# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:41:54 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{S})-5-(hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@H](O)[C@H](O)[C@@H](O)[C@H]2O[C@@H]12
#
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
 HBE  HBE  (2~{R},3~{S},4~{S},5~{R},6~{S})-5-(hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2,3,4-triol  ligand  24  12  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HBE
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
 HBE  C3   C  CH1   0   0.013  -1.7131   0.0544   0.3541
 HBE  C4   C  CH1   0   0.004  -0.9091   0.9058  -0.6229
 HBE  C5   C  CH1   0   0.016   0.5598   0.9491  -0.2138
 HBE  C1   C  CH1   0  -0.002   0.3214  -1.5242   0.2428
 HBE  C2   C  CH1   0  -0.045  -1.0815  -1.2920   0.5801
 HBE  C6   C  CH1   0  -0.319   1.1860  -0.4361  -0.3643
 HBE  O7   O  OH1   0  -0.670   0.7065   1.3637   1.1257
 HBE  O8   O  OH1   0  -0.680  -1.3892   2.2321  -0.6491
 HBE  O9   O  OH1   0  -0.676  -3.0254  -0.0610  -0.1614
 HBE  C10  C  CH2   0  -0.146   2.5919  -0.5219   0.2147
 HBE  O11  O  OH1   0  -0.672   3.3992   0.4548  -0.3966
 HBE  O12  O  O2    0  -0.490  -0.7246  -2.0275  -0.5776
 HBE  H1   H  HCH1  0   0.221  -1.7270   0.5665   1.3234
 HBE  H2   H  HCH1  0   0.213  -0.9711   0.4536  -1.6240
 HBE  H3   H  HCH1  0   0.232   1.0798   1.6398  -0.8912
 HBE  H4   H  HCH1  0   0.251   0.8530  -2.2944   0.8012
 HBE  H5   H  HCH1  0   0.255  -1.5336  -1.8851   1.3752
 HBE  H7   H  HCH1  0   0.266   1.2608  -0.6408  -1.4386
 HBE  H8   H  HOH1  0   0.451   0.2979   2.2308   1.2176
 HBE  H9   H  HOH1  0   0.451  -2.3431   2.2036  -0.7806
 HBE  H10  H  HOH1  0   0.458  -3.6283  -0.2415   0.5658
 HBE  H11  H  HCH2  0   0.205   2.5575  -0.3987   1.3036
 HBE  H12  H  HCH2  0   0.208   2.9754  -1.5336   0.0237
 HBE  H13  H  HOH1  0   0.456   4.2648   0.4321   0.0207

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
 HBE  O11  C10  single  1.407  0.020  1.407
 HBE  C10  C6   single  1.523  0.020  1.523
 HBE  C6   C5   single  1.528  0.020  1.528
 HBE  C6   C1   single  1.517  0.020  1.517
 HBE  O12  C1   single  1.421  0.020  1.421
 HBE  C5   C4   single  1.525  0.020  1.525
 HBE  C5   O7   single  1.410  0.020  1.410
 HBE  C1   C2   single  1.461  0.020  1.461
 HBE  C4   O8   single  1.411  0.020  1.411
 HBE  C4   C3   single  1.525  0.020  1.525
 HBE  C2   C3   single  1.504  0.020  1.504
 HBE  C3   O9   single  1.415  0.020  1.415
 HBE  C3   H1   single  0.970  0.020  1.090
 HBE  C4   H2   single  0.970  0.020  1.090
 HBE  C5   H3   single  0.970  0.020  1.090
 HBE  C1   H4   single  0.970  0.020  1.090
 HBE  C2   H5   single  0.970  0.020  1.090
 HBE  C6   H7   single  0.970  0.020  1.090
 HBE  O7   H8   single  0.850  0.020  0.980
 HBE  O8   H9   single  0.850  0.020  0.980
 HBE  O9   H10  single  0.850  0.020  0.980
 HBE  C10  H11  single  0.970  0.020  1.090
 HBE  C10  H12  single  0.970  0.020  1.090
 HBE  O11  H13  single  0.850  0.020  0.980
 HBE  C2   O12  single  1.417  0.020  1.417

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
 HBE  H1   C3   O9   110.40  3.000
 HBE  H1   C3   C2   106.89  3.000
 HBE  O9   C3   C2   111.79  3.000
 HBE  H1   C3   C4   108.20  3.000
 HBE  O9   C3   C4   107.53  3.000
 HBE  C2   C3   C4   112.00  3.000
 HBE  H2   C4   O8   110.51  3.000
 HBE  H2   C4   C5   108.06  3.000
 HBE  O8   C4   C5   107.82  3.000
 HBE  H2   C4   C3   108.89  3.000
 HBE  O8   C4   C3   110.93  3.000
 HBE  C5   C4   C3   110.59  3.000
 HBE  H3   C5   O7   110.60  3.000
 HBE  H3   C5   C6   108.38  3.000
 HBE  O7   C5   C6   108.52  3.000
 HBE  H3   C5   C4   107.96  3.000
 HBE  O7   C5   C4   111.31  3.000
 HBE  C6   C5   C4   110.03  3.000
 HBE  H4   C1   O12  113.86  3.000
 HBE  H4   C1   C6   115.73  3.000
 HBE  O12  C1   C6   116.27  3.000
 HBE  H4   C1   C2   117.53  3.000
 HBE  O12  C1   C2    58.87  3.000
 HBE  C6   C1   C2   121.71  3.000
 HBE  H5   C2   O12  114.70  3.000
 HBE  O12  C2   C1    59.15  3.000
 HBE  H5   C2   C1   118.69  3.000
 HBE  O12  C2   C3   116.58  3.000
 HBE  H5   C2   C3   114.99  3.000
 HBE  C1   C2   C3   120.70  3.000
 HBE  H7   C6   C10  107.40  3.000
 HBE  H7   C6   C1   107.29  3.000
 HBE  C10  C6   C1   109.50  3.000
 HBE  H7   C6   C5   107.09  3.000
 HBE  C1   C6   C5   112.18  3.000
 HBE  C10  C6   C5   113.08  3.000
 HBE  H8   O7   C5   108.14  3.000
 HBE  H9   O8   C4   108.16  3.000
 HBE  H10  O9   C3   108.74  3.000
 HBE  H12  C10  H11  106.68  3.000
 HBE  H12  C10  O11  111.31  3.000
 HBE  H11  C10  O11  111.81  3.000
 HBE  H12  C10  C6   107.94  3.000
 HBE  H11  C10  C6   110.02  3.000
 HBE  O11  C10  C6   108.99  3.000
 HBE  H13  O11  C10  108.16  3.000
 HBE  C2   O12  C1    61.97  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
 HBE  Var_01  C6  C1  C2   C3    -1.01  30.0  1
 HBE  Var_02  H5  C2  O12  C1  -109.92  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
 HBE  chir_01  C3  C4   C2   O9   positiv
 HBE  chir_02  C4  O8   C3   C5   positiv
 HBE  chir_03  C5  O7   C4   C6   positiv
 HBE  chir_06  C6  C1   C5   C10  negativ
 HBE  chir_07  C1  C6   O12  C2   both
 HBE  chir_08  C2  O12  C3   C1   both

