# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:00:05 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R},6~{R})-6-(methoxymethyl)oxane-2,3,4,5-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H]1O[C@@H](O)[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
 EMZ  EMZ  (2~{R},3~{R},4~{S},5~{R},6~{R})-6-(methoxymethyl)oxane-2,3,4,5-tetrol  D-saccharide  27  13  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EMZ
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
 EMZ  C4   C  CH1   0   0.000  -0.1160   1.3938  -0.1472
 EMZ  C5   C  CH1   0  -0.028   0.8629   0.2524  -0.3962
 EMZ  C6   C  CH2   0  -0.134   2.2700   0.6002   0.0399
 EMZ  C3   C  CH1   0   0.003  -1.5134   0.9439  -0.5633
 EMZ  CAM  C  CH3   0  -0.397   4.4778  -0.1492  -0.0401
 EMZ  O6   O  O2    0  -0.486   3.1453  -0.4025  -0.4046
 EMZ  O5   O  O2    0  -0.496   0.4579  -0.9167   0.2833
 EMZ  C1   C  CH1   0   0.264  -0.7874  -1.4016  -0.1572
 EMZ  O1   O  OH1   0  -0.661  -1.0850  -2.5495   0.5479
 EMZ  C2   C  CH1   0  -0.023  -1.8782  -0.3686   0.1184
 EMZ  O2   O  OH1   0  -0.672  -3.1218  -0.7782  -0.3988
 EMZ  O3   O  OH1   0  -0.674  -2.4106   1.9782  -0.2428
 EMZ  O4   O  OH1   0  -0.672  -0.0643   1.7479   1.2123
 EMZ  H1   H  HCH1  0   0.235   0.1812   2.2369  -0.7889
 EMZ  H2   H  HCH1  0   0.229   0.8766   0.0738  -1.4839
 EMZ  H3   H  HCH2  0   0.207   2.5379   1.5750  -0.3931
 EMZ  H4   H  HCH2  0   0.210   2.3182   0.7086   1.1317
 EMZ  H5   H  HCH1  0   0.213  -1.4936   0.7659  -1.6506
 EMZ  H6   H  HCH3  0   0.234   5.0899  -0.9738  -0.4040
 EMZ  H7   H  HCH3  0   0.204   4.8555   0.7821  -0.4792
 EMZ  H8   H  HCH3  0   0.204   4.6010  -0.0808   1.0474
 EMZ  H9   H  HCH1  0   0.186  -0.7414  -1.5938  -1.2443
 EMZ  H10  H  HOH1  0   0.466  -0.6096  -3.2950   0.1664
 EMZ  H11  H  HCH1  0   0.223  -1.9315  -0.2083   1.2045
 EMZ  H12  H  HOH1  0   0.458  -3.4647  -1.4896   0.1510
 EMZ  H13  H  HOH1  0   0.455  -3.3095   1.6553  -0.3672
 EMZ  H14  H  HOH1  0   0.452  -0.7629   2.3896   1.3795

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
 EMZ  O1   C1   single  1.380  0.020  1.380
 EMZ  O5   C1   single  1.407  0.020  1.407
 EMZ  O5   C5   single  1.412  0.020  1.412
 EMZ  O6   CAM  single  1.405  0.020  1.405
 EMZ  O6   C6   single  1.403  0.020  1.403
 EMZ  C1   C2   single  1.527  0.020  1.527
 EMZ  O2   C2   single  1.408  0.020  1.408
 EMZ  C6   C5   single  1.514  0.020  1.514
 EMZ  C2   C3   single  1.523  0.020  1.523
 EMZ  C5   C4   single  1.524  0.020  1.524
 EMZ  O4   C4   single  1.406  0.020  1.406
 EMZ  C4   C3   single  1.526  0.020  1.526
 EMZ  C3   O3   single  1.406  0.020  1.406
