# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:15:17 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  29  16  .  2023-02-15  2023-02-16
;
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   0.222  -2.0709   1.4334  -0.1656
 A6P  C2    C  CH1   0  -0.014  -3.1663   0.4685  -0.6349
 A6P  C3    C  CH1   0  -0.041  -2.9244  -0.9591  -0.1530
 A6P  C4    C  CH1   0   0.036  -1.5066  -1.3789  -0.5328
 A6P  C5    C  CH1   0  -0.012  -0.5007  -0.3617   0.0037
 A6P  C6    C  CH2   0  -0.177   0.9023  -0.6967  -0.4485
 A6P  O1    O  OH1   0  -0.657  -2.1997   1.6795   1.1925
 A6P  O2    O  OH1   0  -0.667  -4.4490   0.8464  -0.2059
 A6P  O3    O  OH1   0  -0.665  -3.0806  -1.1031   1.2347
 A6P  O4    O  OH1   0  -0.670  -1.1715  -2.6427  -0.0205
 A6P  O5    O  O2    0  -0.507  -0.8107   0.9192  -0.5147
 A6P  O6    O  O2    0  -0.590   1.7939   0.2780   0.1054
 A6P  P     P  P     0   1.456   3.3676   0.0627  -0.0389
 A6P  O1P   O  OH1   0  -0.741   3.7890  -1.0507   1.0282
 A6P  O2P   O  O     0  -0.712   3.8608  -0.3251  -1.3735
 A6P  O3P   O  OH1   0  -0.732   3.8060   1.4821   0.5386
 A6P  H1    H  HCH1  0   0.235  -2.1453   2.3658  -0.7408
 A6P  H2    H  HCH1  0   0.230  -3.1036   0.4533  -1.7325
 A6P  HA    H  HOH1  0   0.461  -1.6788   2.4584   1.4152
 A6P  H3    H  HCH1  0   0.229  -3.6318  -1.6121  -0.6906
 A6P  HB    H  HOH1  0   0.459  -4.6155   1.7597  -0.4609
 A6P  H4    H  HCH1  0   0.221  -1.4441  -1.3664  -1.6317
 A6P  HC    H  HOH1  0   0.449  -3.8157  -0.5472   1.5134
 A6P  H5    H  HCH1  0   0.238  -0.5326  -0.3596   1.1001
 A6P  HD    H  HOH1  0   0.457  -1.7374  -3.3020  -0.4348
 A6P  H6C1  H  HCH2  0   0.251   1.1626  -1.6980  -0.1013
 A6P  H6C2  H  HCH2  0   0.240   0.9652  -0.6796  -1.5401
 A6P  H1P   H  HOH1  0   0.496   3.5403  -0.8682   1.9443
 A6P  H3P   H  HOH1  0   0.504   4.7580   1.6462   0.5012

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  1.386  0.020  1.386
 A6P  C1   O5    single  1.405  0.020  1.405
 A6P  C2   C3    single  1.526  0.020  1.526
 A6P  C2   O2    single  1.404  0.020  1.404
 A6P  C3   C4    single  1.527  0.020  1.527
 A6P  C3   O3    single  1.404  0.020  1.404
 A6P  C4   C5    single  1.528  0.020  1.528
 A6P  C4   O4    single  1.404  0.020  1.404
 A6P  C5   C6    single  1.512  0.020  1.512
 A6P  C5   O5    single  1.416  0.020  1.416
 A6P  C6   O6    single  1.432  0.020  1.432
 A6P  O6   P     single  1.595  0.020  1.595
 A6P  P    O1P   single  1.599  0.020  1.599
 A6P  P    O2P   double  1.475  0.020  1.475
 A6P  P    O3P   single  1.594  0.020  1.594
 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
 A6P  O1P  H1P   single  0.850  0.020  0.980
 A6P  O3P  H3P   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
 A6P  H1    C1   O5    103.97  3.000
 A6P  H1    C1   O1    110.86  3.000
 A6P  O5    C1   O1    113.06  3.000
 A6P  H1    C1   C2    109.00  3.000
 A6P  O5    C1   C2    109.54  3.000
 A6P  O1    C1   C2    110.20  3.000
 A6P  H2    C2   O2    111.15  3.000
 A6P  H2    C2   C3    107.05  3.000
 A6P  O2    C2   C3    107.46  3.000
 A6P  H2    C2   C1    105.87  3.000
 A6P  O2    C2   C1    112.93  3.000
 A6P  C3    C2   C1    112.26  3.000
 A6P  H3    C3   O3    110.48  3.000
 A6P  H3    C3   C4    108.17  3.000
 A6P  O3    C3   C4    108.73  3.000
 A6P  H3    C3   C2    107.36  3.000
 A6P  O3    C3   C2    112.98  3.000
 A6P  C4    C3   C2    109.02  3.000
 A6P  H4    C4   O4    111.15  3.000
 A6P  H4    C4   C5    107.80  3.000
 A6P  O4    C4   C5    108.30  3.000
 A6P  H4    C4   C3    107.33  3.000
 A6P  O4    C4   C3    112.23  3.000
 A6P  C5    C4   C3    109.94  3.000
 A6P  H5    C5   O5    110.97  3.000
 A6P  H5    C5   C6    109.05  3.000
 A6P  O5    C5   C6    107.10  3.000
 A6P  H5    C5   C4    109.45  3.000
 A6P  O5    C5   C4    109.24  3.000
 A6P  C6    C5   C4    111.01  3.000
 A6P  H6C2  C6   H6C1  108.55  3.000
 A6P  H6C2  C6   O6    109.85  3.000
 A6P  H6C1  C6   O6    110.67  3.000
 A6P  H6C2  C6   C5    110.40  3.000
 A6P  H6C1  C6   C5    109.24  3.000
 A6P  O6    C6   C5    108.14  3.000
 A6P  HA    O1   C1    108.66  3.000
 A6P  HB    O2   C2    109.41  3.000
 A6P  HC    O3   C3    108.17  3.000
 A6P  HD    O4   C4    108.60  3.000
 A6P  C5    O5   C1    115.87  3.000
 A6P  P     O6   C6    119.17  3.000
 A6P  O3P   P    O2P   118.04  3.000
 A6P  O3P   P    O1P   107.81  3.000
 A6P  O2P   P    O1P   109.44  3.000
 A6P  O3P   P    O6     96.80  3.000
 A6P  O2P   P    O6    116.58  3.000
 A6P  O1P   P    O6    107.08  3.000
 A6P  H1P   O1P  P     115.68  3.000
 A6P  H3P   O3P  P     114.08  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  -76.50  30.0  3
 A6P  Var_02  H6C1  C6  O6  P    52.06  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
 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

