# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 11:38:08 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: [1-deoxy-beta-L-xylulofuranosato(2-)-kappa~2~O~2~,O~3~](dihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 A1B  A1B  '[1-deoxy-beta-L-xylulofuranosato(2-)-kappa~2~O~2~,O~3~](dihydroxy)borate(1-)'  ligand  22  12  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A1B
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
 A1B  C8   C  CH1    0  -0.118   0.6304   0.3033   0.8217
 A1B  O1   O  OC2    0  -0.492  -0.5194   1.0545   0.9856
 A1B  C7   C  CH1    0  -0.004   1.6322   0.8425  -0.1972
 A1B  O12  O  OH1    0  -0.681   2.5620   1.7154   0.3977
 A1B  C6   C  CH2    0  -0.193   2.2303  -0.4487  -0.7382
 A1B  O5   O  O2     0  -0.535   1.1512  -1.3582  -0.8056
 A1B  C4   C  CT     0   0.490   0.1885  -1.0424   0.2026
 A1B  C11  C  CH3    0  -0.690   0.1135  -2.1954   1.1885
 A1B  O3   O  OC2    0  -0.451  -1.0335  -0.7903  -0.3674
 A1B  B    B  B     -1   0.225  -1.5831   0.5104   0.1085
 A1B  O10  O  OB     0  -0.650  -2.8034   0.2063   0.8411
 A1B  O9   O  OB     0  -0.797  -1.7967   1.4647  -0.9744
 A1B  H1   H  HCH1   0   0.228   1.1549   0.1576   1.7787
 A1B  H2   H  HCH1   0   0.254   1.0746   1.3480  -0.9966
 A1B  H3   H  HOH1   0   0.447   3.1300   2.0647  -0.2960
 A1B  H4   H  HCH2   0   0.246   2.6680  -0.3402  -1.7339
 A1B  H5   H  HCH2   0   0.164   3.0210  -0.8041  -0.0609
 A1B  H6   H  HCH3   0   0.221   1.0835  -2.3931   1.6495
 A1B  H7   H  HCH3   0   0.263  -0.5981  -1.9515   1.9775
 A1B  H8   H  HCH3   0   0.233  -0.2249  -3.1114   0.6993
 A1B  H9   H  H      0   0.433  -3.2878   1.0142   1.0275
 A1B  H10  H  H      0   0.407  -2.5826   1.2251  -1.4715

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
 A1B  O12  C7   single  1.407  0.020  1.407
 A1B  C6   O5   single  1.413  0.020  1.413
 A1B  C6   C7   single  1.522  0.020  1.522
 A1B  O5   C4   single  1.429  0.020  1.429
 A1B  C7   C8   single  1.527  0.020  1.527
 A1B  C11  C4   single  1.519  0.020  1.519
 A1B  C4   C8   single  1.546  0.020  1.546
 A1B  C4   O3   single  1.372  0.020  1.372
 A1B  C8   O1   single  1.383  0.020  1.383
 A1B  O3   B    single  1.490  0.020  1.490
 A1B  O1   B    single  1.482  0.020  1.482
 A1B  B    O9   single  1.459  0.020  1.459
 A1B  B    O10  single  1.455  0.020  1.455
 A1B  C8   H1   single  0.970  0.020  1.090
 A1B  C7   H2   single  0.970  0.020  1.090
 A1B  O12  H3   single  0.850  0.020  0.980
 A1B  C6   H4   single  0.970  0.020  1.090
 A1B  C6   H5   single  0.970  0.020  1.090
 A1B  C11  H6   single  0.970  0.020  1.090
 A1B  C11  H7   single  0.970  0.020  1.090
 A1B  C11  H8   single  0.970  0.020  1.090
 A1B  O10  H9   single  0.850  0.020  0.980
 A1B  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
 A1B  H1   C8   C4   111.66  3.000
 A1B  H1   C8   C7   108.31  3.000
 A1B  C4   C8   C7   103.15  3.000
 A1B  H1   C8   O1   111.40  3.000
 A1B  C4   C8   O1   106.41  3.000
 A1B  C7   C8   O1   115.63  3.000
 A1B  B    O1   C8   109.10  3.000
 A1B  H2   C7   C6   109.35  3.000
 A1B  H2   C7   O12  110.96  3.000
 A1B  C6   C7   O12  114.63  3.000
 A1B  H2   C7   C8   108.37  3.000
 A1B  C6   C7   C8   101.27  3.000
 A1B  O12  C7   C8   111.73  3.000
 A1B  H3   O12  C7   108.08  3.000
 A1B  H5   C6   H4   107.76  3.000
 A1B  H5   C6   O5   111.74  3.000
 A1B  H4   C6   O5   109.05  3.000
 A1B  H5   C6   C7   109.73  3.000
 A1B  H4   C6   C7   113.38  3.000
 A1B  O5   C6   C7   105.24  3.000
 A1B  C4   O5   C6   109.79  3.000
 A1B  O3   C4   C11  111.42  3.000
 A1B  O3   C4   O5   110.34  3.000
 A1B  C11  C4   O5   108.87  3.000
 A1B  O3   C4   C8   105.13  3.000
 A1B  C11  C4   C8   114.52  3.000
 A1B  O5   C4   C8   106.40  3.000
 A1B  H8   C11  H7   108.03  3.000
 A1B  H8   C11  H6   108.21  3.000
 A1B  H7   C11  H6   108.35  3.000
 A1B  H8   C11  C4   111.18  3.000
 A1B  H7   C11  C4   109.40  3.000
 A1B  H6   C11  C4   111.57  3.000
 A1B  B    O3   C4   110.87  3.000
 A1B  O9   B    O10  112.80  3.000
 A1B  O10  B    O3   106.72  3.000
 A1B  O9   B    O3   112.82  3.000
 A1B  O10  B    O1   112.37  3.000
 A1B  O9   B    O1   107.71  3.000
 A1B  O3   B    O1   104.16  3.000
 A1B  H9   O10  B    110.18  3.000
 A1B  H10  O9   B    109.93  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
 A1B  Var_01  O3  B   O1  C8    11.28  30.0  1
 A1B  Var_02  H4  C6  O5  C4  -151.25  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
 A1B  chir_01  C8  C7   C4  O1  positiv
 A1B  chir_02  C7  O12  C8  C6  positiv
 A1B  chir_03  C4  O5   C8  O3  negativ

