# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:18:11 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-O-methyl-D-fructose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]([C@H](O)[C@H](O)CO)C(=O)CO
#
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
 3MF  3MF  '3-O-methyl-D-fructose    '  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_3MF
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
 3MF  C1   C  CH2   0  -0.252  -0.9471   0.9946   2.4840
 3MF  C2   C  C     0   0.346   0.0163  -0.0432   1.9661
 3MF  C3   C  CH1   0  -0.070   0.5867   0.2314   0.5781
 3MF  C4   C  CH1   0  -0.039  -0.4565  -0.1538  -0.4819
 3MF  C5   C  CH1   0  -0.013   0.0491   0.1300  -1.9091
 3MF  C6   C  CH2   0  -0.164  -1.0684  -0.0954  -2.9161
 3MF  O1   O  OH1   0  -0.657  -1.4908   0.5710   3.6959
 3MF  O2   O  O     0  -0.378   0.3304  -1.0118   2.6090
 3MF  O3   O  O2    0  -0.488   1.7380  -0.5187   0.3413
 3MF  O4   O  OH1   0  -0.655  -0.8705  -1.4887  -0.3293
 3MF  O5   O  OH1   0  -0.657   0.5961   1.4221  -2.0124
 3MF  O6   O  OH1   0  -0.670  -0.5444   0.0558  -4.2141
 3MF  H11  H  HCH2  0   0.243  -0.3804   1.9341   2.5711
 3MF  H12  H  HCH2  0   0.237  -1.7113   1.1847   1.7170
 3MF  H3   H  HCH1  0   0.248   0.7812   1.3105   0.4898
 3MF  H4   H  HCH1  0   0.252  -1.3502   0.4572  -0.3100
 3MF  H5   H  HCH1  0   0.239   0.8677  -0.5615  -2.1356
 3MF  H61  H  HCH2  0   0.209  -1.4919  -1.0936  -2.7639
 3MF  H62  H  HCH2  0   0.192  -1.8755   0.6270  -2.7175
 3MF  H71  H  HCH3  0   0.240   3.7442  -0.5995   0.5976
 3MF  H72  H  HCH3  0   0.212   3.0833   1.0449   0.5802
 3MF  H73  H  HCH3  0   0.214   2.8773   0.0163   2.0112
 3MF  HO1  H  HOH1  0   0.463  -2.1154   1.2406   3.9883
 3MF  HO4  H  HOH1  0   0.450  -0.1029  -2.0642  -0.4237
 3MF  HO5  H  HOH1  0   0.446  -0.1164   2.0682  -1.9525
 3MF  HO6  H  HOH1  0   0.456  -1.2478  -0.1314  -4.8418
 3MF  C7   C  CH3   0  -0.406   2.9065   0.0182   0.9174

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
 3MF  C1  C2   single  1.508  0.020  1.508
 3MF  C1  O1   single  1.394  0.020  1.394
 3MF  C1  H11  single  0.970  0.020  1.090
 3MF  C1  H12  single  0.970  0.020  1.090
 3MF  C2  C3   single  1.526  0.020  1.526
 3MF  C2  O2   double  1.204  0.020  1.204
 3MF  C3  C4   single  1.536  0.020  1.536
 3MF  C3  O3   single  1.394  0.020  1.394
 3MF  C3  H3   single  0.970  0.020  1.090
 3MF  C4  C5   single  1.540  0.020  1.540
 3MF  C4  O4   single  1.406  0.020  1.406
 3MF  C4  H4   single  0.970  0.020  1.090
 3MF  C5  C6   single  1.521  0.020  1.521
 3MF  C5  O5   single  1.407  0.020  1.407
 3MF  C5  H5   single  0.970  0.020  1.090
 3MF  C6  O6   single  1.408  0.020  1.408
 3MF  C6  H61  single  0.970  0.020  1.090
 3MF  C6  H62  single  0.970  0.020  1.090
 3MF  C7  O3   single  1.409  0.020  1.409
 3MF  C7  H71  single  0.970  0.020  1.090
 3MF  C7  H72  single  0.970  0.020  1.090
 3MF  C7  H73  single  0.970  0.020  1.090
 3MF  O1  HO1  single  0.850  0.020  0.980
 3MF  O4  HO4  single  0.850  0.020  0.980
 3MF  O5  HO5  single  0.850  0.020  0.980
 3MF  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
 3MF  H12  C1  H11  105.40  3.000
 3MF  H12  C1  O1   112.83  3.000
 3MF  H11  C1  O1   113.04  3.000
 3MF  H12  C1  C2   108.87  3.000
 3MF  H11  C1  C2   106.60  3.000
 3MF  O1   C1  C2   109.79  3.000
 3MF  O2   C2  C3   122.21  3.000
 3MF  O2   C2  C1   122.47  3.000
 3MF  C3   C2  C1   115.31  3.000
 3MF  H3   C3  O3   111.60  3.000
 3MF  H3   C3  C4   108.10  3.000
 3MF  O3   C3  C4   107.97  3.000
 3MF  H3   C3  C2   108.40  3.000
 3MF  O3   C3  C2   111.50  3.000
 3MF  C4   C3  C2   109.19  3.000
 3MF  H4   C4  O4   105.79  3.000
 3MF  H4   C4  C5   108.08  3.000
 3MF  O4   C4  C5   111.85  3.000
 3MF  H4   C4  C3   107.80  3.000
 3MF  O4   C4  C3   111.29  3.000
 3MF  C5   C4  C3   111.73  3.000
 3MF  H5   C5  O5   105.91  3.000
 3MF  H5   C5  C6   108.58  3.000
 3MF  O5   C5  C6   111.91  3.000
 3MF  H5   C5  C4   108.70  3.000
 3MF  O5   C5  C4   111.40  3.000
 3MF  C6   C5  C4   110.18  3.000
 3MF  H62  C6  H61  106.83  3.000
 3MF  H62  C6  O6   111.63  3.000
 3MF  H61  C6  O6   111.72  3.000
 3MF  H62  C6  C5   108.77  3.000
 3MF  H61  C6  C5   109.10  3.000
 3MF  O6   C6  C5   108.72  3.000
 3MF  HO1  O1  C1   107.83  3.000
 3MF  C7   O3  C3   114.22  3.000
 3MF  HO4  O4  C4   108.77  3.000
 3MF  HO5  O5  C5   108.89  3.000
 3MF  HO6  O6  C6   107.99  3.000
 3MF  H73  C7  H72  108.29  3.000
 3MF  H73  C7  H71  108.25  3.000
 3MF  H72  C7  H71  108.49  3.000
 3MF  H73  C7  O3   112.70  3.000
 3MF  H72  C7  O3   111.42  3.000
 3MF  H71  C7  O3   107.56  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
 3MF  Var_01  O1   C1  C2  C3   174.45  30.0  1
 3MF  Var_02  H71  C7  O3  C3  -175.29  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
 3MF  chir_01  C3  C2  C4  O3  positiv
 3MF  chir_02  C4  O4  C3  C5  negativ
 3MF  chir_03  C5  O5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 3MF  plan-1  C1  0.020
 3MF  plan-1  C2  0.020
 3MF  plan-1  C3  0.020
 3MF  plan-1  O2  0.020

