# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:19:56 2021
#   Inital geometry file: a 47 line input string
#   Ligand name: 4-thio-beta-L-ribopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1OC[C@H](S)[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
 Z4V  Z4V  4-thio-beta-L-ribopyranose  L-saccharide  20  10  .  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_Z4V
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
 Z4V  C1   C  CH1   0   0.283  2.6575  -0.3019  -3.5950
 Z4V  C2   C  CH1   0   0.013  3.4213   0.7168  -4.4359
 Z4V  C3   C  CH1   0  -0.029  3.7845   0.1203  -5.8022
 Z4V  C4   C  CH1   0  -0.428  2.5173  -0.4226  -6.4616
 Z4V  C5   C  CH2   0  -0.155  1.7866  -1.3616  -5.5124
 Z4V  O1   O  OH1   0  -0.659  2.2578   0.3015  -2.4223
 Z4V  O2   O  OH1   0  -0.664  4.5535   1.1212  -3.7177
 Z4V  O3   O  OH1   0  -0.665  4.7325  -0.9062  -5.6218
 Z4V  S4   S  S2    0  -0.234  2.9820  -1.2999  -7.9925
 Z4V  O5   O  O2    0  -0.497  1.5012  -0.7069  -4.2960
 Z4V  H1   H  HCH1  0   0.193  3.2915  -1.1832  -3.4009
 Z4V  HO1  H  HOH1  0   0.463  2.0140  -0.3767  -1.7835
 Z4V  H2   H  HCH1  0   0.219  2.7393   1.5601  -4.6244
 Z4V  HO2  H  HOH1  0   0.454  5.0040   1.8076  -4.2198
 Z4V  H3   H  HCH1  0   0.257  4.1950   0.9218  -6.4296
 Z4V  HO3  H  HOH1  0   0.461  5.3418  -0.9007  -6.3647
 Z4V  H4   H  HCH1  0   0.296  1.8710   0.4148  -6.7333
 Z4V  HS4  H  HSH1  0   0.231  1.8617  -1.0502  -8.6774
 Z4V  H51  H  HCH2  0   0.214  2.3866  -2.2657  -5.3461
 Z4V  H52  H  HCH2  0   0.252  0.8336  -1.6734  -5.9409

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
 Z4V  C1  H1   single  0.970  0.020  1.090
 Z4V  C1  O1   single  1.378  0.020  1.378
 Z4V  O1  HO1  single  0.850  0.020  0.980
 Z4V  C1  O5   single  1.412  0.020  1.412
 Z4V  C1  C2   single  1.526  0.020  1.526
 Z4V  C2  H2   single  0.970  0.020  1.090
 Z4V  C2  O2   single  1.400  0.020  1.400
 Z4V  O2  HO2  single  0.850  0.020  0.980
 Z4V  C2  C3   single  1.534  0.020  1.534
 Z4V  C3  H3   single  0.970  0.020  1.090
 Z4V  C3  O3   single  1.409  0.020  1.409
 Z4V  O3  HO3  single  0.850  0.020  0.980
 Z4V  C3  C4   single  1.528  0.020  1.528
 Z4V  C4  H4   single  0.970  0.020  1.090
 Z4V  C4  S4   single  1.825  0.020  1.825
 Z4V  S4  HS4  single  1.200  0.020  1.300
 Z4V  C4  C5   single  1.522  0.020  1.522
 Z4V  C5  O5   single  1.411  0.020  1.411
 Z4V  C5  H51  single  0.970  0.020  1.090
 Z4V  C5  H52  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
 Z4V  H1   C1  O5   109.21  3.000
 Z4V  O5   C1  O1   108.10  3.000
 Z4V  H1   C1  O1   111.52  3.000
 Z4V  O5   C1  C2   109.15  3.000
 Z4V  O1   C1  C2   108.78  3.000
 Z4V  H1   C1  C2   110.04  3.000
 Z4V  H2   C2  O2   111.56  3.000
 Z4V  O2   C2  C3   112.18  3.000
 Z4V  H2   C2  C3   106.97  3.000
 Z4V  C3   C2  C1   110.46  3.000
 Z4V  O2   C2  C1   108.35  3.000
 Z4V  H2   C2  C1   107.20  3.000
 Z4V  H3   C3  O3   110.70  3.000
 Z4V  O3   C3  C4   110.76  3.000
 Z4V  H3   C3  C4   108.84  3.000
 Z4V  C4   C3  C2   109.03  3.000
 Z4V  O3   C3  C2   109.18  3.000
 Z4V  H3   C3  C2   108.28  3.000
 Z4V  H4   C4  S4   108.10  3.000
 Z4V  S4   C4  C5   110.42  3.000
 Z4V  H4   C4  C5   110.12  3.000
 Z4V  C5   C4  C3   110.38  3.000
 Z4V  S4   C4  C3   108.76  3.000
 Z4V  H4   C4  C3   109.00  3.000
 Z4V  H52  C5  H51  107.56  3.000
 Z4V  H52  C5  O5   107.15  3.000
 Z4V  H51  C5  O5   111.23  3.000
 Z4V  H52  C5  C4   110.55  3.000
 Z4V  H51  C5  C4   109.88  3.000
 Z4V  O5   C5  C4   110.40  3.000
 Z4V  HO1  O1  C1   109.24  3.000
 Z4V  HO2  O2  C2   108.47  3.000
 Z4V  HO3  O3  C3   108.88  3.000
 Z4V  HS4  S4  C4    97.28  3.000
 Z4V  C5   O5  C1   113.31  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
 Z4V  Var_01  C4  C5  O5  C1  -62.42  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
 Z4V  chir_01  C1  O1  O5  C2  negativ
 Z4V  chir_02  C2  O2  C1  C3  positiv
 Z4V  chir_03  C3  O3  C2  C4  positiv
 Z4V  chir_04  C4  S4  C3  C5  positiv

