# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:20:30 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 6-O-phosphono-D-glucose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@@H](O)C=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
 G6Q  G6Q  '6-O-phosphono-D-glucose  '  ligand  29  16  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G6Q
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
 G6Q  C1    C  C1    0   0.150   0.6821   0.0148  -5.0052
 G6Q  C2    C  CH1   0  -0.099  -0.1071  -0.4354  -3.7853
 G6Q  C3    C  CH1   0  -0.005   0.3289   0.3458  -2.5405
 G6Q  C4    C  CH1   0  -0.028  -0.3772  -0.1422  -1.2670
 G6Q  C5    C  CH1   0  -0.048   0.4018   0.2420   0.0049
 G6Q  C6    C  CH2   0  -0.175  -0.2727  -0.3448   1.2354
 G6Q  O1    O  O     0  -0.372   1.8714   0.1974  -5.0080
 G6Q  O2    O  OH1   0  -0.656  -1.4813  -0.4395  -4.0598
 G6Q  O3    O  OH1   0  -0.665   0.2036   1.7388  -2.7125
 G6Q  O4    O  OH1   0  -0.660  -1.7082   0.3220  -1.2020
 G6Q  O5    O  OH1   0  -0.650   1.7511  -0.1387  -0.0650
 G6Q  O6    O  O2    0  -0.587   0.4304   0.1332   2.3857
 G6Q  P     P  P     0   1.457  -0.0487  -0.3023   3.8435
 G6Q  O1P   O  O     0  -0.711  -0.2542  -1.7450   4.0692
 G6Q  O2P   O  OH1   0  -0.731   1.1240   0.4203   4.6450
 G6Q  O3P   O  OH1   0  -0.743  -1.4073   0.4836   4.1463
 G6Q  H1    H  H     0   0.205   0.0755   0.1429  -5.9219
 G6Q  H2    H  HCH1  0   0.289   0.1709  -1.4840  -3.6188
 G6Q  H3    H  HCH1  0   0.258   1.3970   0.1489  -2.4298
 G6Q  H4    H  HCH1  0   0.244  -0.4304  -1.2371  -1.3125
 G6Q  H5    H  HCH1  0   0.247   0.4054   1.3349   0.0932
 G6Q  H61   H  HCH2  0   0.246  -1.3225  -0.0496   1.2836
 G6Q  H62   H  HCH2  0   0.241  -0.2331  -1.4386   1.1973
 G6Q  HO2   H  HOH1  0   0.448  -1.8051   0.4635  -4.1376
 G6Q  HO3   H  HOH1  0   0.441  -0.7256   1.9901  -2.6675
 G6Q  HO4   H  HOH1  0   0.454  -1.7263   1.1964  -0.7974
 G6Q  HO5   H  HOH1  0   0.451   1.8065  -1.1002  -0.1149
 G6Q  HOP2  H  HOH1  0   0.504   1.1185   0.2447   5.5954
 G6Q  HOP3  H  HOH1  0   0.496  -1.3646   1.4454   4.0600

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
 G6Q  C1   C2    single  1.521  0.020  1.521
 G6Q  C1   O1    double  1.203  0.020  1.203
 G6Q  C1   H1    single  0.930  0.020  1.080
 G6Q  C2   C3    single  1.533  0.020  1.533
 G6Q  C2   O2    single  1.401  0.020  1.401
 G6Q  C2   H2    single  0.970  0.020  1.090
 G6Q  C3   C4    single  1.536  0.020  1.536
 G6Q  C3   O3    single  1.409  0.020  1.409
 G6Q  C3   H3    single  0.970  0.020  1.090
 G6Q  C4   C5    single  1.540  0.020  1.540
 G6Q  C4   O4    single  1.411  0.020  1.411
 G6Q  C4   H4    single  0.970  0.020  1.090
 G6Q  C5   C6    single  1.521  0.020  1.521
 G6Q  C5   O5    single  1.404  0.020  1.404
