02  C6    N1   C2   O2   180.00   0.0  0
 JZF  CONST_03  C15   N1   C2   C3   180.00   0.0  0
 JZF  CONST_04  C15   N1   C2   O2     0.00   0.0  0
 JZF  Var_01    C4    C3   C2   N1   -23.87  30.0  1
 JZF  Var_02    C4    C5   C6   N1    22.83  30.0  1
 JZF  Var_03    C5    C6   N1   C2    11.10  30.0  1
 JZF  Var_04    C21   C15  N1   C2    87.68  30.0  3
 JZF  Var_05    O4    C21  C15  N1    -4.47  30.0  3
 JZF  Var_06    H117  C17  C16  O5   -60.20  30.0  3
 JZF  Var_07    H116  C16  O5   C21  -60.72  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
 JZF  chir_01  C4   C3   C5   C7   negativ
 JZF  chir_02  C8   OH   C9   C7   negativ
 JZF  chir_03  C9   C14  C10  C8   positiv
 JZF  chir_04  C11  C18  C12  C10  negativ
 JZF  chir_05  C13  C19  C14  C12  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
 JZF  plan-1  N1   0.020
 JZF  plan-1  O3   0.020
 JZF  plan-1  C5   0.020
 JZF  plan-1  C6   0.020
 JZF  plan-2  O1   0.020
 JZF  plan-2  C9   0.020
 JZF  plan-2  C10  0.020
 JZF  plan-2  C11  0.020
 JZF  plan-3  N1   0.020
 JZF  plan-3  C2   0.020
 JZF  plan-3  O2   0.020
 JZF  plan-3  C3   0.020
 JZF  plan-3  C6   0.020
 JZF  plan-3  C15  0.020
 JZF  plan-4  O4   0.020
 JZF  plan-4  O5   0.020
 JZF  plan-4  C15  0.020
 JZF  plan-4  C21  0.020

