# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:45:34 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@H](CO[P](O)(S)=O)[C@@H](O)[C@@H]1F
#
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
 48Z  48Z  2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranose  D-saccharide  23  14  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_48Z
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
 48Z  O1    O  OH1    0  -0.659  2.6985  -2.6299   2.6882
 48Z  P     P  P      0   1.168  5.1177  -3.8926  -3.4415
 48Z  C1    C  CH1    0   0.210  3.3524  -1.9291   1.6818
 48Z  C2    C  CH1    0   0.153  2.3220  -1.0783   0.9551
 48Z  F2    F  F      0  -0.373  2.9930  -0.0515   0.2988
 48Z  C3    C  CH1    0  -0.074  1.7532  -2.0326  -0.0860
 48Z  O3    O  OH1    0  -0.662  0.6490  -2.6842   0.4837
 48Z  C4    C  CH1    0  -0.012  2.9476  -2.9681  -0.3663
 48Z  O4    O  O2     0  -0.506  3.8832  -2.7620   0.6894
 48Z  C5    C  CH2    0  -0.163  3.6013  -2.6648  -1.6982
 48Z  O5    O  O2     0  -0.615  4.7076  -3.5294  -1.8864
 48Z  OP1   O  O      0  -0.758  5.4316  -2.6304  -4.1777
 48Z  OP2   O  OP    -1  -0.762  4.1780  -4.9211  -3.9832
 48Z  SP3   S  S2     0  -0.496  6.9142  -4.9706  -3.0295
 48Z  H2    H  HCH1   0   0.249  1.5672  -0.6384   1.6083
 48Z  H3    H  HCH1   0   0.251  1.4640  -1.4776  -0.9883
 48Z  HO3   H  HOH1   0   0.457  0.3054  -3.3169  -0.1549
 48Z  H4    H  HCH1   0   0.244  2.6138  -4.0128  -0.3649
 48Z  H52   H  HCH2   0   0.215  2.8402  -2.7984  -2.4762
 48Z  H51   H  HCH2   0   0.217  3.9194  -1.6174  -1.7315
 48Z  HSP3  H  HSH1   0   0.218  7.6876  -3.9326  -2.6875
 48Z  HO1   H  HOH1   0   0.461  3.3533  -3.0787   3.2337
 48Z  H1    H  HCH1   0   0.238  4.1783  -1.3301   2.0825

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
 48Z  P    SP3   single  2.135  0.020  2.135
 48Z  P    OP2   deloc   1.495  0.020  1.495
 48Z  P    O5    single  1.649  0.020  1.649
 48Z  C1   O1    single  1.390  0.020  1.390
 48Z  C2   C1    single  1.521  0.020  1.521
 48Z  C2   H2    single  0.970  0.020  1.090
 48Z  F2   C2    single  1.391  0.020  1.391
 48Z  C3   C2    single  1.523  0.020  1.523
 48Z  C3   O3    single  1.403  0.020  1.403
 48Z  C3   H3    single  0.970  0.020  1.090
 48Z  O3   HO3   single  0.850  0.020  0.980
 48Z  C4   C3    single  1.543  0.020  1.543
 48Z  C4   O4    single  1.426  0.020  1.426
 48Z  C4   H4    single  0.970  0.020  1.090
 48Z  O4   C1    single  1.400  0.020  1.400
 48Z  C5   C4    single  1.514  0.020  1.514
 48Z  C5   O5    single  1.417  0.020  1.417
 48Z  C5   H52   single  0.970  0.020  1.090
 48Z  C5   H51   single  0.970  0.020  1.090
 48Z  OP1  P     deloc   1.495  0.020  1.495
 48Z  SP3  HSP3  single  1.200  0.020  1.300
 48Z  O1   HO1   single  0.850  0.020  0.980
 48Z  C1   H1    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
 48Z  HO1   O1   C1   108.98  3.000
 48Z  SP3   P    OP2  104.57  3.000
 48Z  OP2   P    OP1  122.32  3.000
 48Z  SP3   P    OP1  110.16  3.000
 48Z  OP1   P    O5   109.32  3.000
 48Z  OP2   P    O5   109.70  3.000
 48Z  SP3   P    O5    97.96  3.000
 48Z  H1    C1   O4   107.37  3.000
 48Z  H1    C1   C2   112.29  3.000
 48Z  O4    C1   C2   104.53  3.000
 48Z  H1    C1   O1   111.43  3.000
 48Z  O4    C1   O1   113.06  3.000
 48Z  C2    C1   O1   108.01  3.000
 48Z  H2    C2   C3   113.81  3.000
 48Z  C3    C2   F2   108.67  3.000
 48Z  H2    C2   F2   108.58  3.000
 48Z  C3    C2   C1   103.25  3.000
 48Z  F2    C2   C1   108.15  3.000
 48Z  H2    C2   C1   114.09  3.000
 48Z  H3    C3   C4   111.16  3.000
 48Z  C4    C3   O3   113.67  3.000
 48Z  H3    C3   O3   111.17  3.000
 48Z  C4    C3   C2   102.42  3.000
 48Z  H3    C3   C2   110.09  3.000
 48Z  O3    C3   C2   107.91  3.000
 48Z  HO3   O3   C3   108.47  3.000
 48Z  H4    C4   C5   108.86  3.000
 48Z  C5    C4   O4   109.82  3.000
 48Z  H4    C4   O4   109.66  3.000
 48Z  C5    C4   C3   111.87  3.000
 48Z  H4    C4   C3   109.98  3.000
 48Z  O4    C4   C3   106.61  3.000
 48Z  C4    O4   C1   111.23  3.000
 48Z  H51   C5   H52  107.25  3.000
 48Z  H51   C5   O5   110.66  3.000
 48Z  H52   C5   O5   111.92  3.000
 48Z  H51   C5   C4   110.10  3.000
 48Z  H52   C5   C4   107.46  3.000
 48Z  O5    C5   C4   109.37  3.000
 48Z  C5    O5   P    117.00  3.000
 48Z  HSP3  SP3  P     98.28  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
 48Z  Var_01  C4   C5  O5  P   152.01  30.0  2
 48Z  Var_02  SP3  P   O5  C5  173.45  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
 48Z  chir_02  C1  O1  C2  O4  positiv
 48Z  chir_03  C2  F2  C3  C1  negativ
 48Z  chir_04  C3  O3  C2  C4  negativ
 48Z  chir_05  C4  O4  C3  C5  negativ

