# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:55:48 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  22  13  .  2023-02-15  2023-02-16
;
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  OH1   0  -0.580  -2.9137  -0.0807  -1.5957
 HDL  C1    C  C     0   0.517  -2.8252  -0.2096  -0.2876
 HDL  O1B   O  O     0  -0.436  -3.5885  -0.8485   0.3934
 HDL  C2    C  CH1   0  -0.089  -1.6418   0.5420   0.2932
 HDL  O2    O  OH1   0  -0.667  -1.6633   0.4658   1.6899
 HDL  C3    C  CH1   0  -0.025  -0.3383  -0.0498  -0.2588
 HDL  O3    O  OH1   0  -0.657  -0.2472  -1.4234   0.0182
 HDL  C4    C  CH1   0  -0.109   0.8880   0.6997   0.2839
 HDL  O4    O  OH1   0  -0.651   0.8692   2.0564  -0.0609
 HDL  C5    C  C     0   0.506   2.1429   0.0357  -0.2791
 HDL  O5    O  O     0  -0.478   2.4394   0.1462  -1.4566
 HDL  N6    N  NH1   0  -0.364   2.8455  -0.6586   0.6212
 HDL  O6    O  OH1   0  -0.540   4.0306  -1.2328   0.2837
 HDL  HO1A  H  HOH1  0   0.493  -3.6683  -0.5829  -1.9402
 HDL  H2    H  HCH1  0   0.280  -1.7189   1.5883  -0.0256
 HDL  HO2   H  HOH1  0   0.455  -2.3501  -0.1611   1.9524
 HDL  H3    H  HCH1  0   0.271  -0.3412   0.0481  -1.3487
 HDL  HO3   H  HOH1  0   0.447  -0.2974  -1.5529   0.9729
 HDL  H4    H  HCH1  0   0.273   0.8858   0.6546   1.3775
 HDL  HO4   H  HOH1  0   0.451   0.9772   2.1325  -1.0169
 HDL  H8    H  HNH1  0   0.422   2.6382  -0.6433   1.6094
 HDL  H9    H  HOH1  0   0.481   3.8312  -2.1488   0.0479

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  O1A  HO1A  single  0.850  0.020  0.980
 HDL  C1   O1A   single  1.317  0.020  1.317
 HDL  C1   C2    single  1.517  0.020  1.517
 HDL  O1B  C1    double  1.206  0.020  1.206
 HDL  C2   O2    single  1.399  0.020  1.399
 HDL  C2   H2    single  0.970  0.020  1.090
 HDL  O2   HO2   single  0.850  0.020  0.980
 HDL  C3   C2    single  1.534  0.020  1.534
 HDL  C3   O3    single  1.404  0.020  1.404
 HDL  C3   C4    single  1.536  0.020  1.536
 HDL  C3   H3    single  0.970  0.020  1.090
 HDL  O3   HO3   single  0.850  0.020  0.980
 HDL  C4   C5    single  1.527  0.020  1.527
 HDL  C4   H4    single  0.970  0.020  1.090
 HDL  O4   C4    single  1.400  0.020  1.400
 HDL  O4   HO4   single  0.850  0.020  0.980
 HDL  C5   O5    double  1.219  0.020  1.219
 HDL  C5   N6    single  1.337  0.020  1.337
 HDL  N6   O6    single  1.359  0.020  1.359
 HDL  N6   H8    single  0.860  0.020  1.020
 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  HO1A  O1A  C1   110.75  3.000
 HDL  C2    C1   O1B  122.67  3.000
 HDL  O1B   C1   O1A  124.75  3.000
 HDL  C2    C1   O1A  112.58  3.000
 HDL  H2    C2   C3   108.86  3.000
 HDL  C3    C2   O2   110.56  3.000
 HDL  H2    C2   O2   109.95  3.000
 HDL  C3    C2   C1   109.49  3.000
 HDL  H2    C2   C1   107.85  3.000
 HDL  O2    C2   C1   110.07  3.000
 HDL  HO2   O2   C2   108.51  3.000
 HDL  H3    C3   C4   108.08  3.000
 HDL  H3    C3   O3   106.51  3.000
 HDL  C4    C3   O3   110.84  3.000
 HDL  H3    C3   C2   108.76  3.000
 HDL  C4    C3   C2   111.27  3.000
 HDL  O3    C3   C2   111.19  3.000
 HDL  HO3   O3   C3   108.86  3.000
 HDL  H4    C4   C5   110.62  3.000
 HDL  H4    C4   O4   106.62  3.000
 HDL  C5    C4   O4   109.97  3.000
 HDL  O4    C4   C3   112.03  3.000
 HDL  H4    C4   C3   109.34  3.000
 HDL  C5    C4   C3   108.27  3.000
 HDL  HO4   O4   C4   108.60  3.000
 HDL  N6    C5   O5   124.73  3.000
 HDL  N6    C5   C4   114.17  3.000
 HDL  O5    C5   C4   121.09  3.000
 HDL  H8    N6   O6   115.36  3.000
 HDL  H8    N6   C5   122.91  3.000
 HDL  O6    N6   C5   120.70  3.000
 HDL  H9    O6   N6   106.32  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
 HDL  CONST_04  HO1A  O1A  C1  O1B    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
 HDL  plan-2  HO1A  0.020

