# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:23:00 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: methyl (5R)-5-[(1S)-1,2-dihydroxyethyl]-alpha-D-lyxopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H]([C@@H](O)CO)[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
 A1Q  A1Q  'methyl (5R)-5-[(1S)-1,2-dihydroxyethyl]-alpha-D-lyxopyranoside'  D-saccharide  31  15  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A1Q
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
 A1Q  C1    C  CH1   0   0.246   6.1037  30.3784  15.3764
 A1Q  O7    O  OH1   0  -0.668  10.1392  26.9353  13.9282
 A1Q  O1    O  O2    0  -0.494   6.6988  31.5256  14.8653
 A1Q  C2    C  CH1   0  -0.028   5.7385  30.6554  16.8391
 A1Q  O2    O  OH1   0  -0.665   4.9374  29.6187  17.3470
 A1Q  C3    C  CH1   0   0.003   7.0167  30.7354  17.6726
 A1Q  O3    O  OH1   0  -0.670   6.7599  30.8631  19.0510
 A1Q  C4    C  CH1   0   0.026   7.8604  29.4813  17.4721
 A1Q  O4    O  OH1   0  -0.673   9.1033  29.5851  18.1233
 A1Q  C5    C  CH1   0   0.007   8.1369  29.3029  15.9790
 A1Q  O5    O  O2    0  -0.503   6.9152  29.2454  15.2634
 A1Q  C6    C  CH1   0  -0.018   8.9385  28.0438  15.6528
 A1Q  O6    O  OH1   0  -0.670   8.3164  26.8667  16.1176
 A1Q  C7    C  CH2   0  -0.151   9.1525  27.9156  14.1552
 A1Q  C8    C  CH3   0  -0.411   6.9478  31.4916  13.4760
 A1Q  HO7   H  HOH1  0   0.451  10.2455  26.8329  12.9785
 A1Q  H71   H  HCH2  0   0.197   9.4600  28.8937  13.7622
 A1Q  H72   H  HCH2  0   0.200   8.2062  27.6562  13.6660
 A1Q  H6    H  HCH1  0   0.226   9.9254  28.1743  16.1148
 A1Q  HO6   H  HOH1  0   0.453   8.5471  26.7394  17.0419
 A1Q  H5    H  HCH1  0   0.223   8.7414  30.1582  15.6428
 A1Q  H4    H  HCH1  0   0.212   7.2956  28.6125  17.8390
 A1Q  H1    H  HCH1  0   0.230   5.1964  30.1304  14.8041
 A1Q  H3    H  HCH1  0   0.224   7.5982  31.5921  17.3058
 A1Q  HO3   H  HOH1  0   0.454   6.5059  31.7723  19.2369
 A1Q  H2    H  HCH1  0   0.229   5.2148  31.6210  16.8862
 A1Q  HO2   H  HOH1  0   0.453   4.0799  29.6517  16.9113
 A1Q  H81C  H  HCH3  0   0.236   7.2469  32.4939  13.1747
 A1Q  H82C  H  HCH3  0   0.220   7.7501  30.7982  13.2100
 A1Q  H83C  H  HCH3  0   0.211   6.0509  31.2120  12.9127
 A1Q  HO4   H  HOH1  0   0.450   8.9372  29.7459  19.0577

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
 A1Q  O7  C7    single  1.409  0.020  1.409
 A1Q  C7  C6    single  1.518  0.020  1.518
 A1Q  C6  O6    single  1.410  0.020  1.410
 A1Q  C6  C5    single  1.528  0.020  1.528
 A1Q  C5  O5    single  1.417  0.020  1.417
 A1Q  C5  C4    single  1.529  0.020  1.529
 A1Q  O5  C1    single  1.398  0.020  1.398
 A1Q  C4  O4    single  1.407  0.020  1.407
 A1Q  C4  C3    single  1.525  0.020  1.525
 A1Q  C3  O3    single  1.408  0.020  1.408
 A1Q  C3  C2    single  1.528  0.020  1.528
 A1Q  C2  O2    single  1.405  0.020  1.405
 A1Q  C2  C1    single  1.533  0.020  1.533
 A1Q  C1  O1    single  1.390  0.020  1.390
 A1Q  O1  C8    single  1.412  0.020  1.412
 A1Q  O7  HO7   single  0.850  0.020  0.980
