# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 07:34:21 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 1-O-(hydroxyphosphinato)-6-O-phosphono-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H](O[P](O)([O-])=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
 G16  G16  1-O-(hydroxyphosphinato)-6-O-phosphono-alpha-D-glucopyranose  D-saccharide  30  20  .  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_G16
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
 G16  C1   C  CH1    0   0.276  39.3929  69.2730  75.3223
 G16  C2   C  CH1    0   0.013  39.7647  70.6318  74.7154
 G16  C3   C  CH1    0   0.008  38.6090  71.1725  73.8874
 G16  C4   C  CH1    0   0.020  38.2188  70.1479  72.8327
 G16  C5   C  CH1    0   0.005  37.9005  68.8220  73.5248
 G16  C6   C  CH2    0  -0.196  37.5029  67.7199  72.5575
 G16  O1   O  O2     0  -0.663  38.4104  69.4365  76.2597
 G16  O2   O  OH1    0  -0.675  40.1505  71.5022  75.7535
 G16  O3   O  OH1    0  -0.685  39.0147  72.3928  73.2999
 G16  O4   O  OH1    0  -0.739  37.1440  70.6395  72.0896
 G16  O5   O  O2     0  -0.526  39.0307  68.3974  74.2711
 G16  O6   O  O2     0  -0.649  38.4074  67.5685  71.4997
 G16  P    P  P      0   1.259  37.8627  67.8720  69.9186
 G16  O1P  O  O      0  -0.874  36.7914  66.8286  69.6439
 G16  O2P  O  OP    -1  -0.865  39.1464  67.7559  69.1195
 G16  O3P  O  OP    -1  -0.877  37.2905  69.3131  69.9697
 G16  P'   P  P      0   1.214  38.0289  68.1802  77.4020
 G16  O1X  O  OP    -1  -0.891  39.3164  67.3703  77.5203
 G16  O2X  O  O      0  -0.884  37.6656  69.0129  78.6234
 G16  O3X  O  OP    -1  -0.885  36.8584  67.4367  76.7690
 G16  H1   H  HCH1   0   0.183  40.2910  68.8135  75.7544
 G16  H2   H  HCH1   0   0.190  40.6106  70.4534  74.0321
 G16  H3   H  HCH1   0   0.181  37.7455  71.3387  74.5511
 G16  H4   H  HCH1   0   0.167  39.1014  69.9851  72.1911
 G16  H5   H  HCH1   0   0.185  37.0424  68.9695  74.1952
 G16  H61  H  HCH2   0   0.195  37.4279  66.7825  73.1264
 G16  H62  H  HCH2   0   0.181  36.4852  67.9369  72.2130
 G16  HO2  H  HOH1   0   0.443  40.4714  72.3147  75.3511
 G16  HO3  H  HOH1   0   0.440  38.3356  72.6277  72.6577
 G16  HO4  H  HOH1   0   0.450  37.1547  70.1170  71.2108

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
 G16  C1  C2   single  1.534  0.020  1.534
 G16  C1  O1   single  1.368  0.020  1.368
 G16  C1  O5   single  1.415  0.020  1.415
 G16  C1  H1   single  0.970  0.020  1.090
 G16  C2  C3   single  1.521  0.020  1.521
 G16  C2  O2   single  1.409  0.020  1.409
 G16  C2  H2   single  0.970  0.020  1.090
 G16  C3  C4   single  1.521  0.020  1.521
 G16  C3  O3   single  1.414  0.020  1.414
 G16  C3  H3   single  0.970  0.020  1.090
 G16  C4  C5   single  1.529  0.020  1.529
 G16  C4  O4   single  1.396  0.020  1.396
 G16  C4  H4   single  0.970  0.020  1.090
 G16  C5  C6   single  1.519  0.020  1.519
 G16  C5  O5   single  1.419  0.020  1.419
