# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:20:08 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 2,5-anhydro-1-deoxy-1-phosphono-6-O-phosphono-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@H](C[P](O)(O)=O)O[C@@H]1CO[P](O)(O)=O
#
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
 FDQ  FDQ  2,5-anhydro-1-deoxy-1-phosphono-6-O-phosphono-D-glucitol  D-saccharide  32  18  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FDQ
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
 FDQ  P1    P  P     0   1.373   2.9963  -1.4250   0.2166
 FDQ  O1P   O  O     0  -0.709   1.9230  -2.4422   0.2961
 FDQ  O2P   O  OH1   0  -0.748   4.2955  -1.8677  -0.6270
 FDQ  O3P   O  OH1   0  -0.753   3.5093  -1.0733   1.7027
 FDQ  C21   C  CH2   0  -0.790   2.6154   0.1470  -0.5881
 FDQ  C2    C  CH1   0   0.052   1.7234   1.0499   0.2425
 FDQ  C3    C  CH1   0  -0.009   1.2892   2.3391  -0.4420
 FDQ  O3    O  OH1   0  -0.662   0.9597   2.0743  -1.7797
 FDQ  C4    C  CH1   0  -0.065   0.0454   2.6912   0.3889
 FDQ  O4    O  OH1   0  -0.667   0.3865   3.3075   1.6053
 FDQ  C5    C  CH1   0   0.007  -0.5396   1.3090   0.7025
 FDQ  O5    O  O2    0  -0.497   0.5195   0.3762   0.5667
 FDQ  C6    C  CH2   0  -0.180  -1.6705   0.9501  -0.2353
 FDQ  O6    O  O2    0  -0.586  -2.1391  -0.3568   0.1171
 FDQ  P2    P  P     0   1.454  -3.5388  -0.8587  -0.4587
 FDQ  O4P   O  O     0  -0.712  -3.7599  -0.6865  -1.9067
 FDQ  O5P   O  OH1   0  -0.731  -3.4630  -2.3444   0.1134
 FDQ  O6P   O  OH1   0  -0.742  -4.6788  -0.0822   0.3506
 FDQ  HOP2  H  HOH1  0   0.491   4.5422  -2.7942  -0.5017
 FDQ  HOP3  H  HOH1  0   0.489   4.2566  -0.4625   1.7499
 FDQ  H211  H  HCH2  0   0.298   2.1582  -0.0803  -1.5528
 FDQ  H212  H  HCH2  0   0.297   3.5553   0.6675  -0.7882
 FDQ  H2    H  HCH1  0   0.234   2.2548   1.3354   1.1595
 FDQ  H3    H  HCH1  0   0.250   2.0639   3.1113  -0.3565
 FDQ  HO3   H  HOH1  0   0.461   0.6515   2.8907  -2.1863
 FDQ  H4    H  HCH1  0   0.253  -0.6529   3.3108  -0.1901
 FDQ  HO4   H  HOH1  0   0.457   0.7688   4.1695   1.4106
 FDQ  H5    H  HCH1  0   0.249  -0.9175   1.2947   1.7321
 FDQ  H61   H  HCH2  0   0.239  -2.4674   1.6915  -0.1249
 FDQ  H62   H  HCH2  0   0.247  -1.3325   0.9569  -1.2725
 FDQ  HOP5  H  HOH1  0   0.504  -4.1640  -2.9247  -0.2125
 FDQ  HOP6  H  HOH1  0   0.495  -4.6446  -0.1737   1.3124

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
 FDQ  P1   O1P   double  1.481  0.020  1.481
 FDQ  P1   O2P   single  1.611  0.020  1.611
 FDQ  P1   O3P   single  1.611  0.020  1.611
 FDQ  P1   C21   single  1.807  0.020  1.807
 FDQ  O2P  HOP2  single  0.850  0.020  0.980
 FDQ  O3P  HOP3  single  0.850  0.020  0.980
 FDQ  C21  C2    single  1.517  0.020  1.517
 FDQ  C21  H211  single  0.970  0.020  1.090
 FDQ  C21  H212  single  0.970  0.020  1.090
 FDQ  C2   C3    single  1.523  0.020  1.523
 FDQ  C2   O5    single  1.417  0.020  1.417
 FDQ  C2   H2    single  0.970  0.020  1.090
 FDQ  C3   O3    single  1.403  0.020  1.403
 FDQ  C3   C4    single  1.537  0.020  1.537
 FDQ  C3   H3    single  0.970  0.020  1.090
 FDQ  O3   HO3   single  0.850  0.020  0.980
 FDQ  C4   O4    single  1.406  0.020  1.406
