# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 06:55:42 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: [(2~{S})-1,1-bis(oxidanyl)propan-2-yl] [(2~{S},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
 H6Z  H6Z  '[(2~{S})-1,1-bis(oxidanyl)propan-2-yl] [(2~{S},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
;

data_comp_H6Z
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
 H6Z  P1   P  P      0   1.327  -1.4607   0.4179   0.8990
 H6Z  C8   C  CH2    0  -0.162   5.1850  -0.6979   0.2477
 H6Z  C5   C  CH1    0   0.012   2.0077   1.3683  -0.4889
 H6Z  C6   C  CH1    0  -0.013   3.4579   1.1068  -0.0900
 H6Z  O6   O  O2     0  -0.620  -0.2317   0.6180  -0.1715
 H6Z  C2   C  CH1    0  -0.002  -3.9663   0.4311   0.1073
 H6Z  C4   C  CH1    0   0.012   1.0878   0.4376   0.2848
 H6Z  C1   C  CH1    0   0.240  -4.3945  -0.9991  -0.2399
 H6Z  O2   O  OH1    0  -0.665  -4.2461  -1.3033  -1.5939
 H6Z  C3   C  CH3    0  -0.699  -4.7823   1.5017  -0.5959
 H6Z  O3   O  OP    -1  -0.789  -1.4655  -0.9831   1.4387
 H6Z  O4   O  O      0  -0.788  -1.5071   1.5651   1.8613
 H6Z  O5   O  O2     0  -0.619  -2.6054   0.5997  -0.2598
 H6Z  O8   O  OH1    0  -0.674   4.2684   1.9238  -0.9082
 H6Z  C7   C  CH1    0  -0.012   3.7955  -0.3760  -0.2579
 H6Z  OX1  O  O2     0  -0.504   2.8788  -1.1572   0.4889
 H6Z  C9   C  CH1    0   0.236   1.5310  -1.0188   0.1191
 H6Z  OX2  O  OH1    0  -0.664   1.2931  -1.4044  -1.1941
 H6Z  H1   H  HCH2   0   0.203   5.8976  -0.0352  -0.2570
 H6Z  H2   H  HCH2   0   0.195   5.2388  -0.4707   1.3220
 H6Z  H3   H  HCH1   0   0.211   1.9088   1.1544  -1.5650
 H6Z  H4   H  HCH1   0   0.222   3.5760   1.3761   0.9702
 H6Z  H5   H  HCH1   0   0.220  -4.0982   0.5540   1.1898
 H6Z  H6   H  HCH1   0   0.233   1.1801   0.6848   1.3521
 H6Z  H7   H  HOH1   0   0.458  -5.9468  -2.0746   0.1850
 H6Z  H8   H  HOH1   0   0.445  -4.7720  -0.6908  -2.1215
 H6Z  H9   H  HCH3   0   0.222  -4.6524   1.4699  -1.6800
 H6Z  H10  H  HCH3   0   0.237  -5.8439   1.3980  -0.3770
 H6Z  H11  H  HCH3   0   0.248  -4.4692   2.4898  -0.2603
 H6Z  H14  H  HOH1   0   0.462   5.0467   2.1933  -0.4132
 H6Z  H15  H  HCH1   0   0.220   3.7438  -0.6306  -1.3259
 H6Z  H16  H  HOH1   0   0.456   6.3840  -2.2155   0.2285
 H6Z  H17  H  HCH1   0   0.233   0.9813  -1.6478   0.8250
 H6Z  H18  H  HOH1   0   0.461   1.3692  -2.3625  -1.2563
 H6Z  H19  H  HCH1   0   0.217  -3.7281  -1.6947   0.2807
 H6Z  O7   O  OH1    0  -0.666   1.6324   2.6926  -0.2085
 H6Z  H13  H  HOH1   0   0.447   2.2408   3.2711  -0.6804
 H6Z  O9   O  OH1    0  -0.670   5.4691  -2.0510  -0.0162
 H6Z  O1   O  OH1    0  -0.673  -5.7142  -1.1404   0.1991

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
 H6Z  O9   C8   single  1.408  0.020  1.408
 H6Z  C8   C7   single  1.513  0.020  1.513
 H6Z  C6   O8   single  1.412  0.020  1.412
 H6Z  C6   C7   single  1.530  0.020  1.530
 H6Z  C6   C5   single  1.527  0.020  1.527
 H6Z  C7   OX1  single  1.417  0.020  1.417
 H6Z  OX1  C9   single  1.404  0.020  1.404
 H6Z  O7   C5   single  1.405  0.020  1.405
 H6Z  C5   C4   single  1.520  0.020  1.520
 H6Z  C4   C9   single  1.531  0.020  1.531
 H6Z  C4   O6   single  1.408  0.020  1.408
 H6Z  C9   OX2  single  1.389  0.020  1.389
 H6Z  O4   P1   deloc   1.498  0.020  1.498
 H6Z  O5   P1   single  1.639  0.020  1.639
 H6Z  O5   C2   single  1.420  0.020  1.420
 H6Z  O6   P1   single  1.642  0.020  1.642
 H6Z  P1   O3   deloc   1.501  0.020  1.501
 H6Z  C3   C2   single  1.519  0.020  1.519
 H6Z  O2   C1   single  1.396  0.020  1.396
 H6Z  C2   C1   single  1.533  0.020  1.533
 H6Z  C1   O1   single  1.398  0.020  1.398
