# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:09:24 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: D-sorbose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H](O)[C@@H](O)C(=O)CO
#
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
 SDD  SDD  'D-sorbose                '  D-saccharide  24  12  .  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_SDD
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
 SDD  C1   C  CH2   0  -0.258  -2.5039   1.0695  -0.4604
 SDD  O1   O  OH1   0  -0.658  -3.8950   1.1496  -0.3990
 SDD  C2   C  C     0   0.348  -2.0699  -0.3382  -0.1559
 SDD  O2   O  O     0  -0.391  -2.8180  -1.1581   0.3206
 SDD  C3   C  CH1   0  -0.072  -0.6424  -0.7274  -0.5112
 SDD  O3   O  OH1   0  -0.660  -0.3890  -2.0381  -0.1096
 SDD  C4   C  CH1   0  -0.036   0.3521   0.2549   0.1188
 SDD  O4   O  OH1   0  -0.660   0.1947   0.3009   1.5130
 SDD  C5   C  CH1   0   0.013   1.8035  -0.0033  -0.2940
 SDD  O5   O  OH1   0  -0.669   2.2879  -1.1374   0.3827
 SDD  C6   C  CH2   0  -0.178   2.6568   1.2187   0.0162
 SDD  O6   O  OH1   0  -0.677   3.9884   0.9087  -0.3368
 SDD  H1   H  HCH2  0   0.243  -2.0979   1.3533  -1.4412
 SDD  H2   H  HCH2  0   0.250  -2.0135   1.7265   0.2735
 SDD  H3   H  HOH1  0   0.465  -4.1431   2.0668  -0.5477
 SDD  H4   H  HCH1  0   0.250  -0.5625  -0.6237  -1.6067
 SDD  H5   H  HOH1  0   0.448  -1.2310  -2.4180   0.1785
 SDD  H6   H  HCH1  0   0.259   0.1044   1.2508  -0.2642
 SDD  H7   H  HOH1  0   0.447   0.5251  -0.5319   1.8699
 SDD  H8   H  HCH1  0   0.210   1.8191  -0.1558  -1.3849
 SDD  H9   H  HOH1  0   0.449   3.2507  -1.0870   0.3711
 SDD  H10  H  HCH2  0   0.205   2.2760   2.0762  -0.5528
 SDD  H11  H  HCH2  0   0.211   2.5722   1.4648   1.0809
 SDD  H12  H  HOH1  0   0.463   4.5766   1.5243   0.1086

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
 SDD  O1  C1   single  1.395  0.020  1.395
 SDD  O6  C6   single  1.412  0.020  1.412
 SDD  C1  C2   single  1.504  0.020  1.504
 SDD  C6  C5   single  1.522  0.020  1.522
 SDD  C2  C3   single  1.522  0.020  1.522
 SDD  C2  O2   double  1.208  0.020  1.208
 SDD  C3  C4   single  1.533  0.020  1.533
 SDD  C3  O3   single  1.394  0.020  1.394
 SDD  C4  C5   single  1.531  0.020  1.531
 SDD  C4  O4   single  1.404  0.020  1.404
 SDD  C5  O5   single  1.407  0.020  1.407
 SDD  C1  H1   single  0.970  0.020  1.090
 SDD  C1  H2   single  0.970  0.020  1.090
 SDD  O1  H3   single  0.850  0.020  0.980
 SDD  C3  H4   single  0.970  0.020  1.090
 SDD  O3  H5   single  0.850  0.020  0.980
 SDD  C4  H6   single  0.970  0.020  1.090
 SDD  O4  H7   single  0.850  0.020  0.980
 SDD  C5  H8   single  0.970  0.020  1.090
 SDD  O5  H9   single  0.850  0.020  0.980
 SDD  C6  H10  single  0.970  0.020  1.090
 SDD  C6  H11  single  0.970  0.020  1.090
 SDD  O6  H12  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
 SDD  H2   C1  H1   106.05  3.000
 SDD  H2   C1  C2   107.17  3.000
 SDD  H1   C1  C2   108.41  3.000
 SDD  H2   C1  O1   112.38  3.000
 SDD  H1   C1  O1   113.14  3.000
 SDD  C2   C1  O1   109.43  3.000
 SDD  H3   O1  C1   107.78  3.000
 SDD  C3   C2  O2   119.97  3.000
 SDD  O2   C2  C1   122.44  3.000
 SDD  C3   C2  C1   117.56  3.000
 SDD  H4   C3  C4   107.51  3.000
 SDD  H4   C3  O3   111.18  3.000
 SDD  C4   C3  O3   111.47  3.000
 SDD  H4   C3  C2   106.01  3.000
 SDD  O3   C3  C2   110.10  3.000
 SDD  C4   C3  C2   110.40  3.000
 SDD  H5   O3  C3   107.26  3.000
 SDD  H6   C4  C5   105.87  3.000
 SDD  H6   C4  O4   106.98  3.000
 SDD  C5   C4  O4   112.31  3.000
 SDD  H6   C4  C3   106.99  3.000
 SDD  O4   C4  C3   110.88  3.000
 SDD  C5   C4  C3   113.34  3.000
 SDD  H7   O4  C4   107.50  3.000
 SDD  H8   C5  C6   107.76  3.000
 SDD  H8   C5  O5   111.09  3.000
 SDD  C6   C5  O5   110.87  3.000
 SDD  H8   C5  C4   107.68  3.000
 SDD  O5   C5  C4   109.43  3.000
 SDD  C6   C5  C4   109.95  3.000
 SDD  H9   O5  C5   107.22  3.000
 SDD  H11  C6  H10  107.55  3.000
 SDD  H11  C6  O6   111.40  3.000
 SDD  H10  C6  O6   111.67  3.000
 SDD  H11  C6  C5   109.56  3.000
 SDD  H10  C6  C5   109.09  3.000
 SDD  O6   C6  C5   107.54  3.000
 SDD  H12  O6  C6   108.71  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
 SDD  Var_01  C3  C2  C1  O1  164.78  30.0  3

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
 SDD  chir_01  C3  C2  C4  O3  negativ
 SDD  chir_02  C4  O4  C5  C3  negativ
 SDD  chir_03  C5  O5  C4  C6  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
 SDD  plan-1  C1  0.020
 SDD  plan-1  C2  0.020
 SDD  plan-1  O2  0.020
 SDD  plan-1  C3  0.020

