# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:58:01 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-beta-D-glucopyranosyl-1,3,5-triazinane-2,4,6-trione
#   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)N2C(=O)NC(=O)NC2=O
#
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
 C4B  C4B  1-beta-D-glucopyranosyl-1,3,5-triazinane-2,4,6-trione  D-saccharide  33  20  .  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_C4B
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
 C4B  C1'   C  CH1   0   0.214   0.1923  -0.2499   0.3972
 C4B  C2'   C  CH1   0  -0.002   0.7433  -1.5282  -0.2322
 C4B  O2'   O  OH1   0  -0.665  -0.0006  -2.5899   0.3042
 C4B  C3'   C  CH1   0   0.002   2.2225  -1.6097   0.1232
 C4B  O3'   O  OH1   0  -0.671   2.7462  -2.7461  -0.5155
 C4B  C4'   C  CH1   0  -0.003   2.9394  -0.3321  -0.3014
 C4B  O4'   O  OH1   0  -0.671   4.2765  -0.4397   0.1305
 C4B  C5'   C  CH1   0  -0.021   2.2414   0.8830   0.3232
 C4B  O5'   O  O2    0  -0.477   0.8723   0.8853  -0.0377
 C4B  C6'   C  CH2   0  -0.161   2.8411   2.1863  -0.1538
 C4B  O6'   O  OH1   0  -0.667   2.2358   3.2521   0.5350
 C4B  N1    N  NR6   0  -0.630  -1.2273  -0.0517   0.1450
 C4B  C2    C  CR6   0   0.755  -2.0805  -0.0236   1.2411
 C4B  O2    O  O     0  -0.447  -1.7037  -0.1602   2.3790
 C4B  N3    N  NR16  0  -0.721  -3.4030   0.1733   0.9454
 C4B  C4    C  CR6   0   0.687  -3.9440   0.3637  -0.2984
 C4B  O4    O  O     0  -0.446  -5.1214   0.5446  -0.4885
 C4B  N5    N  NR16  0  -0.724  -3.0140   0.3279  -1.3011
 C4B  C6    C  CR6   0   0.765  -1.6638   0.1268  -1.1601
 C4B  O6    O  O     0  -0.439  -0.9279   0.1112  -2.1133
 C4B  H1'   H  HCH1  0   0.268   0.2852  -0.3570   1.4834
 C4B  H2'   H  HCH1  0   0.245   0.6565  -1.4854  -1.3229
 C4B  HO2'  H  HOH1  0   0.458   0.2982  -3.4077  -0.1058
 C4B  H3'   H  HCH1  0   0.211   2.3103  -1.7029   1.2188
 C4B  HO3'  H  HOH1  0   0.455   3.6706  -2.8367  -0.2609
 C4B  H4'   H  HCH1  0   0.230   2.8803  -0.2448  -1.3960
 C4B  HO4'  H  HOH1  0   0.463   4.8468   0.0305  -0.4835
 C4B  H5'   H  HCH1  0   0.225   2.3426   0.8205   1.4195
 C4B  H6'   H  HCH2  0   0.206   3.9213   2.1521   0.0287
 C4B  H6'A  H  HCH2  0   0.201   2.6995   2.2652  -1.2409
 C4B  HO6'  H  HOH1  0   0.457   2.6924   4.0613   0.2888
 C4B  HN3   H  HNR6  0   0.450  -4.0396   0.1953   1.7319
 C4B  HN5   H  HNR6  0   0.451  -3.3488   0.4631  -2.2469

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
 C4B  C1'  C2'   single  1.528  0.020  1.528
 C4B  C1'  O5'   single  1.393  0.020  1.393
