# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 21:36:51 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-deoxy-7-O-phosphono-alpha-D-gluco-hept-2-ulopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(O)O[C@H](CO[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
 QIF  QIF  1-deoxy-7-O-phosphono-alpha-D-gluco-hept-2-ulopyranose  D-saccharide  32  17  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QIF
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
 QIF  C1   C  CT    0   0.442  -1.9440   1.3108   0.0459
 QIF  C2   C  CH1   0   0.041  -3.0292   0.3237  -0.4048
 QIF  C3   C  CH1   0  -0.037  -2.7636  -1.0642   0.1708
 QIF  C4   C  CH1   0   0.025  -1.3642  -1.5282  -0.2111
 QIF  C5   C  CH1   0  -0.018  -0.3509  -0.4777   0.2380
 QIF  C6   C  CH2   0  -0.175   1.0390  -0.8262  -0.2424
 QIF  C7   C  CH3   0  -0.696  -2.0523   2.6462  -0.6714
 QIF  O1   O  OH1   0  -0.666  -2.0626   1.4547   1.4272
 QIF  O2P  O  O     0  -0.712   4.1075  -1.3200   0.0016
 QIF  O2   O  OH1   0  -0.673  -4.2844   0.8178  -0.0218
 QIF  O1P  O  OH1   0  -0.731   4.0177   1.1324   0.9539
 QIF  O3   O  OH1   0  -0.680  -3.7250  -1.9667  -0.3470
 QIF  O3P  O  OH1   0  -0.741   3.6656   0.6034  -1.5478
 QIF  O4   O  OH1   0  -0.673  -1.0337  -2.7492   0.4034
 QIF  O5   O  O2    0  -0.511  -0.6837   0.7807  -0.3118
 QIF  O6   O  O2    0  -0.590   1.9553   0.1261   0.3084
 QIF  P    P  P     0   1.457   3.5020   0.0231  -0.0674
 QIF  H1   H  HCH1  0   0.215  -2.9536   0.2542  -1.5013
 QIF  H2   H  HCH1  0   0.235  -2.8307  -1.0226   1.2650
 QIF  H3   H  HCH1  0   0.213  -1.3126  -1.6131  -1.3088
 QIF  H4   H  HCH1  0   0.234  -0.3453  -0.4397   1.3358
 QIF  H5   H  HCH2  0   0.255   1.2997  -1.8317   0.0894
 QIF  H6   H  HCH2  0   0.237   1.0737  -0.8026  -1.3364
 QIF  H7   H  HCH3  0   0.245  -3.0090   3.1179  -0.4556
 QIF  H8   H  HCH3  0   0.243  -1.2583   3.3216  -0.3453
 QIF  H9   H  HCH3  0   0.238  -1.9665   2.5225  -1.7505
 QIF  H10  H  HOH1  0   0.457  -1.4868   2.1710   1.7200
 QIF  H11  H  HOH1  0   0.450  -4.9500   0.2030  -0.3480
 QIF  H12  H  HOH1  0   0.504   4.9787   1.2349   0.9735
 QIF  H13  H  HOH1  0   0.464  -4.1746  -2.3979   0.3836
 QIF  H14  H  HOH1  0   0.496   3.3571   1.5094  -1.6828
 QIF  H15  H  HOH1  0   0.454  -1.6424  -3.4205   0.0783

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
 QIF  O2P  P    double  1.475  0.020  1.475
 QIF  O3P  P    single  1.598  0.020  1.598
 QIF  P    O1P  single  1.594  0.020  1.594
 QIF  P    O6   single  1.595  0.020  1.595
 QIF  O6   C6   single  1.432  0.020  1.432
 QIF  C6   C5   single  1.511  0.020  1.511
 QIF  O5   C5   single  1.413  0.020  1.413
 QIF  O5   C1   single  1.413  0.020  1.413
 QIF  C7   C1   single  1.520  0.020  1.520
 QIF  C4   C5   single  1.527  0.020  1.527
 QIF  C4   O4   single  1.406  0.020  1.406
 QIF  C4   C3   single  1.523  0.020  1.523
 QIF  C1   C2   single  1.535  0.020  1.535
 QIF  C1   O1   single  1.394  0.020  1.394
 QIF  C2   C3   single  1.526  0.020  1.526
 QIF  C2   O2   single  1.402  0.020  1.402
