# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 06:48:30 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-D-psicofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@](O)(CO)[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
 PSV  PSV  'alpha-D-psicofuranose    '  D-saccharide  24  12  .  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_PSV
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
 PSV  C1   C  CH2   0  -0.159  -41.9477  4.4080  13.4738
 PSV  O1   O  OH1   0  -0.665  -40.6373  4.8340  13.7378
 PSV  C2   C  CT    0   0.464  -41.9926  3.7373  12.1074
 PSV  O2   O  OH1   0  -0.663  -41.1609  2.6350  12.1485
 PSV  C3   C  CH1   0  -0.077  -43.4462  3.3822  11.7201
 PSV  O3   O  OH1   0  -0.674  -43.4127  2.1884  10.9815
 PSV  C4   C  CH1   0  -0.002  -43.8566  4.5680  10.8555
 PSV  O4   O  OH1   0  -0.663  -44.9151  4.2072  10.0144
 PSV  C5   C  CH1   0   0.002  -42.5445  4.9012  10.1434
 PSV  O5   O  O2    0  -0.515  -41.5468  4.6574  11.1183
 PSV  C6   C  CH2   0  -0.157  -42.4771  6.3324   9.6712
 PSV  O6   O  OH1   0  -0.664  -41.2834  6.5332   8.9553
 PSV  H11  H  HCH2  0   0.200  -42.6590  5.2454  13.4755
 PSV  H12  H  HCH2  0   0.203  -42.3053  3.6869  14.2204
 PSV  HO1  H  HOH1  0   0.455  -40.6293  5.2537  14.6025
 PSV  HO2  H  HOH1  0   0.451  -41.4045  2.0395  11.4274
 PSV  H3   H  HCH1  0   0.244  -44.0849  3.2810  12.6072
 PSV  HO3  H  HOH1  0   0.461  -44.2130  2.1284  10.4476
 PSV  H4   H  HCH1  0   0.232  -44.1329  5.4041  11.5134
 PSV  HO4  H  HOH1  0   0.464  -45.2734  4.9939   9.5925
 PSV  H5   H  HCH1  0   0.217  -42.4221  4.2298   9.2808
 PSV  H61  H  HCH2  0   0.197  -43.3602  6.5241   9.0453
 PSV  H62  H  HCH2  0   0.196  -42.5527  6.9956  10.5441
 PSV  HO6  H  HOH1  0   0.454  -41.2581  7.4485   8.6629

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
 PSV  C2  C1   single  1.523  0.020  1.523
 PSV  C1  O1   single  1.403  0.020  1.403
 PSV  C1  H11  single  0.970  0.020  1.090
 PSV  C1  H12  single  0.970  0.020  1.090
 PSV  O1  HO1  single  0.850  0.020  0.980
 PSV  O5  C2   single  1.423  0.020  1.423
 PSV  C3  C2   single  1.546  0.020  1.546
 PSV  C2  O2   single  1.381  0.020  1.381
 PSV  O2  HO2  single  0.850  0.020  0.980
 PSV  C4  C3   single  1.524  0.020  1.524
 PSV  O3  C3   single  1.404  0.020  1.404
 PSV  C3  H3   single  0.970  0.020  1.090
 PSV  O3  HO3  single  0.850  0.020  0.980
 PSV  O4  C4   single  1.399  0.020  1.399
 PSV  C5  C4   single  1.530  0.020  1.530
 PSV  C4  H4   single  0.970  0.020  1.090
 PSV  O4  HO4  single  0.850  0.020  0.980
 PSV  C6  C5   single  1.509  0.020  1.509
 PSV  C5  O5   single  1.416  0.020  1.416
 PSV  C5  H5   single  0.970  0.020  1.090
 PSV  O6  C6   single  1.406  0.020  1.406
 PSV  C6  H61  single  0.970  0.020  1.090
 PSV  C6  H62  single  0.970  0.020  1.090
 PSV  O6  HO6  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
 PSV  H12  C1  H11  106.78  3.000
 PSV  H12  C1  C2   108.14  3.000
 PSV  H11  C1  C2   108.54  3.000
 PSV  H12  C1  O1   112.06  3.000
 PSV  H11  C1  O1   111.90  3.000
 PSV  C2   C1  O1   109.28  3.000
 PSV  HO1  O1  C1   108.03  3.000
 PSV  O5   C2  C3   105.61  3.000
 PSV  C3   C2  O2   112.98  3.000
 PSV  O5   C2  O2   110.37  3.000
 PSV  O2   C2  C1   107.88  3.000
 PSV  C3   C2  C1   110.71  3.000
 PSV  O5   C2  C1   109.25  3.000
 PSV  HO2  O2  C2   108.53  3.000
 PSV  H3   C3  C4   111.94  3.000
 PSV  H3   C3  O3   111.14  3.000
 PSV  C4   C3  O3   111.69  3.000
 PSV  H3   C3  C2   111.46  3.000
 PSV  O3   C3  C2   107.74  3.000
 PSV  C4   C3  C2   102.52  3.000
 PSV  HO3  O3  C3   108.94  3.000
 PSV  H4   C4  C5   109.18  3.000
 PSV  H4   C4  O4   111.45  3.000
 PSV  C5   C4  O4   115.17  3.000
 PSV  H4   C4  C3   108.66  3.000
 PSV  C5   C4  C3   101.69  3.000
 PSV  O4   C4  C3   110.13  3.000
 PSV  HO4  O4  C4   109.55  3.000
 PSV  H5   C5  C6   109.19  3.000
 PSV  H5   C5  O5   110.88  3.000
 PSV  C6   C5  O5   110.32  3.000
 PSV  H5   C5  C4   109.12  3.000
 PSV  O5   C5  C4   104.26  3.000
 PSV  C6   C5  C4   113.00  3.000
 PSV  C5   O5  C2   111.67  3.000
 PSV  H62  C6  H61  106.97  3.000
 PSV  H62  C6  O6   112.13  3.000
 PSV  H61  C6  O6   111.54  3.000
 PSV  H62  C6  C5   108.71  3.000
 PSV  H61  C6  C5   107.92  3.000
 PSV  O6   C6  C5   109.43  3.000
 PSV  HO6  O6  C6   108.25  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
 PSV  chir_01  C2  O5  C3  O2  negativ
 PSV  chir_02  C3  O3  C2  C4  negativ
 PSV  chir_03  C4  O4  C3  C5  negativ
 PSV  chir_04  C5  O5  C4  C6  negativ

