# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:40:43 2021
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC[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
 E9O  E9O  '(2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid'  ligand  49  20  .  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_E9O
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
 E9O  C2   C  CH2   0  -0.324  -1.3274  -14.2567  -54.2260
 E9O  C3   C  CH1   0   0.060  -2.4027  -13.2232  -54.5199
 E9O  O3   O  OH1   0  -0.673  -3.0348  -13.5746  -55.7261
 E9O  N    N  NH1   0  -0.614  -0.6605  -13.9211  -52.9831
 E9O  C7   C  CH1   0  -0.057  -1.5438  -13.9651  -51.8288
 E9O  C5   C  CH1   0  -0.390  -2.6323  -12.8997  -52.0575
 E9O  C6   C  C     0   0.533  -3.5937  -12.7862  -50.9023
 E9O  O62  O  OH1   0  -0.591  -4.2801  -13.9067  -50.7036
 E9O  C4   C  CH1   0   0.023  -3.3892  -13.1888  -53.3602
 E9O  O4   O  OH1   0  -0.677  -4.3611  -12.1948  -53.6117
 E9O  O61  O  O     0  -0.436  -3.7409  -11.7990  -50.2253
 E9O  C8   C  CH2   0  -0.427  -0.7596  -13.7019  -50.5472
 E9O  C9   C  CH2   0  -0.435   0.3149  -14.7393  -50.2366
 E9O  C10  C  CH2   0  -0.411   0.9820  -14.4902  -48.8890
 E9O  C1   C  CH2   0  -0.413   2.0635  -15.5091  -48.5542
 E9O  C11  C  CH2   0  -0.412   2.7332  -15.2501  -47.2105
 E9O  C12  C  CH2   0  -0.412   3.8132  -16.2685  -46.8680
 E9O  C13  C  CH2   0  -0.406   4.4876  -16.0016  -45.5283
 E9O  C14  C  CH2   0  -0.419   5.5634  -17.0223  -45.1784
 E9O  C15  C  CH3   0  -0.662   6.2366  -16.7378  -43.8429
 E9O  H1   H  HCH2  0   0.201  -1.7929  -15.2559  -54.2072
 E9O  H2   H  HCH2  0   0.249  -0.5899  -14.2590  -55.0308
 E9O  H3   H  HCH1  0   0.202  -1.9223  -12.2355  -54.5960
 E9O  H4   H  HOH1  0   0.448  -3.7397  -12.9383  -55.8851
 E9O  H5   H  HNH1  0   0.364   0.1087  -14.5621  -52.8454
 E9O  H7   H  HCH1  0   0.208  -2.0372  -14.9488  -51.7397
 E9O  H8   H  HCH1  0   0.267  -2.1324  -11.9300  -52.1473
 E9O  H9   H  HOH1  0   0.483  -4.8862  -13.7977  -49.9551
 E9O  H10  H  HCH1  0   0.226  -3.8560  -14.1804  -53.2942
 E9O  H11  H  HOH1  0   0.462  -5.2320  -12.5422  -53.4024
 E9O  H12  H  HCH2  0   0.222  -0.3097  -12.7049  -50.6008
 E9O  H13  H  HCH2  0   0.228  -1.4551  -13.6822  -49.7027
 E9O  H14  H  HCH2  0   0.217  -0.1315  -15.7398  -50.2426
 E9O  H15  H  HCH2  0   0.215   1.0894  -14.7423  -51.0103
 E9O  H16  H  HCH2  0   0.210   1.4154  -13.4838  -48.8818
 E9O  H17  H  HCH2  0   0.211   0.2209  -14.4976  -48.1012
 E9O  H18  H  HCH2  0   0.208   1.6279  -16.5146  -48.5539
 E9O  H19  H  HCH2  0   0.208   2.8228  -15.5082  -49.3441
 E9O  H20  H  HCH2  0   0.206   3.1690  -14.2446  -47.2111
 E9O  H21  H  HCH2  0   0.207   1.9731  -15.2492  -46.4213
 E9O  H22  H  HCH2  0   0.206   3.3747  -17.2729  -46.8597
 E9O  H23  H  HCH2  0   0.206   4.5703  -16.2763  -47.6601
 E9O  H24  H  HCH2  0   0.205   4.9293  -14.9986  -45.5381
 E9O  H25  H  HCH2  0   0.206   3.7300  -15.9895  -44.7366
 E9O  H26  H  HCH2  0   0.210   5.1192  -18.0226  -45.1603
 E9O  H27  H  HCH2  0   0.210   6.3173  -17.0408  -45.9715
 E9O  H28  H  HCH3  0   0.225   7.0079  -17.4749  -43.6160
 E9O  H29  H  HCH3  0   0.215   6.7104  -15.7540  -43.8434
