# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:08:40 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C[C@H](C)C(=O)[C@@H](C1)[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
 3HE  3HE  4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione  ligand  43  20  .  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_3HE
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
 3HE  C1   C  CH1   0  -0.248   3.6713  -1.3828   1.1335
 3HE  C2   C  CH2   0  -0.416   4.6547  -0.3122   0.6658
 3HE  C3   C  CH1   0  -0.368   4.2577   0.3380  -0.6688
 3HE  C4   C  C     0   0.447   2.8461   0.8732  -0.5634
 3HE  C5   C  CH1   0  -0.389   1.8093  -0.1374  -0.1089
 3HE  C6   C  CH2   0  -0.448   2.2633  -0.7913   1.2078
 3HE  C12  C  C     0   0.550  -4.1627   0.9812   0.5661
 3HE  N    N  NH1   0  -0.677  -4.8698   0.0996  -0.2233
 3HE  C11  C  C     0   0.549  -4.4134  -1.0739  -0.7823
 3HE  O1   O  O     0  -0.436  -5.1622  -1.7726  -1.4296
 3HE  C10  C  CH2   0  -0.570  -2.9760  -1.4150  -0.5187
 3HE  C13  C  CH2   0  -0.572  -2.7220   0.6430   0.8235
 3HE  C9   C  CH1   0  -0.281  -2.0947  -0.1920  -0.2863
 3HE  C7   C  CH1   0   0.049   0.3950   0.4559  -0.0384
 3HE  O3   O  OH1   0  -0.663   0.2708   1.3873   1.0169
 3HE  O    O  O     0  -0.401   2.5668   2.0180  -0.8401
 3HE  C14  C  CH3   0  -0.653   5.2640   1.3897  -1.1044
 3HE  C    C  CH3   0  -0.665   3.7358  -2.6516   0.2874
 3HE  H1   H  HCH1  0   0.241   3.9552  -1.6627   2.1528
 3HE  H2   H  HCH2  0   0.232   4.7256   0.4721   1.4275
 3HE  H3   H  HCH2  0   0.241   5.6585  -0.7344   0.5672
 3HE  H4   H  HCH1  0   0.263   4.2219  -0.4513  -1.4311
 3HE  H5   H  HCH1  0   0.270   1.7986  -0.9145  -0.8854
 3HE  H6   H  HCH2  0   0.252   1.5519  -1.5701   1.4958
 3HE  H7   H  HCH2  0   0.234   2.2491  -0.0422   2.0053
 3HE  H9   H  HCH2  0   0.285  -2.9507  -2.0589   0.3687
 3HE  H10  H  HCH2  0   0.287  -2.6148  -2.0159  -1.3537
 3HE  H11  H  HCH2  0   0.293  -2.1889   1.5754   0.9936
 3HE  H12  H  HCH2  0   0.280  -2.6893   0.0832   1.7667
 3HE  H13  H  HCH1  0   0.256  -2.0812   0.4017  -1.2079
 3HE  H16  H  HCH1  0   0.237   0.2302   1.0318  -0.9545
 3HE  H17  H  HOH1  0   0.446   0.2075   0.9058   1.8482
 3HE  H18  H  HCH3  0   0.222   5.3377   2.1981  -0.3756
 3HE  H19  H  HCH3  0   0.231   6.2524   0.9388  -1.1993
 3HE  H20  H  HCH3  0   0.234   5.0067   1.8286  -2.0679
 3HE  H21  H  HCH3  0   0.219   3.4488  -2.4904  -0.7533
 3HE  H22  H  HCH3  0   0.231   4.7473  -3.0610   0.2836
 3HE  H23  H  HCH3  0   0.231   3.0725  -3.4188   0.6900
 3HE  C8   C  CH2   0  -0.453  -0.6650  -0.6430   0.0096
 3HE  H8   H  HNH1  0   0.413  -5.8446   0.3261  -0.3877
 3HE  O2   O  O     0  -0.437  -4.7123   1.9585   1.0257
 3HE  H14  H  HCH2  0   0.237  -0.6432  -1.1652   0.9739
 3HE  H15  H  HCH2  0   0.246  -0.3978  -1.3933  -0.7404

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
 3HE  C14  C3   single  1.519  0.020  1.519
