# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:52:54 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  29  17  .  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_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  -0.889  -2.4860  -1.6878   0.8631
 GRX  P     P  P      0   1.149  -2.7206  -0.4490   0.0039
 GRX  O2P   O  OP    -1  -0.906  -2.5095  -0.6401  -1.5016
 GRX  O3P   O  OP    -1  -0.909  -4.0183   0.2925   0.3501
 GRX  C7    C  CH1    0  -0.107  -1.3920   0.7849   0.5121
 GRX  F1    F  F      0  -0.406  -1.8171   2.0605   0.0940
 GRX  C1    C  CH1    0  -0.012  -0.0110   0.5535  -0.0865
 GRX  O5    O  O2     0  -0.481   0.4033  -0.7115   0.3763
 GRX  C5    C  CH1    0  -0.001   1.5947  -1.1846  -0.1978
 GRX  C6    C  CH2    0  -0.156   1.8198  -2.6072   0.2657
 GRX  O6    O  OH1    0  -0.661   0.8334  -3.4464  -0.2807
 GRX  C4    C  CH1    0   0.001   2.7491  -0.2663   0.2167
 GRX  O4    O  OH1    0  -0.675   3.9681  -0.6109  -0.4084
 GRX  C3    C  CH1    0  -0.007   2.4138   1.1539  -0.2049
 GRX  O3    O  OH1    0  -0.678   3.3626   2.0843   0.2689
 GRX  C2    C  CH1    0   0.054   1.0484   1.5914   0.3143
 GRX  O2    O  OH1    0  -0.669   0.7228   2.8563  -0.2091
 GRX  H7    H  HCH1   0   0.159  -1.3009   0.8285   1.6062
 GRX  H1    H  HCH1   0   0.192  -0.1052   0.5458  -1.1835
 GRX  H2    H  HCH1   0   0.190   1.0908   1.6201   1.4164
 GRX  H5    H  HCH1   0   0.202   1.5233  -1.1787  -1.2990
 GRX  H61C  H  HCH2   0   0.192   2.8227  -2.9174  -0.0532
 GRX  H62C  H  HCH2   0   0.192   1.8133  -2.6273   1.3650
 GRX  H4    H  HCH1   0   0.216   2.8466  -0.3004   1.3118
 GRX  HA    H  HOH1   0   0.459   4.4275  -1.2584   0.1329
 GRX  H3    H  HCH1   0   0.204   2.3699   1.1750  -1.3073
 GRX  HB    H  HOH1   0   0.453   4.2071   1.8938  -0.1512
 GRX  HC    H  HOH1   0   0.444   1.4703   3.4383  -0.0352
 GRX  H6    H  HOH1   0   0.452   1.0514  -4.3510  -0.0401

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     deloc   1.526  0.020  1.526
 GRX  P    O2P   deloc   1.532  0.020  1.532
 GRX  P    O3P   deloc   1.534  0.020  1.534
 GRX  P    C7    single  1.883  0.020  1.883
 GRX  C7   F1    single  1.408  0.020  1.408
 GRX  C7   C1    single  1.523  0.020  1.523
 GRX  C1   O5    single  1.409  0.020  1.409
 GRX  C1   C2    single  1.536  0.020  1.536
 GRX  O5   C5    single  1.405  0.020  1.405
 GRX  C5   C6    single  1.513  0.020  1.513
 GRX  C5   C4    single  1.532  0.020  1.532
 GRX  C6   O6    single  1.406  0.020  1.406
 GRX  C4   O4    single  1.413  0.020  1.413
 GRX  C4   C3    single  1.519  0.020  1.519
 GRX  C3   O3    single  1.411  0.020  1.411
 GRX  C3   C2    single  1.525  0.020  1.525
 GRX  C2   O2    single  1.407  0.020  1.407
 GRX  O6   H6    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   102.66  3.000
 GRX  C7    P   O2P   104.46  3.000
 GRX  O3P   P   O2P   113.48  3.000
 GRX  C7    P   O1P   105.76  3.000
 GRX  O3P   P   O1P   113.30  3.000
 GRX  O2P   P   O1P   115.53  3.000
 GRX  H7    C7  C1    108.80  3.000
 GRX  H7    C7  F1    106.55  3.000
 GRX  C1    C7  F1    107.14  3.000
 GRX  H7    C7  P     110.68  3.000
 GRX  C1    C7  P     115.73  3.000
 GRX  F1    C7  P     107.49  3.000
 GRX  H1    C1  C2    108.89  3.000
 GRX  H1    C1  O5    110.24  3.000
 GRX  C2    C1  O5    108.54  3.000
 GRX  H1    C1  C7    108.37  3.000
 GRX  C2    C1  C7    114.84  3.000
 GRX  O5    C1  C7    105.90  3.000
 GRX  C5    O5  C1    114.68  3.000
 GRX  H5    C5  C4    108.39  3.000
 GRX  H5    C5  C6    108.69  3.000
 GRX  C4    C5  C6    111.63  3.000
 GRX  H5    C5  O5    110.56  3.000
 GRX  C4    C5  O5    109.06  3.000
 GRX  C6    C5  O5    108.52  3.000
 GRX  H62C  C6  H61C  106.91  3.000
 GRX  H62C  C6  O6    111.94  3.000
 GRX  H61C  C6  O6    111.08  3.000
 GRX  H62C  C6  C5    108.82  3.000
 GRX  H61C  C6  C5    108.23  3.000
 GRX  O6    C6  C5    109.75  3.000
 GRX  H6    O6  C6    107.78  3.000
 GRX  H4    C4  C3    108.97  3.000
 GRX  H4    C4  O4    110.88  3.000
 GRX  C3    C4  O4    107.20  3.000
 GRX  H4    C4  C5    108.52  3.000
 GRX  C3    C4  C5    108.60  3.000
 GRX  O4    C4  C5    112.59  3.000
 GRX  HA    O4  C4    109.13  3.000
 GRX  H3    C3  C2    107.40  3.000
 GRX  H3    C3  O3    110.47  3.000
 GRX  C2    C3  O3    107.37  3.000
 GRX  H3    C3  C4    107.70  3.000
 GRX  C2    C3  C4    111.80  3.000
 GRX  O3    C3  C4    112.02  3.000
 GRX  HB    O3  C3    108.25  3.000
 GRX  H2    C2  O2    110.92  3.000
 GRX  H2    C2  C3    108.25  3.000
 GRX  O2    C2  C3    109.78  3.000
 GRX  H2    C2  C1    107.74  3.000
 GRX  O2    C2  C1    110.53  3.000
 GRX  C3    C2  C1    109.56  3.000
 GRX  HC    O2  C2    107.25  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