 E9O  H30  H  HCH3  0   0.216   5.5140  -16.7532  -43.0248

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
 E9O  O3   C3   single  1.406  0.020  1.406
 E9O  C3   C2   single  1.520  0.020  1.520
 E9O  C3   C4   single  1.523  0.020  1.523
 E9O  C2   N    single  1.450  0.020  1.450
 E9O  C4   O4   single  1.413  0.020  1.413
 E9O  C4   C5   single  1.534  0.020  1.534
 E9O  N    C7   single  1.454  0.020  1.454
 E9O  C5   C7   single  1.540  0.020  1.540
 E9O  C5   C6   single  1.507  0.020  1.507
 E9O  C7   C8   single  1.525  0.020  1.525
 E9O  C6   O61  double  1.206  0.020  1.206
 E9O  C6   O62  single  1.329  0.020  1.329
 E9O  C8   C9   single  1.526  0.020  1.526
 E9O  C9   C10  single  1.524  0.020  1.524
 E9O  C10  C1   single  1.523  0.020  1.523
 E9O  C1   C11  single  1.524  0.020  1.524
 E9O  C11  C12  single  1.523  0.020  1.523
 E9O  C12  C13  single  1.523  0.020  1.523
 E9O  C13  C14  single  1.524  0.020  1.524
 E9O  C14  C15  single  1.522  0.020  1.522
 E9O  C2   H1   single  0.970  0.020  1.090
 E9O  C2   H2   single  0.970  0.020  1.090
 E9O  C3   H3   single  0.970  0.020  1.090
 E9O  O3   H4   single  0.850  0.020  0.980
 E9O  N    H5   single  0.890  0.020  1.040
 E9O  C7   H7   single  0.970  0.020  1.090
 E9O  C5   H8   single  0.970  0.020  1.090
 E9O  O62  H9   single  0.850  0.020  0.980
 E9O  C4   H10  single  0.970  0.020  1.090
 E9O  O4   H11  single  0.850  0.020  0.980
 E9O  C8   H12  single  0.970  0.020  1.090
 E9O  C8   H13  single  0.970  0.020  1.090
 E9O  C9   H14  single  0.970  0.020  1.090
 E9O  C9   H15  single  0.970  0.020  1.090
 E9O  C10  H16  single  0.970  0.020  1.090
 E9O  C10  H17  single  0.970  0.020  1.090
 E9O  C1   H18  single  0.970  0.020  1.090
 E9O  C1   H19  single  0.970  0.020  1.090
 E9O  C11  H20  single  0.970  0.020  1.090
 E9O  C11  H21  single  0.970  0.020  1.090
 E9O  C12  H22  single  0.970  0.020  1.090
 E9O  C12  H23  single  0.970  0.020  1.090
 E9O  C13  H24  single  0.970  0.020  1.090
 E9O  C13  H25  single  0.970  0.020  1.090
 E9O  C14  H26  single  0.970  0.020  1.090
 E9O  C14  H27  single  0.970  0.020  1.090
 E9O  C15  H28  single  0.970  0.020  1.090
 E9O  C15  H29  single  0.970  0.020  1.090
 E9O  C15  H30  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
 E9O  H2   C2   H1   107.21  3.000
 E9O  H2   C2   N    108.77  3.000
 E9O  H1   C2   N    112.91  3.000
 E9O  H2   C2   C3   109.68  3.000
 E9O  H1   C2   C3   108.72  3.000
 E9O  N    C2   C3   109.50  3.000
 E9O  H3   C3   C4   108.37  3.000
 E9O  H3   C3   O3   111.16  3.000
 E9O  C4   C3   O3   111.57  3.000
 E9O  H3   C3   C2   108.34  3.000
 E9O  C4   C3   C2   109.05  3.000
 E9O  O3   C3   C2   108.29  3.000
 E9O  H4   O3   C3   107.79  3.000
 E9O  H5   N    C7   109.57  3.000
 E9O  H5   N    C2   108.67  3.000
 E9O  C7   N    C2   113.21  3.000
 E9O  H7   C7   C8   108.40  3.000
 E9O  H7   C7   C5   108.21  3.000
 E9O  C8   C7   C5   111.64  3.000
 E9O  H7   C7   N    111.25  3.000
 E9O  C8   C7   N    110.46  3.000
 E9O  C5   C7   N    106.89  3.000
 E9O  H8   C5   C4   108.82  3.000
 E9O  H8   C5   C6   106.71  3.000
 E9O  C4   C5   C6   110.51  3.000
 E9O  H8   C5   C7   107.59  3.000
 E9O  C6   C5   C7   112.90  3.000
 E9O  C4   C5   C7   110.14  3.000
