# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:20:50 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 6-O-phosphono-alpha-D-allopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[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
 A6P  A6P  6-O-phosphono-alpha-D-allopyranose  D-saccharide  27  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A6P
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
 A6P  C1    C  CH1    0   0.224  -2.1793   1.4607  -0.2243
 A6P  C2    C  CH1    0  -0.014  -3.2507   0.4445  -0.6353
 A6P  C3    C  CH1    0  -0.040  -2.9346  -0.9596  -0.1310
 A6P  C4    C  CH1    0   0.043  -1.5080  -1.3267  -0.5369
 A6P  C5    C  CH1    0  -0.016  -0.5240  -0.2624  -0.0568
 A6P  C6    C  CH2    0  -0.125   0.8958  -0.5306  -0.5194
 A6P  O1    O  OH1    0  -0.661  -2.2827   1.7363   1.1332
 A6P  O2    O  OH1    0  -0.669  -4.5356   0.7812  -0.1751
 A6P  O3    O  OH1    0  -0.666  -3.0579  -1.0800   1.2631
 A6P  O4    O  OH1    0  -0.672  -1.1178  -2.5701  -0.0086
 A6P  O5    O  O2     0  -0.508  -0.9155   0.9926  -0.6002
 A6P  O6    O  O2     0  -0.658   1.7389   0.4813  -0.0610
 A6P  P     P  P      0   1.218   3.3922   0.0984   0.1156
 A6P  O1P   O  OP    -1  -0.904   3.4334  -0.9835   1.1897
 A6P  O2P   O  O      0  -0.907   3.8351  -0.3797  -1.2640
 A6P  O3P   O  OP    -1  -0.899   3.9474   1.4513   0.5419
 A6P  H1    H  HCH1   0   0.227  -2.3153   2.3776  -0.8150
 A6P  H2    H  HCH1   0   0.226  -3.2222   0.4062  -1.7338
 A6P  HA    H  HOH1   0   0.458  -1.7608   2.5226   1.3247
 A6P  H3    H  HCH1   0   0.222  -3.6264  -1.6551  -0.6363
 A6P  HB    H  HOH1   0   0.458  -4.7249   1.6980  -0.3998
 A6P  H4    H  HCH1   0   0.206  -1.4763  -1.3396  -1.6378
 A6P  HC    H  HOH1   0   0.446  -3.8009  -0.5362   1.5446
 A6P  H5    H  HCH1   0   0.212  -0.5367  -0.2243   1.0396
 A6P  HD    H  HOH1   0   0.452  -1.7070  -3.2474  -0.3558
 A6P  H6C1  H  HCH2   0   0.184   1.1927  -1.5134  -0.1356
 A6P  H6C2  H  HCH2   0   0.164   0.9055  -0.6040  -1.6186

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
 A6P  C1  C2    single  1.533  0.020  1.533
 A6P  C1  O1    single  1.389  0.020  1.389
 A6P  C1  O5    single  1.399  0.020  1.399
 A6P  C2  C3    single  1.525  0.020  1.525
 A6P  C2  O2    single  1.406  0.020  1.406
 A6P  C3  C4    single  1.528  0.020  1.528
 A6P  C3  O3    single  1.405  0.020  1.405
 A6P  C4  C5    single  1.527  0.020  1.527
 A6P  C4  O4    single  1.406  0.020  1.406
 A6P  C5  C6    single  1.517  0.020  1.517
 A6P  C5  O5    single  1.422  0.020  1.422
 A6P  C6  O6    single  1.395  0.020  1.395
 A6P  O6  P     single  1.706  0.020  1.706
 A6P  P   O1P   deloc   1.525  0.020  1.525
 A6P  P   O2P   deloc   1.526  0.020  1.526
 A6P  P   O3P   deloc   1.523  0.020  1.523
 A6P  C1  H1    single  0.970  0.020  1.090
 A6P  C2  H2    single  0.970  0.020  1.090
 A6P  O1  HA    single  0.850  0.020  0.980
 A6P  C3  H3    single  0.970  0.020  1.090
 A6P  O2  HB    single  0.850  0.020  0.980
 A6P  C4  H4    single  0.970  0.020  1.090
 A6P  O3  HC    single  0.850  0.020  0.980
 A6P  C5  H5    single  0.970  0.020  1.090
 A6P  O4  HD    single  0.850  0.020  0.980
 A6P  C6  H6C1  single  0.970  0.020  1.090
 A6P  C6  H6C2  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
 A6P  H1    C1  O5    104.27  3.000
 A6P  H1    C1  O1    110.52  3.000
 A6P  O5    C1  O1    113.34  3.000
 A6P  H1    C1  C2    108.81  3.000
 A6P  O5    C1  C2    109.73  3.000
 A6P  O1    C1  C2    109.98  3.000
 A6P  H2    C2  O2    111.05  3.000
 A6P  H2    C2  C3    107.04  3.000
 A6P  O2    C2  C3    107.56  3.000
 A6P  H2    C2  C1    105.83  3.000
 A6P  O2    C2  C1    113.10  3.000
 A6P  C3    C2  C1    112.14  3.000
 A6P  H3    C3  O3    110.21  3.000
 A6P  H3    C3  C4    108.20  3.000
 A6P  O3    C3  C4    108.96  3.000
 A6P  H3    C3  C2    107.39  3.000
 A6P  O3    C3  C2    112.89  3.000
 A6P  C4    C3  C2    109.08  3.000
 A6P  H4    C4  O4    110.92  3.000
 A6P  H4    C4  C5    107.69  3.000
 A6P  O4    C4  C5    108.62  3.000
 A6P  H4    C4  C3    107.17  3.000
 A6P  O4    C4  C3    111.82  3.000
 A6P  C5    C4  C3    110.53  3.000
 A6P  H5    C5  O5    110.36  3.000
 A6P  H5    C5  C6    108.77  3.000
 A6P  O5    C5  C6    107.28  3.000
 A6P  H5    C5  C4    109.32  3.000
 A6P  O5    C5  C4    108.51  3.000
 A6P  C6    C5  C4    112.58  3.000
 A6P  H6C2  C6  H6C1  106.70  3.000
 A6P  H6C2  C6  O6    111.78  3.000
 A6P  H6C1  C6  O6    111.82  3.000
 A6P  H6C2  C6  C5    108.92  3.000
 A6P  H6C1  C6  C5    107.77  3.000
 A6P  O6    C6  C5    109.71  3.000
 A6P  HA    O1  C1    108.43  3.000
 A6P  HB    O2  C2    109.35  3.000
 A6P  HC    O3  C3    108.03  3.000
 A6P  HD    O4  C4    108.47  3.000
 A6P  C5    O5  C1    116.18  3.000
 A6P  P     O6  C6    117.19  3.000
 A6P  O3P   P   O2P   115.18  3.000
 A6P  O3P   P   O1P   115.03  3.000
 A6P  O2P   P   O1P   114.00  3.000
 A6P  O3P   P   O6    100.53  3.000
 A6P  O2P   P   O6    104.95  3.000
 A6P  O1P   P   O6    104.97  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
 A6P  Var_01  O1P   P   O6  C6  -63.39  30.0  3
 A6P  Var_02  H6C1  C6  O6  P    35.79  30.0  2

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
 A6P  chir_01  C1  C2  O1  O5  negativ
 A6P  chir_02  C2  O2  C1  C3  negativ
 A6P  chir_03  C3  O3  C2  C4  negativ
 A6P  chir_04  C4  O4  C5  C3  positiv
 A6P  chir_05  C5  O5  C4  C6  negativ

