# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:37:30 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)C(F)(F)[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
 7JZ  7JZ  2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose  D-saccharide  23  13  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7JZ
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
 7JZ  F2A  F  F     0  -0.339  19.9086  68.8140  84.1467
 7JZ  C2   C  CT    0   0.707  19.7918  69.0849  85.4724
 7JZ  F2B  F  F     0  -0.355  18.7959  70.0213  85.5629
 7JZ  C1   C  CH1   0   0.158  21.1011  69.7364  85.9943
 7JZ  C3   C  CH1   0  -0.054  19.3609  67.8351  86.2493
 7JZ  O3   O  OH1   0  -0.654  18.4721  67.0429  85.5215
 7JZ  C4   C  CH1   0  -0.114  20.5865  67.0686  86.7259
 7JZ  O4   O  OH1   0  -0.661  21.2530  66.5780  85.5857
 7JZ  C5   C  CH1   0  -0.001  21.4226  67.9820  87.6312
 7JZ  O5   O  O2    0  -0.498  21.3186  69.3695  87.3066
 7JZ  C6   C  CH2   0  -0.161  22.8637  67.5238  87.7498
 7JZ  O6   O  OH1   0  -0.666  23.4789  68.2606  88.7804
 7JZ  O1   O  OH1   0  -0.647  22.2057  69.4094  85.2199
 7JZ  H1   H  HCH1  0   0.248  20.9406  70.8222  86.0124
 7JZ  H3   H  HCH1  0   0.277  18.8266  68.1836  87.1385
 7JZ  HO3  H  HOH1  0   0.447  18.9740  66.5585  84.8549
 7JZ  H4   H  HCH1  0   0.268  20.2409  66.2350  87.3483
 7JZ  HO4  H  HOH1  0   0.464  21.6700  65.7394  85.8029
 7JZ  H5   H  HCH1  0   0.252  20.9723  67.9120  88.6271
 7JZ  H61  H  HCH2  0   0.198  22.8531  66.4481  87.9786
 7JZ  H62  H  HCH2  0   0.214  23.3852  67.6440  86.7958
 7JZ  HO6  H  HOH1  0   0.453  24.4146  68.0416  88.7858
 7JZ  HO1  H  HOH1  0   0.463  22.2018  69.9338  84.4122

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
 7JZ  F2A  C2   single  1.358  0.020  1.358
 7JZ  C2   F2B  single  1.370  0.020  1.370
 7JZ  C2   C1   single  1.553  0.020  1.553
 7JZ  C2   C3   single  1.533  0.020  1.533
 7JZ  C1   O5   single  1.380  0.020  1.380
 7JZ  C1   O1   single  1.388  0.020  1.388
 7JZ  C1   H1   single  0.970  0.020  1.090
 7JZ  C3   O3   single  1.395  0.020  1.395
 7JZ  C3   C4   single  1.522  0.020  1.522
 7JZ  C3   H3   single  0.970  0.020  1.090
 7JZ  O3   HO3  single  0.850  0.020  0.980
 7JZ  C4   O4   single  1.409  0.020  1.409
 7JZ  C4   C5   single  1.534  0.020  1.534
 7JZ  C4   H4   single  0.970  0.020  1.090
 7JZ  O4   HO4  single  0.850  0.020  0.980
 7JZ  C5   O5   single  1.429  0.020  1.429
 7JZ  C5   C6   single  1.517  0.020  1.517
 7JZ  C5   H5   single  0.970  0.020  1.090
 7JZ  C6   O6   single  1.408  0.020  1.408
 7JZ  C6   H61  single  0.970  0.020  1.090
 7JZ  C6   H62  single  0.970  0.020  1.090
 7JZ  O6   HO6  single  0.850  0.020  0.980
 7JZ  O1   HO1  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
 7JZ  C3   C2  C1   114.12  3.000
 7JZ  C3   C2  F2B  108.62  3.000
 7JZ  C1   C2  F2B  107.70  3.000
 7JZ  C3   C2  F2A  110.86  3.000
 7JZ  C1   C2  F2A  109.83  3.000
 7JZ  F2B  C2  F2A  105.27  3.000
 7JZ  H1   C1  O1   111.01  3.000
 7JZ  H1   C1  O5   105.69  3.000
 7JZ  O1   C1  O5   110.03  3.000
 7JZ  H1   C1  C2   107.29  3.000
 7JZ  O1   C1  C2   112.62  3.000
 7JZ  O5   C1  C2   109.94  3.000
 7JZ  H3   C3  C4   107.40  3.000
 7JZ  H3   C3  O3   107.07  3.000
 7JZ  C4   C3  O3   112.97  3.000
 7JZ  H3   C3  C2   106.82  3.000
 7JZ  C4   C3  C2   110.05  3.000
 7JZ  O3   C3  C2   112.18  3.000
 7JZ  HO3  O3  C3   108.31  3.000
 7JZ  H4   C4  C5   106.83  3.000
 7JZ  H4   C4  O4   110.11  3.000
 7JZ  C5   C4  O4   115.28  3.000
 7JZ  H4   C4  C3   107.87  3.000
 7JZ  C5   C4  C3   108.90  3.000
 7JZ  O4   C4  C3   107.63  3.000
 7JZ  HO4  O4  C4   109.03  3.000
 7JZ  H5   C5  C6   107.47  3.000
 7JZ  H5   C5  O5   103.80  3.000
 7JZ  C6   C5  O5   112.35  3.000
 7JZ  H5   C5  C4   105.93  3.000
 7JZ  C6   C5  C4   112.59  3.000
 7JZ  O5   C5  C4   113.86  3.000
 7JZ  C5   O5  C1   119.06  3.000
 7JZ  H62  C6  H61  107.07  3.000
 7JZ  H62  C6  O6   111.87  3.000
 7JZ  H61  C6  O6   111.32  3.000
 7JZ  H62  C6  C5   110.58  3.000
 7JZ  H61  C6  C5   107.61  3.000
 7JZ  O6   C6  C5   108.31  3.000
 7JZ  HO6  O6  C6   108.07  3.000
 7JZ  HO1  O1  C1   109.66  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
 7JZ  chir_01  C1  C2  O5  O1  negativ
 7JZ  chir_02  C3  O3  C2  C4  positiv
 7JZ  chir_03  C4  O4  C5  C3  negativ
 7JZ  chir_04  C5  O5  C4  C6  negativ

