# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:19:47 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (1R)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](C[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
 YO5  YO5  (1R)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol  D-saccharide  29  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 PERFECT
;

data_comp_YO5
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
 YO5  C2    C  CH1    0   0.048   1.0383  -1.6113  -0.3446
 YO5  C3    C  CH1    0   0.002   2.3535  -1.1292   0.2494
 YO5  C4    C  CH1    0  -0.002   2.6454   0.3030  -0.1690
 YO5  C5    C  CH1    0  -0.003   1.4347   1.1801   0.1729
 YO5  C1    C  CH1    0   0.049  -0.0876  -0.6266  -0.0080
 YO5  C6    C  CH2    0  -0.160   1.6325   2.6061  -0.2949
 YO5  C7    C  CH2    0  -0.755  -1.4120  -1.0001  -0.6416
 YO5  O2    O  OH1    0  -0.676   0.6927  -2.8774   0.1689
 YO5  O3    O  OH1    0  -0.678   3.3686  -2.0168  -0.1643
 YO5  O4    O  OH1    0  -0.676   3.8163   0.7078   0.5112
 YO5  O5    O  O2     0  -0.484   0.2881   0.6631  -0.4516
 YO5  O6    O  OH1    0  -0.664   0.5715   3.4053   0.1684
 YO5  P     P  P      0   1.166  -2.9181  -0.1122   0.0182
 YO5  O2P   O  OP    -1  -0.922  -4.0884  -0.9104  -0.5825
 YO5  O3P   O  OP    -1  -0.916  -2.8008  -0.2544   1.5445
 YO5  O1P   O  O      0  -0.901  -2.8629   1.3346  -0.4764
 YO5  H71C  H  HCH2   0   0.186  -1.3336  -0.8840  -1.7301
 YO5  H72C  H  HCH2   0   0.203  -1.5691  -2.0680  -0.4677
 YO5  H1    H  HCH1   0   0.182  -0.2147  -0.6172   1.0865
 YO5  H2    H  HCH1   0   0.190   1.1436  -1.6481  -1.4413
 YO5  H5    H  HCH1   0   0.199   1.3107   1.1836   1.2703
 YO5  H61C  H  HCH2   0   0.193   2.5948   2.9657   0.0894
 YO5  H62C  H  HCH2   0   0.192   1.7021   2.6145  -1.3924
 YO5  H4    H  HCH1   0   0.215   2.7971   0.3290  -1.2583
 YO5  HA    H  HOH1   0   0.458   4.2785   1.3622  -0.0191
 YO5  H3    H  HCH1   0   0.200   2.2485  -1.1461   1.3475
 YO5  HB    H  HOH1   0   0.451   4.1868  -1.7603   0.2731
 YO5  HC    H  HOH1   0   0.449   1.4030  -3.4910  -0.0443
 YO5  H6O   H  HOH1   0   0.453   0.7650   4.3165  -0.0682

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
 YO5  O1P  P     deloc   1.530  0.020  1.530
 YO5  P    O2P   deloc   1.539  0.020  1.539
 YO5  P    O3P   deloc   1.537  0.020  1.537
 YO5  P    C7    single  1.869  0.020  1.869
 YO5  C7   C1    single  1.515  0.020  1.515
 YO5  C1   O5    single  1.415  0.020  1.415
 YO5  C1   C2    single  1.533  0.020  1.533
 YO5  O5   C5    single  1.404  0.020  1.404
 YO5  C5   C6    single  1.514  0.020  1.514
 YO5  C5   C4    single  1.534  0.020  1.534
 YO5  C6   O6    single  1.407  0.020  1.407
 YO5  C4   O4    single  1.413  0.020  1.413
 YO5  C4   C3    single  1.520  0.020  1.520
 YO5  C3   O3    single  1.410  0.020  1.410
 YO5  C3   C2    single  1.522  0.020  1.522
