# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:02:51 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2-deoxy-2-fluoro-4-O-beta-D-xylopyranosyl-alpha-D-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](O[C@@H]2CO[C@H](O)[C@H](F)[C@H]2O)[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
 FXP  FXP  2-deoxy-2-fluoro-4-O-beta-D-xylopyranosyl-alpha-D-xylopyranose  D-saccharide  36  19  .  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_FXP
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
 FXP  O1    O  OH1   0  -0.661  -4.2617   1.5281   0.1755
 FXP  C1A   C  CH1   0   0.194  -3.9181   0.6175  -0.8113
 FXP  C2A   C  CH1   0   0.151  -3.5579  -0.7049  -0.1433
 FXP  C3A   C  CH1   0  -0.036  -2.2814  -0.6165   0.6837
 FXP  C4A   C  CH1   0  -0.010  -1.1809  -0.0919  -0.2259
 FXP  C5A   C  CH2   0  -0.210  -1.6293   1.2163  -0.8737
 FXP  F2A   F  F     0  -0.373  -4.6087  -1.1109   0.6710
 FXP  O3A   O  OH1   0  -0.662  -1.8984  -1.8751   1.1714
 FXP  O4A   O  O2    0  -0.508  -0.0194   0.1322   0.5489
 FXP  O5A   O  O2    0  -0.493  -2.8324   1.0360  -1.5965
 FXP  C1B   C  CH1   0   0.289   1.1790  -0.0271  -0.1202
 FXP  C2B   C  CH1   0  -0.016   2.2424   0.8077   0.5968
 FXP  C3B   C  CH1   0   0.013   3.5840   0.5867  -0.0840
 FXP  C4B   C  CH1   0  -0.006   3.8799  -0.9076  -0.1629
 FXP  C5B   C  CH2   0  -0.229   2.7083  -1.6374  -0.8137
 FXP  O2B   O  OH1   0  -0.662   1.9312   2.1744   0.5358
 FXP  O3B   O  OH1   0  -0.667   4.5694   1.2811   0.6358
 FXP  O4B   O  OH1   0  -0.670   5.0609  -1.0635  -0.9152
 FXP  O5B   O  O2    0  -0.481   1.5149  -1.3878  -0.1029
 FXP  H1A   H  HCH1  0   0.249  -4.7379   0.4675  -1.5226
 FXP  H2A   H  HCH1  0   0.231  -3.4314  -1.4637  -0.9210
 FXP  H3A   H  HCH1  0   0.234  -2.4302   0.1006   1.5035
 FXP  H4A   H  HCH1  0   0.246  -0.9912  -0.8410  -1.0059
 FXP  H5A   H  HCH2  0   0.225  -1.7336   1.9896  -0.1044
 FXP  H5AA  H  HCH2  0   0.250  -0.8858   1.5630  -1.5929
 FXP  HO3A  H  HOH1  0   0.457  -2.5096  -2.1335   1.8681
 FXP  H1B   H  HCH1  0   0.194   1.0997   0.3212  -1.1668
 FXP  H2B   H  HCH1  0   0.222   2.3103   0.4533   1.6373
 FXP  H3B   H  HCH1  0   0.209   3.5076   0.9681  -1.1166
 FXP  H4B   H  HCH1  0   0.222   4.0100  -1.2882   0.8602
 FXP  H5B   H  HCH2  0   0.216   2.6167  -1.3257  -1.8644
 FXP  H5BA  H  HCH2  0   0.253   2.8713  -2.7161  -0.8009
 FXP  HO2B  H  HOH1  0   0.452   1.1328   2.3225   1.0525
 FXP  HO3B  H  HOH1  0   0.450   5.4187   1.1081   0.2162
 FXP  HO4B  H  HOH1  0   0.461   5.4117  -1.9456  -0.7603
 FXP  H17   H  HOH1  0   0.468  -4.6924   2.2877  -0.2319

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
 FXP  O1   C1A   single  1.386  0.020  1.386
 FXP  C1A  C2A   single  1.525  0.020  1.525
 FXP  C1A  O5A   single  1.404  0.020  1.404
 FXP  C1A  H1A   single  0.970  0.020  1.090
 FXP  C2A  C3A   single  1.523  0.020  1.523
 FXP  C2A  F2A   single  1.390  0.020  1.390
 FXP  C2A  H2A   single  0.970  0.020  1.090
 FXP  C3A  C4A   single  1.521  0.020  1.521
 FXP  C3A  O3A   single  1.403  0.020  1.403
 FXP  C3A  H3A   single  0.970  0.020  1.090
 FXP  C4A  C5A   single  1.527  0.020  1.527
 FXP  C4A  O4A   single  1.414  0.020  1.414
 FXP  C4A  H4A   single  0.970  0.020  1.090
 FXP  C5A  O5A   single  1.415  0.020  1.415
 FXP  C5A  H5A   single  0.970  0.020  1.090
 FXP  C5A  H5AA  single  0.970  0.020  1.090
 FXP  O3A  HO3A  single  0.850  0.020  0.980
 FXP  O4A  C1B   single  1.382  0.020  1.382
 FXP  C1B  C2B   single  1.530  0.020  1.530
 FXP  C1B  O5B   single  1.402  0.020  1.402
 FXP  C1B  H1B   single  0.970  0.020  1.090
 FXP  C2B  C3B   single  1.521  0.020  1.521
