# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:14:34 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 1,4-anhydro-3-deoxy-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1C[C@@H](O)CO1
#
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
 PA3  PA3  1,4-anhydro-3-deoxy-D-erythro-pentitol  ligand  18  8  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PA3
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
 PA3  C1   C  CH2   0  -0.186  -1.0553   1.2053  -0.2309
 PA3  C2   C  CH1   0  -0.008  -1.7522  -0.1429  -0.3384
 PA3  O2   O  OH1   0  -0.674  -2.4060  -0.5110   0.8569
 PA3  C3   C  CH2   0  -0.531  -0.5525  -1.0557  -0.5246
 PA3  C4   C  CH1   0   0.037   0.5318  -0.3930   0.3317
 PA3  O4   O  O2    0  -0.502   0.1311   0.9638   0.5007
 PA3  C5   C  CH2   0  -0.159   1.8924  -0.4813  -0.3224
 PA3  O5   O  OH1   0  -0.673   2.8624   0.0744   0.5333
 PA3  H11  H  HCH2  0   0.204  -0.8376   1.5903  -1.2360
 PA3  H12  H  HCH2  0   0.233  -1.6528   1.9592   0.2892
 PA3  H2   H  HCH1  0   0.231  -2.4350  -0.1710  -1.1957
 PA3  HO2  H  HOH1  0   0.451  -3.1020   0.1297   1.0325
 PA3  H31  H  HCH2  0   0.264  -0.7545  -2.0859  -0.2326
 PA3  H32  H  HCH2  0   0.248  -0.2638  -1.0615  -1.5789
 PA3  H4   H  HCH1  0   0.223   0.5837  -0.8610   1.3224
 PA3  H51  H  HCH2  0   0.199   2.0982  -1.5391  -0.5360
 PA3  H52  H  HCH2  0   0.192   1.8531   0.0374  -1.2912
 PA3  HO5  H  HOH1  0   0.455   3.7224  -0.0253   0.1158

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
 PA3  C1  C2   single  1.521  0.020  1.521
 PA3  C1  O4   single  1.415  0.020  1.415
 PA3  C1  H11  single  0.970  0.020  1.090
 PA3  C1  H12  single  0.970  0.020  1.090
 PA3  C2  O2   single  1.411  0.020  1.411
 PA3  C2  C3   single  1.519  0.020  1.519
 PA3  C2  H2   single  0.970  0.020  1.090
 PA3  O2  HO2  single  0.850  0.020  0.980
 PA3  C3  C4   single  1.532  0.020  1.532
 PA3  C3  H31  single  0.970  0.020  1.090
 PA3  C3  H32  single  0.970  0.020  1.090
 PA3  C4  O4   single  1.425  0.020  1.425
 PA3  C4  C5   single  1.512  0.020  1.512
 PA3  C4  H4   single  0.970  0.020  1.090
 PA3  C5  O5   single  1.408  0.020  1.408
 PA3  C5  H51  single  0.970  0.020  1.090
 PA3  C5  H52  single  0.970  0.020  1.090
 PA3  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
 PA3  H12  C1  H11  107.57  3.000
 PA3  H12  C1  O4   109.27  3.000
 PA3  H11  C1  O4   111.53  3.000
 PA3  H12  C1  C2   113.21  3.000
 PA3  H11  C1  C2   109.68  3.000
 PA3  O4   C1  C2   105.63  3.000
 PA3  H2   C2  C3   112.38  3.000
 PA3  H2   C2  O2   111.53  3.000
 PA3  C3   C2  O2   108.24  3.000
 PA3  H2   C2  C1   111.30  3.000
 PA3  C3   C2  C1   100.33  3.000
 PA3  O2   C2  C1   112.55  3.000
 PA3  HO2  O2  C2   108.42  3.000
 PA3  H32  C3  H31  107.60  3.000
 PA3  H32  C3  C4   110.75  3.000
 PA3  H31  C3  C4   112.97  3.000
 PA3  H32  C3  C2   109.27  3.000
 PA3  H31  C3  C2   112.89  3.000
 PA3  C4   C3  C2   103.33  3.000
 PA3  H4   C4  C5   108.85  3.000
 PA3  H4   C4  O4   108.21  3.000
 PA3  C5   C4  O4   111.10  3.000
 PA3  H4   C4  C3   110.71  3.000
 PA3  C5   C4  C3   111.70  3.000
 PA3  O4   C4  C3   106.21  3.000
 PA3  C4   O4  C1   109.70  3.000
 PA3  H52  C5  H51  106.84  3.000
 PA3  H52  C5  O5   111.95  3.000
 PA3  H51  C5  O5   111.66  3.000
 PA3  H52  C5  C4   108.75  3.000
 PA3  H51  C5  C4   107.99  3.000
 PA3  O5   C5  C4   109.51  3.000
 PA3  HO5  O5  C5   108.15  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
 PA3  Var_01  H11  C1  O4  C4  -93.00  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
 PA3  chir_01  C2  C1  O2  C3  positiv
 PA3  chir_02  C4  O4  C5  C3  positiv

