# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:58:40 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R,3R,4S,5S,6R)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)O[C@@H](C(O)O)[C@@H](O)[C@@H]1OC
#
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
 U9J  U9J  '(2R,3R,4S,5S,6R)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol (non-preferred name)'  L-saccharide  31  15  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U9J
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
 U9J  O4    O  OH1   0  -0.659  26.0145   3.2691  59.4491
 U9J  C4    C  CR16  0   0.016  26.4467   3.0930  60.7752
 U9J  C5    C  CR16  0  -0.037  26.8416   1.6371  61.0759
 U9J  O5    O  O     0  -0.499  25.7671   0.9306  61.6692
 U9J  C6    C  CH1   0   0.250  27.3195   0.8508  59.8629
 U9J  O6A   O  OH1   0  -0.673  28.0223  -0.2589  60.3482
 U9J  O6B   O  OH1   0  -0.663  26.2200   0.4695  59.0982
 U9J  C3    C  CR16  0   0.040  25.3768   3.5353  61.7779
 U9J  O3    O  O2    0  -0.502  25.3829   4.9418  61.8351
 U9J  C3M   C  CH3   0  -0.410  24.1104   5.5411  61.9397
 U9J  C2    C  CR16  0  -0.074  25.6724   2.8685  63.1191
 U9J  O2    O  O2    0  -0.500  24.8405   3.3011  64.1656
 U9J  C2M   C  CH3   0  -0.413  25.4107   4.2602  65.0286
 U9J  C1    C  CR16  0   0.289  25.4358   1.3585  62.9476
 U9J  O1    O  OH1   0  -0.662  26.1704   0.5964  63.8632
 U9J  H4    H  HCR6  0   0.221  27.3452   3.6987  60.9645
 U9J  H5    H  HCR6  0   0.255  27.6907   1.6787  61.7694
 U9J  H61   H  HCH1  0   0.209  27.9916   1.4969  59.2818
 U9J  H6O   H  HOH1  0   0.455  28.5016  -0.6624  59.6169
 U9J  H65   H  HOH1  0   0.459  26.4835   0.4144  58.1751
 U9J  H3    H  HCR6  0   0.223  24.3994   3.1824  61.4134
 U9J  H681  H  HCH3  0   0.232  24.2508   6.6193  61.8704
 U9J  H682  H  HCH3  0   0.214  23.4473   5.2283  61.1256
 U9J  H683  H  HCH3  0   0.215  23.6128   5.3177  62.8868
 U9J  H4O   H  HCR6  0   0.229  26.7275   3.0431  63.3828
 U9J  H6B1  H  HCH3  0   0.234  24.7059   4.4259  65.8425
 U9J  H6B2  H  HCH3  0   0.216  26.3554   3.9083  65.4581
 U9J  H6B3  H  HCH3  0   0.216  25.5983   5.2156  64.5329
 U9J  H1O   H  HCR6  0   0.216  24.3587   1.1700  63.0635
 U9J  H6    H  HOH1  0   0.451  25.9195   4.2163  59.3038
 U9J  HO1   H  HOH1  0   0.454  25.8618   0.8020  64.7526

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
 U9J  O4   C4    single  1.406  0.020  1.406
 U9J  C4   C5    single  1.538  0.020  1.538
 U9J  C4   C3    single  1.531  0.020  1.531
 U9J  C4   H4    single  0.970  0.020  1.090
 U9J  C5   O5    single  1.416  0.020  1.416
 U9J  C5   C6    single  1.522  0.020  1.522
 U9J  C5   H5    single  0.970  0.020  1.090
 U9J  O5   C1    single  1.388  0.020  1.388
 U9J  C6   O6A   single  1.400  0.020  1.400
 U9J  C6   O6B   single  1.392  0.020  1.392
 U9J  C6   H61   single  0.970  0.020  1.090
 U9J  O6A  H6O   single  0.850  0.020  0.980
 U9J  O6B  H65   single  0.850  0.020  0.980
 U9J  C3   O3    single  1.408  0.020  1.408
 U9J  C3   C2    single  1.527  0.020  1.527
 U9J  C3   H3    single  0.970  0.020  1.090