 FXP  C2B  O2B   single  1.403  0.020  1.403
 FXP  C2B  H2B   single  0.970  0.020  1.090
 FXP  C3B  C4B   single  1.525  0.020  1.525
 FXP  C3B  O3B   single  1.404  0.020  1.404
 FXP  C3B  H3B   single  0.970  0.020  1.090
 FXP  C4B  C5B   single  1.526  0.020  1.526
 FXP  C4B  O4B   single  1.409  0.020  1.409
 FXP  C4B  H4B   single  0.970  0.020  1.090
 FXP  C5B  O5B   single  1.411  0.020  1.411
 FXP  C5B  H5B   single  0.970  0.020  1.090
 FXP  C5B  H5BA  single  0.970  0.020  1.090
 FXP  O2B  HO2B  single  0.850  0.020  0.980
 FXP  O3B  HO3B  single  0.850  0.020  0.980
 FXP  O4B  HO4B  single  0.850  0.020  0.980
 FXP  O1   H17   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
 FXP  H17   O1   C1A  109.12  3.000
 FXP  H1A   C1A  O5A  104.86  3.000
 FXP  H1A   C1A  C2A  110.03  3.000
 FXP  O5A   C1A  C2A  108.72  3.000
 FXP  H1A   C1A  O1   111.51  3.000
 FXP  O5A   C1A  O1   113.21  3.000
 FXP  C2A   C1A  O1   108.45  3.000
 FXP  H2A   C2A  F2A  107.53  3.000
 FXP  H2A   C2A  C3A  109.22  3.000
 FXP  F2A   C2A  C3A  109.42  3.000
 FXP  H2A   C2A  C1A  108.51  3.000
 FXP  F2A   C2A  C1A  109.35  3.000
 FXP  C3A   C2A  C1A  112.68  3.000
 FXP  H3A   C3A  O3A  111.27  3.000
 FXP  H3A   C3A  C4A  108.59  3.000
 FXP  O3A   C3A  C4A  108.65  3.000
 FXP  H3A   C3A  C2A  109.22  3.000
 FXP  O3A   C3A  C2A  111.43  3.000
 FXP  C4A   C3A  C2A  107.56  3.000
 FXP  H4A   C4A  O4A  110.82  3.000
 FXP  H4A   C4A  C5A  109.50  3.000
 FXP  O4A   C4A  C5A  109.75  3.000
 FXP  H4A   C4A  C3A  108.33  3.000
 FXP  O4A   C4A  C3A  108.75  3.000
 FXP  C5A   C4A  C3A  109.68  3.000
 FXP  H5AA  C5A  H5A  107.67  3.000
 FXP  H5AA  C5A  O5A  106.45  3.000
 FXP  H5A   C5A  O5A  111.57  3.000
 FXP  H5AA  C5A  C4A  110.59  3.000
 FXP  H5A   C5A  C4A  109.55  3.000
 FXP  O5A   C5A  C4A  110.93  3.000
 FXP  HO3A  O3A  C3A  108.62  3.000
 FXP  C1B   O4A  C4A  115.39  3.000
 FXP  C5A   O5A  C1A  114.20  3.000
 FXP  H1B   C1B  O5B  109.55  3.000
 FXP  H1B   C1B  C2B  108.75  3.000
 FXP  O5B   C1B  C2B  110.93  3.000
 FXP  H1B   C1B  O4A  111.08  3.000
 FXP  O5B   C1B  O4A  108.29  3.000
 FXP  C2B   C1B  O4A  108.23  3.000
 FXP  H2B   C2B  O2B  111.61  3.000
 FXP  H2B   C2B  C3B  108.77  3.000
 FXP  O2B   C2B  C3B  108.53  3.000
 FXP  H2B   C2B  C1B  108.06  3.000
 FXP  O2B   C2B  C1B  110.91  3.000
 FXP  C3B   C2B  C1B  108.90  3.000
 FXP  H3B   C3B  O3B  110.94  3.000
 FXP  H3B   C3B  C4B  107.67  3.000
 FXP  O3B   C3B  C4B  112.02  3.000
 FXP  H3B   C3B  C2B  107.92  3.000
 FXP  O3B   C3B  C2B  108.53  3.000
 FXP  C4B   C3B  C2B  109.67  3.000
 FXP  H4B   C4B  O4B  111.06  3.000
 FXP  H4B   C4B  C5B  108.80  3.000
 FXP  O4B   C4B  C5B  111.28  3.000
 FXP  H4B   C4B  C3B  108.30  3.000
 FXP  O4B   C4B  C3B  107.37  3.000
 FXP  C5B   C4B  C3B  109.98  3.000
 FXP  H5BA  C5B  H5B  107.69  3.000
 FXP  H5BA  C5B  O5B  107.17  3.000
 FXP  H5B   C5B  O5B  111.14  3.000
 FXP  H5BA  C5B  C4B  110.67  3.000
 FXP  H5B   C5B  C4B  109.62  3.000
 FXP  O5B   C5B  C4B  110.48  3.000
 FXP  HO2B  O2B  C2B  108.09  3.000
 FXP  HO3B  O3B  C3B  107.86  3.000
 FXP  HO4B  O4B  C4B  108.74  3.000
 FXP  C5B   O5B  C1B  111.60  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
 FXP  Var_01  C4A  C5A  O5A  C1A  61.08  30.0  1
 FXP  Var_02  C4B  C5B  O5B  C1B  62.39  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
 FXP  chir_01  C1A  O1   C2A  O5A  positiv
 FXP  chir_02  C2A  F2A  C3A  C1A  positiv
 FXP  chir_03  C3A  O3A  C2A  C4A  positiv
 FXP  chir_04  C4A  O4A  C3A  C5A  negativ
 FXP  chir_05  C1B  O4A  O5B  C2B  positiv
 FXP  chir_06  C2B  O2B  C1B  C3B  negativ
 FXP  chir_07  C3B  O3B  C2B  C4B  positiv
 FXP  chir_08  C4B  O4B  C3B  C5B  negativ

