# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 06:50:08 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: (3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@]1(O)COC(=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
 89Y  89Y  (3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-one  D-saccharide  18  10  .  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_89Y
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
 89Y  O10  O  OH1   0  -0.646  -0.8151  -1.9494  -0.2859
 89Y  C09  C  CH1   0  -0.089  -0.6551  -0.5933  -0.5168
 89Y  C07  C  C     0   0.537  -1.6693   0.2884   0.1973
 89Y  O08  O  O     0  -0.424  -2.8045   0.0286   0.4797
 89Y  O06  O  O2    0  -0.434  -1.1091   1.4645   0.4714
 89Y  C05  C  CH2   0  -0.171   0.2761   1.4538   0.0839
 89Y  C03  C  CT    0   0.096   0.6516  -0.0339   0.0289
 89Y  O04  O  OH1   0  -0.665   0.8059  -0.5564   1.3228
 89Y  C02  C  CH2   0  -0.158   1.8593  -0.3125  -0.8436
 89Y  O01  O  OH1   0  -0.673   2.9552   0.3445  -0.2505
 89Y  H1   H  HOH1  0   0.466  -1.5708  -2.2630  -0.7927
 89Y  H2   H  HCH1  0   0.279  -0.7158  -0.3351  -1.5869
 89Y  H3   H  HCH2  0   0.253   0.3775   1.9384  -0.8898
 89Y  H4   H  HCH2  0   0.273   0.8425   2.0190   0.8218
 89Y  H5   H  HOH1  0   0.453   1.6497  -0.2477   1.6732
 89Y  H6   H  HCH2  0   0.231   2.0133  -1.3961  -0.9010
 89Y  H7   H  HCH2  0   0.206   1.6681   0.0456  -1.8630
 89Y  H8   H  HOH1  0   0.466   3.7677   0.0035  -0.6348

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
 89Y  O01  C02  single  1.409  0.020  1.409
 89Y  C02  C03  single  1.516  0.020  1.516
 89Y  C03  C05  single  1.535  0.020  1.535
 89Y  C03  O04  single  1.404  0.020  1.404
 89Y  C03  C09  single  1.523  0.020  1.523
 89Y  C05  O06  single  1.438  0.020  1.438
 89Y  C09  O10  single  1.385  0.020  1.385
 89Y  C09  C07  single  1.522  0.020  1.522
 89Y  O06  C07  single  1.331  0.020  1.331
 89Y  C07  O08  double  1.198  0.020  1.198
 89Y  O10  H1   single  0.850  0.020  0.980
 89Y  C09  H2   single  0.970  0.020  1.090
 89Y  C05  H3   single  0.970  0.020  1.090
 89Y  C05  H4   single  0.970  0.020  1.090
 89Y  O04  H5   single  0.850  0.020  0.980
 89Y  C02  H6   single  0.970  0.020  1.090
 89Y  C02  H7   single  0.970  0.020  1.090
 89Y  O01  H8   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
 89Y  H1   O10  C09  108.78  3.000
 89Y  H2   C09  C03  108.01  3.000
 89Y  H2   C09  C07  106.45  3.000
 89Y  C03  C09  C07  101.01  3.000
 89Y  H2   C09  O10  112.63  3.000
 89Y  C07  C09  O10  114.33  3.000
 89Y  C03  C09  O10  113.52  3.000
 89Y  O06  C07  O08  122.80  3.000
 89Y  O08  C07  C09  128.05  3.000
 89Y  O06  C07  C09  109.15  3.000
 89Y  C05  O06  C07  110.07  3.000
 89Y  H4   C05  H3   109.00  3.000
 89Y  H4   C05  C03  113.59  3.000
 89Y  H3   C05  C03  112.04  3.000
 89Y  H4   C05  O06  108.34  3.000
 89Y  H3   C05  O06  109.04  3.000
 89Y  C03  C05  O06  104.62  3.000
 89Y  C02  C03  O04  112.00  3.000
 89Y  O04  C03  C05  110.76  3.000
 89Y  C02  C03  C05  113.18  3.000
 89Y  O04  C03  C09  106.73  3.000
 89Y  C05  C03  C09   99.14  3.000
 89Y  C02  C03  C09  114.20  3.000
 89Y  H5   O04  C03  108.17  3.000
 89Y  H7   C02  H6   107.37  3.000
 89Y  H7   C02  O01  111.99  3.000
 89Y  H6   C02  O01  111.95  3.000
 89Y  H7   C02  C03  109.63  3.000
 89Y  H6   C02  C03  108.90  3.000
 89Y  O01  C02  C03  106.97  3.000
 89Y  H8   O01  C02  108.89  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
 89Y  Var_01  C03  C05  O06  C07  -21.24  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
 89Y  chir_01  C09  C03  O10  C07  negativ
 89Y  chir_02  C03  C02  C05  C09  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
 89Y  plan-1  C09  0.020
 89Y  plan-1  C07  0.020
 89Y  plan-1  O08  0.020
 89Y  plan-1  O06  0.020

