# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 13:38:00 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: dihydroxy[beta-L-xylulofuranosato(2-)-kappa~2~O~2~,O~3~]borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@]12OC[C@H](O)[C@H]1O[B-](O)(O)O2
#
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
 A2B  A2B  dihydroxy[beta-L-xylulofuranosato(2-)-kappa~2~O~2~,O~3~]borate(1-)  ligand  23  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A2B
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
 A2B  O13  O  OH1    0  -0.674   0.1114   3.0611   0.1105
 A2B  C8   C  CR15   0  -0.037   0.5492  -0.5453  -0.9716
 A2B  O1   O  O      0  -0.582  -0.5440  -1.3941  -0.9810
 A2B  C7   C  CH1    0  -0.005   1.7520  -1.1358  -0.2361
 A2B  O12  O  OH1    0  -0.678   2.9122  -0.5137  -0.7499
 A2B  C6   C  CH2    0  -0.220   1.4591  -0.7188   1.1955
 A2B  O5   O  O2     0  -0.529   0.9148   0.5820   1.0927
 A2B  C4   C  CR5    0   0.480   0.1419   0.6758  -0.1006
 A2B  C11  C  CH2    0  -0.171   0.4587   2.0074  -0.7560
 A2B  O3   O  O      0  -0.584  -1.1976   0.5360   0.1448
 A2B  B    B  B     -1   0.485  -1.6729  -0.8220  -0.2119
 A2B  O10  O  OB     0  -0.739  -1.8899  -1.6957   0.9357
 A2B  O9   O  OB     0  -0.738  -2.8786  -0.6348  -1.0076
 A2B  H1   H  HOH1   0   0.453   0.3095   3.8877  -0.3377
 A2B  H2   H  HCR5   0   0.204   0.8451  -0.2484  -1.9902
 A2B  H4   H  HOH1   0   0.449   3.6561  -0.7406  -0.1836
 A2B  H5   H  HCH2   0   0.210   0.7560  -1.4204   1.6593
 A2B  H6   H  HCH2   0   0.229   2.3538  -0.6812   1.8237
 A2B  H7   H  HCH2   0   0.189  -0.0976   2.0606  -1.7016
 A2B  H8   H  HCH2   0   0.185   1.5263   2.0246  -1.0129
 A2B  H9   H  H      0   0.428  -2.6788  -1.4265   1.4128
 A2B  H10  H  H      0   0.433  -3.3480  -1.4668  -1.1045
 A2B  H3   H  HCH1   0   0.215   1.8004  -2.2267  -0.3446

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
 A2B  C6   O5   single  1.414  0.020  1.414
 A2B  C6   C7   single  1.520  0.020  1.520
 A2B  O12  C7   single  1.413  0.020  1.413
 A2B  O5   C4   single  1.425  0.020  1.425
 A2B  C7   C8   single  1.529  0.020  1.529
 A2B  O13  C11  single  1.408  0.020  1.408
 A2B  C11  C4   single  1.518  0.020  1.518
 A2B  C4   C8   single  1.554  0.020  1.554
 A2B  C4   O3   single  1.369  0.020  1.369
 A2B  C8   O1   single  1.384  0.020  1.384
 A2B  O3   B    single  1.482  0.020  1.482
 A2B  O1   B    single  1.481  0.020  1.481
 A2B  B    O10  single  1.459  0.020  1.459
 A2B  B    O9   single  1.457  0.020  1.457
 A2B  O13  H1   single  0.850  0.020  0.980
 A2B  C8   H2   single  0.970  0.020  1.090
 A2B  C7   H3   single  0.970  0.020  1.090
 A2B  O12  H4   single  0.850  0.020  0.980
 A2B  C6   H5   single  0.970  0.020  1.090
 A2B  C6   H6   single  0.970  0.020  1.090
 A2B  C11  H7   single  0.970  0.020  1.090
 A2B  C11  H8   single  0.970  0.020  1.090
 A2B  O10  H9   single  0.850  0.020  0.980
 A2B  O9   H10  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
 A2B  H1   O13  C11  107.82  3.000
 A2B  H2   C8   C4   112.13  3.000
 A2B  H2   C8   C7   109.74  3.000
 A2B  C4   C8   C7   103.89  3.000
 A2B  H2   C8   O1   111.79  3.000
 A2B  C4   C8   O1   106.18  3.000
 A2B  C7   C8   O1   112.82  3.000
 A2B  B    O1   C8   111.21  3.000
 A2B  H3   C7   C6   111.99  3.000
 A2B  H3   C7   O12  111.44  3.000
 A2B  C6   C7   O12  112.33  3.000
 A2B  H3   C7   C8   111.79  3.000
 A2B  O12  C7   C8   107.52  3.000
 A2B  C6   C7   C8   101.28  3.000
 A2B  H4   O12  C7   108.48  3.000
 A2B  H6   C6   H5   107.67  3.000
 A2B  H6   C6   O5   108.97  3.000
 A2B  H5   C6   O5   111.88  3.000
 A2B  H6   C6   C7   113.13  3.000
 A2B  H5   C6   C7   110.29  3.000
 A2B  O5   C6   C7   104.96  3.000
 A2B  C4   O5   C6   109.29  3.000
 A2B  O3   C4   C11  111.79  3.000
 A2B  O3   C4   O5   111.96  3.000
 A2B  C11  C4   O5   107.83  3.000
 A2B  O3   C4   C8   106.06  3.000
 A2B  C11  C4   C8   113.12  3.000
 A2B  O5   C4   C8   105.99  3.000
 A2B  H8   C11  H7   106.87  3.000
 A2B  H8   C11  C4   108.52  3.000
 A2B  H7   C11  C4   107.97  3.000
 A2B  H8   C11  O13  111.84  3.000
 A2B  H7   C11  O13  111.64  3.000
 A2B  C4   C11  O13  109.85  3.000
 A2B  B    O3   C4   111.36  3.000
 A2B  O9   B    O10  112.56  3.000
 A2B  O9   B    O3   106.20  3.000
 A2B  O10  B    O3   114.02  3.000
 A2B  O9   B    O1   113.39  3.000
 A2B  O10  B    O1   106.90  3.000
 A2B  O3   B    O1   103.55  3.000
 A2B  H9   O10  B    110.19  3.000
 A2B  H10  O9   B    110.39  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
 A2B  Var_01  O3  B   O1  C8    5.91  30.0  1
 A2B  Var_02  H5  C6  O5  C4  -85.12  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
 A2B  chir_01  C8  C7   C4  O1  positiv
 A2B  chir_02  C7  O12  C8  C6  positiv
 A2B  chir_03  C4  O5   C8  O3  negativ

