# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 07:37:29 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: [(2~{S})-1,1-bis(oxidanyl)propan-2-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O[P](O)(=O)O[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O)C(O)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
 H6Q  H6Q  '[(2~{S})-1,1-bis(oxidanyl)propan-2-yl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate'  D-saccharide  39  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_H6Q
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
 H6Q  C8   C  CH2    0  -0.160   5.2898  -0.0664   0.0375
 H6Q  C5   C  CH1    0   0.011   1.5783   0.8198  -0.5430
 H6Q  C6   C  CH1    0  -0.003   3.0546   1.0790  -0.2542
 H6Q  O6   O  O2     0  -0.616  -0.2545  -0.6415  -0.0537
 H6Q  C2   C  CH1    0  -0.047  -3.7796   0.7136   0.0480
 H6Q  C4   C  CH1    0   0.008   1.0396  -0.2722   0.3666
 H6Q  C1   C  CH1    0   0.290  -4.4897  -0.1169  -1.0331
 H6Q  O2   O  OH1    0  -0.680  -5.8503  -0.0967  -0.6825
 H6Q  C3   C  CH3    0  -0.669  -4.1377   2.1839  -0.0462
 H6Q  P1   P  P      0   1.366  -1.5798  -0.4628   0.8757
 H6Q  O4   O  O      0  -0.775  -1.2486   0.1594   2.1923
 H6Q  O5   O  O2     0  -0.615  -2.3690   0.5891  -0.1000
 H6Q  O7   O  OH1    0  -0.659   0.8002   1.9712  -0.3509
 H6Q  O8   O  OH1    0  -0.673   3.5060   2.0066  -1.2163
 H6Q  C7   C  CH1    0  -0.022   3.8295  -0.2410  -0.3146
 H6Q  O9   O  OH1    0  -0.669   5.9540  -1.2934  -0.1450
 H6Q  OX1  O  O2     0  -0.499   3.2606  -1.1466   0.6079
 H6Q  C9   C  CH1    0   0.276   1.9363  -1.5046   0.2910
 H6Q  OX2  O  OH1    0  -0.653   1.4974  -2.4228   1.2177
 H6Q  H1   H  HCH2   0   0.203   5.7086   0.7163  -0.6059
 H6Q  H2   H  HCH2   0   0.200   5.3690   0.2915   1.0736
 H6Q  H3   H  HCH1   0   0.207   1.5020   0.4645  -1.5849
 H6Q  H4   H  HCH1   0   0.223   3.1453   1.4881   0.7623
 H6Q  H5   H  HCH1   0   0.219  -4.1044   0.3367   1.0282
 H6Q  H6   H  HCH1   0   0.239   1.0325   0.0907   1.4011
 H6Q  H7   H  HOH1   0   0.450  -3.4661  -1.6630  -0.3696
 H6Q  H8   H  HOH1   0   0.454  -6.3690  -0.3659  -1.4470
 H6Q  H11  H  HCH3   0   0.224  -3.8532   2.5972  -1.0161
 H6Q  H13  H  HOH1   0   0.448   1.1265   2.6498  -0.9513
 H6Q  H14  H  HOH1   0   0.462   4.2110   2.5374  -0.8361
 H6Q  H15  H  HCH1   0   0.219   3.7580  -0.6418  -1.3398
 H6Q  H16  H  HOH1   0   0.457   6.8868  -1.1577   0.0435
 H6Q  H17  H  HCH1   0   0.189   1.9089  -1.9125  -0.7351
 H6Q  H18  H  HOH1   0   0.465   1.8250  -3.2970   0.9824
 H6Q  H19  H  HCH1   0   0.170  -4.3510   0.3788  -2.0063
 H6Q  H9   H  HCH3   0   0.232  -5.2080   2.3322   0.0847
 H6Q  O1   O  OH1    0  -0.716  -4.0065  -1.4099  -1.1600
 H6Q  O3   O  OP    -1  -0.794  -2.3478  -1.7673   0.8471
 H6Q  H10  H  HCH3   0   0.237  -3.6238   2.7513   0.7297

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
 H6Q  O9   C8   single  1.407  0.020  1.407
 H6Q  C8   C7   single  1.512  0.020  1.512
 H6Q  O8   C6   single  1.411  0.020  1.411
 H6Q  C6   C7   single  1.532  0.020  1.532
 H6Q  C6   C5   single  1.526  0.020  1.526
 H6Q  C7   OX1  single  1.412  0.020  1.412
 H6Q  OX1  C9   single  1.408  0.020  1.408
 H6Q  O7   C5   single  1.403  0.020  1.403
 H6Q  C5   C4   single  1.520  0.020  1.520
 H6Q  C4   C9   single  1.526  0.020  1.526
 H6Q  C4   O6   single  1.410  0.020  1.410
 H6Q  O4   P1   deloc   1.493  0.020  1.493
 H6Q  C9   OX2  single  1.376  0.020  1.376
 H6Q  O5   P1   single  1.638  0.020  1.638
 H6Q  O5   C2   single  1.424  0.020  1.424
 H6Q  C3   C2   single  1.516  0.020  1.516
 H6Q  P1   O6   single  1.629  0.020  1.629
 H6Q  P1   O3   deloc   1.514  0.020  1.514
 H6Q  O2   C1   single  1.405  0.020  1.405
