# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:55:34 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@@H]1NC[C@@H](O)[C@H](O)[C@H]1C(O)=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
 E8X  E8X  '(2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid'  ligand  40  17  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E8X
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
 E8X  C6   C  C     0   0.551  -33.6013  33.6963  -31.2705
 E8X  C5   C  CH1   0  -0.403  -33.7687  34.5005  -30.0063
 E8X  C4   C  CH1   0   0.066  -33.8928  33.5436  -28.8244
 E8X  O4   O  OH1   0  -0.673  -32.7187  32.7667  -28.7896
 E8X  C3   C  CH1   0   0.023  -34.1095  34.3310  -27.5428
 E8X  O3   O  OH1   0  -0.676  -34.2743  33.3965  -26.4980
 E8X  C2   C  CH2   0  -0.354  -35.3317  35.2354  -27.7021
 E8X  C7   C  CH1   0  -0.072  -35.0104  35.4237  -30.0937
 E8X  C8   C  CH2   0  -0.436  -34.8813  36.4215  -31.2400
 E8X  C9   C  CH2   0  -0.404  -36.0722  37.3595  -31.3939
 E8X  N    N  NH1   0  -0.577  -35.2425  36.1210  -28.8439
 E8X  O61  O  O     0  -0.448  -34.4030  32.8799  -31.6570
 E8X  O62  O  OH1   0  -0.586  -32.4911  33.9911  -31.9337
 E8X  C10  C  CH2   0  -0.420  -35.8788  38.3459  -32.5390
 E8X  C11  C  CH2   0  -0.416  -37.0571  39.2955  -32.7247
 E8X  C12  C  CH2   0  -0.426  -36.7736  40.4526  -33.6803
 E8X  C13  C  CH3   0  -0.667  -36.3975  40.0169  -35.0909
 E8X  H1   H  HCH1  0   0.263  -32.8887  35.1354  -29.8566
 E8X  H2   H  HCH1  0   0.208  -34.7764  32.9046  -28.9819
 E8X  H3   H  HOH1  0   0.452  -32.7801  32.1615  -28.0430
 E8X  H4   H  HCH1  0   0.206  -33.2232  34.9614  -27.3704
 E8X  H5   H  HOH1  0   0.457  -34.2254  33.8640  -25.6586
 E8X  H6   H  HCH2  0   0.247  -35.4703  35.8353  -26.7991
 E8X  H7   H  HCH2  0   0.226  -36.2254  34.6103  -27.8083
 E8X  H8   H  HCH1  0   0.229  -35.8856  34.7875  -30.2756
 E8X  H9   H  HCH2  0   0.232  -34.7456  35.8771  -32.1793
 E8X  H10  H  HCH2  0   0.218  -33.9676  37.0116  -31.0999
 E8X  H11  H  HCH2  0   0.218  -36.2324  37.9075  -30.4626
 E8X  H12  H  HCH2  0   0.208  -36.9796  36.7690  -31.5609
 E8X  H13  H  HNH1  0   0.344  -34.5120  36.8084  -28.6929
 E8X  H15  H  HOH1  0   0.479  -32.4450  33.4667  -32.7478
 E8X  H16  H  HCH2  0   0.213  -35.6977  37.7935  -33.4664
 E8X  H17  H  HCH2  0   0.206  -34.9699  38.9318  -32.3574
 E8X  H18  H  HCH2  0   0.214  -37.3414  39.7074  -31.7509
 E8X  H19  H  HCH2  0   0.207  -37.9270  38.7333  -33.0810
 E8X  H20  H  HCH2  0   0.209  -35.9694  41.0681  -33.2649
 E8X  H21  H  HCH2  0   0.219  -37.6544  41.0990  -33.7250
 E8X  H22  H  HCH3  0   0.226  -36.2527  40.8783  -35.7439
