# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:02:39 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (4~{S},6~{R})-2,2,6-trimethyl-1,3-dioxan-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@@H](O)OC(C)(C)O1
#
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
 D6K  D6K  (4~{S},6~{R})-2,2,6-trimethyl-1,3-dioxan-4-ol  ligand  24  10  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D6K
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
 D6K  CAA  C  CH3   0  -0.676   2.6195   1.1903   0.1634
 D6K  CAC  C  CH3   0  -0.684  -1.9917   1.5302  -0.5215
 D6K  CAE  C  CH3   0  -0.688  -1.4006   0.2605   1.5497
 D6K  CAH  C  CH2   0  -0.477   1.3525  -0.8281  -0.6607
 D6K  CAI  C  CH1   0   0.019   1.3733   0.3432   0.3065
 D6K  CAK  C  CT    0   0.470  -1.0024   0.5599   0.1035
 D6K  CAL  C  CH1   0   0.240   0.0065  -1.5299  -0.6250
 D6K  OAF  O  OH1   0  -0.663  -0.0495  -2.3149   0.5290
 D6K  OAG  O  O2    0  -0.507   0.2563   1.1789   0.0291
 D6K  OAJ  O  O2    0  -0.518  -1.0473  -0.6016  -0.7109
 D6K  H1   H  HCH3  0   0.226   2.7152   1.5828  -0.8505
 D6K  H2   H  HCH3  0   0.238   2.6096   2.0304   0.8588
 D6K  H3   H  HCH3  0   0.232   3.5045   0.5909   0.3773
 D6K  H4   H  HCH3  0   0.232  -2.0308   2.4572   0.0504
 D6K  H5   H  HCH3  0   0.238  -1.7092   1.7680  -1.5479
 D6K  H6   H  HCH3  0   0.233  -2.9936   1.1012  -0.5297
 D6K  H7   H  HCH3  0   0.232  -2.3847  -0.2080   1.5749
 D6K  H8   H  HCH3  0   0.245  -0.7058  -0.4022   2.0606
 D6K  H9   H  HCH3  0   0.227  -1.4601   1.1918   2.1137
 D6K  H11  H  HCH2  0   0.247   2.1501  -1.5382  -0.4347
 D6K  H12  H  HCH1  0   0.217   1.3210  -0.0294   1.3377
 D6K  H13  H  HCH1  0   0.226  -0.1182  -2.1552  -1.5166
 D6K  H14  H  HOH1  0   0.456  -0.8769  -2.8087   0.5307
 D6K  H10  H  HCH2  0   0.237   1.5265  -0.4594  -1.6756

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
 D6K  CAE  CAK  single  1.530  0.020  1.530
 D6K  OAF  CAL  single  1.397  0.020  1.397
 D6K  CAC  CAK  single  1.520  0.020  1.520
 D6K  CAK  OAJ  single  1.419  0.020  1.419
 D6K  CAK  OAG  single  1.405  0.020  1.405
 D6K  OAJ  CAL  single  1.407  0.020  1.407
 D6K  CAL  CAH  single  1.518  0.020  1.518
 D6K  OAG  CAI  single  1.422  0.020  1.422
 D6K  CAI  CAH  single  1.519  0.020  1.519
 D6K  CAI  CAA  single  1.514  0.020  1.514
 D6K  CAA  H1   single  0.970  0.020  1.090
 D6K  CAA  H2   single  0.970  0.020  1.090
 D6K  CAA  H3   single  0.970  0.020  1.090
 D6K  CAC  H4   single  0.970  0.020  1.090
 D6K  CAC  H5   single  0.970  0.020  1.090
 D6K  CAC  H6   single  0.970  0.020  1.090
 D6K  CAE  H7   single  0.970  0.020  1.090
 D6K  CAE  H8   single  0.970  0.020  1.090
 D6K  CAE  H9   single  0.970  0.020  1.090
 D6K  CAH  H10  single  0.970  0.020  1.090
 D6K  CAH  H11  single  0.970  0.020  1.090
 D6K  CAI  H12  single  0.970  0.020  1.090
 D6K  CAL  H13  single  0.970  0.020  1.090
 D6K  OAF  H14  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
 D6K  H3   CAA  H2   107.81  3.000
 D6K  H3   CAA  H1   107.98  3.000
 D6K  H2   CAA  H1   108.43  3.000
 D6K  H3   CAA  CAI  110.01  3.000
 D6K  H2   CAA  CAI  111.31  3.000
 D6K  H1   CAA  CAI  111.18  3.000
 D6K  H6   CAC  H5   108.46  3.000
 D6K  H6   CAC  H4   107.81  3.000
 D6K  H5   CAC  H4   108.51  3.000
 D6K  H6   CAC  CAK  110.49  3.000
 D6K  H5   CAC  CAK  110.95  3.000
 D6K  H4   CAC  CAK  110.52  3.000
 D6K  H9   CAE  H8   108.19  3.000
 D6K  H9   CAE  H7   107.80  3.000
 D6K  H8   CAE  H7   107.70  3.000
 D6K  H9   CAE  CAK  109.64  3.000
 D6K  H8   CAE  CAK  113.40  3.000
 D6K  H7   CAE  CAK  109.94  3.000
 D6K  H11  CAH  H10  107.17  3.000
 D6K  H11  CAH  CAL  110.01  3.000
 D6K  H10  CAH  CAL  108.58  3.000
 D6K  H11  CAH  CAI  111.08  3.000
 D6K  H10  CAH  CAI  109.19  3.000
 D6K  CAL  CAH  CAI  110.70  3.000
 D6K  H12  CAI  OAG  110.19  3.000
 D6K  H12  CAI  CAH  109.62  3.000
 D6K  OAG  CAI  CAH  108.55  3.000
 D6K  H12  CAI  CAA  108.54  3.000
 D6K  CAH  CAI  CAA  112.50  3.000
 D6K  OAG  CAI  CAA  107.42  3.000
 D6K  OAJ  CAK  OAG  111.01  3.000
 D6K  OAG  CAK  CAE  111.69  3.000
 D6K  OAJ  CAK  CAE  111.97  3.000
 D6K  OAG  CAK  CAC  106.27  3.000
 D6K  OAJ  CAK  CAC  105.42  3.000
 D6K  CAE  CAK  CAC  110.14  3.000
 D6K  H13  CAL  OAJ  103.98  3.000
 D6K  H13  CAL  OAF  110.29  3.000
 D6K  OAJ  CAL  OAF  113.03  3.000
 D6K  H13  CAL  CAH  110.20  3.000
 D6K  OAJ  CAL  CAH  110.95  3.000
 D6K  OAF  CAL  CAH  108.34  3.000
 D6K  H14  OAF  CAL  108.90  3.000
 D6K  CAK  OAG  CAI  115.76  3.000
 D6K  CAL  OAJ  CAK  118.77  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
 D6K  Var_01  OAJ  CAK  OAG  CAI  -53.52  30.0  1
 D6K  Var_02  OAG  CAK  OAJ  CAL   47.80  30.0  1
 D6K  Var_03  H7   CAE  CAK  OAG  179.34  30.0  3
 D6K  Var_04  H4   CAC  CAK  OAG  -62.65  30.0  3

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
 D6K  chir_01  CAI  OAG  CAH  CAA  negativ
 D6K  chir_02  CAL  OAJ  OAF  CAH  positiv

