# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 19:40:50 2021
#   Inital geometry file: a 55 line input string
#   Ligand name: beta-L-altropyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[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
 3MK  3MK  'beta-L-altropyranose     '  L-saccharide  24  12  .  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_3MK
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
 3MK  C1   C  CR16  0   0.241  4.8996  -12.6827  26.3433
 3MK  O1   O  OH1   0  -0.664  4.1113  -11.6317  26.8089
 3MK  C2   C  CR16  0  -0.017  6.3573  -12.3328  26.5919
 3MK  O2   O  OH1   0  -0.670  6.5638  -12.2384  27.9781
 3MK  C3   C  CR16  0  -0.006  6.7631  -11.0632  25.8327
 3MK  O3   O  OH1   0  -0.673  8.1331  -11.2010  25.5316
 3MK  C4   C  CR16  0  -0.012  5.9033  -10.8914  24.5681
 3MK  O4   O  OH1   0  -0.678  6.6491  -10.1709  23.6153
 3MK  C5   C  CR16  0   0.005  5.4841  -12.2619  24.0303
 3MK  O5   O  O     0  -0.515  4.6870  -12.9566  24.9847
 3MK  C6   C  CH2   0  -0.193  4.7123  -12.1956  22.7307
 3MK  O6   O  OH1   0  -0.671  3.6226  -11.3145  22.8636
 3MK  H1   H  HCR6  0   0.232  4.6475  -13.6125  26.8676
 3MK  HO1  H  HOH1  0   0.459  3.1857  -11.8969  26.7776
 3MK  H2   H  HCR6  0   0.230  6.9428  -13.1627  26.1703
 3MK  HO2  H  HOH1  0   0.455  7.5122  -12.2095  28.1377
 3MK  H3   H  HCR6  0   0.222  6.5975  -10.1943  26.4839
 3MK  HO3  H  HOH1  0   0.451  8.4116  -10.4183  25.0447
 3MK  H4   H  HCR6  0   0.238  5.0042  -10.3409  24.8553
 3MK  HO4  H  HOH1  0   0.461  6.0407   -9.6560  23.0778
 3MK  H5   H  HCR6  0   0.223  6.3936  -12.8448  23.8172
 3MK  H61  H  HCH2  0   0.206  5.4056  -11.8774  21.9430
 3MK  H62  H  HCH2  0   0.217  4.3880  -13.2107  22.4650
 3MK  HO6  H  HOH1  0   0.458  3.2056  -11.2224  22.0027

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
 3MK  C1  O1   single  1.394  0.020  1.394
 3MK  C1  C2   single  1.520  0.020  1.520
 3MK  C1  O5   single  1.402  0.020  1.402
 3MK  C2  O2   single  1.405  0.020  1.405
 3MK  C2  C3   single  1.534  0.020  1.534
 3MK  C3  O3   single  1.410  0.020  1.410
 3MK  C3  C4   single  1.539  0.020  1.539
 3MK  C4  O4   single  1.408  0.020  1.408
 3MK  C4  C5   single  1.531  0.020  1.531
 3MK  C5  O5   single  1.424  0.020  1.424
 3MK  C5  C6   single  1.513  0.020  1.513
 3MK  C6  O6   single  1.408  0.020  1.408
 3MK  C1  H1   single  0.970  0.020  1.090
 3MK  O1  HO1  single  0.850  0.020  0.980
 3MK  C2  H2   single  0.970  0.020  1.090
 3MK  O2  HO2  single  0.850  0.020  0.980
 3MK  C3  H3   single  0.970  0.020  1.090
 3MK  O3  HO3  single  0.850  0.020  0.980
 3MK  C4  H4   single  0.970  0.020  1.090
 3MK  O4  HO4  single  0.850  0.020  0.980
 3MK  C5  H5   single  0.970  0.020  1.090
 3MK  C6  H61  single  0.970  0.020  1.090
 3MK  C6  H62  single  0.970  0.020  1.090
 3MK  O6  HO6  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
 3MK  H1   C1  O5   105.23  3.000
 3MK  H1   C1  C2   109.72  3.000
 3MK  O5   C1  C2   110.42  3.000
 3MK  H1   C1  O1   110.46  3.000
 3MK  O5   C1  O1   112.66  3.000
 3MK  C2   C1  O1   108.32  3.000
 3MK  HO1  O1  C1   108.97  3.000
 3MK  H2   C2  C3   107.10  3.000
 3MK  H2   C2  O2   110.53  3.000
 3MK  C3   C2  O2   113.20  3.000
 3MK  H2   C2  C1   105.92  3.000
 3MK  C3   C2  C1   111.31  3.000
 3MK  O2   C2  C1   108.54  3.000
 3MK  HO2  O2  C2   108.10  3.000
 3MK  H3   C3  C4   108.34  3.000
 3MK  H3   C3  O3   110.52  3.000
 3MK  C4   C3  O3   112.23  3.000
 3MK  H3   C3  C2   108.75  3.000
 3MK  C4   C3  C2   110.57  3.000
 3MK  O3   C3  C2   106.38  3.000
 3MK  HO3  O3  C3   108.04  3.000
 3MK  H4   C4  C5   108.54  3.000
 3MK  H4   C4  O4   110.84  3.000
 3MK  C5   C4  O4   111.43  3.000
 3MK  H4   C4  C3   107.45  3.000
 3MK  C5   C4  C3   109.99  3.000
 3MK  O4   C4  C3   108.50  3.000
 3MK  HO4  O4  C4   108.49  3.000
 3MK  H5   C5  C6   106.16  3.000
 3MK  H5   C5  O5   109.50  3.000
 3MK  C6   C5  O5   108.15  3.000
 3MK  H5   C5  C4   108.40  3.000
 3MK  C6   C5  C4   113.72  3.000
 3MK  O5   C5  C4   110.76  3.000
 3MK  C5   O5  C1   117.98  3.000
 3MK  H62  C6  H61  106.33  3.000
 3MK  H62  C6  O6   111.89  3.000
 3MK  H61  C6  O6   112.06  3.000
 3MK  H62  C6  C5   108.54  3.000
 3MK  H61  C6  C5   107.89  3.000
 3MK  O6   C6  C5   109.95  3.000
 3MK  HO6  O6  C6   108.14  3.000

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
 3MK  chir_01  C1  O1  C2  O5  positiv
 3MK  chir_02  C2  O2  C1  C3  negativ
 3MK  chir_03  C3  O3  C2  C4  positiv
 3MK  chir_04  C4  O4  C5  C3  negativ
 3MK  chir_05  C5  O5  C4  C6  positiv

