# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:04:24 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: D-allitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO
#
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
 X9X  X9X  'D-allitol                '  ligand  26  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X9X
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
 X9X  OAA  O  OH1   0  -0.684   4.3119   0.3046  -0.3404
 X9X  CAG  C  CH2   0  -0.096   3.1454   0.4510   0.4354
 X9X  CAI  C  CH1   0  -0.034   1.9409   0.0185  -0.3866
 X9X  OAC  O  OH1   0  -0.628   2.0362  -1.3352  -0.7645
 X9X  CAK  C  CH1   0   0.010   0.6441   0.3624   0.3743
 X9X  OAE  O  OH1   0  -0.703   0.4788   1.7621   0.3882
 X9X  CAL  C  CH1   0   0.013  -0.5718  -0.4344  -0.1575
 X9X  OAF  O  OH1   0  -0.662  -0.5710  -1.7293   0.4012
 X9X  CAJ  C  CH1   0  -0.030  -1.9077   0.2946   0.0702
 X9X  OAD  O  OH1   0  -0.632  -1.9473   1.4698  -0.7272
 X9X  CAH  C  CH2   0  -0.167  -3.0992  -0.6053  -0.2126
 X9X  OAB  O  OH1   0  -0.677  -4.2771   0.1372  -0.0024
 X9X  H1   H  HOH1  0   0.454   5.0629   0.5622   0.2009
 X9X  H2   H  HCH2  0   0.172   3.1839  -0.1661   1.3460
 X9X  H3   H  HCH2  0   0.181   3.0045   1.4889   0.7605
 X9X  H4   H  HCH1  0   0.193   1.9430   0.5885  -1.3271
 X9X  H5   H  HOH1  0   0.398   1.8578  -1.8873   0.0042
 X9X  H6   H  HCH1  0   0.252   0.7703   0.0557   1.4248
 X9X  H7   H  HOH1  0   0.433  -0.2300   1.9947  -0.2300
 X9X  H8   H  HCH1  0   0.231  -0.4697  -0.5863  -1.2390
 X9X  H9   H  HOH1  0   0.449  -0.6751  -1.6521   1.3566
 X9X  H10  H  HCH1  0   0.230  -1.9716   0.6411   1.1082
 X9X  H11  H  HOH1  0   0.435  -2.0006   1.2131  -1.6559
 X9X  H12  H  HCH2  0   0.224  -3.0327  -0.9793  -1.2460
 X9X  H13  H  HCH2  0   0.196  -3.0545  -1.4793   0.4443
 X9X  H14  H  HOH1  0   0.442  -5.0234  -0.4583  -0.1130

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
 X9X  OAB  CAH  single  1.408  0.020  1.408
 X9X  CAH  CAJ  single  1.520  0.020  1.520
 X9X  CAJ  OAD  single  1.421  0.020  1.421
 X9X  CAJ  CAL  single  1.539  0.020  1.539
 X9X  OAA  CAG  single  1.409  0.020  1.409
 X9X  OAC  CAI  single  1.409  0.020  1.409
 X9X  CAK  CAL  single  1.548  0.020  1.548
 X9X  CAK  CAI  single  1.542  0.020  1.542
 X9X  CAK  OAE  single  1.409  0.020  1.409
 X9X  CAL  OAF  single  1.410  0.020  1.410
 X9X  CAG  CAI  single  1.521  0.020  1.521
 X9X  OAA  H1   single  0.850  0.020  0.980
 X9X  CAG  H2   single  0.970  0.020  1.090
 X9X  CAG  H3   single  0.970  0.020  1.090
 X9X  CAI  H4   single  0.970  0.020  1.090
 X9X  OAC  H5   single  0.850  0.020  0.980
 X9X  CAK  H6   single  0.970  0.020  1.090
 X9X  OAE  H7   single  0.850  0.020  0.980
 X9X  CAL  H8   single  0.970  0.020  1.090
 X9X  OAF  H9   single  0.850  0.020  0.980
 X9X  CAJ  H10  single  0.970  0.020  1.090
 X9X  OAD  H11  single  0.850  0.020  0.980
 X9X  CAH  H12  single  0.970  0.020  1.090
 X9X  CAH  H13  single  0.970  0.020  1.090
 X9X  OAB  H14  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
 X9X  H1   OAA  CAG  108.00  3.000
 X9X  H3   CAG  H2   106.86  3.000
 X9X  H3   CAG  CAI  109.12  3.000
 X9X  H2   CAG  CAI  108.38  3.000
 X9X  H3   CAG  OAA  111.60  3.000
 X9X  H2   CAG  OAA  111.62  3.000
 X9X  CAI  CAG  OAA  109.18  3.000
 X9X  H4   CAI  CAK  107.93  3.000
 X9X  H4   CAI  OAC  105.58  3.000
 X9X  CAK  CAI  OAC  113.80  3.000
 X9X  H4   CAI  CAG  108.26  3.000
 X9X  CAK  CAI  CAG  109.61  3.000
 X9X  OAC  CAI  CAG  111.39  3.000
 X9X  H5   OAC  CAI  108.92  3.000
 X9X  H6   CAK  CAL  105.92  3.000
 X9X  H6   CAK  OAE  106.29  3.000
 X9X  CAL  CAK  OAE  114.99  3.000
 X9X  H6   CAK  CAI  108.18  3.000
 X9X  OAE  CAK  CAI  108.96  3.000
 X9X  CAL  CAK  CAI  112.09  3.000
 X9X  H7   OAE  CAK  108.54  3.000
 X9X  H8   CAL  CAJ  106.99  3.000
 X9X  H8   CAL  OAF  105.27  3.000
 X9X  CAJ  CAL  OAF  112.14  3.000
 X9X  H8   CAL  CAK  109.69  3.000
 X9X  OAF  CAL  CAK  109.64  3.000
 X9X  CAJ  CAL  CAK  112.78  3.000
 X9X  H9   OAF  CAL  108.60  3.000
 X9X  H10  CAJ  CAH  108.52  3.000
 X9X  H10  CAJ  OAD  105.57  3.000
 X9X  CAH  CAJ  OAD  111.31  3.000
 X9X  H10  CAJ  CAL  109.91  3.000
 X9X  OAD  CAJ  CAL  109.45  3.000
 X9X  CAH  CAJ  CAL  111.88  3.000
 X9X  H11  OAD  CAJ  108.76  3.000
 X9X  H13  CAH  H12  106.84  3.000
 X9X  H13  CAH  OAB  111.45  3.000
 X9X  H12  CAH  OAB  111.70  3.000
 X9X  H13  CAH  CAJ  109.22  3.000
 X9X  H12  CAH  CAJ  109.17  3.000
 X9X  OAB  CAH  CAJ  108.41  3.000
 X9X  H14  OAB  CAH  107.79  3.000

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
 X9X  chir_01  CAI  OAC  CAK  CAG  negativ
 X9X  chir_02  CAK  OAE  CAI  CAL  positiv
 X9X  chir_03  CAL  OAF  CAK  CAJ  positiv
 X9X  chir_04  CAJ  OAD  CAL  CAH  positiv