 E8X  H23  H  HCH3  0   0.221  -35.4710  39.4410  -35.1033
 E8X  H24  H  HCH3  0   0.214  -37.1775  39.3949  -35.5350

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
 E8X  C13  C12  single  1.523  0.020  1.523
 E8X  C12  C11  single  1.527  0.020  1.527
 E8X  C11  C10  single  1.525  0.020  1.525
 E8X  C10  C9   single  1.524  0.020  1.524
 E8X  O61  C6   double  1.208  0.020  1.208
 E8X  O62  C6   single  1.326  0.020  1.326
 E8X  C9   C8   single  1.524  0.020  1.524
 E8X  C6   C5   single  1.508  0.020  1.508
 E8X  C8   C7   single  1.525  0.020  1.525
 E8X  C5   C7   single  1.550  0.020  1.550
 E8X  C5   C4   single  1.526  0.020  1.526
 E8X  C7   N    single  1.450  0.020  1.450
 E8X  O4   C4   single  1.408  0.020  1.408
 E8X  C4   C3   single  1.520  0.020  1.520
 E8X  N    C2   single  1.448  0.020  1.448
 E8X  C3   C2   single  1.529  0.020  1.529
 E8X  C3   O3   single  1.411  0.020  1.411
 E8X  C5   H1   single  0.970  0.020  1.090
 E8X  C4   H2   single  0.970  0.020  1.090
 E8X  O4   H3   single  0.850  0.020  0.980
 E8X  C3   H4   single  0.970  0.020  1.090
 E8X  O3   H5   single  0.850  0.020  0.980
 E8X  C2   H6   single  0.970  0.020  1.090
 E8X  C2   H7   single  0.970  0.020  1.090
 E8X  C7   H8   single  0.970  0.020  1.090
 E8X  C8   H9   single  0.970  0.020  1.090
 E8X  C8   H10  single  0.970  0.020  1.090
 E8X  C9   H11  single  0.970  0.020  1.090
 E8X  C9   H12  single  0.970  0.020  1.090
 E8X  N    H13  single  0.890  0.020  1.040
 E8X  O62  H15  single  0.850  0.020  0.980
 E8X  C10  H16  single  0.970  0.020  1.090
 E8X  C10  H17  single  0.970  0.020  1.090
 E8X  C11  H18  single  0.970  0.020  1.090
 E8X  C11  H19  single  0.970  0.020  1.090
 E8X  C12  H20  single  0.970  0.020  1.090
 E8X  C12  H21  single  0.970  0.020  1.090
 E8X  C13  H22  single  0.970  0.020  1.090
 E8X  C13  H23  single  0.970  0.020  1.090
 E8X  C13  H24  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
 E8X  O62  C6   O61  123.08  3.000
 E8X  O62  C6   C5   113.18  3.000
 E8X  O61  C6   C5   123.73  3.000
 E8X  H1   C5   C7   107.83  3.000
 E8X  H1   C5   C4   108.84  3.000
 E8X  C7   C5   C4   110.62  3.000
 E8X  H1   C5   C6   109.55  3.000
 E8X  C4   C5   C6   108.90  3.000
 E8X  C7   C5   C6   111.07  3.000
 E8X  H2   C4   C3   107.86  3.000
 E8X  H2   C4   O4   110.62  3.000
 E8X  C3   C4   O4   112.57  3.000
 E8X  H2   C4   C5   108.56  3.000
 E8X  C3   C4   C5   109.87  3.000
 E8X  O4   C4   C5   107.29  3.000
 E8X  H3   O4   C4   108.22  3.000
 E8X  H4   C3   C2   108.73  3.000
 E8X  H4   C3   O3   110.92  3.000
 E8X  C2   C3   O3   112.05  3.000
 E8X  H4   C3   C4   108.30  3.000
 E8X  O3   C3   C4   107.33  3.000
