# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:13:27 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{S})-3-oxidanylbutoxy]oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)CCO[C@H]1O[C@H](CO)[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
 EBQ  EBQ  (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{S})-3-oxidanylbutoxy]oxane-3,4,5-triol  D-saccharide  37  17  .  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_EBQ
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
 EBQ  O17  O  OH1   0  -0.668   4.6890   0.1826   0.8180
 EBQ  C9   C  CH1   0   0.022   4.1778   0.2967  -0.4988
 EBQ  C16  C  CH3   0  -0.678   5.2008  -0.1457  -1.5347
 EBQ  C8   C  CH2   0  -0.492   2.8596  -0.4530  -0.6658
 EBQ  C7   C  CH2   0  -0.127   1.8074  -0.0270   0.3391
 EBQ  O1   O  O2    0  -0.499   0.6022  -0.7067   0.0332
 EBQ  C1   C  CH1   0   0.249  -0.3664  -0.6536   1.0225
 EBQ  C2   C  CH1   0  -0.016  -1.5252  -1.5700   0.6220
 EBQ  O2   O  OH1   0  -0.668  -1.1004  -2.8707   0.3049
 EBQ  C3   C  CH1   0  -0.010  -2.2502  -0.9973  -0.5889
 EBQ  O3   O  OH1   0  -0.676  -3.4184  -1.7267  -0.8902
 EBQ  C4   C  CH1   0   0.034  -2.6750   0.4399  -0.3097
 EBQ  O4   O  OH1   0  -0.673  -3.2179   1.0479  -1.4560
 EBQ  C5   C  CH1   0  -0.012  -1.4688   1.2645   0.1377
 EBQ  O5   O  O2    0  -0.505  -0.8449   0.6438   1.2497
 EBQ  C6   C  CH2   0  -0.161  -1.8680   2.6591   0.5712
 EBQ  O6   O  OH1   0  -0.670  -0.7023   3.3924   0.8655
 EBQ  H1   H  HOH1  0   0.441   4.8645  -0.7491   0.9902
 EBQ  H2   H  HCH1  0   0.221   3.9855   1.3660  -0.6354
 EBQ  H3   H  HCH3  0   0.220   5.4182  -1.2129  -1.4417
 EBQ  H4   H  HCH3  0   0.227   4.8330   0.0299  -2.5463
 EBQ  H5   H  HCH2  0   0.233   2.4863  -0.2713  -1.6778
 EBQ  H6   H  HCH2  0   0.225   3.0374  -1.5314  -0.5823
 EBQ  H7   H  HCH2  0   0.204   2.1290  -0.2707   1.3592
 EBQ  H8   H  HCH2  0   0.207   1.6639   1.0598   0.2955
 EBQ  H9   H  HCH1  0   0.229   0.0522  -0.9691   1.9899
 EBQ  H10  H  HCH1  0   0.227  -2.2270  -1.5806   1.4681
 EBQ  H11  H  HOH1  0   0.458  -0.9131  -3.3431   1.1216
 EBQ  H12  H  HCH1  0   0.219  -1.5650  -0.9919  -1.4497
 EBQ  H13  H  HOH1  0   0.455  -3.1600  -2.5888  -1.2303
 EBQ  H14  H  HCH1  0   0.209  -3.4085   0.4263   0.5133
 EBQ  H15  H  HOH1  0   0.454  -3.9756   0.5268  -1.7413
 EBQ  H16  H  HCH1  0   0.227  -0.7659   1.3464  -0.7041
 EBQ  H17  H  HCH2  0   0.211  -2.4432   3.1233  -0.2365
 EBQ  H18  H  HCH2  0   0.195  -2.5343   2.5850   1.4422
 EBQ  H19  H  HOH1  0   0.456  -0.9680   4.2832   1.1104
 EBQ  H20  H  HCH3  0   0.235   6.1360   0.4035  -1.4189

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
 EBQ  C16  C9   single  1.522  0.020  1.522
 EBQ  C8   C9   single  1.526  0.020  1.526
 EBQ  C8   C7   single  1.516  0.020  1.516
 EBQ  C9   O17  single  1.417  0.020  1.417
 EBQ  C7   O1   single  1.417  0.020  1.417
 EBQ  O1   C1   single  1.386  0.020  1.386
 EBQ  O2   C2   single  1.405  0.020  1.405
 EBQ  C1   C2   single  1.531  0.020  1.531
 EBQ  C1   O5   single  1.401  0.020  1.401
 EBQ  C2   C3   single  1.523  0.020  1.523
 EBQ  C3   O3   single  1.410  0.020  1.410
 EBQ  C3   C4   single  1.524  0.020  1.524
 EBQ  O5   C5   single  1.418  0.020  1.418
 EBQ  C5   C4   single  1.528  0.020  1.528
 EBQ  C5   C6   single  1.514  0.020  1.514
 EBQ  C4   O4   single  1.407  0.020  1.407
 EBQ  C6   O6   single  1.408  0.020  1.408
 EBQ  O17  H1   single  0.850  0.020  0.980
 EBQ  C9   H2   single  0.970  0.020  1.090
 EBQ  C16  H3   single  0.970  0.020  1.090