 A1Q  C7  H71   single  0.970  0.020  1.090
 A1Q  C7  H72   single  0.970  0.020  1.090
 A1Q  C6  H6    single  0.970  0.020  1.090
 A1Q  O6  HO6   single  0.850  0.020  0.980
 A1Q  C5  H5    single  0.970  0.020  1.090
 A1Q  C4  H4    single  0.970  0.020  1.090
 A1Q  C1  H1    single  0.970  0.020  1.090
 A1Q  C3  H3    single  0.970  0.020  1.090
 A1Q  O3  HO3   single  0.850  0.020  0.980
 A1Q  C2  H2    single  0.970  0.020  1.090
 A1Q  O2  HO2   single  0.850  0.020  0.980
 A1Q  C8  H81C  single  0.970  0.020  1.090
 A1Q  C8  H82C  single  0.970  0.020  1.090
 A1Q  C8  H83C  single  0.970  0.020  1.090
 A1Q  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
 A1Q  H1    C1  O5    104.70  3.000
 A1Q  H1    C1  C2    109.90  3.000
 A1Q  O5    C1  C2    111.22  3.000
 A1Q  H1    C1  O1    110.34  3.000
 A1Q  C2    C1  O1    107.68  3.000
 A1Q  O5    C1  O1    113.00  3.000
 A1Q  HO7   O7  C7    108.10  3.000
 A1Q  C8    O1  C1    114.68  3.000
 A1Q  H2    C2  C3    109.21  3.000
 A1Q  H2    C2  O2    111.16  3.000
 A1Q  C3    C2  O2    108.56  3.000
 A1Q  H2    C2  C1    108.24  3.000
 A1Q  O2    C2  C1    110.33  3.000
 A1Q  C3    C2  C1    109.31  3.000
 A1Q  HO2   O2  C2    108.60  3.000
 A1Q  H3    C3  C4    107.74  3.000
 A1Q  H3    C3  O3    110.66  3.000
 A1Q  C4    C3  O3    107.72  3.000
 A1Q  H3    C3  C2    107.54  3.000
 A1Q  O3    C3  C2    112.72  3.000
 A1Q  C4    C3  C2    110.37  3.000
 A1Q  HO3   O3  C3    108.85  3.000
 A1Q  H4    C4  C5    109.07  3.000
 A1Q  H4    C4  O4    110.96  3.000
 A1Q  C5    C4  O4    107.50  3.000
 A1Q  H4    C4  C3    108.78  3.000
 A1Q  O4    C4  C3    111.54  3.000
 A1Q  C5    C4  C3    108.94  3.000
 A1Q  HO4   O4  C4    108.01  3.000
 A1Q  H5    C5  C6    106.69  3.000
 A1Q  H5    C5  O5    110.55  3.000
 A1Q  C6    C5  O5    108.12  3.000
 A1Q  H5    C5  C4    107.89  3.000
 A1Q  O5    C5  C4    109.99  3.000
 A1Q  C6    C5  C4    113.55  3.000
 A1Q  C5    O5  C1    115.26  3.000
 A1Q  H6    C6  C7    107.37  3.000
 A1Q  H6    C6  O6    110.93  3.000
 A1Q  C7    C6  O6    108.47  3.000
 A1Q  H6    C6  C5    106.50  3.000
 A1Q  O6    C6  C5    112.71  3.000
 A1Q  C7    C6  C5    110.74  3.000
 A1Q  HO6   O6  C6    108.76  3.000
 A1Q  H72   C7  H71   107.03  3.000
 A1Q  H72   C7  C6    109.78  3.000
 A1Q  H71   C7  C6    108.50  3.000
 A1Q  H72   C7  O7    111.58  3.000
 A1Q  H71   C7  O7    111.46  3.000
 A1Q  C6    C7  O7    108.44  3.000
 A1Q  H83C  C8  H82C  108.29  3.000
 A1Q  H83C  C8  H81C  108.53  3.000
 A1Q  H82C  C8  H81C  108.36  3.000
 A1Q  H83C  C8  O1    111.57  3.000
 A1Q  H82C  C8  O1    112.59  3.000
 A1Q  H81C  C8  O1    107.38  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
 A1Q  Var_01  H81C  C8  O1  C1  170.32  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
 A1Q  chir_01  C1  O5  C2  O1  negativ
 A1Q  chir_02  C2  O2  C1  C3  positiv
 A1Q  chir_03  C3  O3  C2  C4  positiv
 A1Q  chir_04  C4  O4  C3  C5  negativ
 A1Q  chir_05  C5  O5  C6  C4  positiv
 A1Q  chir_06  C6  O6  C5  C7  positiv

