# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:28:01 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxopiperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@H](NC(=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
 EVA  EVA  '(2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxopiperidine-2-carboxylic acid'  ligand  21  13  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EVA
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
 EVA  C     C  C      0   0.471   2.3964   0.4327   0.0002
 EVA  N     N  NR16   0  -0.631   0.1302   1.3624   0.2453
 EVA  O     O  O      0  -0.567   2.7606   1.6031  -0.1575
 EVA  CA    C  CR16   0  -0.252   0.9394   0.1831   0.4545
 EVA  CB    C  CR16   0   0.030   0.3238  -1.0386  -0.2353
 EVA  CG    C  CR16   0   0.026  -1.1262  -1.1559   0.1962
 EVA  OG    O  OH1    0  -0.695   1.0229  -2.1971   0.1139
 EVA  CAE   C  CR6    0   0.491  -1.1893   1.3960   0.0423
 EVA  OAJ   O  OH1    0  -0.666  -3.1745   0.0415   0.2347
 EVA  OAK   O  O      0  -0.504  -1.8464   2.4302   0.0428
 EVA  CD1   C  CR16   0  -0.085  -1.8765   0.0738  -0.2923
 EVA  OD2   O  OH1    0  -0.668  -1.6674  -2.3317  -0.3497
 EVA  OXT   O  OC    -1  -0.603   3.0946  -0.6022  -0.1353
 EVA  HN    H  HNR6   0   0.389   0.6061   2.2454   0.3722
 EVA  HA    H  HCR6   0   0.260   0.9835  -0.0433   1.5307
 EVA  HB    H  HCR6   0   0.201   0.3493  -0.8702  -1.3267
 EVA  HG    H  HCR6   0   0.213  -1.1621  -1.1800   1.2982
 EVA  HOG   H  HOH1   0   0.440   1.9628  -1.9164   0.0452
 EVA  HOAJ  H  HOH1   0   0.454  -3.6445   0.8227  -0.0770
 EVA  HD1   H  HCR6   0   0.243  -1.8952   0.0307  -1.3945
 EVA  HOD2  H  HOH1   0   0.452  -2.5901  -2.3932  -0.0821

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
 EVA  O    C     deloc   1.236  0.020  1.236
 EVA  OXT  C     deloc   1.256  0.020  1.256
 EVA  C    CA    single  1.546  0.020  1.546
 EVA  N    CAE   single  1.335  0.020  1.335
 EVA  N    CA    single  1.446  0.020  1.446
 EVA  N    HN    single  0.860  0.020  1.020
 EVA  CA   CB    single  1.532  0.020  1.532
 EVA  CA   HA    single  0.970  0.020  1.090
 EVA  CB   OG    single  1.397  0.020  1.397
 EVA  CB   CG    single  1.517  0.020  1.517
 EVA  CB   HB    single  0.970  0.020  1.090
 EVA  CD1  CG    single  1.521  0.020  1.521
 EVA  CG   OD2   single  1.405  0.020  1.405
 EVA  CG   HG    single  0.970  0.020  1.090
 EVA  OG   HOG   single  0.850  0.020  0.980
 EVA  OAK  CAE   double  1.225  0.020  1.225
 EVA  CAE  CD1   single  1.527  0.020  1.527
 EVA  CD1  OAJ   single  1.401  0.020  1.401
 EVA  OAJ  HOAJ  single  0.850  0.020  0.980
 EVA  CD1  HD1   single  0.970  0.020  1.090
 EVA  OD2  HOD2  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
 EVA  OXT   C    CA   114.99  3.000
 EVA  CA    C    O    117.91  3.000
 EVA  OXT   C    O    127.07  3.000
 EVA  HN    N    CAE  117.53  3.000
 EVA  HN    N    CA   115.52  3.000
 EVA  CAE   N    CA   126.56  3.000
 EVA  HA    CA   CB   107.00  3.000
 EVA  HA    CA   N    109.38  3.000
 EVA  CB    CA   N    111.13  3.000
 EVA  HA    CA   C    106.42  3.000
 EVA  CB    CA   C    112.02  3.000
 EVA  N     CA   C    110.68  3.000
 EVA  HB    CB   OG   111.21  3.000
 EVA  HB    CB   CG   108.35  3.000
 EVA  OG    CB   CG   110.05  3.000
 EVA  HB    CB   CA   108.30  3.000
 EVA  CG    CB   CA   108.51  3.000
 EVA  OG    CB   CA   110.34  3.000
 EVA  HG    CG   OD2  110.94  3.000
 EVA  HG    CG   CD1  108.81  3.000
 EVA  OD2   CG   CD1  111.21  3.000
 EVA  HG    CG   CB   108.48  3.000
 EVA  OD2   CG   CB   108.80  3.000
 EVA  CD1   CG   CB   108.51  3.000
 EVA  HOG   OG   CB   102.95  3.000
 EVA  CD1   CAE  OAK  119.31  3.000
 EVA  CD1   CAE  N    117.14  3.000
 EVA  OAK   CAE  N    123.44  3.000
 EVA  HOAJ  OAJ  CD1  108.15  3.000
 EVA  HD1   CD1  OAJ  111.05  3.000
 EVA  HD1   CD1  CAE  105.10  3.000
 EVA  OAJ   CD1  CAE  110.76  3.000
 EVA  HD1   CD1  CG   107.31  3.000
 EVA  OAJ   CD1  CG   108.51  3.000
 EVA  CAE   CD1  CG   114.05  3.000
 EVA  HOD2  OD2  CG   108.34  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
 EVA  CONST_01  CD1  CAE  N    CA     0.00  0.0  0
 EVA  CONST_02  OAK  CAE  N    CA   180.00  0.0  0
 EVA  CONST_03  HN   N    CAE  CD1  180.00  0.0  0

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
 EVA  chir_01  CA   C    N    CB   negativ
 EVA  chir_02  CB   OG   CA   CG   positiv
 EVA  chir_03  CG   OD2  CD1  CB   positiv
 EVA  chir_04  CD1  OAJ  CG   CAE  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
 EVA  plan-1  N    0.020
 EVA  plan-1  CA   0.020
 EVA  plan-1  CAE  0.020
 EVA  plan-1  OAK  0.020
 EVA  plan-1  CD1  0.020
 EVA  plan-1  HN   0.020
 EVA  plan-2  C    0.020
 EVA  plan-2  O    0.020
 EVA  plan-2  CA   0.020
 EVA  plan-2  OXT  0.020