 3HE  C3   C4   single  1.513  0.020  1.513
 3HE  C3   C2   single  1.537  0.020  1.537
 3HE  O    C4   double  1.210  0.020  1.210
 3HE  C4   C5   single  1.517  0.020  1.517
 3HE  C    C1   single  1.526  0.020  1.526
 3HE  C2   C1   single  1.527  0.020  1.527
 3HE  C5   C7   single  1.535  0.020  1.535
 3HE  C5   C6   single  1.539  0.020  1.539
 3HE  C1   C6   single  1.529  0.020  1.529
 3HE  C7   C8   single  1.528  0.020  1.528
 3HE  C7   O3   single  1.413  0.020  1.413
 3HE  C10  C11  single  1.501  0.020  1.501
 3HE  C10  C9   single  1.525  0.020  1.525
 3HE  O1   C11  double  1.212  0.020  1.212
 3HE  C8   C9   single  1.528  0.020  1.528
 3HE  C11  N    single  1.378  0.020  1.378
 3HE  C9   C13  single  1.524  0.020  1.524
 3HE  C13  C12  single  1.502  0.020  1.502
 3HE  N    C12  single  1.379  0.020  1.379
 3HE  C12  O2   double  1.212  0.020  1.212
 3HE  C1   H1   single  0.970  0.020  1.090
 3HE  C2   H2   single  0.970  0.020  1.090
 3HE  C2   H3   single  0.970  0.020  1.090
 3HE  C3   H4   single  0.970  0.020  1.090
 3HE  C5   H5   single  0.970  0.020  1.090
 3HE  C6   H6   single  0.970  0.020  1.090
 3HE  C6   H7   single  0.970  0.020  1.090
 3HE  N    H8   single  0.860  0.020  1.020
 3HE  C10  H9   single  0.970  0.020  1.090
 3HE  C10  H10  single  0.970  0.020  1.090
 3HE  C13  H11  single  0.970  0.020  1.090
 3HE  C13  H12  single  0.970  0.020  1.090
 3HE  C9   H13  single  0.970  0.020  1.090
 3HE  C8   H14  single  0.970  0.020  1.090
 3HE  C8   H15  single  0.970  0.020  1.090
 3HE  C7   H16  single  0.970  0.020  1.090
 3HE  O3   H17  single  0.850  0.020  0.980
 3HE  C14  H18  single  0.970  0.020  1.090
 3HE  C14  H19  single  0.970  0.020  1.090
 3HE  C14  H20  single  0.970  0.020  1.090
 3HE  C    H21  single  0.970  0.020  1.090
 3HE  C    H22  single  0.970  0.020  1.090
 3HE  C    H23  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
 3HE  H1   C1   C    107.02  3.000
 3HE  H1   C1   C6   107.01  3.000
 3HE  C    C1   C6   112.80  3.000
 3HE  H1   C1   C2   107.30  3.000
 3HE  C6   C1   C2   109.67  3.000
 3HE  C    C1   C2   112.69  3.000
 3HE  H3   C2   H2   106.24  3.000
 3HE  H3   C2   C3   108.80  3.000
 3HE  H2   C2   C3   108.52  3.000
 3HE  H3   C2   C1   110.37  3.000
 3HE  H2   C2   C1   109.30  3.000
 3HE  C3   C2   C1   113.34  3.000
 3HE  H4   C3   C14  108.67  3.000
 3HE  H4   C3   C4   105.80  3.000
 3HE  C14  C3   C4   113.14  3.000
 3HE  H4   C3   C2   107.90  3.000
 3HE  C4   C3   C2   109.28  3.000
 3HE  C14  C3   C2   111.76  3.000
 3HE  O    C4   C5   122.73  3.000
 3HE  C5   C4   C3   115.00  3.000
 3HE  O    C4   C3   122.27  3.000
 3HE  H5   C5   C7   107.27  3.000
 3HE  H5   C5   C6   107.89  3.000
 3HE  C7   C5   C6   113.37  3.000
 3HE  H5   C5   C4   105.43  3.000
 3HE  C6   C5   C4   109.74  3.000
 3HE  C7   C5   C4   112.69  3.000
 3HE  H7   C6   H6   106.69  3.000
 3HE  H7   C6   C5   109.20  3.000
 3HE  H6   C6   C5   109.64  3.000
