# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:56:04 2021
#   Inital geometry file: a 47 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R})-oxane-2,3,4,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](O)[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
 SEJ  SEJ  (2~{R},3~{S},4~{R},5~{R})-oxane-2,3,4,5-tetrol  D-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 OK
;

data_comp_SEJ
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
 SEJ  C1   C  CH1   0   0.215  22.4089  22.3964  30.0970
 SEJ  C2   C  CH1   0   0.005  21.6905  23.1250  28.9512
 SEJ  C3   C  CH1   0   0.021  20.7069  22.1878  28.2634
 SEJ  C4   C  CH1   0  -0.031  19.7632  21.5731  29.2980
 SEJ  C5   C  CH2   0  -0.228  20.5860  20.9213  30.3976
 SEJ  O1   O  OH1   0  -0.663  23.2625  21.4435  29.5509
 SEJ  O2   O  OH1   0  -0.666  22.5969  23.6049  27.9935
 SEJ  O3   O  OH1   0  -0.667  20.0259  22.9157  27.2741
 SEJ  O4   O  OH1   0  -0.669  18.9222  22.5884  29.7941
 SEJ  O5   O  O2    0  -0.492  21.4841  21.8402  30.9928
 SEJ  H1   H  HCH1  0   0.231  22.9687  23.1264  30.6951
 SEJ  H2   H  HCH1  0   0.222  21.1259  23.9497  29.4072
 SEJ  H3   H  HCH1  0   0.217  21.2716  21.3555  27.8186
 SEJ  H4   H  HCH1  0   0.227  19.1763  20.7801  28.8089
 SEJ  H51  H  HCH2  0   0.246  19.9360  20.5601  31.1978
 SEJ  H52  H  HCH2  0   0.218  21.1119  20.0488  29.9933
 SEJ  HO2  H  HOH1  0   0.452  23.1286  24.2973  28.3983
 SEJ  HO3  H  HOH1  0   0.450  19.4491  22.3109  26.7965
 SEJ  HO4  H  HOH1  0   0.453  18.3025  22.1875  30.4113
 SEJ  HO1  H  HOH1  0   0.461  23.8647  21.1371  30.2372

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
 SEJ  O3  C3   single  1.404  0.020  1.404
 SEJ  O2  C2   single  1.403  0.020  1.403
 SEJ  C3  C2   single  1.523  0.020  1.523
 SEJ  C3  C4   single  1.529  0.020  1.529
 SEJ  C2  C1   single  1.536  0.020  1.536
 SEJ  C4  O4   single  1.409  0.020  1.409
 SEJ  C4  C5   single  1.520  0.020  1.520
 SEJ  O1  C1   single  1.391  0.020  1.391
 SEJ  C1  O5   single  1.402  0.020  1.402
 SEJ  C5  O5   single  1.416  0.020  1.416
 SEJ  C1  H1   single  0.970  0.020  1.090
 SEJ  C2  H2   single  0.970  0.020  1.090
 SEJ  C3  H3   single  0.970  0.020  1.090
 SEJ  C4  H4   single  0.970  0.020  1.090
 SEJ  C5  H51  single  0.970  0.020  1.090
 SEJ  C5  H52  single  0.970  0.020  1.090
 SEJ  O2  HO2  single  0.850  0.020  0.980
 SEJ  O3  HO3  single  0.850  0.020  0.980
 SEJ  O4  HO4  single  0.850  0.020  0.980
 SEJ  O1  HO1  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
 SEJ  H1   C1  O5   104.60  3.000
 SEJ  H1   C1  O1   110.90  3.000
 SEJ  O5   C1  O1   112.57  3.000
 SEJ  H1   C1  C2   109.24  3.000
 SEJ  O5   C1  C2   110.86  3.000
 SEJ  O1   C1  C2   108.61  3.000
 SEJ  H2   C2  O2   111.01  3.000
 SEJ  H2   C2  C3   108.51  3.000
 SEJ  O2   C2  C3   108.63  3.000
 SEJ  H2   C2  C1   106.67  3.000
 SEJ  C3   C2  C1   110.31  3.000
 SEJ  O2   C2  C1   111.67  3.000
 SEJ  H3   C3  O3   110.88  3.000
 SEJ  H3   C3  C4   106.63  3.000
 SEJ  O3   C3  C4   112.69  3.000
 SEJ  H3   C3  C2   108.47  3.000
 SEJ  C4   C3  C2   109.90  3.000
 SEJ  O3   C3  C2   108.20  3.000
 SEJ  H4   C4  O4   110.93  3.000
 SEJ  H4   C4  C5   107.52  3.000
 SEJ  O4   C4  C5   112.18  3.000
 SEJ  H4   C4  C3   108.54  3.000
 SEJ  C5   C4  C3   109.13  3.000
 SEJ  O4   C4  C3   108.48  3.000
 SEJ  H52  C5  H51  107.01  3.000
 SEJ  H52  C5  O5   111.55  3.000
 SEJ  H51  C5  O5   106.50  3.000
 SEJ  H52  C5  C4   109.52  3.000
 SEJ  H51  C5  C4   110.46  3.000
 SEJ  O5   C5  C4   111.66  3.000
 SEJ  HO1  O1  C1   108.78  3.000
 SEJ  HO2  O2  C2   108.42  3.000
 SEJ  HO3  O3  C3   108.32  3.000
 SEJ  HO4  O4  C4   108.07  3.000
 SEJ  C5   O5  C1   114.02  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
 SEJ  Var_01  C4  C5  O5  C1  -59.93  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
 SEJ  chir_01  C1  C2  O1  O5  positiv
 SEJ  chir_02  C2  O2  C1  C3  positiv
 SEJ  chir_03  C3  O3  C2  C4  negativ
 SEJ  chir_04  C4  O4  C3  C5  negativ

