# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 06:16:00 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 1,4-anhydro-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC[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
 R1X  R1X  '1,4-anhydro-D-ribitol    '  D-saccharide  19  9  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R1X
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
 R1X  O2'   O  OH1   0  -0.667   2.6212   0.1183   0.6869
 R1X  C2'   C  CH1   0  -0.014   1.2450   0.3519   0.5801
 R1X  C3'   C  CH1   0  -0.041   0.5175  -0.9065   0.1067
 R1X  O3'   O  OH1   0  -0.671   1.1882  -1.5220  -0.9656
 R1X  C1'   C  CH2   0  -0.176   0.8325   1.3512  -0.4968
 R1X  O4'   O  O2    0  -0.500  -0.5037   1.0170  -0.8180
 R1X  C4'   C  CH1   0  -0.009  -0.7908  -0.3206  -0.4149
 R1X  C5'   C  CH2   0  -0.153  -1.8831  -0.3355   0.6364
 R1X  O5'   O  OH1   0  -0.669  -3.0344   0.2666   0.0965
 R1X  HO2'  H  HOH1  0   0.462   3.0493   0.9181   1.0069
 R1X  H2'   H  HCH1  0   0.220   0.8162   0.6572   1.5444
 R1X  H3'   H  HCH1  0   0.240   0.3498  -1.6138   0.9301
 R1X  HO3'  H  HOH1  0   0.451   2.0853  -1.7299  -0.6837
 R1X  H1'   H  HCH2  0   0.230   0.8694   2.3879  -0.1541
 R1X  H1'A  H  HCH2  0   0.204   1.4925   1.2586  -1.3687
 R1X  H4'   H  HCH1  0   0.241  -1.1372  -0.8920  -1.2850
 R1X  H5'   H  HCH2  0   0.203  -2.0655  -1.3804   0.9184
 R1X  H5'A  H  HCH2  0   0.194  -1.5398   0.1843   1.5421
 R1X  HO5'  H  HOH1  0   0.456  -3.7408   0.1920   0.7441

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
 R1X  O2'  C2'   single  1.400  0.020  1.400
 R1X  O2'  HO2'  single  0.850  0.020  0.980
 R1X  C1'  C2'   single  1.526  0.020  1.526
 R1X  C2'  C3'   single  1.529  0.020  1.529
 R1X  C2'  H2'   single  0.970  0.020  1.090
 R1X  O3'  C3'   single  1.407  0.020  1.407
 R1X  C3'  C4'   single  1.525  0.020  1.525
 R1X  C3'  H3'   single  0.970  0.020  1.090
 R1X  O3'  HO3'  single  0.850  0.020  0.980
 R1X  C1'  O4'   single  1.414  0.020  1.414
 R1X  C1'  H1'   single  0.970  0.020  1.090
 R1X  C1'  H1'A  single  0.970  0.020  1.090
 R1X  O4'  C4'   single  1.426  0.020  1.426
 R1X  C4'  C5'   single  1.516  0.020  1.516
 R1X  C4'  H4'   single  0.970  0.020  1.090
 R1X  C5'  O5'   single  1.407  0.020  1.407
 R1X  C5'  H5'   single  0.970  0.020  1.090
 R1X  C5'  H5'A  single  0.970  0.020  1.090
 R1X  O5'  HO5'  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
 R1X  HO2'  O2'  C2'  108.91  3.000
 R1X  H2'   C2'  C1'  109.38  3.000
 R1X  H2'   C2'  C3'  108.35  3.000
 R1X  C1'   C2'  C3'  101.06  3.000
 R1X  H2'   C2'  O2'  111.29  3.000
 R1X  C3'   C2'  O2'  110.73  3.000
 R1X  C1'   C2'  O2'  115.40  3.000
 R1X  H3'   C3'  C4'  111.88  3.000
 R1X  H3'   C3'  O3'  111.26  3.000
 R1X  C4'   C3'  O3'  108.44  3.000
 R1X  H3'   C3'  C2'  111.75  3.000
 R1X  C4'   C3'  C2'  101.41  3.000
 R1X  O3'   C3'  C2'  111.68  3.000
 R1X  HO3'  O3'  C3'  108.39  3.000
 R1X  H1'A  C1'  H1'  107.99  3.000
 R1X  H1'A  C1'  O4'  111.58  3.000
 R1X  H1'   C1'  O4'  109.11  3.000
 R1X  H1'A  C1'  C2'  110.05  3.000
 R1X  H1'   C1'  C2'  113.01  3.000
 R1X  O4'   C1'  C2'  105.13  3.000
 R1X  C4'   O4'  C1'  110.34  3.000
 R1X  H4'   C4'  C5'  108.50  3.000
 R1X  H4'   C4'  O4'  109.14  3.000
 R1X  C5'   C4'  O4'  110.50  3.000
 R1X  H4'   C4'  C3'  110.00  3.000
 R1X  C5'   C4'  C3'  112.15  3.000
 R1X  O4'   C4'  C3'  106.51  3.000
 R1X  H5'A  C5'  H5'  106.88  3.000
 R1X  H5'A  C5'  O5'  111.68  3.000
 R1X  H5'   C5'  O5'  111.72  3.000
 R1X  H5'A  C5'  C4'  109.97  3.000
 R1X  H5'   C5'  C4'  107.90  3.000
 R1X  O5'   C5'  C4'  108.62  3.000
 R1X  HO5'  O5'  C5'  108.04  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
 R1X  Var_01  H1'  C1'  O4'  C4'  -141.60  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
 R1X  chir_01  C2'  O2'  C1'  C3'  negativ
 R1X  chir_02  C3'  O3'  C4'  C2'  positiv
 R1X  chir_03  C4'  O4'  C3'  C5'  negativ