 EBQ  C16  H4   single  0.970  0.020  1.090
 EBQ  C8   H5   single  0.970  0.020  1.090
 EBQ  C8   H6   single  0.970  0.020  1.090
 EBQ  C7   H7   single  0.970  0.020  1.090
 EBQ  C7   H8   single  0.970  0.020  1.090
 EBQ  C1   H9   single  0.970  0.020  1.090
 EBQ  C2   H10  single  0.970  0.020  1.090
 EBQ  O2   H11  single  0.850  0.020  0.980
 EBQ  C3   H12  single  0.970  0.020  1.090
 EBQ  O3   H13  single  0.850  0.020  0.980
 EBQ  C4   H14  single  0.970  0.020  1.090
 EBQ  O4   H15  single  0.850  0.020  0.980
 EBQ  C5   H16  single  0.970  0.020  1.090
 EBQ  C6   H17  single  0.970  0.020  1.090
 EBQ  C6   H18  single  0.970  0.020  1.090
 EBQ  O6   H19  single  0.850  0.020  0.980
 EBQ  C16  H20  single  0.970  0.020  1.090

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
 EBQ  H1   O17  C9   108.04  3.000
 EBQ  H2   C9   C8   108.33  3.000
 EBQ  H2   C9   C16  108.48  3.000
 EBQ  C8   C9   C16  111.31  3.000
 EBQ  H2   C9   O17  104.95  3.000
 EBQ  C8   C9   O17  111.95  3.000
 EBQ  C16  C9   O17  111.51  3.000
 EBQ  H20  C16  H4   107.85  3.000
 EBQ  H20  C16  H3   108.18  3.000
 EBQ  H4   C16  H3   107.65  3.000
 EBQ  H20  C16  C9   110.96  3.000
 EBQ  H4   C16  C9   110.97  3.000
 EBQ  H3   C16  C9   111.08  3.000
 EBQ  H6   C8   H5   106.81  3.000
 EBQ  H6   C8   C7   109.79  3.000
 EBQ  H5   C8   C7   109.25  3.000
 EBQ  H6   C8   C9   109.57  3.000
 EBQ  H5   C8   C9   108.33  3.000
 EBQ  C7   C8   C9   112.89  3.000
 EBQ  H8   C7   H7   107.18  3.000
 EBQ  H8   C7   O1   110.82  3.000
 EBQ  H7   C7   O1   110.09  3.000
 EBQ  H8   C7   C8   110.05  3.000
 EBQ  H7   C7   C8   110.51  3.000
 EBQ  O1   C7   C8   108.20  3.000
 EBQ  C1   O1   C7   114.96  3.000
 EBQ  H9   C1   O5   104.64  3.000
 EBQ  H9   C1   C2   110.26  3.000
 EBQ  O5   C1   C2   109.77  3.000
 EBQ  H9   C1   O1   110.54  3.000
 EBQ  O5   C1   O1   112.95  3.000
 EBQ  C2   C1   O1   108.63  3.000
 EBQ  H10  C2   C3   108.16  3.000
 EBQ  H10  C2   O2   110.97  3.000
 EBQ  C3   C2   O2   108.22  3.000
 EBQ  H10  C2   C1   106.72  3.000
 EBQ  C3   C2   C1   110.08  3.000
 EBQ  O2   C2   C1   112.61  3.000
 EBQ  H11  O2   C2   108.78  3.000
 EBQ  H12  C3   C4   108.19  3.000
 EBQ  H12  C3   O3   110.57  3.000
 EBQ  C4   C3   O3   107.22  3.000
 EBQ  H12  C3   C2   109.11  3.000
 EBQ  C4   C3   C2   109.97  3.000
 EBQ  O3   C3   C2   111.71  3.000
 EBQ  H13  O3   C3   108.45  3.000
 EBQ  H14  C4   C5   108.25  3.000
 EBQ  H14  C4   O4   110.91  3.000
 EBQ  C5   C4   O4   108.06  3.000
 EBQ  H14  C4   C3   108.09  3.000
 EBQ  O4   C4   C3   111.46  3.000
 EBQ  C5   C4   C3   110.02  3.000
 EBQ  H15  O4   C4   108.14  3.000
 EBQ  H16  C5   C6   108.61  3.000
 EBQ  H16  C5   O5   110.59  3.000
 EBQ  C6   C5   O5   107.14  3.000
 EBQ  H16  C5   C4   108.69  3.000
 EBQ  C6   C5   C4   111.89  3.000
 EBQ  O5   C5   C4   109.92  3.000
 EBQ  C5   O5   C1   115.36  3.000
 EBQ  H18  C6   H17  107.14  3.000
 EBQ  H18  C6   O6   111.80  3.000
 EBQ  H17  C6   O6   111.60  3.000
 EBQ  H18  C6   C5   108.95  3.000
 EBQ  H17  C6   C5   108.53  3.000
 EBQ  O6   C6   C5   108.74  3.000
 EBQ  H19  O6   C6   107.88  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
 EBQ  Var_01  H7  C7  O1  C1   45.63  30.0  1
 EBQ  Var_02  O1  C7  C8  C9  175.69  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
 EBQ  chir_01  C9  C16  C8  O17  negativ
 EBQ  chir_02  C1  O1   O5  C2   negativ
 EBQ  chir_03  C2  O2   C1  C3   negativ
 EBQ  chir_04  C3  O3   C2  C4   positiv
 EBQ  chir_05  C4  O4   C3  C5   negativ
 EBQ  chir_06  C5  O5   C4  C6   negativ

