# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:58:27 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (1S)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[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
 GPM  GPM  (1S)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol  D-saccharide  29  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GPM
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
 GPM  C1   C  CH1    0   0.000   0.0178   0.8088  -0.7338
 GPM  C2   C  CH1    0   0.043  -1.3416   1.5168  -0.6713
 GPM  C3   C  CH1    0  -0.005  -2.2055   0.8846   0.4079
 GPM  C4   C  CH1    0  -0.009  -2.3195  -0.6168   0.1813
 GPM  C5   C  CH1    0   0.017  -0.9451  -1.2641  -0.0575
 GPM  C6   C  CH2    0  -0.162  -1.1449  -2.6805  -0.5599
 GPM  C7   C  CH2    0  -0.761   0.9069   1.0325   0.4796
 GPM  O2   O  OH1    0  -0.677  -1.1429   2.8937  -0.4528
 GPM  O3   O  OH1    0  -0.680  -3.4736   1.5073   0.3667
 GPM  O4   O  OH1    0  -0.676  -2.9735  -1.1605   1.3126
 GPM  O5   O  O2     0  -0.498  -0.2371  -0.5519  -1.0421
 GPM  O6   O  OH1    0  -0.658   0.0851  -3.3488  -0.6760
 GPM  P    P  P      0   1.168   2.6024   0.2570   0.3976
 GPM  O1P  O  O      0  -0.888   2.4237  -1.2437   0.6451
 GPM  O2P  O  OP    -1  -0.917   3.1253   0.6042  -1.0061
 GPM  O3P  O  OP    -1  -0.922   3.3717   0.9665   1.5257
 GPM  H1   H  HCH1   0   0.218   0.5603   1.1902  -1.6036
 GPM  H2   H  HCH1   0   0.203  -1.8421   1.3551  -1.6404
 GPM  H3   H  HCH1   0   0.208  -1.7351   1.0569   1.3872
 GPM  H4   H  HCH1   0   0.207  -2.9286  -0.7641  -0.7236
 GPM  H5   H  HCH1   0   0.213  -0.3801  -1.2909   0.8831
 GPM  H61  H  HCH2   0   0.185  -1.8114  -3.2016   0.1401
 GPM  H62  H  HCH2   0   0.188  -1.6742  -2.6340  -1.5235
 GPM  H71  H  HCH2   0   0.206   1.0440   2.1136   0.5738
 GPM  H72  H  HCH2   0   0.195   0.4183   0.7203   1.4086
 GPM  HO2  H  HOH1   0   0.447  -2.0078   3.3138  -0.4110
 GPM  HO3  H  HOH1   0   0.450  -3.9969   1.1668   1.0992
 GPM  HO4  H  HOH1   0   0.456  -3.4805  -1.9306   1.0439
 GPM  HO6  H  HOH1   0   0.449  -0.1004  -4.2353  -0.9983

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
 GPM  C1  C2   single  1.534  0.020  1.534
 GPM  C1  C7   single  1.521  0.020  1.521
 GPM  C1  O5   single  1.418  0.020  1.418
 GPM  C1  H1   single  0.970  0.020  1.090
 GPM  C2  C3   single  1.520  0.020  1.520
 GPM  C2  O2   single  1.408  0.020  1.408
 GPM  C2  H2   single  0.970  0.020  1.090
 GPM  C3  C4   single  1.523  0.020  1.523
 GPM  C3  O3   single  1.413  0.020  1.413
 GPM  C3  H3   single  0.970  0.020  1.090
 GPM  C4  C5   single  1.538  0.020  1.538
 GPM  C4  O4   single  1.415  0.020  1.415
 GPM  C4  H4   single  0.970  0.020  1.090
 GPM  C5  C6   single  1.516  0.020  1.516
 GPM  C5  O5   single  1.406  0.020  1.406