 G16  C5  H5   single  0.970  0.020  1.090
 G16  C6  O6   single  1.400  0.020  1.400
 G16  C6  H61  single  0.970  0.020  1.090
 G16  C6  H62  single  0.970  0.020  1.090
 G16  O1  P'   single  1.740  0.020  1.740
 G16  O2  HO2  single  0.850  0.020  0.980
 G16  O3  HO3  single  0.850  0.020  0.980
 G16  O4  HO4  single  0.850  0.020  0.980
 G16  O6  P    single  1.700  0.020  1.700
 G16  P   O1P  deloc   1.520  0.020  1.520
 G16  P   O2P  deloc   1.517  0.020  1.517
 G16  P   O3P  deloc   1.551  0.020  1.551
 G16  P'  O1X  deloc   1.526  0.020  1.526
 G16  P'  O2X  deloc   1.522  0.020  1.522
 G16  P'  O3X  deloc   1.524  0.020  1.524

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
 G16  H1   C1  O5   104.06  3.000
 G16  H1   C1  O1   111.60  3.000
 G16  O5   C1  O1   113.53  3.000
 G16  H1   C1  C2   109.16  3.000
 G16  O5   C1  C2   108.43  3.000
 G16  O1   C1  C2   109.84  3.000
 G16  H2   C2  O2   110.29  3.000
 G16  H2   C2  C3   107.65  3.000
 G16  O2   C2  C3   112.93  3.000
 G16  H2   C2  C1   106.74  3.000
 G16  O2   C2  C1   108.80  3.000
 G16  C3   C2  C1   110.25  3.000
 G16  H3   C3  O3   110.19  3.000
 G16  H3   C3  C4   108.55  3.000
 G16  O3   C3  C4   111.52  3.000
 G16  H3   C3  C2   108.73  3.000
 G16  O3   C3  C2   108.36  3.000
 G16  C4   C3  C2   109.44  3.000
 G16  H4   C4  O4   111.00  3.000
 G16  H4   C4  C5   107.57  3.000
 G16  O4   C4  C5   112.71  3.000
 G16  H4   C4  C3   107.30  3.000
 G16  O4   C4  C3   109.23  3.000
 G16  C5   C4  C3   108.88  3.000
 G16  H5   C5  O5   109.95  3.000
 G16  H5   C5  C6   106.34  3.000
 G16  O5   C5  C6   109.03  3.000
 G16  H5   C5  C4   108.80  3.000
 G16  O5   C5  C4   109.37  3.000
 G16  C6   C5  C4   113.28  3.000
 G16  H62  C6  H61  105.56  3.000
 G16  H62  C6  O6   112.56  3.000
 G16  H61  C6  O6   110.06  3.000
 G16  H62  C6  C5   107.43  3.000
 G16  H61  C6  C5   107.88  3.000
 G16  O6   C6  C5   112.98  3.000
 G16  P'   O1  C1   121.40  3.000
 G16  HO2  O2  C2   107.77  3.000
 G16  HO3  O3  C3   106.57  3.000
 G16  HO4  O4  C4   105.63  3.000
 G16  C5   O5  C1   114.16  3.000
 G16  P    O6  C6   118.46  3.000
 G16  O3P  P   O2P  113.62  3.000
 G16  O3P  P   O1P  112.55  3.000
 G16  O2P  P   O1P  116.66  3.000
 G16  O3P  P   O6   104.68  3.000
 G16  O2P  P   O6   101.84  3.000
 G16  O1P  P   O6   105.74  3.000
 G16  O3X  P'  O2X  114.63  3.000
 G16  O3X  P'  O1X  114.92  3.000
 G16  O2X  P'  O1X  115.44  3.000
 G16  O3X  P'  O1   104.35  3.000
 G16  O2X  P'  O1   100.61  3.000
 G16  O1X  P'  O1   104.42  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
 G16  Var_01  O1X  P'  O1  C1   25.47  30.0  3
 G16  Var_02  O1P  P   O6  C6  -63.78  30.0  3
 G16  Var_03  H61  C6  O6  P   122.89  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
 G16  chir_01  C1  C2  O1  O5  negativ
 G16  chir_02  C2  O2  C1  C3  negativ
 G16  chir_03  C3  O3  C2  C4  positiv
 G16  chir_04  C4  O4  C5  C3  positiv
 G16  chir_05  C5  O5  C4  C6  negativ

