# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:34:13 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{S})-3,4,5-tris(oxidanyl)piperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CN[C@@H]([C@@H](O)[C@@H]1O)C(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
 CN0  CN0  '(2~{S},3~{R},4~{R},5~{S})-3,4,5-tris(oxidanyl)piperidine-2-carboxylic acid'  ligand  22  12  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CN0
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
 CN0  C10  C  C      0   0.450  -28.3217  -0.0580  22.5188
 CN0  O01  O  OH1    0  -0.673  -29.6727   2.0710  17.4344
 CN0  C02  C  CH1    0   0.044  -29.2776   1.2107  18.4791
 CN0  C03  C  CH2    0  -0.337  -28.1854   1.9137  19.2809
 CN0  N04  N  NH1    0  -0.578  -27.7348   1.1697  20.4376
 CN0  C05  C  CH1    0  -0.295  -28.8143   0.7801  21.3194
 CN0  C06  C  CH1    0   0.044  -29.9451   0.0323  20.5809
 CN0  O07  O  OH1    0  -0.713  -31.0385  -0.2364  21.4209
 CN0  C08  C  CH1    0   0.010  -30.4334   0.8642  19.4036
 CN0  O09  O  OH1    0  -0.678  -31.4090   0.1858  18.6404
 CN0  O11  O  O      0  -0.557  -27.1096  -0.2270  22.6793
 CN0  O12  O  OC    -1  -0.616  -29.2423  -0.5191  23.2507
 CN0  H11  H  HOH1   0   0.444  -30.3998   1.6532  16.9613
 CN0  H31  H  HCH2   0   0.216  -28.5691   2.8844  19.6165
 CN0  H1   H  HNH1   0   0.334  -27.2084   0.3537  20.1512
 CN0  H51  H  HCH1   0   0.230  -29.2557   1.7027  21.7276
 CN0  H61  H  HCH1   0   0.171  -29.5156  -0.9054  20.1799
 CN0  H71  H  HOH1   0   0.436  -30.6046  -0.4264  22.2895
 CN0  H81  H  HCH1   0   0.187  -30.8434   1.8076  19.8038
 CN0  H91  H  HOH1   0   0.448  -32.1720   0.0258  19.2046
 CN0  H21  H  HCH1   0   0.190  -28.8639   0.2715  18.0755
 CN0  H32  H  HCH2   0   0.241  -27.3281   2.1189  18.6358

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
 CN0  O01  C02  single  1.410  0.020  1.410
 CN0  C02  C03  single  1.526  0.020  1.526
 CN0  C02  C08  single  1.520  0.020  1.520
 CN0  O09  C08  single  1.412  0.020  1.412
 CN0  C03  N04  single  1.447  0.020  1.447
 CN0  C08  C06  single  1.522  0.020  1.522
 CN0  N04  C05  single  1.447  0.020  1.447
 CN0  C06  C05  single  1.544  0.020  1.544
 CN0  C06  O07  single  1.405  0.020  1.405
 CN0  C05  C10  single  1.544  0.020  1.544
 CN0  O11  C10  deloc   1.234  0.020  1.234
 CN0  C10  O12  deloc   1.263  0.020  1.263
 CN0  O01  H11  single  0.850  0.020  0.980
 CN0  C02  H21  single  0.970  0.020  1.090
 CN0  C03  H32  single  0.970  0.020  1.090
 CN0  C03  H31  single  0.970  0.020  1.090
 CN0  N04  H1   single  0.890  0.020  1.040
 CN0  C05  H51  single  0.970  0.020  1.090
 CN0  C06  H61  single  0.970  0.020  1.090
 CN0  O07  H71  single  0.850  0.020  0.980
 CN0  C08  H81  single  0.970  0.020  1.090
 CN0  O09  H91  single  0.850  0.020  0.980

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
 CN0  O12  C10  O11  126.18  3.000
 CN0  O12  C10  C05  114.57  3.000
 CN0  O11  C10  C05  119.25  3.000
 CN0  H11  O01  C02  108.12  3.000
 CN0  H21  C02  C08  108.28  3.000
 CN0  H21  C02  C03  108.43  3.000
 CN0  C08  C02  C03  109.24  3.000
 CN0  H21  C02  O01  110.71  3.000
 CN0  C08  C02  O01  112.13  3.000
 CN0  C03  C02  O01  107.98  3.000
 CN0  H31  C03  H32  106.81  3.000
 CN0  H31  C03  N04  108.63  3.000
 CN0  H32  C03  N04  108.92  3.000
 CN0  H31  C03  C02  108.55  3.000
 CN0  H32  C03  C02  109.74  3.000
 CN0  N04  C03  C02  113.95  3.000
 CN0  H1   N04  C05  110.07  3.000
 CN0  H1   N04  C03  110.50  3.000
 CN0  C05  N04  C03  113.15  3.000
 CN0  H51  C05  C06  106.83  3.000
 CN0  H51  C05  N04  107.41  3.000
 CN0  C06  C05  N04  112.66  3.000
 CN0  H51  C05  C10  107.14  3.000
 CN0  C06  C05  C10  110.02  3.000
 CN0  N04  C05  C10  112.43  3.000
 CN0  H61  C06  C08  107.90  3.000
 CN0  H61  C06  O07  110.90  3.000
 CN0  C08  C06  O07  108.51  3.000
 CN0  H61  C06  C05  107.43  3.000
 CN0  O07  C06  C05  112.13  3.000
 CN0  C08  C06  C05  109.89  3.000
 CN0  H71  O07  C06  102.73  3.000
 CN0  H81  C08  O09  110.48  3.000
 CN0  H81  C08  C06  107.82  3.000
 CN0  O09  C08  C06  112.15  3.000
 CN0  H81  C08  C02  107.95  3.000
 CN0  C06  C08  C02  110.56  3.000
 CN0  O09  C08  C02  107.82  3.000
 CN0  H91  O09  C08  108.10  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
 CN0  Var_01  C05  N04  C03  C02  -53.73  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
 CN0  chir_01  C02  O01  C03  C08  negativ
 CN0  chir_02  C05  N04  C06  C10  negativ
 CN0  chir_03  C06  O07  C05  C08  positiv
 CN0  chir_04  C08  O09  C06  C02  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
 CN0  plan-1  C10  0.020
 CN0  plan-1  C05  0.020
 CN0  plan-1  O11  0.020
 CN0  plan-1  O12  0.020

