# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:44:12 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (1R)-1,5-anhydro-1-[(S)-fluoro(phosphono)methyl]-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)[C@@H](F)[P](O)(O)=O
#
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
 GRX  GRX  (1R)-1,5-anhydro-1-[(S)-fluoro(phosphono)methyl]-D-glucitol  D-saccharide  31  17  .  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_GRX
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
 GRX  O1P   O  O     0  -0.692  -2.3907  -1.5763   1.2566
 GRX  P     P  P     0   1.360  -2.5333  -0.5010   0.2543
 GRX  O2P   O  OH1   0  -0.741  -2.3593  -1.0566  -1.2406
 GRX  O3P   O  OH1   0  -0.747  -3.9333   0.2881   0.2810
 GRX  C7    C  CH1   0  -0.116  -1.3970   0.9432   0.4235
 GRX  F1    F  F     0  -0.359  -1.9468   2.0030  -0.2793
 GRX  C1    C  CH1   0  -0.009  -0.0051   0.6490  -0.1221
 GRX  O5    O  O2    0  -0.490   0.3183  -0.6438   0.3088
 GRX  C5    C  CH1   0  -0.019   1.5070  -1.1495  -0.2660
 GRX  C6    C  CH2   0  -0.171   1.6613  -2.5897   0.1656
 GRX  O6    O  OH1   0  -0.643   0.6262  -3.3551  -0.3961
 GRX  C4    C  CH1   0  -0.003   2.6858  -0.2784   0.1831
 GRX  O4    O  OH1   0  -0.658   3.8858  -0.6491  -0.4586
 GRX  C3    C  CH1   0   0.004   2.4108   1.1773  -0.1792
 GRX  O3    O  OH1   0  -0.660   3.3891   2.0427   0.3415
 GRX  C2    C  CH1   0   0.030   1.0606   1.6292   0.3647
 GRX  O2    O  OH1   0  -0.652   0.7229   2.9184  -0.0719
 GRX  H2P   H  HOH1  0   0.488  -2.6352  -0.4574  -1.9464
 GRX  H3P   H  HOH1  0   0.495  -4.6994  -0.2905   0.4014
 GRX  H7    H  HCH1  0   0.268  -1.3574   1.2119   1.4839
 GRX  H1    H  HCH1  0   0.238  -0.0563   0.6945  -1.2221
 GRX  H2    H  HCH1  0   0.238   1.0896   1.5761   1.4649
 GRX  H5    H  HCH1  0   0.247   1.4359  -1.1096  -1.3653
 GRX  H61C  H  HCH2  0   0.204   2.6457  -2.9408  -0.1671
 GRX  H62C  H  HCH2  0   0.218   1.6585  -2.6331   1.2639
 GRX  H4    H  HCH1  0   0.228   2.7820  -0.3575   1.2755
 GRX  HA    H  HOH1  0   0.439   4.3470  -1.2960   0.0819
 GRX  H3    H  HCH1  0   0.201   2.3686   1.2501  -1.2790
 GRX  HB    H  HOH1  0   0.437   4.2321   1.8287  -0.0713
 GRX  HC    H  HOH1  0   0.435   1.4068   3.5250   0.2308
 GRX  H6    H  HOH1  0   0.429   0.7719  -4.2728  -0.1498

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
 GRX  O1P  P     double  1.477  0.020  1.477
 GRX  P    O2P   single  1.604  0.020  1.604
 GRX  P    O3P   single  1.607  0.020  1.607
 GRX  P    C7    single  1.845  0.020  1.845
 GRX  C7   F1    single  1.385  0.020  1.385
 GRX  C7   C1    single  1.524  0.020  1.524
 GRX  C1   O5    single  1.401  0.020  1.401
 GRX  C1   C2    single  1.528  0.020  1.528
 GRX  O5   C5    single  1.414  0.020  1.414
 GRX  C5   C6    single  1.511  0.020  1.511
 GRX  C5   C4    single  1.533  0.020  1.533
 GRX  C6   O6    single  1.405  0.020  1.405
 GRX  C4   O4    single  1.410  0.020  1.410
 GRX  C4   C3    single  1.525  0.020  1.525
 GRX  C3   O3    single  1.406  0.020  1.406