 U9J  O3   C3M   single  1.410  0.020  1.410
 U9J  C3M  H681  single  0.970  0.020  1.090
 U9J  C3M  H682  single  0.970  0.020  1.090
 U9J  C3M  H683  single  0.970  0.020  1.090
 U9J  C2   O2    single  1.405  0.020  1.405
 U9J  C2   C1    single  1.538  0.020  1.538
 U9J  C2   H4O   single  0.970  0.020  1.090
 U9J  O2   C2M   single  1.411  0.020  1.411
 U9J  C2M  H6B1  single  0.970  0.020  1.090
 U9J  C2M  H6B2  single  0.970  0.020  1.090
 U9J  C2M  H6B3  single  0.970  0.020  1.090
 U9J  C1   O1    single  1.400  0.020  1.400
 U9J  C1   H1O   single  0.970  0.020  1.090
 U9J  O4   H6    single  0.850  0.020  0.980
 U9J  O1   HO1   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
 U9J  H6    O4   C4    107.21  3.000
 U9J  H4    C4   C3    107.39  3.000
 U9J  H4    C4   C5    106.13  3.000
 U9J  C3    C4   C5    108.95  3.000
 U9J  H4    C4   O4    110.15  3.000
 U9J  C3    C4   O4    111.51  3.000
 U9J  C5    C4   O4    112.45  3.000
 U9J  H5    C5   C6    106.28  3.000
 U9J  H5    C5   O5    109.96  3.000
 U9J  C6    C5   O5    108.32  3.000
 U9J  H5    C5   C4    106.64  3.000
 U9J  C6    C5   C4    114.44  3.000
 U9J  O5    C5   C4    111.05  3.000
 U9J  C1    O5   C5    114.40  3.000
 U9J  H61   C6   O6B   110.71  3.000
 U9J  H61   C6   O6A   110.01  3.000
 U9J  O6B   C6   O6A   111.69  3.000
 U9J  H61   C6   C5    108.05  3.000
 U9J  O6B   C6   C5    109.34  3.000
 U9J  O6A   C6   C5    106.90  3.000
 U9J  H6O   O6A  C6    108.59  3.000
 U9J  H65   O6B  C6    109.06  3.000
 U9J  H3    C3   C2    108.82  3.000
 U9J  H3    C3   O3    109.72  3.000
 U9J  C2    C3   O3    113.57  3.000
 U9J  H3    C3   C4    108.11  3.000
 U9J  C2    C3   C4    108.29  3.000
 U9J  O3    C3   C4    108.19  3.000
 U9J  C3M   O3   C3    115.07  3.000
 U9J  H683  C3M  H682  108.06  3.000
 U9J  H683  C3M  H681  108.42  3.000
 U9J  H682  C3M  H681  108.25  3.000
 U9J  H683  C3M  O3    112.84  3.000
 U9J  H682  C3M  O3    111.69  3.000
 U9J  H681  C3M  O3    107.43  3.000
 U9J  H4O   C2   C1    109.25  3.000
 U9J  H4O   C2   O2    109.88  3.000
 U9J  C1    C2   O2    107.11  3.000
 U9J  H4O   C2   C3    109.06  3.000
 U9J  C1    C2   C3    107.52  3.000
 U9J  O2    C2   C3    113.90  3.000
 U9J  C2M   O2   C2    115.19  3.000
 U9J  H6B3  C2M  H6B2  108.10  3.000
 U9J  H6B3  C2M  H6B1  108.48  3.000
 U9J  H6B2  C2M  H6B1  108.28  3.000
 U9J  H6B3  C2M  O2    112.73  3.000
 U9J  H6B2  C2M  O2    111.71  3.000
 U9J  H6B1  C2M  O2    107.40  3.000
 U9J  H1O   C1   O1    110.61  3.000
 U9J  H1O   C1   C2    107.89  3.000
 U9J  O1    C1   C2    112.39  3.000
 U9J  H1O   C1   O5    106.14  3.000
 U9J  O1    C1   O5    108.02  3.000
 U9J  C2    C1   O5    111.63  3.000
 U9J  HO1   O1   C1    108.63  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
 U9J  Var_01  H681  C3M  O3  C3  -174.24  30.0  3
 U9J  Var_02  H6B1  C2M  O2  C2  -174.21  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
 U9J  chir_01  C4  O4  C5  C3  positiv
 U9J  chir_02  C5  O5  C4  C6  positiv
 U9J  chir_03  C3  O3  C2  C4  positiv
 U9J  chir_04  C2  O2  C1  C3  negativ
 U9J  chir_05  C1  O1  O5  C2  positiv

