# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 23:01:04 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 4-deoxy-L-threo-hex-5-ulosuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CC(=O)C(O)=O)[C@@H](O)C=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
 D54  D54  '4-deoxy-L-threo-hex-5-ulosuronic acid'  ligand  19  12  .  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_D54
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
 D54  OAA   O  O      0  -0.377  -4.2422   0.1458   0.2225
 D54  OAB   O  OH1    0  -0.667  -2.1472  -1.4994   0.5749
 D54  OAC   O  O      0  -0.393   1.6564   1.6040  -0.5015
 D54  OAD   O  O      0  -0.577   2.9941  -1.5418   0.0289
 D54  CAE   C  C1     0   0.154  -3.2938   0.3144  -0.5023
 D54  CAF   C  CH1    0  -0.084  -2.0599  -0.5443  -0.4413
 D54  CAG   C  CH1    0   0.016  -0.8423   0.3650  -0.2411
 D54  CAH   C  CH2    0  -0.580   0.4502  -0.4352  -0.2356
 D54  CAI   C  C      0   0.240   1.6934   0.4192  -0.2691
 D54  CAJ   C  C      0   0.349   3.0531  -0.3021  -0.0349
 D54  OAK   O  OH1    0  -0.663  -1.0000   1.1353   0.9284
 D54  OAL   O  OC    -1  -0.581   4.0433   0.4357   0.0534
 D54  HAE   H  H      0   0.220  -3.2804   1.1062  -1.2688
 D54  HAF   H  HCH1   0   0.258  -1.9722  -1.0207  -1.4316
 D54  HAG   H  HCH1   0   0.249  -0.8226   1.0735  -1.0747
 D54  HAH   H  HCH2   0   0.270   0.4942  -1.1040   0.6279
 D54  HAHA  H  HCH2   0   0.274   0.4913  -1.0982  -1.1073
 D54  HOAK  H  HOH1   0   0.443  -1.0803   0.5312   1.6756
 D54  HOAB  H  HOH1   0   0.451  -3.0232  -1.4328   0.9777

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
 D54  OAA  CAE   double  1.206  0.020  1.206
 D54  OAB  CAF   single  1.397  0.020  1.397
 D54  OAB  HOAB  single  0.850  0.020  0.980
 D54  CAI  OAC   double  1.208  0.020  1.208
 D54  OAD  CAJ   deloc   1.243  0.020  1.243
 D54  CAF  CAE   single  1.504  0.020  1.504
 D54  CAE  HAE   single  0.930  0.020  1.080
 D54  CAF  CAG   single  1.533  0.020  1.533
 D54  CAF  HAF   single  0.970  0.020  1.090
 D54  OAK  CAG   single  1.409  0.020  1.409
 D54  CAG  CAH   single  1.520  0.020  1.520
 D54  CAG  HAG   single  0.970  0.020  1.090
 D54  CAH  CAI   single  1.509  0.020  1.509
 D54  CAH  HAH   single  0.970  0.020  1.090
 D54  CAH  HAHA  single  0.970  0.020  1.090
 D54  CAI  CAJ   single  1.557  0.020  1.557
 D54  CAJ  OAL   deloc   1.238  0.020  1.238
 D54  OAK  HOAK  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
 D54  HOAB  OAB  CAF  108.21  3.000
 D54  HAE   CAE  CAF  115.36  3.000
 D54  HAE   CAE  OAA  121.89  3.000
 D54  CAF   CAE  OAA  122.75  3.000
 D54  HAF   CAF  CAG  108.09  3.000
 D54  HAF   CAF  CAE  105.99  3.000
 D54  CAG   CAF  CAE  108.55  3.000
 D54  HAF   CAF  OAB  111.28  3.000
 D54  CAG   CAF  OAB  111.10  3.000
 D54  CAE   CAF  OAB  111.62  3.000
 D54  HAG   CAG  OAK  106.28  3.000
 D54  HAG   CAG  CAH  109.17  3.000
 D54  OAK   CAG  CAH  112.32  3.000
 D54  HAG   CAG  CAF  107.39  3.000
 D54  CAH   CAG  CAF  111.33  3.000
 D54  OAK   CAG  CAF  110.10  3.000
 D54  HAHA  CAH  HAH  104.87  3.000
 D54  HAHA  CAH  CAI  107.10  3.000
 D54  HAH   CAH  CAI  109.32  3.000
 D54  HAHA  CAH  CAG  110.33  3.000
 D54  HAH   CAH  CAG  111.05  3.000
 D54  CAI   CAH  CAG  113.73  3.000
 D54  CAJ   CAI  CAH  116.99  3.000
 D54  CAJ   CAI  OAC  120.67  3.000
 D54  CAH   CAI  OAC  122.31  3.000
 D54  OAL   CAJ  CAI  115.67  3.000
 D54  OAL   CAJ  OAD  128.96  3.000
 D54  CAI   CAJ  OAD  115.37  3.000
 D54  HOAK  OAK  CAG  108.06  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
 D54  Var_01  CAG  CAH  CAI  OAC   -11.55  30.0  2
 D54  Var_02  OAD  CAJ  CAI  OAC  -171.34  30.0  2

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
 D54  chir_01  CAF  OAB  CAE  CAG  negativ
 D54  chir_02  CAG  OAK  CAF  CAH  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
 D54  plan-1  OAC  0.020
 D54  plan-1  CAH  0.020
 D54  plan-1  CAI  0.020
 D54  plan-1  CAJ  0.020
 D54  plan-2  OAD  0.020
 D54  plan-2  CAI  0.020
 D54  plan-2  CAJ  0.020
 D54  plan-2  OAL  0.020
 D54  plan-3  OAA  0.020
 D54  plan-3  CAE  0.020
 D54  plan-3  CAF  0.020
 D54  plan-3  HAE  0.020

