# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:39:04 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  22  13  .  2021-08-09  2021-08-09  
;
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   0.546   2.3122   0.6032  -0.1371
 EVA  N     N  NR16  0  -0.638   0.1173   1.3832   0.4652
 EVA  O     O  O     0  -0.416   2.5321   1.6478  -0.6877
 EVA  CA    C  CR16  0  -0.183   0.9943   0.2412   0.5320
 EVA  CB    C  CR16  0   0.002   0.3863  -1.0346  -0.1046
 EVA  CG    C  CR16  0   0.025  -1.0911  -1.1189   0.2450
 EVA  OG    O  OH1   0  -0.655   1.0086  -2.1844   0.3857
 EVA  CAE   C  CR6   0   0.500  -1.1941   1.3982   0.1810
 EVA  OAJ   O  OH1   0  -0.662  -3.1519   0.0117   0.0044
 EVA  OAK   O  O     0  -0.484  -1.8786   2.4039   0.2812
 EVA  CD1   C  CR16  0  -0.089  -1.7975   0.0983  -0.3298
 EVA  OD2   O  OH1   0  -0.662  -1.5936  -2.3055  -0.3039
 EVA  OXT   O  OH1   0  -0.595   3.1910  -0.3836  -0.0347
 EVA  HN    H  HNR6  0   0.406   0.5041   2.2606   0.7850
 EVA  HA    H  HCR6  0   0.307   1.2069   0.0018   1.5815
 EVA  HB    H  HCR6  0   0.246   0.4736  -0.9651  -1.1989
 EVA  HG    H  HCR6  0   0.231  -1.1987  -1.1089   1.3422
 EVA  HOG   H  HOH1  0   0.459   1.8976  -2.2419   0.0216
 EVA  HOAJ  H  HOH1  0   0.459  -3.6093   0.7769  -0.3604
 EVA  HD1   H  HCR6  0   0.253  -1.6518   0.0943  -1.4229
 EVA  HOD2  H  HOH1  0   0.456  -2.5388  -2.3448  -0.1230
 EVA  HOXT  H  HOH1  0   0.494   4.0158  -0.1554  -0.4914

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     double  1.201  0.020  1.201
 EVA  OXT  C     single  1.325  0.020  1.325
 EVA  C    CA    single  1.522  0.020  1.522
 EVA  N    CAE   single  1.342  0.020  1.342
 EVA  N    CA    single  1.441  0.020  1.441
 EVA  N    HN    single  0.860  0.020  1.020
 EVA  CA   CB    single  1.550  0.020  1.550
 EVA  CA   HA    single  0.970  0.020  1.090
 EVA  CB   OG    single  1.396  0.020  1.396
 EVA  CB   CG    single  1.521  0.020  1.521
 EVA  CB   HB    single  0.970  0.020  1.090
 EVA  CD1  CG    single  1.520  0.020  1.520
 EVA  CG   OD2   single  1.401  0.020  1.401
 EVA  CG   HG    single  0.970  0.020  1.090
 EVA  OG   HOG   single  0.850  0.020  0.980
 EVA  OAK  CAE   double  1.221  0.020  1.221
 EVA  CAE  CD1   single  1.521  0.020  1.521
 EVA  CD1  OAJ   single  1.398  0.020  1.398
 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
 EVA  OXT  HOXT  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   111.29  3.000
 EVA  CA    C    O    124.54  3.000
 EVA  OXT   C    O    124.17  3.000
 EVA  HN    N    CAE  115.54  3.000
 EVA  HN    N    CA   116.12  3.000
 EVA  CAE   N    CA   127.83  3.000
 EVA  HA    CA   CB   106.81  3.000
 EVA  HA    CA   N    109.58  3.000
 EVA  CB    CA   N    113.23  3.000
 EVA  HA    CA   C    107.74  3.000
 EVA  CB    CA   C    110.79  3.000
 EVA  N     CA   C    108.55  3.000
 EVA  HB    CB   OG   111.47  3.000
 EVA  HB    CB   CG   108.03  3.000
 EVA  OG    CB   CG   107.86  3.000
 EVA  HB    CB   CA   108.99  3.000
 EVA  CG    CB   CA   109.41  3.000
 EVA  OG    CB   CA   111.02  3.000
 EVA  HG    CG   OD2  111.27  3.000
 EVA  HG    CG   CD1  108.89  3.000
 EVA  OD2   CG   CD1  111.31  3.000
 EVA  HG    CG   CB   108.85  3.000
 EVA  OD2   CG   CB   107.78  3.000
 EVA  CD1   CG   CB   108.67  3.000
 EVA  HOG   OG   CB   109.15  3.000
 EVA  CD1   CAE  OAK  120.61  3.000
 EVA  CD1   CAE  N    116.68  3.000
 EVA  OAK   CAE  N    122.67  3.000
 EVA  HOAJ  OAJ  CD1  108.68  3.000
 EVA  HD1   CD1  OAJ  111.40  3.000
 EVA  HD1   CD1  CAE  106.47  3.000
 EVA  OAJ   CD1  CAE  110.91  3.000
 EVA  HD1   CD1  CG   108.09  3.000
 EVA  OAJ   CD1  CG   108.07  3.000
 EVA  CAE   CD1  CG   111.89  3.000
 EVA  HOD2  OD2  CG   108.24  3.000
 EVA  HOXT  OXT  C    110.62  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
 EVA  CONST_04  HOXT  OXT  C    CA   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
 EVA  plan-2  HOXT  0.020