 EMZ  C4   H1   single  0.970  0.020  1.090
 EMZ  C5   H2   single  0.970  0.020  1.090
 EMZ  C6   H3   single  0.970  0.020  1.090
 EMZ  C6   H4   single  0.970  0.020  1.090
 EMZ  C3   H5   single  0.970  0.020  1.090
 EMZ  CAM  H6   single  0.970  0.020  1.090
 EMZ  CAM  H7   single  0.970  0.020  1.090
 EMZ  CAM  H8   single  0.970  0.020  1.090
 EMZ  C1   H9   single  0.970  0.020  1.090
 EMZ  O1   H10  single  0.850  0.020  0.980
 EMZ  C2   H11  single  0.970  0.020  1.090
 EMZ  O2   H12  single  0.850  0.020  0.980
 EMZ  O3   H13  single  0.850  0.020  0.980
 EMZ  O4   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
 EMZ  H1   C4   O4  111.16  3.000
 EMZ  H1   C4   C3  108.31  3.000
 EMZ  O4   C4   C3  111.82  3.000
 EMZ  H1   C4   C5  107.76  3.000
 EMZ  C3   C4   C5  108.84  3.000
 EMZ  O4   C4   C5  108.84  3.000
 EMZ  H2   C5   O5  110.14  3.000
 EMZ  H2   C5   C6  108.05  3.000
 EMZ  O5   C5   C6  108.56  3.000
 EMZ  H2   C5   C4  106.89  3.000
 EMZ  C6   C5   C4  112.20  3.000
 EMZ  O5   C5   C4  110.94  3.000
 EMZ  H4   C6   H3  107.05  3.000
 EMZ  H4   C6   O6  110.98  3.000
 EMZ  H3   C6   O6  110.89  3.000
 EMZ  H4   C6   C5  110.48  3.000
 EMZ  H3   C6   C5  108.46  3.000
 EMZ  O6   C6   C5  108.93  3.000
 EMZ  H5   C3   O3  110.80  3.000
 EMZ  H5   C3   C2  107.86  3.000
 EMZ  O3   C3   C2  112.27  3.000
 EMZ  H5   C3   C4  107.47  3.000
 EMZ  O3   C3   C4  107.78  3.000
 EMZ  C2   C3   C4  110.57  3.000
 EMZ  H8   CAM  H7  107.78  3.000
 EMZ  H8   CAM  H6  108.38  3.000
 EMZ  H7   CAM  H6  108.39  3.000
 EMZ  H8   CAM  O6  112.03  3.000
 EMZ  H7   CAM  O6  112.08  3.000
 EMZ  H6   CAM  O6  108.05  3.000
 EMZ  CAM  O6   C6  112.38  3.000
 EMZ  C1   O5   C5  112.87  3.000
 EMZ  H9   C1   C2  108.96  3.000
 EMZ  H9   C1   O1  111.53  3.000
 EMZ  C2   C1   O1  108.44  3.000
 EMZ  H9   C1   O5  109.34  3.000
 EMZ  C2   C1   O5  110.03  3.000
 EMZ  O1   C1   O5  108.52  3.000
 EMZ  H10  O1   C1  109.58  3.000
 EMZ  H11  C2   O2  111.27  3.000
 EMZ  H11  C2   C1  108.16  3.000
 EMZ  O2   C2   C1  111.58  3.000
 EMZ  H11  C2   C3  109.15  3.000
 EMZ  O2   C2   C3  107.33  3.000
 EMZ  C1   C2   C3  109.32  3.000
 EMZ  H12  O2   C2  108.66  3.000
 EMZ  H13  O3   C3  108.63  3.000
 EMZ  H14  O4   C4  108.00  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
 EMZ  Var_01  H6  CAM  O6  C6   179.09  30.0  3
 EMZ  Var_02  H3  C6   O6  CAM   60.56  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
 EMZ  chir_01  C4  C5  O4  C3  positiv
 EMZ  chir_02  C5  O5  C4  C6  negativ
 EMZ  chir_03  C3  O3  C4  C2  negativ
 EMZ  chir_04  C1  O1  O5  C2  positiv
 EMZ  chir_05  C2  O2  C1  C3  negativ