 YO5  C2   O2    single  1.409  0.020  1.409
 YO5  O6   H6O   single  0.850  0.020  0.980
 YO5  C7   H71C  single  0.970  0.020  1.090
 YO5  C7   H72C  single  0.970  0.020  1.090
 YO5  C1   H1    single  0.970  0.020  1.090
 YO5  C2   H2    single  0.970  0.020  1.090
 YO5  C5   H5    single  0.970  0.020  1.090
 YO5  C6   H61C  single  0.970  0.020  1.090
 YO5  C6   H62C  single  0.970  0.020  1.090
 YO5  C4   H4    single  0.970  0.020  1.090
 YO5  O4   HA    single  0.850  0.020  0.980
 YO5  C3   H3    single  0.970  0.020  1.090
 YO5  O3   HB    single  0.850  0.020  0.980
 YO5  O2   HC    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
 YO5  H2    C2  O2    110.85  3.000
 YO5  H2    C2  C1    108.06  3.000
 YO5  O2    C2  C1    108.48  3.000
 YO5  H2    C2  C3    108.44  3.000
 YO5  O2    C2  C3    110.75  3.000
 YO5  C1    C2  C3    110.22  3.000
 YO5  H3    C3  O3    110.53  3.000
 YO5  H3    C3  C4    107.86  3.000
 YO5  O3    C3  C4    111.96  3.000
 YO5  H3    C3  C2    107.55  3.000
 YO5  O3    C3  C2    107.95  3.000
 YO5  C4    C3  C2    110.92  3.000
 YO5  H4    C4  O4    110.83  3.000
 YO5  H4    C4  C5    108.43  3.000
 YO5  O4    C4  C5    112.52  3.000
 YO5  H4    C4  C3    108.74  3.000
 YO5  O4    C4  C3    107.24  3.000
 YO5  C5    C4  C3    109.01  3.000
 YO5  H5    C5  O5    110.58  3.000
 YO5  H5    C5  C6    108.59  3.000
 YO5  O5    C5  C6    108.42  3.000
 YO5  H5    C5  C4    108.18  3.000
 YO5  C6    C5  C4    111.51  3.000
 YO5  O5    C5  C4    109.57  3.000
 YO5  H1    C1  O5    109.53  3.000
 YO5  H1    C1  C7    108.47  3.000
 YO5  O5    C1  C7    109.01  3.000
 YO5  H1    C1  C2    107.96  3.000
 YO5  O5    C1  C2    108.76  3.000
 YO5  C7    C1  C2    113.07  3.000
 YO5  H62C  C6  H61C  106.95  3.000
 YO5  H62C  C6  O6    111.84  3.000
 YO5  H61C  C6  O6    111.10  3.000
 YO5  H62C  C6  C5    108.90  3.000
 YO5  H61C  C6  C5    108.38  3.000
 YO5  O6    C6  C5    109.57  3.000
 YO5  H72C  C7  H71C  105.74  3.000
 YO5  H72C  C7  P     106.98  3.000
 YO5  H71C  C7  P     110.95  3.000
 YO5  H72C  C7  C1    107.45  3.000
 YO5  H71C  C7  C1    109.05  3.000
 YO5  P     C7  C1    116.09  3.000
 YO5  HC    O2  C2    108.12  3.000
 YO5  HB    O3  C3    108.11  3.000
 YO5  HA    O4  C4    109.15  3.000
 YO5  C1    O5  C5    114.39  3.000
 YO5  H6O   O6  C6    107.80  3.000
 YO5  O1P   P   O3P   113.93  3.000
 YO5  O3P   P   O2P   113.43  3.000
 YO5  O1P   P   O2P   113.07  3.000
 YO5  O3P   P   C7    104.19  3.000
 YO5  O2P   P   C7    103.22  3.000
 YO5  O1P   P   C7    107.82  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
 YO5  Var_01  O1P  P  C7  C1  72.01  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
 YO5  chir_01  C2  C1  C3  O2  negativ
 YO5  chir_02  C3  O3  C2  C4  positiv
 YO5  chir_03  C4  O4  C5  C3  positiv
 YO5  chir_04  C5  O5  C6  C4  positiv
 YO5  chir_05  C1  O5  C7  C2  negativ

