# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:07:06 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-beta-D-glucopyranosyl-4-(hydroxymethyl)-1H-1,2,3-triazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)n2cc(CO)nn2
#
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
 RUG  RUG  1-beta-D-glucopyranosyl-4-(hydroxymethyl)-1H-1,2,3-triazole  D-saccharide  33  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RUG
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
 RUG  O2   O  OH1   0  -0.670   0.0269   2.5178  -0.5030
 RUG  C2   C  CH1   0  -0.023   0.7233   1.4617   0.1094
 RUG  C3   C  CH1   0  -0.009   2.1883   1.4562  -0.3168
 RUG  O3   O  OH1   0  -0.671   2.8723   2.5837   0.1741
 RUG  C4   C  CH1   0   0.035   2.8969   0.2128   0.2109
 RUG  O4   O  OH1   0  -0.670   4.2036   0.1163  -0.2962
 RUG  C5   C  CH1   0  -0.024   2.1245  -1.0314  -0.2285
 RUG  C6   C  CH2   0  -0.157   2.7104  -2.3070   0.3358
 RUG  O6   O  OH1   0  -0.670   2.0231  -3.4016  -0.2210
 RUG  O5   O  O2    0  -0.483   0.7846  -0.9388   0.2277
 RUG  C1   C  CH1   0   0.227   0.0937   0.1392  -0.3257
 RUG  N1   N  NR5   0  -0.304  -1.2790   0.0450   0.1008
 RUG  C7   C  CR15  0  -0.069  -2.3691  -0.1976  -0.6533
 RUG  N2   N  N     0  -0.100  -1.6089   0.2419   1.3640
 RUG  N3   N  N     0  -0.311  -2.8868   0.1287   1.4588
 RUG  C8   C  CR5   0   0.105  -3.4043  -0.1421   0.2398
 RUG  C9   C  CH2   0  -0.203  -4.8629  -0.3341   0.0097
 RUG  O9   O  OH1   0  -0.666  -5.0712  -0.4156  -1.3767
 RUG  HO2  H  HOH1  0   0.467  -0.1973   3.1731   0.1620
 RUG  H2   H  HCH1  0   0.251   0.6724   1.5261   1.2028
 RUG  H3   H  HCH1  0   0.222   2.2280   1.4250  -1.4169
 RUG  HO3  H  HOH1  0   0.458   2.6515   3.3411  -0.3762
 RUG  H4   H  HCH1  0   0.218   2.8973   0.2497   1.3120
 RUG  HO4  H  HOH1  0   0.456   4.6960   0.8889  -0.0000
 RUG  H5   H  HCH1  0   0.233   2.1442  -1.0887  -1.3288
 RUG  H6   H  HCH2  0   0.217   3.7779  -2.3325   0.0950
 RUG  H6A  H  HCH2  0   0.200   2.6272  -2.2845   1.4311
 RUG  HO6  H  HOH1  0   0.458   2.4474  -4.2071   0.0874
 RUG  H1   H  HCH1  0   0.257   0.0805   0.0848  -1.4230
 RUG  H7   H  HCR5  0   0.315  -2.3161  -0.3808  -1.7122
 RUG  H9   H  HCH2  0   0.226  -5.1939  -1.2428   0.5286
 RUG  H9A  H  HCH2  0   0.223  -5.4123   0.5002   0.4642
 RUG  HO9  H  HOH1  0   0.464  -5.9978  -0.6202  -1.5304

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
 RUG  O2  C2   single    1.405  0.020  1.405
 RUG  O2  HO2  single    0.850  0.020  0.980
 RUG  C3  C2   single    1.526  0.020  1.526
 RUG  C2  C1   single    1.528  0.020  1.528
 RUG  C2  H2   single    0.970  0.020  1.090
 RUG  O3  C3   single    1.407  0.020  1.407
 RUG  C3  C4   single    1.525  0.020  1.525
 RUG  C3  H3   single    0.970  0.020  1.090
 RUG  O3  HO3  single    0.850  0.020  0.980
 RUG  O4  C4   single    1.405  0.020  1.405
 RUG  C4  C5   single    1.529  0.020  1.529
 RUG  C4  H4   single    0.970  0.020  1.090
 RUG  O4  HO4  single    0.850  0.020  0.980
 RUG  C5  C6   single    1.513  0.020  1.513
 RUG  C5  O5   single    1.418  0.020  1.418
 RUG  C5  H5   single    0.970  0.020  1.090
 RUG  O6  C6   single    1.407  0.020  1.407
 RUG  C6  H6   single    0.970  0.020  1.090
 RUG  C6  H6A  single    0.970  0.020  1.090
 RUG  O6  HO6  single    0.850  0.020  0.980
 RUG  C1  O5   single    1.395  0.020  1.395
 RUG  C1  N1   single    1.440  0.020  1.440
 RUG  C1  H1   single    0.970  0.020  1.090
 RUG  C7  N1   aromatic  1.348  0.020  1.348
