# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:10:09 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2~{R},3~{R},4~{R},5~{S})-5-[(1~{R})-1-oxidanylethyl]oxolane-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H]1O[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
 GYE  GYE  (2~{R},3~{R},4~{R},5~{S})-5-[(1~{R})-1-oxidanylethyl]oxolane-2,3,4-triol  D-saccharide  23  11  .  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_GYE
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
 GYE  O3   O  OH1   0  -0.667   0.2688  -2.0884   1.1653
 GYE  C4   C  CH1   0  -0.050   1.6374  -0.2841   0.1747
 GYE  C5   C  CH1   0   0.267   1.1877   1.0252  -0.4618
 GYE  O4   O  OH1   0  -0.672  -2.0124  -0.2931  -1.3450
 GYE  C    C  CH3   0  -0.694  -3.0222   0.9253   0.4987
 GYE  O    O  O2    0  -0.512  -0.1130   1.2458   0.0480
 GYE  C1   C  CH1   0   0.027  -2.0721  -0.1801   0.0607
 GYE  C2   C  CH1   0   0.039  -0.6605   0.0446   0.5762
 GYE  C3   C  CH1   0  -0.014   0.3346  -1.0592   0.2157
 GYE  O1   O  OH1   0  -0.659   2.0371   2.0580  -0.1109
 GYE  O2   O  OH1   0  -0.664   2.6266  -0.9744  -0.5355
 GYE  H10  H  HOH1  0   0.457   0.7693  -2.8400   0.8340
 GYE  H3   H  HCH1  0   0.222   1.9528  -0.0727   1.2087
 GYE  H4   H  HCH1  0   0.194   1.1357   0.9204  -1.5560
 GYE  H6   H  HCH3  0   0.235  -4.0370   0.7204   0.1528
 GYE  H7   H  HCH3  0   0.226  -3.0575   0.9972   1.5867
 GYE  H5   H  HCH3  0   0.231  -2.7183   1.8940   0.1015
 GYE  H    H  HCH1  0   0.208  -2.4116  -1.1230   0.5150
 GYE  H1   H  HCH1  0   0.227  -0.7169   0.1181   1.6717
 GYE  H2   H  HCH1  0   0.227   0.1228  -1.4387  -0.7934
 GYE  H8   H  HOH1  0   0.465   1.9265   2.7894  -0.7271
 GYE  H9   H  HOH1  0   0.457   3.4651  -0.5167  -0.4202
 GYE  H11  H  HOH1  0   0.453  -2.8888  -0.5286  -1.6639

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
 GYE  O4  C1   single  1.412  0.020  1.412
 GYE  C   C1   single  1.522  0.020  1.522
 GYE  C1  C2   single  1.520  0.020  1.520
 GYE  C2  O    single  1.422  0.020  1.422
 GYE  C2  C3   single  1.529  0.020  1.529
 GYE  O   C5   single  1.414  0.020  1.414
 GYE  C3  O3   single  1.402  0.020  1.402
 GYE  C3  C4   single  1.517  0.020  1.517
 GYE  C5  C4   single  1.524  0.020  1.524
 GYE  C5  O1   single  1.383  0.020  1.383
 GYE  C4  O2   single  1.400  0.020  1.400
 GYE  O3  H10  single  0.850  0.020  0.980
 GYE  C4  H3   single  0.970  0.020  1.090
 GYE  C5  H4   single  0.970  0.020  1.090
 GYE  O4  H11  single  0.850  0.020  0.980
 GYE  C   H6   single  0.970  0.020  1.090
 GYE  C   H7   single  0.970  0.020  1.090
 GYE  C   H5   single  0.970  0.020  1.090
 GYE  C1  H    single  0.970  0.020  1.090
 GYE  C2  H1   single  0.970  0.020  1.090
 GYE  C3  H2   single  0.970  0.020  1.090
 GYE  O1  H8   single  0.850  0.020  0.980
 GYE  O2  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
 GYE  H10  O3  C3  108.42  3.000
 GYE  H3   C4  O2  111.62  3.000
 GYE  H3   C4  C3  108.59  3.000
 GYE  O2   C4  C3  111.64  3.000
 GYE  H3   C4  C5  108.17  3.000
 GYE  O2   C4  C5  114.86  3.000
 GYE  C3   C4  C5  101.36  3.000
 GYE  H4   C5  O1  110.64  3.000
 GYE  H4   C5  O   109.26  3.000
 GYE  O1   C5  O   110.92  3.000
 GYE  H4   C5  C4  110.34  3.000
 GYE  O1   C5  C4  110.76  3.000
 GYE  O    C5  C4  104.77  3.000
 GYE  H11  O4  C1  108.13  3.000
 GYE  H5   C   H7  108.29  3.000
 GYE  H5   C   H6  108.09  3.000
 GYE  H7   C   H6  107.36  3.000
 GYE  H5   C   C1  111.50  3.000
 GYE  H7   C   C1  110.80  3.000
 GYE  H6   C   C1  110.66  3.000
 GYE  C2   O   C5  110.87  3.000
 GYE  H    C1  C2  105.86  3.000
 GYE  H    C1  C   108.12  3.000
 GYE  C2   C1  C   112.02  3.000
 GYE  H    C1  O4  110.83  3.000
 GYE  C2   C1  O4  108.08  3.000
 GYE  C    C1  O4  111.79  3.000
 GYE  H1   C2  C3  108.46  3.000
 GYE  H1   C2  C1  107.47  3.000
 GYE  C3   C2  C1  114.70  3.000
 GYE  H1   C2  O   109.48  3.000
 GYE  C3   C2  O   105.76  3.000
 GYE  C1   C2  O   110.89  3.000
 GYE  H2   C3  C2  109.90  3.000
 GYE  H2   C3  C4  108.50  3.000
 GYE  C2   C3  C4  101.33  3.000
 GYE  H2   C3  O3  111.07  3.000
 GYE  C4   C3  O3  115.71  3.000
 GYE  C2   C3  O3  109.86  3.000
 GYE  H8   O1  C5  109.54  3.000
 GYE  H9   O2  C4  108.69  3.000

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
 GYE  chir_01  C4  C3  C5  O2  positiv
 GYE  chir_02  C5  O   O1  C4  negativ
 GYE  chir_03  C1  O4  C2  C   negativ
 GYE  chir_04  C2  O   C3  C1  positiv
 GYE  chir_05  C3  O3  C2  C4  negativ

