# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:52:01 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 1-O-phosphono-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[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
 G1P  G1P  1-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 GRAND
;

data_comp_G1P
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
 G1P  C1   C  CH1    0   0.271  28.7166   3.4542  53.2500
 G1P  C2   C  CH1    0   0.019  28.5709   2.4200  54.3699
 G1P  C3   C  CH1    0  -0.005  27.7775   1.2210  53.8696
 G1P  C4   C  CH1    0   0.004  26.4310   1.6881  53.3330
 G1P  C5   C  CH1    0   0.005  26.6418   2.7924  52.2885
 G1P  C6   C  CH2    0  -0.199  25.3477   3.3764  51.7620
 G1P  O1   O  O2     0  -0.662  29.4533   2.9339  52.2282
 G1P  O2   O  OH1    0  -0.671  29.8545   2.0627  54.8189
 G1P  O3   O  OH1    0  -0.675  27.6300   0.3245  54.9502
 G1P  O4   O  OH1    0  -0.676  25.7775   0.5672  52.7745
 G1P  O5   O  O2     0  -0.519  27.4131   3.8405  52.8387
 G1P  O6   O  OH1    0  -0.669  24.5651   3.8655  52.8265
 G1P  P    P  P      0   1.205  30.5756   3.8851  51.2944
 G1P  O1P  O  O      0  -0.882  30.2309   3.4411  49.8810
 G1P  O2P  O  OP    -1  -0.886  30.2283   5.3298  51.6320
 G1P  O3P  O  OP    -1  -0.882  31.9297   3.4136  51.8054
 G1P  H1   H  HCH1   0   0.195  29.1525   4.3761  53.6533
 G1P  H2   H  HCH1   0   0.193  27.9950   2.8928  55.1818
 G1P  H3   H  HCH1   0   0.203  28.3366   0.7470  53.0493
 G1P  H4   H  HCH1   0   0.211  25.8552   2.0954  54.1748
 G1P  H5   H  HCH1   0   0.209  27.1530   2.3502  51.4213
 G1P  H61  H  HCH2   0   0.212  25.5917   4.1670  51.0396
 G1P  H62  H  HCH2   0   0.200  24.8257   2.5933  51.1979
 G1P  HO2  H  HOH1   0   0.444  29.7481   1.4259  55.5323
 G1P  HO3  H  HOH1   0   0.448  27.2448  -0.4906  54.6139
 G1P  HO4  H  HOH1   0   0.454  24.8283   0.7167  52.7986
 G1P  HO6  H  HOH1   0   0.454  23.7152   4.1412  52.4728

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
 G1P  C1  C2   single  1.531  0.020  1.531
 G1P  C1  O1   single  1.363  0.020  1.363
 G1P  C1  O5   single  1.420  0.020  1.420
 G1P  C1  H1   single  0.970  0.020  1.090
 G1P  C2  C3   single  1.522  0.020  1.522
 G1P  C2  O2   single  1.406  0.020  1.406
 G1P  C2  H2   single  0.970  0.020  1.090
 G1P  C3  C4   single  1.523  0.020  1.523
 G1P  C3  O3   single  1.412  0.020  1.412
 G1P  C3  H3   single  0.970  0.020  1.090
 G1P  C4  C5   single  1.535  0.020  1.535
 G1P  C4  O4   single  1.413  0.020  1.413
 G1P  C4  H4   single  0.970  0.020  1.090
 G1P  C5  C6   single  1.514  0.020  1.514
 G1P  C5  O5   single  1.413  0.020  1.413
 G1P  C5  H5   single  0.970  0.020  1.090
 G1P  C6  O6   single  1.409  0.020  1.409
 G1P  C6  H61  single  0.970  0.020  1.090
 G1P  C6  H62  single  0.970  0.020  1.090
 G1P  O1  P    single  1.743  0.020  1.743
 G1P  O2  HO2  single  0.850  0.020  0.980
 G1P  O3  HO3  single  0.850  0.020  0.980
 G1P  O4  HO4  single  0.850  0.020  0.980
 G1P  O6  HO6  single  0.850  0.020  0.980
 G1P  P   O1P  deloc   1.521  0.020  1.521
 G1P  P   O2P  deloc   1.524  0.020  1.524
 G1P  P   O3P  deloc   1.522  0.020  1.522

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
 G1P  H1   C1  O5   104.04  3.000
 G1P  H1   C1  O1   112.45  3.000
 G1P  O5   C1  O1   112.50  3.000
 G1P  H1   C1  C2   109.67  3.000
 G1P  O5   C1  C2   107.95  3.000
 G1P  O1   C1  C2   109.99  3.000
 G1P  H2   C2  O2   110.54  3.000
 G1P  H2   C2  C3   107.92  3.000
 G1P  O2   C2  C3   112.37  3.000
 G1P  H2   C2  C1   107.38  3.000
 G1P  O2   C2  C1   108.56  3.000
 G1P  C3   C2  C1   109.94  3.000
 G1P  H3   C3  O3   110.49  3.000
 G1P  H3   C3  C4   108.59  3.000
 G1P  O3   C3  C4   111.85  3.000
 G1P  H3   C3  C2   108.64  3.000
 G1P  O3   C3  C2   107.64  3.000
 G1P  C4   C3  C2   109.58  3.000
 G1P  H4   C4  O4   110.78  3.000
 G1P  H4   C4  C5   109.08  3.000
 G1P  O4   C4  C5   111.44  3.000
 G1P  H4   C4  C3   107.89  3.000
 G1P  O4   C4  C3   107.76  3.000
 G1P  C5   C4  C3   109.82  3.000
 G1P  H5   C5  O5   110.59  3.000
 G1P  H5   C5  C6   106.16  3.000
 G1P  O5   C5  C6   108.41  3.000
 G1P  H5   C5  C4   108.14  3.000
 G1P  O5   C5  C4   110.11  3.000
 G1P  C6   C5  C4   113.38  3.000
 G1P  H62  C6  H61  106.33  3.000
 G1P  H62  C6  O6   111.83  3.000
 G1P  H61  C6  O6   111.75  3.000
 G1P  H62  C6  C5   108.06  3.000
 G1P  H61  C6  C5   108.45  3.000
 G1P  O6   C6  C5   110.24  3.000
 G1P  P    O1  C1   122.78  3.000
 G1P  HO2  O2  C2   107.70  3.000
 G1P  HO3  O3  C3   108.19  3.000
 G1P  HO4  O4  C4   108.88  3.000
 G1P  C5   O5  C1   114.33  3.000
 G1P  HO6  O6  C6   108.23  3.000
 G1P  O3P  P   O2P  114.97  3.000
 G1P  O3P  P   O1P  115.03  3.000
 G1P  O2P  P   O1P  115.54  3.000
 G1P  O3P  P   O1   102.94  3.000
 G1P  O2P  P   O1   104.60  3.000
 G1P  O1P  P   O1   101.10  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
 G1P  Var_01  O1P  P  O1  C1  -134.80  30.0  3

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
 G1P  chir_01  C1  C2  O1  O5  negativ
 G1P  chir_02  C2  O2  C1  C3  negativ
 G1P  chir_03  C3  O3  C2  C4  positiv
 G1P  chir_04  C4  O4  C5  C3  positiv
 G1P  chir_05  C5  O5  C4  C6  negativ