 H6Q  C2   C1   single  1.537  0.020  1.537
 H6Q  C1   O1   single  1.386  0.020  1.386
 H6Q  C8   H1   single  0.970  0.020  1.090
 H6Q  C8   H2   single  0.970  0.020  1.090
 H6Q  C5   H3   single  0.970  0.020  1.090
 H6Q  C6   H4   single  0.970  0.020  1.090
 H6Q  C2   H5   single  0.970  0.020  1.090
 H6Q  C4   H6   single  0.970  0.020  1.090
 H6Q  O1   H7   single  0.850  0.020  0.980
 H6Q  O2   H8   single  0.850  0.020  0.980
 H6Q  C3   H9   single  0.970  0.020  1.090
 H6Q  C3   H10  single  0.970  0.020  1.090
 H6Q  C3   H11  single  0.970  0.020  1.090
 H6Q  O7   H13  single  0.850  0.020  0.980
 H6Q  O8   H14  single  0.850  0.020  0.980
 H6Q  C7   H15  single  0.970  0.020  1.090
 H6Q  O9   H16  single  0.850  0.020  0.980
 H6Q  C9   H17  single  0.970  0.020  1.090
 H6Q  OX2  H18  single  0.850  0.020  0.980
 H6Q  C1   H19  single  0.970  0.020  1.090

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
 H6Q  H2   C8   H1   107.06  3.000
 H6Q  H2   C8   O9   111.85  3.000
 H6Q  H1   C8   O9   111.47  3.000
 H6Q  H2   C8   C7   109.07  3.000
 H6Q  H1   C8   C7   108.34  3.000
 H6Q  O9   C8   C7   108.96  3.000
 H6Q  H3   C5   O7   110.81  3.000
 H6Q  H3   C5   C4   108.01  3.000
 H6Q  O7   C5   C4   108.12  3.000
 H6Q  H3   C5   C6   107.47  3.000
 H6Q  C4   C5   C6   110.59  3.000
 H6Q  O7   C5   C6   111.79  3.000
 H6Q  H4   C6   C7   108.38  3.000
 H6Q  H4   C6   O8   111.08  3.000
 H6Q  C7   C6   O8   112.20  3.000
 H6Q  H4   C6   C5   108.53  3.000
 H6Q  C7   C6   C5   109.60  3.000
 H6Q  O8   C6   C5   106.98  3.000
 H6Q  P1   O6   C4   123.24  3.000
 H6Q  H5   C2   O5   110.82  3.000
 H6Q  H5   C2   C3   108.55  3.000
 H6Q  O5   C2   C3   108.20  3.000
 H6Q  H5   C2   C1   107.78  3.000
 H6Q  C3   C2   C1   111.79  3.000
 H6Q  O5   C2   C1   109.71  3.000
 H6Q  H6   C4   C9   108.53  3.000
 H6Q  H6   C4   O6   111.23  3.000
 H6Q  C9   C4   O6   108.24  3.000
 H6Q  H6   C4   C5   109.23  3.000
 H6Q  O6   C4   C5   109.58  3.000
 H6Q  C9   C4   C5   110.02  3.000
 H6Q  H19  C1   O2   109.63  3.000
 H6Q  H19  C1   O1   107.17  3.000
 H6Q  O2   C1   O1   111.95  3.000
 H6Q  H19  C1   C2   108.68  3.000
 H6Q  O1   C1   C2   114.04  3.000
 H6Q  O2   C1   C2   105.31  3.000
 H6Q  H8   O2   C1   108.64  3.000
 H6Q  H11  C3   H10  108.21  3.000
 H6Q  H11  C3   H9   108.14  3.000
 H6Q  H10  C3   H9   107.89  3.000
 H6Q  H11  C3   C2   111.14  3.000
 H6Q  H10  C3   C2   110.44  3.000
 H6Q  H9   C3   C2   110.91  3.000
 H6Q  O5   P1   O4   111.38  3.000
 H6Q  O5   P1   O3   107.32  3.000
 H6Q  O4   P1   O3   119.22  3.000
 H6Q  O3   P1   O6   107.91  3.000
 H6Q  O5   P1   O6    97.05  3.000
 H6Q  O4   P1   O6   111.62  3.000
 H6Q  P1   O5   C2   118.15  3.000
 H6Q  H13  O7   C5   107.76  3.000
 H6Q  H14  O8   C6   109.15  3.000
 H6Q  H15  C7   OX1  110.36  3.000
 H6Q  H15  C7   C6   108.48  3.000
 H6Q  OX1  C7   C6   108.85  3.000
 H6Q  H15  C7   C8   108.72  3.000
 H6Q  OX1  C7   C8   108.11  3.000
 H6Q  C6   C7   C8   112.32  3.000
 H6Q  H16  O9   C8   108.03  3.000
 H6Q  C9   OX1  C7   113.26  3.000
 H6Q  H17  C9   OX2  111.79  3.000
 H6Q  H17  C9   OX1  109.04  3.000
 H6Q  OX2  C9   OX1  108.54  3.000
 H6Q  H17  C9   C4   109.25  3.000
 H6Q  OX2  C9   C4   108.55  3.000
 H6Q  OX1  C9   C4   109.65  3.000
 H6Q  H18  OX2  C9   109.44  3.000
 H6Q  H7   O1   C1   110.83  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
 H6Q  Var_01  O4  P1  O6  C4  1.23  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
 H6Q  chir_01  C5  C6   O7   C4   positiv
 H6Q  chir_02  C6  O8   C5   C7   negativ
 H6Q  chir_03  C2  O5   C3   C1   negativ
 H6Q  chir_04  C4  O6   C5   C9   positiv
 H6Q  chir_06  C7  C8   C6   OX1  positiv
 H6Q  chir_07  C9  OX2  OX1  C4   positiv