 E9O  O61  C6   O62  122.90  3.000
 E9O  O62  C6   C5   112.37  3.000
 E9O  O61  C6   C5   124.73  3.000
 E9O  H9   O62  C6   110.10  3.000
 E9O  H10  C4   O4   110.71  3.000
 E9O  H10  C4   C5   109.20  3.000
 E9O  O4   C4   C5   110.98  3.000
 E9O  H10  C4   C3   107.51  3.000
 E9O  C5   C4   C3   109.35  3.000
 E9O  O4   C4   C3   109.02  3.000
 E9O  H11  O4   C4   109.30  3.000
 E9O  H13  C8   H12  106.41  3.000
 E9O  H13  C8   C9   107.63  3.000
 E9O  H12  C8   C9   109.86  3.000
 E9O  H13  C8   C7   108.95  3.000
 E9O  H12  C8   C7   109.09  3.000
 E9O  C9   C8   C7   114.57  3.000
 E9O  H15  C9   H14  106.38  3.000
 E9O  H15  C9   C10  108.40  3.000
 E9O  H14  C9   C10  109.42  3.000
 E9O  H15  C9   C8   110.87  3.000
 E9O  H14  C9   C8   109.44  3.000
 E9O  C10  C9   C8   112.16  3.000
 E9O  H17  C10  H16  106.04  3.000
 E9O  H17  C10  C1   109.32  3.000
 E9O  H16  C10  C1   109.40  3.000
 E9O  H17  C10  C9   109.31  3.000
 E9O  H16  C10  C9   109.21  3.000
 E9O  C1   C10  C9   113.31  3.000
 E9O  H19  C1   H18  106.05  3.000
 E9O  H19  C1   C11  109.34  3.000
 E9O  H18  C1   C11  109.29  3.000
 E9O  H19  C1   C10  109.46  3.000
 E9O  H18  C1   C10  109.37  3.000
 E9O  C11  C1   C10  113.09  3.000
 E9O  H21  C11  H20  105.99  3.000
 E9O  H21  C11  C12  109.29  3.000
 E9O  H20  C11  C12  109.36  3.000
 E9O  H21  C11  C1   109.30  3.000
 E9O  H20  C11  C1   109.29  3.000
 E9O  C12  C11  C1   113.34  3.000
 E9O  H23  C12  H22  105.98  3.000
 E9O  H23  C12  C13  109.34  3.000
 E9O  H22  C12  C13  109.33  3.000
 E9O  H23  C12  C11  109.39  3.000
 E9O  H22  C12  C11  109.31  3.000
 E9O  C13  C12  C11  113.23  3.000
 E9O  H25  C13  H24  105.96  3.000
 E9O  H25  C13  C14  109.24  3.000
 E9O  H24  C13  C14  109.31  3.000
 E9O  H25  C13  C12  109.34  3.000
 E9O  H24  C13  C12  109.32  3.000
 E9O  C14  C13  C12  113.40  3.000
 E9O  H27  C14  H26  106.02  3.000
 E9O  H27  C14  C15  109.53  3.000
 E9O  H26  C14  C15  109.61  3.000
 E9O  H27  C14  C13  109.35  3.000
 E9O  H26  C14  C13  109.24  3.000
 E9O  C15  C14  C13  112.86  3.000
 E9O  H30  C15  H29  107.47  3.000
 E9O  H30  C15  H28  107.62  3.000
 E9O  H29  C15  H28  107.59  3.000
 E9O  H30  C15  C14  111.23  3.000
 E9O  H29  C15  C14  111.09  3.000
 E9O  H28  C15  C14  111.65  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
 E9O  CONST_01  H9   O62  C6   C5    180.00   0.0  0
 E9O  Var_01    C7   N    C2   C3     63.45  30.0  1
 E9O  Var_02    C10  C9   C8   C7   -175.13  30.0  3
 E9O  Var_03    C1   C10  C9   C8   -179.81  30.0  3
 E9O  Var_04    C11  C1   C10  C9    179.62  30.0  3
 E9O  Var_05    C12  C11  C1   C10   179.83  30.0  3
 E9O  Var_06    C13  C12  C11  C1    179.61  30.0  3
 E9O  Var_07    C14  C13  C12  C11   179.69  30.0  3
 E9O  Var_08    C15  C14  C13  C12   179.55  30.0  3
 E9O  Var_09    H28  C15  C14  C13  -179.54  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
 E9O  chir_01  C3  O3  C2  C4  positiv
 E9O  chir_02  C7  N   C8  C5  negativ
 E9O  chir_03  C5  C4  C7  C6  positiv
 E9O  chir_04  C4  O4  C5  C3  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
 E9O  plan-1  C5   0.020
 E9O  plan-1  C6   0.020
 E9O  plan-1  O62  0.020
 E9O  plan-1  O61  0.020
 E9O  plan-1  H9   0.020

