# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:35:53 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 1-(hydroxyamino)-D-lyxuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)[C@@H](O)[C@@H](O)[C@H](O)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
 HDL  HDL  '1-(hydroxyamino)-D-lyxuronic acid'  D-saccharide  21  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HDL
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
 HDL  O1A  O  OC    -1  -0.590  -2.9847   0.1066  -1.5707
 HDL  C1   C  C      0   0.409  -2.8729  -0.0297  -0.3446
 HDL  O1B  O  O      0  -0.606  -3.6584  -0.6084   0.4397
 HDL  C2   C  CH1    0  -0.136  -1.6272   0.5864   0.3348
 HDL  O2   O  OH1    0  -0.697  -1.6768   0.3277   1.7166
 HDL  C3   C  CH1    0  -0.007  -0.3538  -0.0047  -0.2594
 HDL  O3   O  OH1    0  -0.669  -0.2882  -1.3950  -0.0422
 HDL  C4   C  CH1    0  -0.107   0.9129   0.6652   0.2983
 HDL  O4   O  OH1    0  -0.655   0.9728   2.0324  -0.0051
 HDL  C5   C  C      0   0.507   2.1295  -0.0474  -0.2840
 HDL  O5   O  O      0  -0.480   2.4591   0.1119  -1.4468
 HDL  N6   N  NH1    0  -0.367   2.7985  -0.8085   0.5935
 HDL  O6   O  OH1    0  -0.543   3.7759  -1.6524   0.1589
 HDL  H2   H  HCH1   0   0.222  -1.6340   1.6678   0.1411
 HDL  HO2  H  HOH1   0   0.434  -2.5138  -0.1714   1.7975
 HDL  H3   H  HCH1   0   0.243  -0.3762   0.1481  -1.3431
 HDL  HO3  H  HOH1   0   0.439  -0.4997  -1.5520   0.8863
 HDL  H4   H  HCH1   0   0.262   0.9098   0.5882   1.3907
 HDL  HO4  H  HOH1   0   0.447   1.0408   2.1273  -0.9628
 HDL  H8   H  HNH1   0   0.416   2.4235  -1.0326   1.5042
 HDL  H9   H  HOH1   0   0.480   4.6126  -1.1951   0.3130

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
 HDL  C1   O1A  deloc   1.239  0.020  1.239
 HDL  C1   C2   single  1.547  0.020  1.547
 HDL  O1B  C1   deloc   1.252  0.020  1.252
 HDL  C2   O2   single  1.407  0.020  1.407
 HDL  C2   H2   single  0.970  0.020  1.090
 HDL  O2   HO2  single  0.850  0.020  0.980
 HDL  C3   C2   single  1.524  0.020  1.524
 HDL  C3   O3   single  1.409  0.020  1.409
 HDL  C3   C4   single  1.538  0.020  1.538
 HDL  C3   H3   single  0.970  0.020  1.090
 HDL  O3   HO3  single  0.850  0.020  0.980
 HDL  C4   C5   single  1.525  0.020  1.525
 HDL  C4   H4   single  0.970  0.020  1.090
 HDL  O4   C4   single  1.402  0.020  1.402
 HDL  O4   HO4  single  0.850  0.020  0.980
 HDL  C5   O5   double  1.219  0.020  1.219
 HDL  C5   N6   single  1.340  0.020  1.340
 HDL  N6   O6   single  1.362  0.020  1.362
 HDL  N6   H8   single  0.890  0.020  1.040
 HDL  O6   H9   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
 HDL  C2   C1  O1B  114.47  3.000
 HDL  O1B  C1  O1A  127.91  3.000
 HDL  C2   C1  O1A  117.62  3.000
 HDL  H2   C2  C3   108.55  3.000
 HDL  C3   C2  O2   109.94  3.000
 HDL  H2   C2  O2   110.73  3.000
 HDL  C3   C2  C1   110.31  3.000
 HDL  H2   C2  C1   108.03  3.000
 HDL  O2   C2  C1   109.26  3.000
 HDL  HO2  O2  C2   101.85  3.000
 HDL  H3   C3  C4   108.37  3.000
 HDL  H3   C3  O3   106.94  3.000
 HDL  C4   C3  O3   109.61  3.000
 HDL  H3   C3  C2   108.34  3.000
 HDL  C4   C3  C2   112.20  3.000
 HDL  O3   C3  C2   111.19  3.000
 HDL  HO3  O3  C3   107.37  3.000
 HDL  H4   C4  C5   110.50  3.000
 HDL  H4   C4  O4   106.53  3.000
 HDL  C5   C4  O4   109.81  3.000
 HDL  O4   C4  C3   112.43  3.000
 HDL  H4   C4  C3   109.20  3.000
 HDL  C5   C4  C3   108.37  3.000
 HDL  HO4  O4  C4   108.29  3.000
 HDL  N6   C5  O5   124.31  3.000
 HDL  N6   C5  C4   114.42  3.000
 HDL  O5   C5  C4   121.25  3.000
 HDL  H8   N6  O6   114.62  3.000
 HDL  H8   N6  C5   122.06  3.000
 HDL  O6   N6  C5   120.06  3.000
 HDL  H9   O6  N6   106.10  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
 HDL  CONST_01  O6  N6  C5  C4  180.00  0.0  0
 HDL  CONST_02  O6  N6  C5  O5    0.00  0.0  0
 HDL  CONST_03  H8  N6  C5  C4    0.00  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
 HDL  chir_01  C2  C1  O2  C3  negativ
 HDL  chir_02  C3  O3  C2  C4  negativ
 HDL  chir_03  C4  O4  C3  C5  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
 HDL  plan-1  C4   0.020
 HDL  plan-1  C5   0.020
 HDL  plan-1  O5   0.020
 HDL  plan-1  N6   0.020
 HDL  plan-1  O6   0.020
 HDL  plan-1  H8   0.020
 HDL  plan-2  O1A  0.020
 HDL  plan-2  C1   0.020
 HDL  plan-2  O1B  0.020
 HDL  plan-2  C2   0.020

