# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 20:57:04 2021
#   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  23  12  .  2022-03-15  2022-11-17
;
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   0.528  -28.3111   0.0778  22.4623
 CN0  O01  O  OH1   0  -0.673  -29.7096   2.1033  17.4175
 CN0  C02  C  CH1   0   0.043  -29.3017   1.2595  18.4673
 CN0  C03  C  CH2   0  -0.347  -28.2218   1.9861  19.2627
 CN0  N04  N  NH1   0  -0.586  -27.7654   1.2411  20.4190
 CN0  C05  C  CH1   0  -0.228  -28.8528   0.8866  21.3059
 CN0  C06  C  CH1   0   0.013  -29.9644   0.0871  20.5853
 CN0  O07  O  OH1   0  -0.669  -31.0725  -0.1653  21.4152
 CN0  C08  C  CH1   0   0.006  -30.4590   0.8973  19.3888
 CN0  O09  O  OH1   0  -0.674  -31.4009   0.1750  18.6324
 CN0  O11  O  O     0  -0.437  -27.3876  -0.6913  22.3633
 CN0  O12  O  OH1   0  -0.581  -28.9873   0.2730  23.5830
 CN0  H11  H  HOH1  0   0.451  -30.3796   1.6440  16.9011
 CN0  H32  H  HCH2  0   0.258  -27.3637   2.1935  18.6211
 CN0  H31  H  HCH2  0   0.232  -28.6128   2.9525  19.5994
 CN0  H1   H  HNH1  0   0.352  -27.2661   0.4090  20.1267
 CN0  H51  H  HCH1  0   0.274  -29.2970   1.8104  21.6929
 CN0  H61  H  HCH1  0   0.229  -29.5243  -0.8502  20.2143
 CN0  H71  H  HOH1  0   0.462  -30.9669  -1.0196  21.8423
 CN0  H81  H  HCH1  0   0.208  -30.9003   1.8340  19.7701
 CN0  H91  H  HOH1  0   0.453  -32.1758   0.0206  19.1821
 CN0  H2   H  HOH1  0   0.484  -28.6476  -0.3058  24.2831
 CN0  H21  H  HCH1  0   0.204  -28.8715   0.3237  18.0749

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  1.407  0.020  1.407
 CN0  C02  C03  single  1.525  0.020  1.525
 CN0  C02  C08  single  1.523  0.020  1.523
 CN0  O09  C08  single  1.407  0.020  1.407
 CN0  C03  N04  single  1.449  0.020  1.449
 CN0  C08  C06  single  1.527  0.020  1.527
 CN0  N04  C05  single  1.447  0.020  1.447
 CN0  C06  C05  single  1.547  0.020  1.547
 CN0  C06  O07  single  1.407  0.020  1.407
 CN0  C05  C10  single  1.512  0.020  1.512
 CN0  O11  C10  double  1.206  0.020  1.206
 CN0  C10  O12  single  1.323  0.020  1.323
 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
 CN0  O12  H2   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  123.70  3.000
 CN0  O12  C10  C05  112.70  3.000
 CN0  O11  C10  C05  123.57  3.000
 CN0  H11  O01  C02  108.41  3.000
 CN0  H21  C02  C08  108.06  3.000
 CN0  H21  C02  C03  108.29  3.000
 CN0  C08  C02  C03  109.62  3.000
 CN0  H21  C02  O01  110.89  3.000
 CN0  C08  C02  O01  111.94  3.000
 CN0  C03  C02  O01  107.97  3.000
 CN0  H31  C03  H32  107.08  3.000
 CN0  H31  C03  N04  108.70  3.000
 CN0  H32  C03  N04  108.61  3.000
 CN0  H31  C03  C02  109.13  3.000
 CN0  H32  C03  C02  109.92  3.000
 CN0  N04  C03  C02  113.21  3.000
 CN0  H1   N04  C05  110.23  3.000
 CN0  H1   N04  C03  110.30  3.000
 CN0  C05  N04  C03  112.23  3.000
 CN0  H51  C05  C06  108.00  3.000
 CN0  H51  C05  N04  108.33  3.000
 CN0  C06  C05  N04  112.39  3.000
 CN0  H51  C05  C10  109.04  3.000
 CN0  C06  C05  C10  109.71  3.000
 CN0  N04  C05  C10  109.31  3.000
 CN0  H61  C06  C08  108.51  3.000
 CN0  H61  C06  O07  111.17  3.000
 CN0  C08  C06  O07  107.59  3.000
 CN0  H61  C06  C05  108.06  3.000
 CN0  O07  C06  C05  112.56  3.000
 CN0  C08  C06  C05  108.87  3.000
 CN0  H71  O07  C06  109.58  3.000
 CN0  H81  C08  O09  110.72  3.000
 CN0  H81  C08  C06  108.01  3.000
 CN0  O09  C08  C06  111.44  3.000
 CN0  H81  C08  C02  108.12  3.000
 CN0  C06  C08  C02  110.73  3.000
 CN0  O09  C08  C02  107.78  3.000
 CN0  H91  O09  C08  108.31  3.000
 CN0  H2   O12  C10  110.14  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  CONST_01  H2   O12  C10  C05  180.00   0.0  0
 CN0  Var_01    C05  N04  C03  C02  -55.80  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
 CN0  plan-1  H2   0.020

