# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:49:27 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 5-deoxy-5-fluoro-D-xylulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(=O)[C@@H](O)[C@H](O)CF
#
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
 5FX  5FX  5-deoxy-5-fluoro-D-xylulose  ligand  19  10  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5FX
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
 5FX  C1    C  CH2   0  -0.257  -1.9579  -0.9627  -0.4033
 5FX  O1    O  OH1   0  -0.655  -3.3329  -0.9409  -0.1776
 5FX  C2    C  C     0   0.357  -1.3735   0.3772  -0.0536
 5FX  O2    O  O     0  -0.383  -1.9903   1.2234   0.5459
 5FX  C3    C  CH1   0  -0.105   0.0470   0.6677  -0.5190
 5FX  O3    O  OH1   0  -0.668   0.4828   1.8960  -0.0133
 5FX  C4    C  CH1   0  -0.082   1.0098  -0.4281  -0.0583
 5FX  O4    O  OH1   0  -0.644   0.9624  -0.5758   1.3381
 5FX  C5    C  CH2   0   0.021   2.4119  -0.1504  -0.5666
 5FX  F     F  F     0  -0.370   3.2347  -1.2251  -0.2615
 5FX  H11C  H  HCH2  0   0.251  -1.4421  -1.7126   0.2152
 5FX  H12C  H  HCH2  0   0.244  -1.6938  -1.1969  -1.4442
 5FX  H1    H  HOH1  0   0.465  -3.6744  -1.8205  -0.3636
 5FX  H3    H  HCH1  0   0.267   0.0196   0.6745  -1.6208
 5FX  HA    H  HOH1  0   0.457  -0.2899   2.3639   0.3343
 5FX  H4    H  HCH1  0   0.272   0.6910  -1.3827  -0.4868
 5FX  HB    H  HOH1  0   0.428   1.1244   0.2876   1.7342
 5FX  H51C  H  HCH2  0   0.197   2.4038  -0.0215  -1.6510
 5FX  H52C  H  HCH2  0   0.201   2.8402   0.7453  -0.1127

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
 5FX  C1  O1    single  1.394  0.020  1.394
 5FX  C1  C2    single  1.503  0.020  1.503
 5FX  C2  O2    double  1.207  0.020  1.207
 5FX  C2  C3    single  1.523  0.020  1.523
 5FX  C3  O3    single  1.398  0.020  1.398
 5FX  C3  C4    single  1.530  0.020  1.530
 5FX  C4  O4    single  1.405  0.020  1.405
 5FX  C4  C5    single  1.517  0.020  1.517
 5FX  C5  F     single  1.387  0.020  1.387
 5FX  C1  H11C  single  0.970  0.020  1.090
 5FX  C1  H12C  single  0.970  0.020  1.090
 5FX  O1  H1    single  0.850  0.020  0.980
 5FX  C3  H3    single  0.970  0.020  1.090
 5FX  O3  HA    single  0.850  0.020  0.980
 5FX  C4  H4    single  0.970  0.020  1.090
 5FX  O4  HB    single  0.850  0.020  0.980
 5FX  C5  H51C  single  0.970  0.020  1.090
 5FX  C5  H52C  single  0.970  0.020  1.090

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
 5FX  H12C  C1  H11C  105.93  3.000
 5FX  H12C  C1  C2    108.47  3.000
 5FX  H11C  C1  C2    107.12  3.000
 5FX  H12C  C1  O1    113.19  3.000
 5FX  H11C  C1  O1    112.46  3.000
 5FX  C2    C1  O1    109.39  3.000
 5FX  H1    O1  C1    107.74  3.000
 5FX  C3    C2  O2    119.67  3.000
 5FX  C3    C2  C1    117.49  3.000
 5FX  O2    C2  C1    122.82  3.000
 5FX  H3    C3  C4    108.73  3.000
 5FX  H3    C3  O3    111.34  3.000
 5FX  C4    C3  O3    108.92  3.000
 5FX  H3    C3  C2    106.47  3.000
 5FX  C4    C3  C2    111.01  3.000
 5FX  O3    C3  C2    110.36  3.000
 5FX  HA    O3  C3    107.81  3.000
 5FX  H4    C4  C5    107.34  3.000
 5FX  H4    C4  O4    106.72  3.000
 5FX  C5    C4  O4    112.55  3.000
 5FX  H4    C4  C3    108.89  3.000
 5FX  C5    C4  C3    110.47  3.000
 5FX  O4    C4  C3    110.69  3.000
 5FX  HB    O4  C4    107.98  3.000
 5FX  H52C  C5  H51C  108.60  3.000
 5FX  H52C  C5  F     108.14  3.000
 5FX  H51C  C5  F     108.31  3.000
 5FX  H52C  C5  C4    111.93  3.000
 5FX  H51C  C5  C4    110.33  3.000
 5FX  F     C5  C4    109.43  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
 5FX  Var_01  O2  C2  C1  O1  11.86  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
 5FX  chir_01  C3  C2  O3  C4  negativ
 5FX  chir_02  C4  O4  C3  C5  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 5FX  plan-1  C1  0.020
 5FX  plan-1  C2  0.020
 5FX  plan-1  O2  0.020
 5FX  plan-1  C3  0.020

