# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:51:29 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{R})-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
 J5B  J5B  (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{R})-3-oxidanylbutoxy]oxane-3,4,5-triol  D-saccharide  37  17  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J5B
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
 J5B  C1   C  CH1   0   0.273  14.1671   7.2330  28.1502
 J5B  O1   O  O2    0  -0.514  14.3140   7.8827  26.9276
 J5B  C2   C  CH1   0   0.001  12.6785   7.0778  28.4531
 J5B  O2   O  OH1   0  -0.664  12.0701   6.4328  27.3672
 J5B  C3   C  CH1   0  -0.010  12.0459   8.4276  28.7718
 J5B  O3   O  OH1   0  -0.669  10.7109   8.1804  29.1437
 J5B  C4   C  CH1   0   0.010  12.8325   9.1079  29.8848
 J5B  O4   O  OH1   0  -0.672  12.2725  10.3860  30.0844
 J5B  C5   C  CH1   0  -0.018  14.3090   9.2011  29.4833
 J5B  O5   O  O2    0  -0.501  14.8098   7.9017  29.1950
 J5B  C6   C  CH2   0  -0.196  15.1970   9.8117  30.5452
 J5B  O6   O  OH1   0  -0.667  15.0767   9.0853  31.7443
 J5B  C7   C  CH2   0  -0.163  15.6311   7.8599  26.3934
 J5B  C8   C  CH2   0  -0.497  15.6614   8.6269  25.0862
 J5B  C9   C  CH1   0   0.050  15.3133  10.1099  25.2203
 J5B  C10  C  CH3   0  -0.671  15.6416  10.8725  23.9501
 J5B  O9   O  OH1   0  -0.689  13.9403  10.3171  25.4977
 J5B  H1   H  HCH1  0   0.237  14.6413   6.2432  28.1066
 J5B  H2   H  HCH1  0   0.223  12.6165   6.4622  29.3637
 J5B  HO2  H  HOH1  0   0.452  11.1572   6.2437  27.6063
 J5B  H3   H  HCH1  0   0.215  12.0825   9.0667  27.8764
 J5B  HO3  H  HOH1  0   0.451  10.2685   9.0270  29.2625
 J5B  H4   H  HCH1  0   0.223  12.7463   8.4921  30.7894
 J5B  HO4  H  HOH1  0   0.458  12.4291  10.6581  30.9933
 J5B  H5   H  HCH1  0   0.229  14.3868   9.8524  28.6006
 J5B  H61  H  HCH2  0   0.218  16.2295   9.8189  30.1714
 J5B  H62  H  HCH2  0   0.207  14.9034  10.8614  30.6672
 J5B  HO6  H  HOH1  0   0.457  15.5812   9.5397  32.4246
 J5B  H12  H  HCH2  0   0.228  15.9442   6.8211  26.2309
 J5B  H13  H  HCH2  0   0.215  16.3418   8.3104  27.0951
 J5B  H14  H  HCH2  0   0.232  15.0030   8.1566  24.3488
 J5B  H15  H  HCH2  0   0.239  16.6792   8.5389  24.6969
 J5B  H16  H  HCH1  0   0.183  15.9299  10.5210  26.0363
 J5B  H17  H  HCH3  0   0.232  15.3659  11.9240  24.0412
 J5B  H18  H  HCH3  0   0.224  16.7104  10.8261  23.7421
 J5B  H19  H  HOH1  0   0.453  13.6812   9.6791  26.1715
 J5B  H20  H  HCH3  0   0.220  15.1113  10.4547  23.0920

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
 J5B  C10  C9   single  1.517  0.020  1.517
 J5B  C9   C8   single  1.529  0.020  1.529
 J5B  C9   O9   single  1.416  0.020  1.416
 J5B  C8   C7   single  1.516  0.020  1.516
 J5B  C7   O1   single  1.421  0.020  1.421
 J5B  O1   C1   single  1.392  0.020  1.392
 J5B  O2   C2   single  1.402  0.020  1.402
 J5B  C1   C2   single  1.527  0.020  1.527
 J5B  C1   O5   single  1.397  0.020  1.397
 J5B  C2   C3   single  1.524  0.020  1.524
 J5B  C3   O3   single  1.408  0.020  1.408
 J5B  C3   C4   single  1.523  0.020  1.523
 J5B  O5   C5   single  1.422  0.020  1.422
 J5B  C5   C4   single  1.533  0.020  1.533
 J5B  C5   C6   single  1.513  0.020  1.513
 J5B  C4   O4   single  1.410  0.020  1.410
 J5B  C6   O6   single  1.407  0.020  1.407
 J5B  C1   H1   single  0.970  0.020  1.090
 J5B  C2   H2   single  0.970  0.020  1.090
 J5B  O2   HO2  single  0.850  0.020  0.980
 J5B  C3   H3   single  0.970  0.020  1.090
