# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:22:14 2020
#   Inital geometry file: a 35 line input string
#   Ligand name: 1,4-dioxane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1COCCO1
#
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
 DIO  DIO  '1,4-dioxane              '  ligand  14  6  .  2020-11-11  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DIO
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
 DIO  C1    C  CH2   0  -0.200  -1.1646   0.1913   0.7386
 DIO  C2    C  CH2   0  -0.200   1.1601   0.2256   0.7330
 DIO  C1'   C  CH2   0  -0.200  -1.1616  -0.2749  -0.7037
 DIO  C2'   C  CH2   0  -0.200   1.1634  -0.2418  -0.7090
 DIO  O1    O  O2    0  -0.489   0.0058  -0.2325   1.4074
 DIO  O1'   O  O2    0  -0.489  -0.0069   0.1816  -1.3782
 DIO  H11   H  HCH2  0   0.206  -1.2520   1.2869   0.7747
 DIO  H12   H  HCH2  0   0.239  -2.0207  -0.2302   1.2684
 DIO  H21   H  HCH2  0   0.239   2.0307  -0.1707   1.2588
 DIO  H22   H  HCH2  0   0.206   1.2159   1.3232   0.7687
 DIO  H1'1  H  HCH2  0   0.206  -1.2197  -1.3724  -0.7399
 DIO  H1'2  H  HCH2  0   0.239  -2.0315   0.1232  -1.2294
 DIO  H2'1  H  HCH2  0   0.206   1.2516  -1.3372  -0.7440
 DIO  H2'2  H  HCH2  0   0.239   2.0195   0.1795  -1.2391

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
 DIO  C1   C1'   single  1.516  0.020  1.516
 DIO  C1   O1    single  1.413  0.020  1.413
 DIO  C1   H11   single  0.970  0.020  1.090
 DIO  C1   H12   single  0.970  0.020  1.090
 DIO  C2   C2'   single  1.516  0.020  1.516
 DIO  C2   O1    single  1.413  0.020  1.413
 DIO  C2   H21   single  0.970  0.020  1.090
 DIO  C2   H22   single  0.970  0.020  1.090
 DIO  C1'  O1'   single  1.413  0.020  1.413
 DIO  C1'  H1'1  single  0.970  0.020  1.090
 DIO  C1'  H1'2  single  0.970  0.020  1.090
 DIO  C2'  O1'   single  1.413  0.020  1.413
 DIO  C2'  H2'1  single  0.970  0.020  1.090
 DIO  C2'  H2'2  single  0.970  0.020  1.090

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
 DIO  H12   C1   H11   107.85  3.000
 DIO  H12   C1   O1    107.70  3.000
 DIO  H11   C1   O1    110.43  3.000
 DIO  H12   C1   C1'   110.16  3.000
 DIO  H11   C1   C1'   109.75  3.000
 DIO  O1    C1   C1'   110.89  3.000
 DIO  H22   C2   H21   107.84  3.000
 DIO  H22   C2   O1    110.46  3.000
 DIO  H21   C2   O1    107.69  3.000
 DIO  H22   C2   C2'   109.79  3.000
 DIO  H21   C2   C2'   110.15  3.000
 DIO  O1    C2   C2'   110.84  3.000
 DIO  H1'2  C1'  H1'1  107.83  3.000
 DIO  H1'2  C1'  O1'   107.67  3.000
 DIO  H1'1  C1'  O1'   110.48  3.000
 DIO  H1'2  C1'  C1    110.15  3.000
 DIO  H1'1  C1'  C1    109.76  3.000
 DIO  O1'   C1'  C1    110.88  3.000
 DIO  H2'2  C2'  H2'1  107.83  3.000
 DIO  H2'2  C2'  O1'   107.69  3.000
 DIO  H2'1  C2'  O1'   110.48  3.000
 DIO  H2'2  C2'  C2    110.17  3.000
 DIO  H2'1  C2'  C2    109.74  3.000
 DIO  O1'   C2'  C2    110.87  3.000
 DIO  C2    O1   C1    110.70  3.000
 DIO  C2'   O1'  C1'   110.73  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
 DIO  Var_01  C2'   C2   O1   C1   -56.56  30.0  1
 DIO  Var_02  C1'   C1   O1   C2    56.53  30.0  1
 DIO  Var_03  O1'   C1'  C1   O1   -56.56  30.0  1
 DIO  Var_04  O1'   C2'  C2   O1    56.65  30.0  1
 DIO  Var_05  H2'1  C2'  O1'  C1'   65.38  30.0  1
 DIO  Var_06  H1'1  C1'  O1'  C2'  -65.48  30.0  1

