# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 02:56:30 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2R,3S,4R,5R,6R)-2,6-difluoro-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@]1(F)O[C@H](F)[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
 B0D  B0D  '(2R,3S,4R,5R,6R)-2,6-difluoro-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol (non-preferred name)'  L-saccharide  23  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_B0D
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
 B0D  F1    F  F     0  -0.349  -2.1808  -1.8419  -0.2109
 B0D  F2    F  F     0  -0.373   1.2720  -0.6639   1.4141
 B0D  CX1   C  CH1   0   0.398  -1.3051  -0.9390   0.3326
 B0D  CX2   C  CH1   0  -0.070  -1.7634   0.4787   0.0438
 B0D  OX2   O  OH1   0  -0.660  -2.0155   0.6862  -1.3177
 B0D  CX3   C  CH1   0  -0.063  -0.6561   1.4427   0.4900
 B0D  OX3   O  OH1   0  -0.660  -0.5409   1.4439   1.8911
 B0D  CX4   C  CH1   0   0.000   0.7168   1.0576  -0.0844
 B0D  OX4   O  OH1   0  -0.661   0.8029   1.3407  -1.4531
 B0D  CX5   C  CT    0   0.583   0.9942  -0.4434   0.0696
 B0D  OX5   O  O2    0  -0.507  -0.0878  -1.2279  -0.2869
 B0D  CX6   C  CH2   0  -0.207   2.1719  -0.9634  -0.7381
 B0D  OX6   O  OH1   0  -0.669   3.2986  -0.1900  -0.4271
 B0D  HX1   H  HCH1  0   0.207  -1.2660  -1.1273   1.4093
 B0D  HX2   H  HCH1  0   0.249  -2.6580   0.6820   0.6520
 B0D  HOX2  H  HOH1  0   0.456  -2.7926   0.1786  -1.5707
 B0D  HX3   H  HCH1  0   0.251  -0.9073   2.4453   0.1140
 B0D  HOX3  H  HOH1  0   0.459  -1.3560   1.7923   2.2659
 B0D  HX4   H  HCH1  0   0.243   1.4815   1.5991   0.4873
 B0D  HOX4  H  HOH1  0   0.459   0.5839   2.2673  -1.5925
 B0D  HX6   H  HCH2  0   0.232   2.3128  -2.0191  -0.4721
 B0D  HX6A  H  HCH2  0   0.218   1.9174  -0.9270  -1.8022
 B0D  HOX6  H  HOH1  0   0.465   4.0626  -0.5889  -0.8526

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
 B0D  F1   CX1   single  1.370  0.020  1.370
 B0D  F2   CX5   single  1.390  0.020  1.390
 B0D  CX1  CX2   single  1.518  0.020  1.518
 B0D  CX1  OX5   single  1.396  0.020  1.396
 B0D  CX2  OX2   single  1.400  0.020  1.400
 B0D  CX2  CX3   single  1.534  0.020  1.534
 B0D  CX3  OX3   single  1.406  0.020  1.406
 B0D  CX3  CX4   single  1.537  0.020  1.537
 B0D  CX4  OX4   single  1.400  0.020  1.400
 B0D  CX4  CX5   single  1.534  0.020  1.534
 B0D  CX5  OX5   single  1.383  0.020  1.383
 B0D  CX5  CX6   single  1.520  0.020  1.520
 B0D  CX6  OX6   single  1.402  0.020  1.402
 B0D  CX1  HX1   single  0.970  0.020  1.090
 B0D  CX2  HX2   single  0.970  0.020  1.090
 B0D  OX2  HOX2  single  0.850  0.020  0.980
 B0D  CX3  HX3   single  0.970  0.020  1.090
 B0D  OX3  HOX3  single  0.850  0.020  0.980
 B0D  CX4  HX4   single  0.970  0.020  1.090
 B0D  OX4  HOX4  single  0.850  0.020  0.980
 B0D  CX6  HX6   single  0.970  0.020  1.090
 B0D  CX6  HX6A  single  0.970  0.020  1.090
 B0D  OX6  HOX6  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
 B0D  HX1   CX1  OX5  111.72  3.000
 B0D  HX1   CX1  CX2  111.03  3.000
 B0D  OX5   CX1  CX2  111.85  3.000
 B0D  HX1   CX1  F1   107.45  3.000
 B0D  OX5   CX1  F1   104.18  3.000
 B0D  CX2   CX1  F1   110.31  3.000
 B0D  HX2   CX2  CX3  108.05  3.000
 B0D  HX2   CX2  OX2  111.32  3.000
 B0D  CX3   CX2  OX2  108.64  3.000
 B0D  HX2   CX2  CX1  108.22  3.000
 B0D  CX3   CX2  CX1  108.28  3.000
 B0D  OX2   CX2  CX1  112.20  3.000
 B0D  HOX2  OX2  CX2  108.84  3.000
 B0D  HX3   CX3  CX4  107.74  3.000
 B0D  HX3   CX3  OX3  111.02  3.000
 B0D  CX4   CX3  OX3  107.42  3.000
 B0D  HX3   CX3  CX2  107.97  3.000
 B0D  CX4   CX3  CX2  112.24  3.000
 B0D  OX3   CX3  CX2  110.45  3.000
 B0D  HOX3  OX3  CX3  108.60  3.000
 B0D  HX4   CX4  CX5  107.72  3.000
 B0D  HX4   CX4  OX4  111.50  3.000
 B0D  CX5   CX4  OX4  106.55  3.000
 B0D  HX4   CX4  CX3  107.70  3.000
 B0D  CX5   CX4  CX3  111.66  3.000
 B0D  OX4   CX4  CX3  111.68  3.000
 B0D  HOX4  OX4  CX4  108.80  3.000
 B0D  CX6   CX5  OX5  105.97  3.000
 B0D  CX6   CX5  CX4  114.93  3.000
 B0D  OX5   CX5  CX4  112.80  3.000
 B0D  CX6   CX5  F2   107.75  3.000
 B0D  OX5   CX5  F2   108.39  3.000
 B0D  CX4   CX5  F2   106.76  3.000
 B0D  CX5   OX5  CX1  116.77  3.000
 B0D  HX6A  CX6  HX6  107.30  3.000
 B0D  HX6A  CX6  OX6  112.60  3.000
 B0D  HX6   CX6  OX6  111.94  3.000
 B0D  HX6A  CX6  CX5  108.97  3.000
 B0D  HX6   CX6  CX5  107.44  3.000
 B0D  OX6   CX6  CX5  108.44  3.000
 B0D  HOX6  OX6  CX6  108.17  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
 B0D  chir_01  CX1  F1   CX2  OX5  positiv
 B0D  chir_02  CX2  OX2  CX1  CX3  negativ
 B0D  chir_03  CX3  OX3  CX2  CX4  positiv
 B0D  chir_04  CX4  OX4  CX5  CX3  positiv
 B0D  chir_05  CX5  OX5  CX6  CX4  negativ