 C4B  C1'  N1    single  1.455  0.020  1.455
 C4B  C2'  O2'   single  1.403  0.020  1.403
 C4B  C2'  C3'   single  1.523  0.020  1.523
 C4B  C3'  O3'   single  1.405  0.020  1.405
 C4B  C3'  C4'   single  1.525  0.020  1.525
 C4B  C4'  O4'   single  1.409  0.020  1.409
 C4B  C4'  C5'   single  1.534  0.020  1.534
 C4B  C5'  O5'   single  1.416  0.020  1.416
 C4B  C5'  C6'   single  1.512  0.020  1.512
 C4B  C6'  O6'   single  1.406  0.020  1.406
 C4B  N1   C2    single  1.389  0.020  1.389
 C4B  N1   C6    single  1.388  0.020  1.388
 C4B  C2   O2    double  1.206  0.020  1.206
 C4B  C2   N3    single  1.369  0.020  1.369
 C4B  N3   C4    single  1.370  0.020  1.370
 C4B  C4   O4    double  1.206  0.020  1.206
 C4B  C4   N5    single  1.368  0.020  1.368
 C4B  N5   C6    single  1.372  0.020  1.372
 C4B  C6   O6    double  1.204  0.020  1.204
 C4B  C1'  H1'   single  0.970  0.020  1.090
 C4B  C2'  H2'   single  0.970  0.020  1.090
 C4B  O2'  HO2'  single  0.850  0.020  0.980
 C4B  C3'  H3'   single  0.970  0.020  1.090
 C4B  O3'  HO3'  single  0.850  0.020  0.980
 C4B  C4'  H4'   single  0.970  0.020  1.090
 C4B  O4'  HO4'  single  0.850  0.020  0.980
 C4B  C5'  H5'   single  0.970  0.020  1.090
 C4B  C6'  H6'   single  0.970  0.020  1.090
 C4B  C6'  H6'A  single  0.970  0.020  1.090
 C4B  O6'  HO6'  single  0.850  0.020  0.980
 C4B  N3   HN3   single  0.860  0.020  1.020
 C4B  N5   HN5   single  0.860  0.020  1.020

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
 C4B  H1'   C1'  N1   105.54  3.000
 C4B  H1'   C1'  O5'  110.36  3.000
 C4B  N1    C1'  O5'  108.12  3.000
 C4B  H1'   C1'  C2'  107.22  3.000
 C4B  N1    C1'  C2'  113.22  3.000
 C4B  O5'   C1'  C2'  112.16  3.000
 C4B  H2'   C2'  C3'  108.14  3.000
 C4B  H2'   C2'  O2'  111.62  3.000
 C4B  C3'   C2'  O2'  112.66  3.000
 C4B  H2'   C2'  C1'  110.43  3.000
 C4B  C3'   C2'  C1'  107.39  3.000
 C4B  O2'   C2'  C1'  106.53  3.000
 C4B  HO2'  O2'  C2'  108.39  3.000
 C4B  H3'   C3'  C4'  108.05  3.000
 C4B  H3'   C3'  O3'  110.71  3.000
 C4B  C4'   C3'  O3'  112.07  3.000
 C4B  H3'   C3'  C2'  108.27  3.000
 C4B  C4'   C3'  C2'  110.28  3.000
 C4B  O3'   C3'  C2'  107.41  3.000
 C4B  HO3'  O3'  C3'  108.28  3.000
 C4B  H4'   C4'  C5'  108.54  3.000
 C4B  H4'   C4'  O4'  111.23  3.000
 C4B  C5'   C4'  O4'  111.55  3.000
 C4B  H4'   C4'  C3'  108.56  3.000
 C4B  C5'   C4'  C3'  109.65  3.000
 C4B  O4'   C4'  C3'  107.26  3.000
 C4B  HO4'  O4'  C4'  109.26  3.000
 C4B  H5'   C5'  C6'  109.03  3.000
 C4B  H5'   C5'  O5'  110.01  3.000
 C4B  C6'   C5'  O5'  107.56  3.000