 H6Z  C8   H1   single  0.970  0.020  1.090
 H6Z  C8   H2   single  0.970  0.020  1.090
 H6Z  C5   H3   single  0.970  0.020  1.090
 H6Z  C6   H4   single  0.970  0.020  1.090
 H6Z  C2   H5   single  0.970  0.020  1.090
 H6Z  C4   H6   single  0.970  0.020  1.090
 H6Z  O1   H7   single  0.850  0.020  0.980
 H6Z  O2   H8   single  0.850  0.020  0.980
 H6Z  C3   H9   single  0.970  0.020  1.090
 H6Z  C3   H10  single  0.970  0.020  1.090
 H6Z  C3   H11  single  0.970  0.020  1.090
 H6Z  O7   H13  single  0.850  0.020  0.980
 H6Z  O8   H14  single  0.850  0.020  0.980
 H6Z  C7   H15  single  0.970  0.020  1.090
 H6Z  O9   H16  single  0.850  0.020  0.980
 H6Z  C9   H17  single  0.970  0.020  1.090
 H6Z  OX2  H18  single  0.850  0.020  0.980
 H6Z  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
 H6Z  O5   P1   O4   110.34  3.000
 H6Z  O5   P1   O3   110.82  3.000
 H6Z  O4   P1   O3   118.92  3.000
 H6Z  O3   P1   O6   110.51  3.000
 H6Z  O5   P1   O6    92.77  3.000
 H6Z  O4   P1   O6   110.40  3.000
 H6Z  H2   C8   H1   107.05  3.000
 H6Z  H2   C8   O9   111.84  3.000
 H6Z  H1   C8   O9   111.32  3.000
 H6Z  H2   C8   C7   109.11  3.000
 H6Z  H1   C8   C7   108.33  3.000
 H6Z  O9   C8   C7   109.10  3.000
 H6Z  H3   C5   O7   110.74  3.000
 H6Z  H3   C5   C4   108.90  3.000
 H6Z  O7   C5   C4   108.29  3.000
 H6Z  H3   C5   C6   107.90  3.000
 H6Z  C4   C5   C6   109.69  3.000
 H6Z  O7   C5   C6   111.29  3.000
 H6Z  H4   C6   C7   108.62  3.000
 H6Z  H4   C6   O8   110.80  3.000
 H6Z  C7   C6   O8   111.75  3.000
 H6Z  H4   C6   C5   108.17  3.000
 H6Z  C7   C6   C5   110.30  3.000
 H6Z  O8   C6   C5   107.14  3.000
 H6Z  C4   O6   P1   118.33  3.000
 H6Z  H5   C2   O5   110.92  3.000
 H6Z  H5   C2   C3   108.25  3.000
 H6Z  O5   C2   C3   108.15  3.000
 H6Z  H5   C2   C1   107.12  3.000
 H6Z  C3   C2   C1   113.75  3.000
 H6Z  O5   C2   C1   108.67  3.000
 H6Z  H6   C4   C9   107.13  3.000
 H6Z  H6   C4   O6   111.38  3.000
 H6Z  C9   C4   O6   110.98  3.000
 H6Z  H6   C4   C5   107.80  3.000
 H6Z  O6   C4   C5   108.89  3.000
 H6Z  C9   C4   C5   110.61  3.000
 H6Z  H19  C1   O2   104.96  3.000
 H6Z  H19  C1   O1   111.16  3.000
 H6Z  O2   C1   O1   112.52  3.000
 H6Z  H19  C1   C2   108.36  3.000
 H6Z  O1   C1   C2   106.67  3.000
 H6Z  O2   C1   C2   113.17  3.000
 H6Z  H8   O2   C1   109.54  3.000
 H6Z  H11  C3   H10  107.74  3.000
 H6Z  H11  C3   H9   107.33  3.000
 H6Z  H10  C3   H9   108.22  3.000
 H6Z  H11  C3   C2   110.02  3.000
 H6Z  H10  C3   C2   111.32  3.000
 H6Z  H9   C3   C2   112.03  3.000
 H6Z  C2   O5   P1   118.26  3.000
 H6Z  H14  O8   C6   109.19  3.000
 H6Z  H15  C7   OX1  110.72  3.000
 H6Z  H15  C7   C6   108.71  3.000
 H6Z  OX1  C7   C6   109.49  3.000
 H6Z  H15  C7   C8   108.58  3.000
 H6Z  OX1  C7   C8   107.50  3.000
 H6Z  C6   C7   C8   111.85  3.000
 H6Z  C9   OX1  C7   115.33  3.000
 H6Z  H17  C9   OX2  111.37  3.000
 H6Z  H17  C9   OX1  104.82  3.000
 H6Z  OX2  C9   OX1  112.70  3.000
 H6Z  H17  C9   C4   109.37  3.000
 H6Z  OX2  C9   C4   108.46  3.000
 H6Z  OX1  C9   C4   110.06  3.000
 H6Z  H18  OX2  C9   108.88  3.000
 H6Z  H13  O7   C5   107.44  3.000
 H6Z  H16  O9   C8   107.99  3.000
 H6Z  H7   O1   C1   108.76  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
 H6Z  Var_01  O4  P1  O6  C4  72.61  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
 H6Z  chir_02  C5  C6   O7   C4  positiv
 H6Z  chir_03  C6  O8   C5   C7  negativ
 H6Z  chir_04  C2  O5   C3   C1  negativ
 H6Z  chir_05  C4  O6   C5   C9  positiv
 H6Z  chir_06  C7  OX1  C6   C8  negativ
 H6Z  chir_07  C9  OX1  OX2  C4  positiv

