# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 22:31:15 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 3,6-dideoxy-alpha-D-arabino-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O)[C@@H](O)C[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
 TYV  TYV  3,6-dideoxy-alpha-D-arabino-hexopyranose  D-saccharide  22  10  .  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_TYV
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
 TYV  C1   C  CH1   0   0.241  69.3464  48.2111  89.1936
 TYV  C2   C  CH1   0   0.006  68.9220  48.5229  87.7614
 TYV  C3   C  CH2   0  -0.526  70.1208  48.4227  86.8240
 TYV  C4   C  CH1   0   0.060  71.2771  49.2707  87.3292
 TYV  C5   C  CH1   0   0.024  71.6060  48.8804  88.7739
 TYV  C6   C  CH3   0  -0.698  72.6668  49.7638  89.3996
 TYV  O1   O  OH1   0  -0.667  69.6073  46.8438  89.2627
 TYV  O2   O  OH1   0  -0.669  68.3762  49.8243  87.7906
 TYV  O4   O  OH1   0  -0.669  72.3810  49.0610  86.4761
 TYV  O5   O  O2    0  -0.502  70.4405  48.9921  89.5848
 TYV  H1   H  HCH1  0   0.226  68.5428  48.4976  89.8838
 TYV  H2   H  HCH1  0   0.225  68.1612  47.7902  87.4616
 TYV  H31  H  HCH2  0   0.236  70.4374  47.3777  86.7544
 TYV  H32  H  HCH2  0   0.250  69.8311  48.7297  85.8143
 TYV  H4   H  HCH1  0   0.200  70.9752  50.3275  87.3204
 TYV  H5   H  HCH1  0   0.205  71.9668  47.8425  88.7698
 TYV  H61  H  HCH3  0   0.242  72.8417  49.4837  90.4386
 TYV  H62  H  HCH3  0   0.230  73.6166  49.6602  88.8754
 TYV  H63  H  HCH3  0   0.226  72.3749  50.8155  89.3720
 TYV  HO1  H  HOH1  0   0.457  69.7492  46.5999  90.1839
 TYV  HO2  H  HOH1  0   0.451  68.1214  50.0638  86.8942
 TYV  HO4  H  HOH1  0   0.450  73.0206  49.7648  86.6196

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
 TYV  C1  C2   single  1.526  0.020  1.526
 TYV  C1  O1   single  1.394  0.020  1.394
 TYV  C1  O5   single  1.400  0.020  1.400
 TYV  C1  H1   single  0.970  0.020  1.090
 TYV  C2  C3   single  1.525  0.020  1.525
 TYV  C2  O2   single  1.412  0.020  1.412
 TYV  C2  H2   single  0.970  0.020  1.090
 TYV  C3  C4   single  1.520  0.020  1.520
 TYV  C3  H31  single  0.970  0.020  1.090
 TYV  C3  H32  single  0.970  0.020  1.090
 TYV  C4  C5   single  1.532  0.020  1.532
 TYV  C4  O4   single  1.411  0.020  1.411
 TYV  C4  H4   single  0.970  0.020  1.090
 TYV  C5  C6   single  1.516  0.020  1.516
 TYV  C5  O5   single  1.424  0.020  1.424
 TYV  C5  H5   single  0.970  0.020  1.090
 TYV  C6  H61  single  0.970  0.020  1.090
 TYV  C6  H62  single  0.970  0.020  1.090
 TYV  C6  H63  single  0.970  0.020  1.090
 TYV  O1  HO1  single  0.850  0.020  0.980
 TYV  O2  HO2  single  0.850  0.020  0.980
 TYV  O4  HO4  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
 TYV  H1   C1  O5   104.53  3.000
 TYV  H1   C1  O1   111.23  3.000
 TYV  O5   C1  O1   112.78  3.000
 TYV  H1   C1  C2   109.47  3.000
 TYV  O5   C1  C2   111.44  3.000
 TYV  O1   C1  C2   107.40  3.000
 TYV  H2   C2  O2   110.67  3.000
 TYV  H2   C2  C3   109.45  3.000
 TYV  O2   C2  C3   112.17  3.000
 TYV  H2   C2  C1   108.22  3.000
 TYV  O2   C2  C1   106.05  3.000
 TYV  C3   C2  C1   110.17  3.000
 TYV  H32  C3  H31  106.61  3.000
 TYV  H32  C3  C4   110.57  3.000
 TYV  H31  C3  C4   109.50  3.000
 TYV  H32  C3  C2   109.91  3.000
 TYV  H31  C3  C2   109.23  3.000
 TYV  C4   C3  C2   110.91  3.000
 TYV  H4   C4  O4   110.68  3.000
 TYV  H4   C4  C5   108.14  3.000
 TYV  O4   C4  C5   111.37  3.000
 TYV  H4   C4  C3   108.95  3.000
 TYV  O4   C4  C3   108.14  3.000
 TYV  C5   C4  C3   109.54  3.000
 TYV  H5   C5  O5   110.17  3.000
 TYV  H5   C5  C6   108.80  3.000
 TYV  O5   C5  C6   106.98  3.000
 TYV  H5   C5  C4   107.91  3.000
 TYV  O5   C5  C4   109.95  3.000
 TYV  C6   C5  C4   113.02  3.000
 TYV  H63  C6  H62  108.20  3.000
 TYV  H63  C6  H61  108.33  3.000
 TYV  H62  C6  H61  107.10  3.000
 TYV  H63  C6  C5   111.34  3.000
 TYV  H62  C6  C5   110.86  3.000
 TYV  H61  C6  C5   110.85  3.000
 TYV  HO1  O1  C1   108.87  3.000
 TYV  HO2  O2  C2   108.22  3.000
 TYV  HO4  O4  C4   108.74  3.000
 TYV  C5   O5  C1   115.89  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
 TYV  chir_01  C1  C2  O1  O5  negativ
 TYV  chir_02  C2  O2  C1  C3  positiv
 TYV  chir_03  C4  O4  C3  C5  negativ
 TYV  chir_04  C5  O5  C4  C6  negativ