 RUG  N1  N2   aromatic  1.320  0.020  1.320
 RUG  C7  C8   aromatic  1.368  0.020  1.368
 RUG  C7  H7   single    0.930  0.020  1.080
 RUG  N2  N3   aromatic  1.286  0.020  1.286
 RUG  C8  N3   aromatic  1.352  0.020  1.352
 RUG  C8  C9   single    1.489  0.020  1.489
 RUG  C9  O9   single    1.404  0.020  1.404
 RUG  C9  H9   single    0.970  0.020  1.090
 RUG  C9  H9A  single    0.970  0.020  1.090
 RUG  O9  HO9  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
 RUG  HO2  O2  C2  109.08  3.000
 RUG  H2   C2  C1  108.40  3.000
 RUG  H2   C2  C3  108.87  3.000
 RUG  C1   C2  C3  108.24  3.000
 RUG  H2   C2  O2  111.55  3.000
 RUG  C1   C2  O2  108.79  3.000
 RUG  C3   C2  O2  110.90  3.000
 RUG  H3   C3  C4  107.80  3.000
 RUG  H3   C3  O3  110.71  3.000
 RUG  C4   C3  O3  107.86  3.000
 RUG  H3   C3  C2  108.29  3.000
 RUG  C4   C3  C2  110.63  3.000
 RUG  O3   C3  C2  111.49  3.000
 RUG  HO3  O3  C3  108.64  3.000
 RUG  H4   C4  C5  108.33  3.000
 RUG  H4   C4  O4  111.27  3.000
 RUG  C5   C4  O4  108.07  3.000
 RUG  H4   C4  C3  108.58  3.000
 RUG  C5   C4  C3  109.23  3.000
 RUG  O4   C4  C3  111.30  3.000
 RUG  HO4  O4  C4  108.03  3.000
 RUG  H5   C5  O5  109.96  3.000
 RUG  H5   C5  C6  108.77  3.000
 RUG  O5   C5  C6  107.52  3.000
 RUG  H5   C5  C4  108.67  3.000
 RUG  O5   C5  C4  109.37  3.000
 RUG  C6   C5  C4  112.54  3.000
 RUG  H6A  C6  H6  107.08  3.000
 RUG  H6A  C6  O6  111.92  3.000
 RUG  H6   C6  O6  111.79  3.000
 RUG  H6A  C6  C5  108.98  3.000
 RUG  H6   C6  C5  108.37  3.000
 RUG  O6   C6  C5  108.61  3.000
 RUG  HO6  O6  C6  108.02  3.000
 RUG  C1   O5  C5  113.00  3.000
 RUG  H1   C1  N1  106.32  3.000
 RUG  H1   C1  O5  111.34  3.000
 RUG  N1   C1  O5  107.70  3.000
 RUG  H1   C1  C2  109.40  3.000
 RUG  N1   C1  C2  111.41  3.000
 RUG  O5   C1  C2  110.60  3.000
 RUG  N2   N1  C7  111.11  3.000
 RUG  N2   N1  C1  120.77  3.000
 RUG  C7   N1  C1  128.10  3.000
 RUG  H7   C7  C8  133.36  3.000
 RUG  H7   C7  N1  122.79  3.000
 RUG  C8   C7  N1  103.85  3.000
 RUG  N3   N2  N1  107.79  3.000
 RUG  C8   N3  N2  109.36  3.000
 RUG  C9   C8  N3  122.70  3.000
 RUG  C9   C8  C7  129.42  3.000
 RUG  N3   C8  C7  107.89  3.000
 RUG  H9A  C9  H9  106.41  3.000
 RUG  H9A  C9  O9  112.26  3.000
 RUG  H9   C9  O9  111.96  3.000
 RUG  H9A  C9  C8  109.17  3.000
 RUG  H9   C9  C8  109.21  3.000
 RUG  O9   C9  C8  107.78  3.000
 RUG  HO9  O9  C9  108.24  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
 RUG  CONST_01  N3  C8  C7  N1    0.00   0.0  0
 RUG  CONST_02  C8  N3  N2  N1    0.00   0.0  0
 RUG  CONST_03  N3  N2  N1  C7    0.00   0.0  0
 RUG  CONST_04  N2  N3  C8  C7    0.00   0.0  0
 RUG  CONST_05  C8  C7  N1  N2    0.00   0.0  0
 RUG  CONST_06  C8  C7  N1  C1  180.00   0.0  0
 RUG  CONST_07  N3  N2  N1  C1  180.00   0.0  0
 RUG  CONST_08  C9  C8  C7  N1  180.00   0.0  0
 RUG  CONST_09  C9  C8  N3  N2  180.00   0.0  0
 RUG  CONST_10  H7  C7  N1  C1    0.00   0.0  0
 RUG  Var_01    O9  C9  C8  C7   -8.06  30.0  2

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
 RUG  chir_01  C2  O2  C3  C1  positiv
 RUG  chir_02  C3  O3  C2  C4  positiv
 RUG  chir_03  C4  O4  C5  C3  positiv
 RUG  chir_04  C5  O5  C4  C6  negativ
 RUG  chir_05  C1  O5  N1  C2  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
 RUG  plan-1  C1  0.020
 RUG  plan-1  N1  0.020
 RUG  plan-1  C7  0.020
 RUG  plan-1  N2  0.020
 RUG  plan-1  N3  0.020
 RUG  plan-1  C8  0.020
 RUG  plan-1  C9  0.020
 RUG  plan-1  H7  0.020

