# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 20:54:08 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  31  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 OK
;

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   0.050   1.0259  -1.6582  -0.3923
 YO5  C3    C  CH1   0   0.000   2.3431  -1.1683   0.1940
 YO5  C4    C  CH1   0   0.000   2.5836   0.2942  -0.1623
 YO5  C5    C  CH1   0  -0.012   1.3653   1.1265   0.2556
 YO5  C1    C  CH1   0   0.037  -0.0925  -0.7116   0.0417
 YO5  C6    C  CH2   0  -0.158   1.4978   2.5763  -0.1532
 YO5  C7    C  CH2   0  -0.799  -1.4298  -1.0962  -0.5683
 YO5  O2    O  OH1   0  -0.673   0.6998  -2.9488   0.0573
 YO5  O3    O  OH1   0  -0.674   3.3649  -2.0048  -0.2917
 YO5  O4    O  OH1   0  -0.673   3.7571   0.6994   0.5087
 YO5  O5    O  O2    0  -0.485   0.2101   0.5996  -0.3615
 YO5  O6    O  OH1   0  -0.662   0.4243   3.3088   0.3831
 YO5  P     P  P     0   1.383  -2.7473   0.0951  -0.2237
 YO5  O2P   O  OH1   0  -0.750  -4.0340  -0.8655  -0.3818
 YO5  O3P   O  OH1   0  -0.751  -2.6515   0.4659   1.3405
 YO5  O1P   O  O     0  -0.708  -2.8015   1.3353  -1.0303
 YO5  H3P   H  HOH1  0   0.487  -2.7157  -0.2810   1.9494
 YO5  H2P   H  HOH1  0   0.490  -4.8704  -0.3825  -0.4290
 YO5  H71C  H  HCH2  0   0.290  -1.3474  -1.1882  -1.6549
 YO5  H72C  H  HCH2  0   0.303  -1.7320  -2.0718  -0.1855
 YO5  H1    H  HCH1  0   0.221  -0.1711  -0.7606   1.1393
 YO5  H2    H  HCH1  0   0.213   1.0964  -1.6254  -1.4911
 YO5  H5    H  HCH1  0   0.216   1.2650   1.0735   1.3527
 YO5  H61C  H  HCH2  0   0.200   2.4601   2.9502   0.2167
 YO5  H62C  H  HCH2  0   0.196   1.5296   2.6358  -1.2503
 YO5  H4    H  HCH1  0   0.223   2.7054   0.3758  -1.2522
 YO5  HA    H  HOH1  0   0.462   4.2075   1.3665  -0.0162
 YO5  H3    H  HCH1  0   0.209   2.2677  -1.2413   1.2919
 YO5  HB    H  HOH1  0   0.454   4.1886  -1.7547   0.1393
 YO5  HC    H  HOH1  0   0.456   1.3894  -3.5554  -0.2312
 YO5  H6O   H  HOH1  0   0.454   0.5647   4.2357   0.1702

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     double  1.480  0.020  1.480
 YO5  P    O2P   single  1.613  0.020  1.613
 YO5  P    O3P   single  1.610  0.020  1.610
 YO5  P    C7    single  1.809  0.020  1.809
 YO5  C7   C1    single  1.519  0.020  1.519
 YO5  C1   O5    single  1.405  0.020  1.405
 YO5  C1   C2    single  1.528  0.020  1.528
 YO5  O5   C5    single  1.412  0.020  1.412
 YO5  C5   C6    single  1.512  0.020  1.512
 YO5  C5   C4    single  1.534  0.020  1.534
 YO5  C6   O6    single  1.406  0.020  1.406
 YO5  C4   O4    single  1.411  0.020  1.411
 YO5  C4   C3    single  1.524  0.020  1.524
 YO5  C3   O3    single  1.407  0.020  1.407
 YO5  C3   C2    single  1.523  0.020  1.523
 YO5  C2   O2    single  1.405  0.020  1.405
 YO5  O6   H6O   single  0.850  0.020  0.980
 YO5  O3P  H3P   single  0.850  0.020  0.980
 YO5  O2P  H2P   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    111.18  3.000
 YO5  H2    C2   C1    108.16  3.000
 YO5  O2    C2   C1    107.96  3.000
 YO5  H2    C2   C3    108.61  3.000
 YO5  O2    C2   C3    111.90  3.000
 YO5  C1    C2   C3    108.93  3.000
 YO5  H3    C3   O3    110.74  3.000
 YO5  H3    C3   C4    107.87  3.000
 YO5  O3    C3   C4    112.03  3.000
 YO5  H3    C3   C2    107.63  3.000
 YO5  O3    C3   C2    107.70  3.000
 YO5  C4    C3   C2    110.80  3.000
 YO5  H4    C4   O4    110.97  3.000
 YO5  H4    C4   C5    108.53  3.000
 YO5  O4    C4   C5    112.04  3.000
 YO5  H4    C4   C3    108.68  3.000
 YO5  O4    C4   C3    107.19  3.000
 YO5  C5    C4   C3    109.37  3.000
 YO5  H5    C5   O5    110.02  3.000
 YO5  H5    C5   C6    108.84  3.000
 YO5  O5    C5   C6    108.15  3.000
 YO5  H5    C5   C4    108.49  3.000
 YO5  C6    C5   C4    112.15  3.000
 YO5  O5    C5   C4    109.17  3.000
 YO5  H1    C1   O5    110.05  3.000
 YO5  H1    C1   C7    109.03  3.000
 YO5  O5    C1   C7    108.10  3.000
 YO5  H1    C1   C2    107.92  3.000
 YO5  O5    C1   C2    109.82  3.000
 YO5  C7    C1   C2    111.92  3.000
 YO5  H62C  C6   H61C  107.02  3.000
 YO5  H62C  C6   O6    112.00  3.000
 YO5  H61C  C6   O6    111.33  3.000
 YO5  H62C  C6   C5    108.92  3.000
 YO5  H61C  C6   C5    108.22  3.000
 YO5  O6    C6   C5    109.24  3.000
 YO5  H72C  C7   H71C  107.12  3.000
 YO5  H72C  C7   P     108.68  3.000
 YO5  H71C  C7   P     107.43  3.000
 YO5  H72C  C7   C1    109.23  3.000
 YO5  H71C  C7   C1    110.72  3.000
 YO5  P     C7   C1    113.44  3.000
 YO5  HC    O2   C2    108.46  3.000
 YO5  HB    O3   C3    108.20  3.000
 YO5  HA    O4   C4    109.23  3.000
 YO5  C1    O5   C5    113.53  3.000
 YO5  H6O   O6   C6    107.84  3.000
 YO5  O1P   P    O3P   109.79  3.000
 YO5  O3P   P    O2P   106.24  3.000
 YO5  O1P   P    O2P   114.59  3.000
 YO5  O3P   P    C7    107.06  3.000
 YO5  O2P   P    C7     99.79  3.000
 YO5  O1P   P    C7    118.32  3.000
 YO5  H2P   O2P  P     113.40  3.000
 YO5  H3P   O3P  P     115.49  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  79.31  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
 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

