# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 08:29:14 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 6-O-phosphono-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@H](CO[P](O)(O)=O)[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
 G6P  G6P  6-O-phosphono-alpha-D-glucopyranose  D-saccharide  27  16  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G6P
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
 G6P  C1   C  CH1    0   0.226  44.9898  11.4543  14.0084
 G6P  C2   C  CH1    0  -0.038  43.6501  12.1432  13.7006
 G6P  C3   C  CH1    0  -0.015  43.5247  12.4567  12.2154
 G6P  C4   C  CH1    0   0.038  44.7401  13.2439  11.7432
 G6P  C5   C  CH1    0  -0.032  46.0201  12.4909  12.1072
 G6P  C6   C  CH2    0  -0.118  47.2667  13.2934  11.7774
 G6P  O1   O  OH1    0  -0.656  45.0494  10.1226  13.6102
 G6P  O2   O  OH1    0  -0.662  42.5426  11.3589  14.0678
 G6P  O3   O  OH1    0  -0.668  42.3805  13.2301  11.9402
 G6P  O4   O  OH1    0  -0.668  44.7167  13.4266  10.3483
 G6P  O5   O  O2     0  -0.496  46.0401  12.2301  13.5016
 G6P  O6   O  O2     0  -0.659  48.4070  12.5381  12.0304
 G6P  P    P  P      0   1.220  49.8928  13.1348  11.3964
 G6P  O1P  O  OP    -1  -0.902  50.0129  14.5423  11.9757
 G6P  O2P  O  OP    -1  -0.888  50.8714  12.1102  11.9533
 G6P  O3P  O  O      0  -0.901  49.7061  13.0955   9.8815
 G6P  H1   H  HCH1   0   0.233  45.1501  11.4462  15.0906
 G6P  H2   H  HCH1   0   0.226  43.6573  13.0982  14.2452
 G6P  H3   H  HCH1   0   0.207  43.4925  11.5165  11.6393
 G6P  H4   H  HCH1   0   0.204  44.7486  14.2126  12.2690
 G6P  H5   H  HCH1   0   0.206  46.0454  11.5510  11.5344
 G6P  H61  H  HCH2   0   0.159  47.2394  14.2219  12.3703
 G6P  H62  H  HCH2   0   0.175  47.2005  13.5972  10.7251
 G6P  HO1  H  HOH1   0   0.451  44.5994   9.9843  12.7705
 G6P  HO2  H  HOH1   0   0.457  42.4668  11.3553  15.0272
 G6P  HO3  H  HOH1   0   0.453  41.6001  12.6952  12.1163
 G6P  HO4  H  HOH1   0   0.450  43.9063  13.8943  10.1218

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
 G6P  C1  C2   single  1.538  0.020  1.538
 G6P  C1  O1   single  1.391  0.020  1.391
 G6P  C1  O5   single  1.401  0.020  1.401
 G6P  C1  H1   single  0.970  0.020  1.090
 G6P  C2  C3   single  1.523  0.020  1.523
 G6P  C2  O2   single  1.406  0.020  1.406
 G6P  C2  H2   single  0.970  0.020  1.090
 G6P  C3  C4   single  1.523  0.020  1.523
 G6P  C3  O3   single  1.408  0.020  1.408
 G6P  C3  H3   single  0.970  0.020  1.090
 G6P  C4  C5   single  1.529  0.020  1.529
 G6P  C4  O4   single  1.407  0.020  1.407
 G6P  C4  H4   single  0.970  0.020  1.090
 G6P  C5  C6   single  1.519  0.020  1.519
 G6P  C5  O5   single  1.419  0.020  1.419
 G6P  C5  H5   single  0.970  0.020  1.090
 G6P  C6  O6   single  1.391  0.020  1.391
 G6P  C6  H61  single  0.970  0.020  1.090
 G6P  C6  H62  single  0.970  0.020  1.090
 G6P  O1  HO1  single  0.850  0.020  0.980
 G6P  O2  HO2  single  0.850  0.020  0.980
 G6P  O3  HO3  single  0.850  0.020  0.980
 G6P  O4  HO4  single  0.850  0.020  0.980
 G6P  O6  P    single  1.722  0.020  1.722
 G6P  P   O1P  deloc   1.527  0.020  1.527
 G6P  P   O2P  deloc   1.522  0.020  1.522
 G6P  P   O3P  deloc   1.527  0.020  1.527

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
 G6P  H1   C1  O5   104.60  3.000
 G6P  H1   C1  O1   105.65  3.000
 G6P  O5   C1  O1   113.23  3.000
 G6P  H1   C1  C2   109.21  3.000
 G6P  O5   C1  C2   109.44  3.000
 G6P  O1   C1  C2   114.13  3.000
 G6P  H2   C2  O2   111.12  3.000
 G6P  H2   C2  C3   107.75  3.000
 G6P  O2   C2  C3   107.74  3.000
 G6P  H2   C2  C1   106.52  3.000
 G6P  O2   C2  C1   112.59  3.000
 G6P  C3   C2  C1   111.05  3.000
 G6P  H3   C3  O3   110.02  3.000
 G6P  H3   C3  C4   107.57  3.000
 G6P  O3   C3  C4   107.69  3.000
 G6P  H3   C3  C2   109.65  3.000
 G6P  O3   C3  C2   111.75  3.000
 G6P  C4   C3  C2   110.06  3.000
 G6P  H4   C4  O4   111.04  3.000
 G6P  H4   C4  C5   108.23  3.000
 G6P  O4   C4  C5   108.29  3.000
 G6P  H4   C4  C3   108.21  3.000
 G6P  O4   C4  C3   111.17  3.000
 G6P  C5   C4  C3   109.85  3.000
 G6P  H5   C5  O5   110.74  3.000
 G6P  H5   C5  C6   108.62  3.000
 G6P  O5   C5  C6   107.40  3.000
 G6P  H5   C5  C4   108.41  3.000
 G6P  O5   C5  C4   109.65  3.000
 G6P  C6   C5  C4   112.03  3.000
 G6P  H62  C6  H61  106.33  3.000
 G6P  H62  C6  O6   111.98  3.000
 G6P  H61  C6  O6   112.33  3.000
 G6P  H62  C6  C5   107.76  3.000
 G6P  H61  C6  C5   107.94  3.000
 G6P  O6   C6  C5   110.27  3.000
 G6P  HO1  O1  C1   111.54  3.000
 G6P  HO2  O2  C2   108.94  3.000
 G6P  HO3  O3  C3   108.53  3.000
 G6P  HO4  O4  C4   108.08  3.000
 G6P  C5   O5  C1   116.55  3.000
 G6P  P    O6  C6   116.88  3.000
 G6P  O3P  P   O2P  115.10  3.000
 G6P  O3P  P   O1P  114.19  3.000
 G6P  O2P  P   O1P  115.54  3.000
 G6P  O3P  P   O6   104.53  3.000
 G6P  O2P  P   O6   100.76  3.000
 G6P  O1P  P   O6   104.34  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
 G6P  Var_01  O1P  P   O6  C6   56.33  30.0  3
 G6P  Var_02  H61  C6  O6  P   -72.77  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
 G6P  chir_01  C1  C2  O1  O5  negativ
 G6P  chir_02  C2  O2  C1  C3  negativ
 G6P  chir_03  C3  O3  C2  C4  positiv
 G6P  chir_04  C4  O4  C5  C3  positiv
 G6P  chir_05  C5  O5  C4  C6  negativ