 3HE  H7   C6   C1   108.20  3.000
 3HE  H6   C6   C1   109.66  3.000
 3HE  C5   C6   C1   113.24  3.000
 3HE  C13  C12  N    116.49  3.000
 3HE  N    C12  O2   120.02  3.000
 3HE  C13  C12  O2   123.47  3.000
 3HE  H8   N    C11  116.29  3.000
 3HE  H8   N    C12  116.29  3.000
 3HE  C11  N    C12  127.39  3.000
 3HE  C10  C11  O1   123.70  3.000
 3HE  O1   C11  N    120.21  3.000
 3HE  C10  C11  N    116.09  3.000
 3HE  H10  C10  H9   106.77  3.000
 3HE  H10  C10  C9   111.54  3.000
 3HE  H9   C10  C9   109.52  3.000
 3HE  H10  C10  C11  107.95  3.000
 3HE  H9   C10  C11  107.32  3.000
 3HE  C9   C10  C11  113.45  3.000
 3HE  H12  C13  H11  106.76  3.000
 3HE  H12  C13  C9   109.52  3.000
 3HE  H11  C13  C9   112.45  3.000
 3HE  H12  C13  C12  106.91  3.000
 3HE  H11  C13  C12  107.70  3.000
 3HE  C9   C13  C12  113.16  3.000
 3HE  H13  C9   C8   108.13  3.000
 3HE  H13  C9   C13  108.69  3.000
 3HE  C8   C9   C13  113.94  3.000
 3HE  H13  C9   C10  108.26  3.000
 3HE  C13  C9   C10  108.20  3.000
 3HE  C8   C9   C10  109.48  3.000
 3HE  H16  C7   O3   105.37  3.000
 3HE  H16  C7   C8   107.48  3.000
 3HE  O3   C7   C8   112.94  3.000
 3HE  H16  C7   C5   107.67  3.000
 3HE  O3   C7   C5   111.71  3.000
 3HE  C8   C7   C5   111.26  3.000
 3HE  H17  O3   C7   108.72  3.000
 3HE  H20  C14  H19  107.68  3.000
 3HE  H20  C14  H18  107.95  3.000
 3HE  H19  C14  H18  107.66  3.000
 3HE  H20  C14  C3   112.08  3.000
 3HE  H19  C14  C3   109.82  3.000
 3HE  H18  C14  C3   111.48  3.000
 3HE  H23  C    H22  107.52  3.000
 3HE  H23  C    H21  107.21  3.000
 3HE  H22  C    H21  107.20  3.000
 3HE  H23  C    C1   110.75  3.000
 3HE  H22  C    C1   110.67  3.000
 3HE  H21  C    C1   113.24  3.000
 3HE  H15  C8   H14  105.74  3.000
 3HE  H15  C8   C7   107.60  3.000
 3HE  H14  C8   C7   110.87  3.000
 3HE  H15  C8   C9   107.35  3.000
 3HE  H14  C8   C9   109.23  3.000
 3HE  C7   C8   C9   115.52  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
 3HE  CONST_01  C13  C12  N    C11    0.00   0.0  0
 3HE  CONST_02  C11  N    C12  O2   180.00   0.0  0
 3HE  CONST_03  H8   N    C12  C13  180.00   0.0  0
 3HE  Var_01    C10  C11  N    C12   -1.15  30.0  1
 3HE  Var_02    C9   C10  C11  N    -27.87  30.0  1
 3HE  Var_03    C9   C13  C12  N     27.21  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
 3HE  chir_01  C1  C    C2  C6   negativ
 3HE  chir_02  C3  C14  C4  C2   positiv
 3HE  chir_03  C5  C6   C7  C4   negativ
 3HE  chir_04  C9  C13  C8  C10  negativ
 3HE  chir_05  C7  O3   C5  C8   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
 3HE  plan-1  C3   0.020
 3HE  plan-1  C4   0.020
 3HE  plan-1  C5   0.020
 3HE  plan-1  O    0.020
 3HE  plan-2  N    0.020
 3HE  plan-2  C11  0.020
 3HE  plan-2  O1   0.020
 3HE  plan-2  C10  0.020
 3HE  plan-3  C12  0.020
 3HE  plan-3  N    0.020
 3HE  plan-3  C11  0.020
 3HE  plan-3  C13  0.020
 3HE  plan-3  H8   0.020
 3HE  plan-3  O2   0.020

