# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:15:53 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  31  16  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.012   0.0223   0.8680  -0.6767
 GPM  C2    C  CH1   0   0.036  -1.3308   1.5739  -0.5512
 GPM  C3    C  CH1   0  -0.007  -2.2135   0.8614   0.4613
 GPM  C4    C  CH1   0  -0.003  -2.3263  -0.6159   0.1089
 GPM  C5    C  CH1   0  -0.007  -0.9377  -1.2411  -0.0747
 GPM  C6    C  CH2   0  -0.159  -1.0596  -2.6453  -0.6300
 GPM  C7    C  CH2   0  -0.814   0.9182   1.0798   0.5471
 GPM  O2    O  OH1   0  -0.672  -1.0999   2.9173  -0.2126
 GPM  O3    O  OH1   0  -0.675  -3.4706   1.4975   0.4411
 GPM  O4    O  OH1   0  -0.673  -3.0416  -1.2445   1.1517
 GPM  O5    O  O2    0  -0.489  -0.1767  -0.4869  -0.9993
 GPM  O6    O  OH1   0  -0.658   0.2064  -3.2500  -0.6916
 GPM  P     P  P     0   1.385   2.4643   0.1459   0.4925
 GPM  O1P   O  O     0  -0.701   2.4219  -1.2707   0.9209
 GPM  O2P   O  OH1   0  -0.752   3.0344   0.2409  -1.0108
 GPM  O3P   O  OH1   0  -0.749   3.4033   1.1000   1.3915
 GPM  H1    H  HCH1  0   0.263   0.5366   1.2914  -1.5431
 GPM  H2    H  HCH1  0   0.231  -1.8218   1.5012  -1.5345
 GPM  H3    H  HCH1  0   0.215  -1.7619   0.9482   1.4619
 GPM  H4    H  HCH1  0   0.222  -2.8732  -0.6934  -0.8421
 GPM  H5    H  HCH1  0   0.223  -0.4311  -1.2863   0.8999
 GPM  H61   H  HCH2  0   0.196  -1.7414  -3.2101   0.0179
 GPM  H62   H  HCH2  0   0.195  -1.5345  -2.5875  -1.6204
 GPM  H71   H  HCH2  0   0.309   1.1584   2.1416   0.6211
 GPM  H72   H  HCH2  0   0.292   0.4277   0.8114   1.4858
 GPM  HO2   H  HOH1  0   0.455  -1.9519   3.3555  -0.1168
 GPM  HO3   H  HOH1  0   0.454  -4.0183   1.1044   1.1283
 GPM  HO4   H  HOH1  0   0.461  -3.5905  -1.9413   0.7830
 GPM  HO6   H  HOH1  0   0.452   0.0865  -4.1391  -1.0372
 GPM  HOP2  H  HOH1  0   0.488   3.2101   1.1327  -1.3376
 GPM  HOP3  H  HOH1  0   0.490   4.2278   0.6789   1.6710

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  1.531  0.020  1.531
 GPM  C1   C7    single  1.531  0.020  1.531
 GPM  C1   O5    single  1.407  0.020  1.407
 GPM  C1   H1    single  0.970  0.020  1.090
 GPM  C2   C3    single  1.521  0.020  1.521
 GPM  C2   O2    single  1.404  0.020  1.404
 GPM  C2   H2    single  0.970  0.020  1.090
 GPM  C3   C4    single  1.523  0.020  1.523
 GPM  C3   O3    single  1.409  0.020  1.409
 GPM  C3   H3    single  0.970  0.020  1.090
 GPM  C4   C5    single  1.534  0.020  1.534
 GPM  C4   O4    single  1.412  0.020  1.412
 GPM  C4   H4    single  0.970  0.020  1.090
 GPM  C5   C6    single  1.515  0.020  1.515
 GPM  C5   O5    single  1.415  0.020  1.415
 GPM  C5   H5    single  0.970  0.020  1.090
 GPM  C6   O6    single  1.404  0.020  1.404
 GPM  C6   H61   single  0.970  0.020  1.090
 GPM  C6   H62   single  0.970  0.020  1.090
 GPM  C7   P     single  1.807  0.020  1.807
 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   double  1.481  0.020  1.481
 GPM  P    O2P   single  1.611  0.020  1.611
 GPM  P    O3P   single  1.613  0.020  1.613
 GPM  O2P  HOP2  single  0.850  0.020  0.980
 GPM  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
 GPM  H1    C1   O5   104.95  3.000
 GPM  H1    C1   C7   107.73  3.000
 GPM  O5    C1   C7   113.52  3.000
 GPM  H1    C1   C2   107.59  3.000
 GPM  O5    C1   C2   109.74  3.000
 GPM  C7    C1   C2   112.81  3.000
 GPM  H2    C2   O2   110.59  3.000
 GPM  H2    C2   C3   107.74  3.000
 GPM  O2    C2   C3   112.53  3.000
 GPM  H2    C2   C1   106.87  3.000
 GPM  O2    C2   C1   108.39  3.000
 GPM  C3    C2   C1   110.58  3.000
 GPM  H3    C3   O3   110.08  3.000
 GPM  H3    C3   C4   108.49  3.000
 GPM  O3    C3   C4   111.63  3.000
 GPM  H3    C3   C2   109.27  3.000
 GPM  O3    C3   C2   107.27  3.000
 GPM  C4    C3   C2   110.09  3.000
 GPM  H4    C4   O4   110.81  3.000
 GPM  H4    C4   C5   108.54  3.000
 GPM  O4    C4   C5   111.44  3.000
 GPM  H4    C4   C3   107.78  3.000
 GPM  O4    C4   C3   107.37  3.000
 GPM  C5    C4   C3   110.86  3.000
 GPM  H5    C5   O5   110.69  3.000
 GPM  H5    C5   C6   108.90  3.000
 GPM  O5    C5   C6   107.32  3.000
 GPM  H5    C5   C4   109.14  3.000
 GPM  O5    C5   C4   110.35  3.000
 GPM  C6    C5   C4   110.42  3.000
 GPM  H62   C6   H61  106.89  3.000
 GPM  H62   C6   O6   111.86  3.000
 GPM  H61   C6   O6   111.37  3.000
 GPM  H62   C6   C5   108.43  3.000
 GPM  H61   C6   C5   108.10  3.000
 GPM  O6    C6   C5   110.04  3.000
 GPM  H72   C7   H71  106.24  3.000
 GPM  H72   C7   P    106.44  3.000
 GPM  H71   C7   P    108.45  3.000
 GPM  H72   C7   C1   112.96  3.000
 GPM  H71   C7   C1   108.52  3.000
 GPM  P     C7   C1   113.89  3.000
 GPM  HO2   O2   C2   108.28  3.000
 GPM  HO3   O3   C3   108.24  3.000
 GPM  HO4   O4   C4   109.20  3.000
 GPM  C5    O5   C1   116.07  3.000
 GPM  HO6   O6   C6   107.55  3.000
 GPM  O3P   P    O2P  106.22  3.000
 GPM  O3P   P    O1P  114.93  3.000
 GPM  O2P   P    O1P  109.67  3.000
 GPM  O3P   P    C7   100.11  3.000
 GPM  O2P   P    C7   107.49  3.000
 GPM  O1P   P    C7   117.47  3.000
 GPM  HOP2  O2P  P    115.76  3.000
 GPM  HOP3  O3P  P    113.58  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  -82.59  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