 E8X  C2   C3   C4   109.43  3.000
 E8X  H5   O3   C3   108.55  3.000
 E8X  H7   C2   H6   106.85  3.000
 E8X  H7   C2   N    108.83  3.000
 E8X  H6   C2   N    108.89  3.000
 E8X  H7   C2   C3   108.95  3.000
 E8X  H6   C2   C3   109.88  3.000
 E8X  N    C2   C3   113.25  3.000
 E8X  H8   C7   N    107.10  3.000
 E8X  H8   C7   C8   108.80  3.000
 E8X  N    C7   C8   110.29  3.000
 E8X  H8   C7   C5   107.64  3.000
 E8X  N    C7   C5   111.48  3.000
 E8X  C8   C7   C5   111.36  3.000
 E8X  H10  C8   H9   105.91  3.000
 E8X  H10  C8   C9   109.43  3.000
 E8X  H9   C8   C9   108.45  3.000
 E8X  H10  C8   C7   109.06  3.000
 E8X  H9   C8   C7   109.29  3.000
 E8X  C9   C8   C7   114.36  3.000
 E8X  H12  C9   H11  106.20  3.000
 E8X  H12  C9   C10  109.85  3.000
 E8X  H11  C9   C10  109.55  3.000
 E8X  H12  C9   C8   109.33  3.000
 E8X  H11  C9   C8   109.71  3.000
 E8X  C10  C9   C8   112.04  3.000
 E8X  H13  N    C7   109.81  3.000
 E8X  H13  N    C2   109.97  3.000
 E8X  C7   N    C2   113.30  3.000
 E8X  H15  O62  C6   109.84  3.000
 E8X  H17  C10  H16  105.84  3.000
 E8X  H17  C10  C11  109.15  3.000
 E8X  H16  C10  C11  109.81  3.000
 E8X  H17  C10  C9   109.07  3.000
 E8X  H16  C10  C9   109.33  3.000
 E8X  C11  C10  C9   113.36  3.000
 E8X  H19  C11  H18  106.04  3.000
 E8X  H19  C11  C12  109.44  3.000
 E8X  H18  C11  C12  108.64  3.000
 E8X  H19  C11  C10  109.50  3.000
 E8X  H18  C11  C10  109.07  3.000
 E8X  C12  C11  C10  113.86  3.000
 E8X  H21  C12  H20  105.96  3.000
 E8X  H21  C12  C13  109.27  3.000
 E8X  H20  C12  C13  109.32  3.000
 E8X  H21  C12  C11  108.90  3.000
 E8X  H20  C12  C11  108.96  3.000
 E8X  C13  C12  C11  114.11  3.000
 E8X  H24  C13  H23  107.54  3.000
 E8X  H24  C13  H22  107.53  3.000
 E8X  H23  C13  H22  107.30  3.000
 E8X  H24  C13  C12  111.29  3.000
 E8X  H23  C13  C12  111.79  3.000
 E8X  H22  C13  C12  111.18  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
 E8X  CONST_01  H15  O62  C6   C5   180.00   0.0  0
 E8X  Var_01    C7   N    C2   C3    55.42  30.0  1
 E8X  Var_02    C10  C9   C8   C7   179.13  30.0  1
 E8X  Var_03    C11  C10  C9   C8   179.71  30.0  1
 E8X  Var_04    C12  C11  C10  C9   168.91  30.0  1
 E8X  Var_05    C13  C12  C11  C10   59.68  30.0  2
 E8X  Var_06    H22  C13  C12  C11  177.26  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
 E8X  chir_01  C5  C6  C7  C4  negativ
 E8X  chir_02  C4  O4  C5  C3  positiv
 E8X  chir_03  C3  O3  C4  C2  negativ
 E8X  chir_04  C7  N   C8  C5  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
 E8X  plan-1  C6   0.020
 E8X  plan-1  C5   0.020
 E8X  plan-1  O61  0.020
 E8X  plan-1  O62  0.020
 E8X  plan-1  H15  0.020

