# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:08:28 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: alpha-D-lyxopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@H](O)[C@@H](O)[C@H]1O
#
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
 LDY  LDY  'alpha-D-lyxopyranose     '  D-saccharide  20  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LDY
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
 LDY  C5   C  CH2   0  -0.224  35.1846  25.8577  -41.8475
 LDY  O5   O  O2    0  -0.488  34.3031  26.9389  -41.6377
 LDY  C1   C  CH1   0   0.273  34.4612  27.9571  -42.5958
 LDY  C2   C  CH1   0  -0.020  34.1320  27.4172  -43.9861
 LDY  O2   O  OH1   0  -0.670  34.3471  28.3840  -44.9854
 LDY  C3   C  CH1   0  -0.025  35.0243  26.2204  -44.3153
 LDY  O3   O  OH1   0  -0.668  36.3754  26.5992  -44.4341
 LDY  C4   C  CH1   0   0.006  34.9458  25.1863  -43.1937
 LDY  O4   O  OH1   0  -0.667  33.6700  24.5957  -43.2808
 LDY  O1   O  OH1   0  -0.662  33.5700  28.9743  -42.3095
 LDY  H51  H  HCH2  0   0.249  35.0180  25.1473  -41.0338
 LDY  H52  H  HCH2  0   0.214  36.2319  26.1812  -41.7830
 LDY  H1   H  HCH1  0   0.184  35.5027  28.3203  -42.5772
 LDY  H2   H  HCH1  0   0.220  33.0873  27.0756  -43.9754
 LDY  HO2  H  HOH1  0   0.453  33.8329  29.1691  -44.7701
 LDY  H3   H  HCH1  0   0.233  34.6652  25.7605  -45.2479
 LDY  HO3  H  HOH1  0   0.450  36.4212  27.3669  -45.0140
 LDY  H4   H  HCH1  0   0.227  35.7418  24.4434  -43.3475
 LDY  HO4  H  HOH1  0   0.453  33.5761  23.9570  -42.5671
 LDY  HO1  H  HOH1  0   0.463  33.9305  29.5358  -41.6152

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
 LDY  C4  C5   single  1.523  0.020  1.523
 LDY  C5  O5   single  1.411  0.020  1.411
 LDY  C5  H51  single  0.970  0.020  1.090
 LDY  C5  H52  single  0.970  0.020  1.090
 LDY  C1  O5   single  1.407  0.020  1.407
 LDY  C2  C1   single  1.527  0.020  1.527
 LDY  C1  O1   single  1.382  0.020  1.382
 LDY  C1  H1   single  0.970  0.020  1.090
 LDY  O2  C2   single  1.407  0.020  1.407
 LDY  C3  C2   single  1.529  0.020  1.529
 LDY  C2  H2   single  0.970  0.020  1.090
 LDY  O2  HO2  single  0.850  0.020  0.980
 LDY  O3  C3   single  1.408  0.020  1.408
 LDY  C3  C4   single  1.528  0.020  1.528
 LDY  C3  H3   single  0.970  0.020  1.090
 LDY  O3  HO3  single  0.850  0.020  0.980
 LDY  C4  O4   single  1.409  0.020  1.409
 LDY  C4  H4   single  0.970  0.020  1.090
 LDY  O4  HO4  single  0.850  0.020  0.980
 LDY  O1  HO1  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
 LDY  H52  C5  H51  107.05  3.000
 LDY  H52  C5  C4   109.36  3.000
 LDY  H51  C5  C4   110.34  3.000
 LDY  H52  C5  O5   111.19  3.000
 LDY  H51  C5  O5   106.98  3.000
 LDY  C4   C5  O5   111.80  3.000
 LDY  C1   O5  C5   112.52  3.000
 LDY  H1   C1  O1   111.28  3.000
 LDY  H1   C1  C2   109.59  3.000
 LDY  O1   C1  C2   108.04  3.000
 LDY  H1   C1  O5   109.44  3.000
 LDY  O1   C1  O5   108.60  3.000
 LDY  C2   C1  O5   109.87  3.000
 LDY  H2   C2  C3   108.27  3.000
 LDY  H2   C2  O2   111.46  3.000
 LDY  C3   C2  O2   107.20  3.000
 LDY  H2   C2  C1   107.81  3.000
 LDY  C3   C2  C1   110.30  3.000
 LDY  O2   C2  C1   111.76  3.000
 LDY  HO2  O2  C2   108.65  3.000
 LDY  H3   C3  C4   108.82  3.000
 LDY  H3   C3  O3   110.74  3.000
 LDY  C4   C3  O3   107.06  3.000
 LDY  H3   C3  C2   108.62  3.000
 LDY  C4   C3  C2   109.99  3.000
 LDY  O3   C3  C2   111.57  3.000
 LDY  HO3  O3  C3   108.11  3.000
 LDY  H4   C4  O4   111.33  3.000
 LDY  H4   C4  C3   108.51  3.000
 LDY  O4   C4  C3   106.56  3.000
 LDY  H4   C4  C5   107.93  3.000
 LDY  O4   C4  C5   112.43  3.000
 LDY  C3   C4  C5   110.03  3.000
 LDY  HO4  O4  C4   108.71  3.000
 LDY  HO1  O1  C1   109.70  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
 LDY  Var_01  C4  C5  O5  C1  -61.63  30.0  1

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
 LDY  chir_01  C1  O5  C2  O1  negativ
 LDY  chir_02  C2  O2  C1  C3  positiv
 LDY  chir_03  C3  O3  C2  C4  positiv
 LDY  chir_04  C4  O4  C3  C5  negativ