 GRX  C3   C2    single  1.524  0.020  1.524
 GRX  C2   O2    single  1.402  0.020  1.402
 GRX  O6   H6    single  0.850  0.020  0.980
 GRX  O2P  H2P   single  0.850  0.020  0.980
 GRX  O3P  H3P   single  0.850  0.020  0.980
 GRX  C7   H7    single  0.970  0.020  1.090
 GRX  C1   H1    single  0.970  0.020  1.090
 GRX  C2   H2    single  0.970  0.020  1.090
 GRX  C5   H5    single  0.970  0.020  1.090
 GRX  C6   H61C  single  0.970  0.020  1.090
 GRX  C6   H62C  single  0.970  0.020  1.090
 GRX  C4   H4    single  0.970  0.020  1.090
 GRX  O4   HA    single  0.850  0.020  0.980
 GRX  C3   H3    single  0.970  0.020  1.090
 GRX  O3   HB    single  0.850  0.020  0.980
 GRX  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
 GRX  C7    P    O3P    98.66  3.000
 GRX  C7    P    O2P   106.84  3.000
 GRX  O3P   P    O2P   106.26  3.000
 GRX  C7    P    O1P   116.63  3.000
 GRX  O3P   P    O1P   115.48  3.000
 GRX  O2P   P    O1P   111.70  3.000
 GRX  H2P   O2P  P     115.79  3.000
 GRX  H3P   O3P  P     113.46  3.000
 GRX  H7    C7   C1    111.17  3.000
 GRX  H7    C7   F1    108.54  3.000
 GRX  C1    C7   F1    109.18  3.000
 GRX  H7    C7   P     107.65  3.000
 GRX  C1    C7   P     112.24  3.000
 GRX  F1    C7   P     107.93  3.000
 GRX  H1    C1   C2    108.91  3.000
 GRX  H1    C1   O5    110.85  3.000
 GRX  C2    C1   O5    109.46  3.000
 GRX  H1    C1   C7    107.87  3.000
 GRX  C2    C1   C7    113.53  3.000
 GRX  O5    C1   C7    106.20  3.000
 GRX  C5    O5   C1    113.52  3.000
 GRX  H5    C5   C4    108.74  3.000
 GRX  H5    C5   C6    109.02  3.000
 GRX  C4    C5   C6    112.29  3.000
 GRX  H5    C5   O5    109.77  3.000
 GRX  C4    C5   O5    108.92  3.000
 GRX  C6    C5   O5    108.09  3.000
 GRX  H62C  C6   H61C  107.03  3.000
 GRX  H62C  C6   O6    112.10  3.000
 GRX  H61C  C6   O6    111.45  3.000
 GRX  H62C  C6   C5    108.83  3.000
 GRX  H61C  C6   C5    108.06  3.000
 GRX  O6    C6   C5    109.26  3.000
 GRX  H6    O6   C6    107.82  3.000
 GRX  H4    C4   C3    108.69  3.000
 GRX  H4    C4   O4    111.02  3.000
 GRX  C3    C4   O4    107.23  3.000
 GRX  H4    C4   C5    108.51  3.000
 GRX  C3    C4   C5    109.52  3.000
 GRX  O4    C4   C5    111.81  3.000
 GRX  HA    O4   C4    109.23  3.000
 GRX  H3    C3   C2    107.60  3.000
 GRX  H3    C3   O3    110.81  3.000
 GRX  C2    C3   O3    107.56  3.000
 GRX  H3    C3   C4    107.87  3.000
 GRX  C2    C3   C4    110.97  3.000
 GRX  O3    C3   C4    111.96  3.000
 GRX  HB    O3   C3    108.28  3.000
 GRX  H2    C2   O2    111.20  3.000
 GRX  H2    C2   C3    108.59  3.000
 GRX  O2    C2   C3    112.01  3.000
 GRX  H2    C2   C1    107.80  3.000
 GRX  O2    C2   C1    108.83  3.000
 GRX  C3    C2   C1    108.30  3.000
 GRX  HC    O2   C2    108.07  3.000

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
 GRX  chir_01  C7  P   F1  C1  positiv
 GRX  chir_02  C1  O5  C2  C7  positiv
 GRX  chir_03  C5  O5  C6  C4  positiv
 GRX  chir_04  C4  O4  C5  C3  positiv
 GRX  chir_05  C3  O3  C4  C2  negativ
 GRX  chir_06  C2  O2  C1  C3  negativ

