# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 18:08:04 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: beta-L-ribopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CO[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
 0MK  0MK  'beta-L-ribopyranose      '  L-saccharide  20  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0MK
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
 0MK  C1   C  CH1   0   0.275  -10.2549  -28.7539  -26.0910
 0MK  C2   C  CH1   0  -0.025   -9.2107  -29.5648  -26.8560
 0MK  C3   C  CH1   0  -0.054   -9.8554  -30.2471  -28.0611
 0MK  C4   C  CH1   0   0.030  -10.5669  -29.1887  -28.9021
 0MK  C5   C  CH2   0  -0.206  -11.5269  -28.3832  -28.0339
 0MK  O1   O  OH1   0  -0.662   -9.6127  -28.0864  -25.0647
 0MK  O2   O  OH1   0  -0.667   -8.6415  -30.5724  -26.0581
 0MK  O3   O  OH1   0  -0.663  -10.7963  -31.2145  -27.6649
 0MK  O4   O  OH1   0  -0.664  -11.3079  -29.7373  -29.9609
 0MK  O5   O  O2    0  -0.492  -10.8371  -27.8015  -26.9493
 0MK  H1   H  HCH1  0   0.188  -11.0368  -29.4267  -25.7021
 0MK  H2   H  HCH1  0   0.217   -8.4461  -28.8635  -27.2251
 0MK  H3   H  HCH1  0   0.231   -9.0571  -30.7048  -28.6674
 0MK  H4   H  HCH1  0   0.215   -9.7927  -28.5019  -29.2739
 0MK  H51  H  HCH2  0   0.247  -11.9600  -27.5649  -28.6108
 0MK  H52  H  HCH2  0   0.213  -12.3516  -29.0203  -27.6866
 0MK  HO1  H  HOH1  0   0.464  -10.2513  -27.8504  -24.3834
 0MK  HO2  H  HOH1  0   0.452   -8.3134  -30.1727  -25.2454
 0MK  HO3  H  HOH1  0   0.448  -10.3679  -31.7988  -27.0299
 0MK  HO4  H  HOH1  0   0.452  -10.7001  -30.1635  -30.5735

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
 0MK  O4  C4   single  1.404  0.020  1.404
 0MK  C4  C5   single  1.524  0.020  1.524
 0MK  C4  C3   single  1.528  0.020  1.528
 0MK  C5  O5   single  1.411  0.020  1.411
 0MK  C3  O3   single  1.406  0.020  1.406
 0MK  C3  C2   single  1.528  0.020  1.528
 0MK  O5  C1   single  1.408  0.020  1.408
 0MK  C2  C1   single  1.527  0.020  1.527
 0MK  C2  O2   single  1.406  0.020  1.406
 0MK  C1  O1   single  1.382  0.020  1.382
 0MK  C1  H1   single  0.970  0.020  1.090
 0MK  C2  H2   single  0.970  0.020  1.090
 0MK  C3  H3   single  0.970  0.020  1.090
 0MK  C4  H4   single  0.970  0.020  1.090
 0MK  C5  H51  single  0.970  0.020  1.090
 0MK  C5  H52  single  0.970  0.020  1.090
 0MK  O1  HO1  single  0.850  0.020  0.980
 0MK  O2  HO2  single  0.850  0.020  0.980
 0MK  O3  HO3  single  0.850  0.020  0.980
 0MK  O4  HO4  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
 0MK  H1   C1  O5   109.54  3.000
 0MK  H1   C1  O1   111.24  3.000
 0MK  O5   C1  O1   108.54  3.000
 0MK  H1   C1  C2   109.73  3.000
 0MK  O1   C1  C2   108.09  3.000
 0MK  O5   C1  C2   109.66  3.000
 0MK  H2   C2  O2   111.44  3.000
 0MK  H2   C2  C3   108.24  3.000
 0MK  O2   C2  C3   107.37  3.000
 0MK  H2   C2  C1   107.73  3.000
 0MK  O2   C2  C1   111.91  3.000
 0MK  C3   C2  C1   110.10  3.000
 0MK  H3   C3  O3   110.73  3.000
 0MK  H3   C3  C4   108.80  3.000
 0MK  O3   C3  C4   108.66  3.000
 0MK  H3   C3  C2   108.29  3.000
 0MK  O3   C3  C2   111.55  3.000
 0MK  C4   C3  C2   108.75  3.000
 0MK  H4   C4  O4   111.14  3.000
 0MK  H4   C4  C5   107.81  3.000
 0MK  O4   C4  C5   107.67  3.000
 0MK  H4   C4  C3   106.92  3.000
 0MK  C5   C4  C3   110.23  3.000
 0MK  O4   C4  C3   112.97  3.000
 0MK  H52  C5  H51  107.71  3.000
 0MK  H52  C5  O5   111.29  3.000
 0MK  H51  C5  O5   106.94  3.000
 0MK  H52  C5  C4   110.26  3.000
 0MK  H51  C5  C4   110.20  3.000
 0MK  O5   C5  C4   110.35  3.000
 0MK  HO1  O1  C1   109.60  3.000
 0MK  HO2  O2  C2   108.63  3.000
 0MK  HO3  O3  C3   107.78  3.000
 0MK  HO4  O4  C4   108.65  3.000
 0MK  C5   O5  C1   113.07  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
 0MK  Var_01  C4  C5  O5  C1  -61.85  30.0  1

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
 0MK  chir_01  C1  O5  C2  O1  negativ
 0MK  chir_02  C2  O2  C1  C3  positiv
 0MK  chir_03  C3  O3  C2  C4  positiv
 0MK  chir_04  C4  O4  C3  C5  positiv