 FDQ  C4   C5    single  1.533  0.020  1.533
 FDQ  C4   H4    single  0.970  0.020  1.090
 FDQ  O4   HO4   single  0.850  0.020  0.980
 FDQ  C5   O5    single  1.418  0.020  1.418
 FDQ  C5   C6    single  1.512  0.020  1.512
 FDQ  C5   H5    single  0.970  0.020  1.090
 FDQ  C6   O6    single  1.432  0.020  1.432
 FDQ  C6   H61   single  0.970  0.020  1.090
 FDQ  C6   H62   single  0.970  0.020  1.090
 FDQ  O6   P2    single  1.595  0.020  1.595
 FDQ  P2   O4P   double  1.475  0.020  1.475
 FDQ  P2   O5P   single  1.594  0.020  1.594
 FDQ  P2   O6P   single  1.599  0.020  1.599
 FDQ  O5P  HOP5  single  0.850  0.020  0.980
 FDQ  O6P  HOP6  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
 FDQ  C21   P1   O3P   106.74  3.000
 FDQ  C21   P1   O2P   100.13  3.000
 FDQ  O3P   P1   O2P   106.63  3.000
 FDQ  C21   P1   O1P   117.96  3.000
 FDQ  O3P   P1   O1P   109.34  3.000
 FDQ  O2P   P1   O1P   115.08  3.000
 FDQ  HOP2  O2P  P1    113.65  3.000
 FDQ  HOP3  O3P  P1    115.42  3.000
 FDQ  H212  C21  H211  107.31  3.000
 FDQ  H212  C21  C2    108.81  3.000
 FDQ  H211  C21  C2    111.20  3.000
 FDQ  H212  C21  P1    108.34  3.000
 FDQ  H211  C21  P1    107.50  3.000
 FDQ  C2    C21  P1    113.46  3.000
 FDQ  H2    C2   O5    110.11  3.000
 FDQ  H2    C2   C3    107.06  3.000
 FDQ  O5    C2   C3    105.25  3.000
 FDQ  H2    C2   C21   109.13  3.000
 FDQ  O5    C2   C21   109.99  3.000
 FDQ  C3    C2   C21   115.18  3.000
 FDQ  H3    C3   C4    111.60  3.000
 FDQ  H3    C3   O3    111.90  3.000
 FDQ  C4    C3   O3    111.64  3.000
 FDQ  H3    C3   C2    111.07  3.000
 FDQ  C4    C3   C2    100.47  3.000
 FDQ  O3    C3   C2    109.62  3.000
 FDQ  HO3   O3   C3    108.53  3.000
 FDQ  H4    C4   C5    111.95  3.000
 FDQ  H4    C4   O4    111.29  3.000
 FDQ  C5    C4   O4    108.11  3.000
 FDQ  H4    C4   C3    111.02  3.000
 FDQ  C5    C4   C3    102.29  3.000
 FDQ  O4    C4   C3    111.83  3.000
 FDQ  HO4   O4   C4    108.30  3.000
 FDQ  H5    C5   C6    108.74  3.000
 FDQ  H5    C5   O5    109.80  3.000
 FDQ  C6    C5   O5    110.07  3.000
 FDQ  H5    C5   C4    109.58  3.000
 FDQ  C6    C5   C4    111.86  3.000
 FDQ  O5    C5   C4    106.77  3.000
 FDQ  C5    O5   C2    110.11  3.000
 FDQ  H62   C6   H61   108.51  3.000
 FDQ  H62   C6   O6    109.93  3.000
 FDQ  H61   C6   O6    110.81  3.000
 FDQ  H62   C6   C5    110.88  3.000
 FDQ  H61   C6   C5    108.74  3.000
 FDQ  O6    C6   C5    107.98  3.000
 FDQ  P2    O6   C6    119.05  3.000
 FDQ  O6P   P2   O5P   107.75  3.000
 FDQ  O6P   P2   O4P   109.46  3.000
 FDQ  O5P   P2   O4P   117.93  3.000
 FDQ  O6P   P2   O6    106.87  3.000
 FDQ  O5P   P2   O6     97.01  3.000
 FDQ  O4P   P2   O6    116.70  3.000
 FDQ  HOP5  O5P  P2    113.83  3.000
 FDQ  HOP6  O6P  P2    115.61  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
 FDQ  Var_01  C2   C21  P1  O1P  73.27  30.0  3
 FDQ  Var_02  O4P  P2   O6  C6   48.53  30.0  3
 FDQ  Var_03  H61  C6   O6  P2   46.54  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
 FDQ  chir_01  C2  C21  C3  O5  negativ
 FDQ  chir_02  C3  O3   C4  C2  negativ
 FDQ  chir_03  C4  O4   C3  C5  negativ
 FDQ  chir_04  C5  O5   C4  C6  negativ