 QIF  C3   O3   single  1.417  0.020  1.417
 QIF  C2   H1   single  0.970  0.020  1.090
 QIF  C3   H2   single  0.970  0.020  1.090
 QIF  C4   H3   single  0.970  0.020  1.090
 QIF  C5   H4   single  0.970  0.020  1.090
 QIF  C6   H5   single  0.970  0.020  1.090
 QIF  C6   H6   single  0.970  0.020  1.090
 QIF  C7   H7   single  0.970  0.020  1.090
 QIF  C7   H8   single  0.970  0.020  1.090
 QIF  C7   H9   single  0.970  0.020  1.090
 QIF  O1   H10  single  0.850  0.020  0.980
 QIF  O2   H11  single  0.850  0.020  0.980
 QIF  O1P  H12  single  0.850  0.020  0.980
 QIF  O3   H13  single  0.850  0.020  0.980
 QIF  O3P  H14  single  0.850  0.020  0.980
 QIF  O4   H15  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
 QIF  O5   C1   O1   111.44  3.000
 QIF  O1   C1   C7   111.77  3.000
 QIF  O5   C1   C7   105.88  3.000
 QIF  O1   C1   C2   107.29  3.000
 QIF  C7   C1   C2   112.10  3.000
 QIF  O5   C1   C2   108.36  3.000
 QIF  H1   C2   O2   110.83  3.000
 QIF  H1   C2   C3   107.83  3.000
 QIF  O2   C2   C3   111.92  3.000
 QIF  H1   C2   C1   106.53  3.000
 QIF  O2   C2   C1   109.04  3.000
 QIF  C3   C2   C1   110.56  3.000
 QIF  H2   C3   O3   110.32  3.000
 QIF  H2   C3   C4   108.53  3.000
 QIF  O3   C3   C4   109.74  3.000
 QIF  H2   C3   C2   109.34  3.000
 QIF  O3   C3   C2   108.87  3.000
 QIF  C4   C3   C2   110.03  3.000
 QIF  H3   C4   O4   110.93  3.000
 QIF  H3   C4   C5   108.35  3.000
 QIF  O4   C4   C5   108.23  3.000
 QIF  H3   C4   C3   108.43  3.000
 QIF  O4   C4   C3   111.77  3.000
 QIF  C5   C4   C3   109.05  3.000
 QIF  H4   C5   O5   111.06  3.000
 QIF  H4   C5   C6   108.73  3.000
 QIF  O5   C5   C6   107.36  3.000
 QIF  H4   C5   C4   108.72  3.000
 QIF  O5   C5   C4   109.99  3.000
 QIF  C6   C5   C4   110.99  3.000
 QIF  H6   C6   H5   108.44  3.000
 QIF  H6   C6   O6   110.48  3.000
 QIF  H5   C6   O6   110.08  3.000
 QIF  H6   C6   C5   109.99  3.000
 QIF  H5   C6   C5   109.62  3.000
 QIF  O6   C6   C5   108.23  3.000
 QIF  H9   C7   H8   107.98  3.000
 QIF  H9   C7   H7   108.34  3.000
 QIF  H8   C7   H7   108.17  3.000
 QIF  H9   C7   C1   111.23  3.000
 QIF  H8   C7   C1   110.53  3.000
 QIF  H7   C7   C1   110.49  3.000
 QIF  H10  O1   C1   109.07  3.000
 QIF  H11  O2   C2   107.53  3.000
 QIF  H12  O1P  P    114.11  3.000
 QIF  H13  O3   C3   109.01  3.000
 QIF  H14  O3P  P    115.92  3.000
 QIF  H15  O4   C4   108.01  3.000
 QIF  C5   O5   C1   116.46  3.000
 QIF  P    O6   C6   119.15  3.000
 QIF  O6   P    O3P  107.10  3.000
 QIF  O6   P    O1P   96.77  3.000
 QIF  O3P  P    O1P  107.92  3.000
 QIF  O6   P    O2P  116.47  3.000
 QIF  O1P  P    O2P  118.10  3.000
 QIF  O3P  P    O2P  109.39  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
 QIF  Var_01  O2P  P   O6  C6  -46.10  30.0  2
 QIF  Var_02  H5   C6  O6  P    61.87  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
 QIF  chir_01  C1  O5  C2  O1  negativ
 QIF  chir_02  C2  O2  C1  C3  negativ
 QIF  chir_03  C3  O3  C2  C4  positiv
 QIF  chir_04  C4  O4  C3  C5  negativ
 QIF  chir_05  C5  O5  C4  C6  negativ