 C4B  H5'   C5'  C4'  108.55  3.000
 C4B  C6'   C5'  C4'  111.96  3.000
 C4B  O5'   C5'  C4'  109.72  3.000
 C4B  C5'   O5'  C1'  113.03  3.000
 C4B  H6'A  C6'  H6'  107.09  3.000
 C4B  H6'A  C6'  O6'  112.01  3.000
 C4B  H6'   C6'  O6'  111.49  3.000
 C4B  H6'A  C6'  C5'  108.84  3.000
 C4B  H6'   C6'  C5'  108.15  3.000
 C4B  O6'   C6'  C5'  109.16  3.000
 C4B  HO6'  O6'  C6'  107.95  3.000
 C4B  C6    N1   C2   123.11  3.000
 C4B  C6    N1   C1'  119.16  3.000
 C4B  C2    N1   C1'  117.71  3.000
 C4B  N3    C2   O2   121.44  3.000
 C4B  N3    C2   N1   115.19  3.000
 C4B  O2    C2   N1   123.37  3.000
 C4B  HN3   N3   C4   117.01  3.000
 C4B  HN3   N3   C2   116.29  3.000
 C4B  C4    N3   C2   126.70  3.000
 C4B  N5    C4   O4   123.50  3.000
 C4B  N5    C4   N3   113.17  3.000
 C4B  O4    C4   N3   123.34  3.000
 C4B  HN5   N5   C6   116.17  3.000
 C4B  HN5   N5   C4   117.15  3.000
 C4B  C6    N5   C4   126.68  3.000
 C4B  O6    C6   N5   121.45  3.000
 C4B  O6    C6   N1   123.40  3.000
 C4B  N5    C6   N1   115.15  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
 C4B  CONST_01  N3   C2  N1  C1'  180.00  0.0  0
 C4B  CONST_02  N5   C6  N1  C1'  180.00  0.0  0
 C4B  CONST_03  C4   N3  C2  N1     0.00  0.0  0
 C4B  CONST_04  C4   N5  C6  N1     0.00  0.0  0
 C4B  CONST_05  N5   C6  N1  C2     0.00  0.0  0
 C4B  CONST_06  N5   C4  N3  C2     0.00  0.0  0
 C4B  CONST_07  C6   N1  C2  N3     0.00  0.0  0
 C4B  CONST_08  C6   N5  C4  N3     0.00  0.0  0
 C4B  CONST_09  O2   C2  N1  C1'    0.00  0.0  0
 C4B  CONST_10  O6   C6  N1  C1'    0.00  0.0  0
 C4B  CONST_11  O6   C6  N1  C2   180.00  0.0  0
 C4B  CONST_12  O4   C4  N3  C2   180.00  0.0  0
 C4B  CONST_13  C6   N1  C2  O2   180.00  0.0  0
 C4B  CONST_14  C4   N3  C2  O2   180.00  0.0  0
 C4B  CONST_15  O6   C6  N5  C4   180.00  0.0  0
 C4B  CONST_16  C6   N5  C4  O4   180.00  0.0  0
 C4B  CONST_17  HN3  N3  C2  N1   180.00  0.0  0
 C4B  CONST_18  HN5  N5  C6  N1   180.00  0.0  0

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
 C4B  chir_01  C1'  C2'  O5'  N1   negativ
 C4B  chir_02  C2'  O2'  C1'  C3'  negativ
 C4B  chir_03  C3'  O3'  C2'  C4'  positiv
 C4B  chir_04  C4'  O4'  C5'  C3'  positiv
 C4B  chir_05  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
 C4B  plan-1  C1'  0.020
 C4B  plan-1  N1   0.020
 C4B  plan-1  C2   0.020
 C4B  plan-1  O2   0.020
 C4B  plan-1  N3   0.020
 C4B  plan-1  C4   0.020
 C4B  plan-1  O4   0.020
 C4B  plan-1  N5   0.020
 C4B  plan-1  C6   0.020
 C4B  plan-1  O6   0.020
 C4B  plan-1  HN3  0.020
 C4B  plan-1  HN5  0.020