 GPM  C5  H5   single  0.970  0.020  1.090
 GPM  C6  O6   single  1.405  0.020  1.405
 GPM  C6  H61  single  0.970  0.020  1.090
 GPM  C6  H62  single  0.970  0.020  1.090
 GPM  C7  P    single  1.866  0.020  1.866
 GPM  C7  H71  single  0.970  0.020  1.090
 GPM  C7  H72  single  0.970  0.020  1.090
 GPM  O2  HO2  single  0.850  0.020  0.980
 GPM  O3  HO3  single  0.850  0.020  0.980
 GPM  O4  HO4  single  0.850  0.020  0.980
 GPM  O6  HO6  single  0.850  0.020  0.980
 GPM  P   O1P  deloc   1.531  0.020  1.531
 GPM  P   O2P  deloc   1.538  0.020  1.538
 GPM  P   O3P  deloc   1.539  0.020  1.539

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
 GPM  H1   C1  O5   104.52  3.000
 GPM  H1   C1  C7   107.05  3.000
 GPM  O5   C1  C7   114.81  3.000
 GPM  H1   C1  C2   108.12  3.000
 GPM  O5   C1  C2   107.00  3.000
 GPM  C7   C1  C2   114.69  3.000
 GPM  H2   C2  O2   110.11  3.000
 GPM  H2   C2  C3   107.76  3.000
 GPM  O2   C2  C3   112.13  3.000
 GPM  H2   C2  C1   107.39  3.000
 GPM  O2   C2  C1   109.42  3.000
 GPM  C3   C2  C1   109.92  3.000
 GPM  H3   C3  O3   109.91  3.000
 GPM  H3   C3  C4   108.60  3.000
 GPM  O3   C3  C4   111.28  3.000
 GPM  H3   C3  C2   108.90  3.000
 GPM  O3   C3  C2   107.82  3.000
 GPM  C4   C3  C2   110.30  3.000
 GPM  H4   C4  O4   110.49  3.000
 GPM  H4   C4  C5   108.09  3.000
 GPM  O4   C4  C5   112.05  3.000
 GPM  H4   C4  C3   107.20  3.000
 GPM  O4   C4  C3   107.13  3.000
 GPM  C5   C4  C3   111.79  3.000
 GPM  H5   C5  O5   110.68  3.000
 GPM  H5   C5  C6   109.21  3.000
 GPM  O5   C5  C6   107.90  3.000
 GPM  H5   C5  C4   109.71  3.000
 GPM  O5   C5  C4   110.22  3.000
 GPM  C6   C5  C4   109.08  3.000
 GPM  H62  C6  H61  106.64  3.000
 GPM  H62  C6  O6   111.65  3.000
 GPM  H61  C6  O6   111.00  3.000
 GPM  H62  C6  C5   108.31  3.000
 GPM  H61  C6  C5   108.18  3.000
 GPM  O6   C6  C5   110.89  3.000
 GPM  H72  C7  H71  105.35  3.000
 GPM  H72  C7  P    108.91  3.000
 GPM  H71  C7  P    107.50  3.000
 GPM  H72  C7  C1   111.96  3.000
 GPM  H71  C7  C1   106.70  3.000
 GPM  P    C7  C1   115.78  3.000
 GPM  HO2  O2  C2   107.87  3.000
 GPM  HO3  O3  C3   108.05  3.000
 GPM  HO4  O4  C4   109.17  3.000
 GPM  C5   O5  C1   115.09  3.000
 GPM  HO6  O6  C6   107.31  3.000
 GPM  O3P  P   O2P  113.27  3.000
 GPM  O3P  P   O1P  113.06  3.000
 GPM  O2P  P   O1P  114.11  3.000
 GPM  O3P  P   C7   103.32  3.000
 GPM  O2P  P   C7   104.79  3.000
 GPM  O1P  P   C7   107.11  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
 GPM  Var_01  O1P  P  C7  C1  -75.78  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
 GPM  chir_01  C1  C2  C7  O5  negativ
 GPM  chir_02  C2  O2  C1  C3  negativ
 GPM  chir_03  C3  O3  C2  C4  positiv
 GPM  chir_04  C4  O4  C5  C3  positiv
 GPM  chir_05  C5  O5  C6  C4  positiv