 G6Q  C5   H5    single  0.970  0.020  1.090
 G6Q  C6   O6    single  1.430  0.020  1.430
 G6Q  C6   H61   single  0.970  0.020  1.090
 G6Q  C6   H62   single  0.970  0.020  1.090
 G6Q  O2   HO2   single  0.850  0.020  0.980
 G6Q  O3   HO3   single  0.850  0.020  0.980
 G6Q  O4   HO4   single  0.850  0.020  0.980
 G6Q  O5   HO5   single  0.850  0.020  0.980
 G6Q  O6   P     single  1.595  0.020  1.595
 G6Q  P    O1P   double  1.475  0.020  1.475
 G6Q  P    O2P   single  1.594  0.020  1.594
 G6Q  P    O3P   single  1.598  0.020  1.598
 G6Q  O2P  HOP2  single  0.850  0.020  0.980
 G6Q  O3P  HOP3  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
 G6Q  H1    C1   O1   121.48  3.000
 G6Q  H1    C1   C2   114.47  3.000
 G6Q  O1    C1   C2   124.03  3.000
 G6Q  H2    C2   O2   105.98  3.000
 G6Q  H2    C2   C3   106.95  3.000
 G6Q  O2    C2   C3   116.07  3.000
 G6Q  H2    C2   C1   105.85  3.000
 G6Q  O2    C2   C1   110.65  3.000
 G6Q  C3    C2   C1   110.66  3.000
 G6Q  H3    C3   O3   106.12  3.000
 G6Q  H3    C3   C4   107.97  3.000
 G6Q  O3    C3   C4   111.99  3.000
 G6Q  H3    C3   C2   105.59  3.000
 G6Q  O3    C3   C2   112.29  3.000
 G6Q  C4    C3   C2   112.38  3.000
 G6Q  H4    C4   O4   106.53  3.000
 G6Q  H4    C4   C5   107.92  3.000
 G6Q  O4    C4   C5   110.91  3.000
 G6Q  H4    C4   C3   107.76  3.000
 G6Q  O4    C4   C3   111.55  3.000
 G6Q  C5    C4   C3   111.90  3.000
 G6Q  H5    C5   O5   105.73  3.000
 G6Q  H5    C5   C6   108.72  3.000
 G6Q  O5    C5   C6   111.21  3.000
 G6Q  H5    C5   C4   108.47  3.000
 G6Q  O5    C5   C4   112.17  3.000
 G6Q  C6    C5   C4   110.34  3.000
 G6Q  H62   C6   H61  107.84  3.000
 G6Q  H62   C6   O6   110.12  3.000
 G6Q  H61   C6   O6   110.30  3.000
 G6Q  H62   C6   C5   109.95  3.000
 G6Q  H61   C6   C5   110.97  3.000
 G6Q  O6    C6   C5   107.68  3.000
 G6Q  HO2   O2   C2   110.06  3.000
 G6Q  HO3   O3   C3   109.74  3.000
 G6Q  HO4   O4   C4   109.61  3.000
 G6Q  HO5   O5   C5   109.16  3.000
 G6Q  P     O6   C6   119.74  3.000
 G6Q  O3P   P    O2P  107.89  3.000
 G6Q  O3P   P    O1P  109.49  3.000
 G6Q  O2P   P    O1P  117.98  3.000
 G6Q  O3P   P    O6   107.11  3.000
 G6Q  O2P   P    O6    96.60  3.000
 G6Q  O1P   P    O6   116.67  3.000
 G6Q  HOP2  O2P  P    114.08  3.000
 G6Q  HOP3  O3P  P    115.77  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
 G6Q  Var_01  O1P  P   O6  C6  50.36  30.0  3
 G6Q  Var_02  H61  C6  O6  P   58.34  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
 G6Q  chir_01  C2  C1  C3  O2  negativ
 G6Q  chir_02  C3  O3  C2  C4  positiv
 G6Q  chir_03  C4  O4  C3  C5  negativ
 G6Q  chir_04  C5  O5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 G6Q  plan-1  C1  0.020
 G6Q  plan-1  C2  0.020
 G6Q  plan-1  O1  0.020
 G6Q  plan-1  H1  0.020