 J5B  O3   HO3  single  0.850  0.020  0.980
 J5B  C4   H4   single  0.970  0.020  1.090
 J5B  O4   HO4  single  0.850  0.020  0.980
 J5B  C5   H5   single  0.970  0.020  1.090
 J5B  C6   H61  single  0.970  0.020  1.090
 J5B  C6   H62  single  0.970  0.020  1.090
 J5B  O6   HO6  single  0.850  0.020  0.980
 J5B  C7   H12  single  0.970  0.020  1.090
 J5B  C7   H13  single  0.970  0.020  1.090
 J5B  C8   H14  single  0.970  0.020  1.090
 J5B  C8   H15  single  0.970  0.020  1.090
 J5B  C9   H16  single  0.970  0.020  1.090
 J5B  C10  H17  single  0.970  0.020  1.090
 J5B  C10  H18  single  0.970  0.020  1.090
 J5B  O9   H19  single  0.850  0.020  0.980
 J5B  C10  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
 J5B  H1   C1   O5   105.21  3.000
 J5B  H1   C1   C2   109.71  3.000
 J5B  O5   C1   C2   110.42  3.000
 J5B  H1   C1   O1   109.88  3.000
 J5B  O5   C1   O1   112.63  3.000
 J5B  C2   C1   O1   108.93  3.000
 J5B  C7   O1   C1   114.85  3.000
 J5B  H2   C2   C3   107.39  3.000
 J5B  H2   C2   O2   111.04  3.000
 J5B  C3   C2   O2   112.91  3.000
 J5B  H2   C2   C1   106.00  3.000
 J5B  C3   C2   C1   110.85  3.000
 J5B  O2   C2   C1   108.43  3.000
 J5B  HO2  O2   C2   108.04  3.000
 J5B  H3   C3   C4   108.54  3.000
 J5B  H3   C3   O3   110.39  3.000
 J5B  C4   C3   O3   112.03  3.000
 J5B  H3   C3   C2   109.28  3.000
 J5B  C4   C3   C2   109.51  3.000
 J5B  O3   C3   C2   107.05  3.000
 J5B  HO3  O3   C3   108.30  3.000
 J5B  H4   C4   C5   109.00  3.000
 J5B  H4   C4   O4   111.14  3.000
 J5B  C5   C4   O4   111.39  3.000
 J5B  H4   C4   C3   108.12  3.000
 J5B  O4   C4   C3   107.65  3.000
 J5B  C5   C4   C3   109.46  3.000
 J5B  HO4  O4   C4   109.01  3.000
 J5B  H5   C5   C6   106.43  3.000
 J5B  H5   C5   O5   110.71  3.000
 J5B  C6   C5   O5   107.72  3.000
 J5B  H5   C5   C4   108.32  3.000
 J5B  C6   C5   C4   113.95  3.000
 J5B  O5   C5   C4   109.68  3.000
 J5B  C5   O5   C1   115.27  3.000
 J5B  H62  C6   H61  106.45  3.000
 J5B  H62  C6   O6   112.11  3.000
 J5B  H61  C6   O6   111.95  3.000
 J5B  H62  C6   C5   107.89  3.000
 J5B  H61  C6   C5   108.40  3.000
 J5B  O6   C6   C5   109.86  3.000
 J5B  HO6  O6   C6   108.32  3.000
 J5B  H13  C7   H12  107.40  3.000
 J5B  H13  C7   C8   109.34  3.000
 J5B  H12  C7   C8   110.23  3.000
 J5B  H13  C7   O1   110.71  3.000
 J5B  H12  C7   O1   109.59  3.000
 J5B  C8   C7   O1   109.54  3.000
 J5B  H15  C8   H14  106.58  3.000
 J5B  H15  C8   C9   108.74  3.000
 J5B  H14  C8   C9   109.80  3.000
 J5B  H15  C8   C7   106.56  3.000
 J5B  H14  C8   C7   110.58  3.000
 J5B  C9   C8   C7   114.24  3.000
 J5B  H16  C9   O9   110.05  3.000
 J5B  H16  C9   C10  108.14  3.000
 J5B  O9   C9   C10  107.47  3.000
 J5B  H16  C9   C8   107.41  3.000
 J5B  O9   C9   C8   112.32  3.000
 J5B  C10  C9   C8   111.39  3.000
 J5B  H20  C10  H18  108.06  3.000
 J5B  H20  C10  H17  108.17  3.000
 J5B  H18  C10  H17  107.75  3.000
 J5B  H20  C10  C9   111.13  3.000
 J5B  H18  C10  C9   110.51  3.000
 J5B  H17  C10  C9   111.09  3.000
 J5B  H19  O9   C9   107.51  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
 J5B  Var_01  C8  C7  O1  C1  -178.58  30.0  1
 J5B  Var_02  C9  C8  C7  O1    62.50  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
 J5B  chir_01  C1  O1   C2  O5  positiv
 J5B  chir_02  C2  O2   C1  C3  negativ
 J5B  chir_03  C3  O3   C2  C4  positiv
 J5B  chir_04  C4  O4   C5  C3  positiv
 J5B  chir_05  C5  O5   C4  C6  negativ
 J5B  chir_06  C9  C10  C8  O9  positiv

