# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:39:24 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-thioxo-6-oxa-1,3-diazaspiro[4.5]decan-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(NC(=S)NC2=O)[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
 GL4  GL4  (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-thioxo-6-oxa-1,3-diazaspiro[4.5]decan-4-one  D-saccharide  29  17  .  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_GL4
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
 GL4  C1   C  CT    0   0.337  -0.0647  -0.1790  -0.4009
 GL4  C2   C  CH1   0  -0.003  -1.4081  -0.4964   0.2609
 GL4  O2   O  OH1   0  -0.662  -2.3882  -0.0010  -0.6066
 GL4  C3   C  CH1   0  -0.004  -1.4930   0.0907   1.6613
 GL4  O3   O  OH1   0  -0.670  -2.6998  -0.3748   2.2135
 GL4  C4   C  CH1   0  -0.007  -0.2836  -0.3490   2.4747
 GL4  O4   O  OH1   0  -0.669  -0.3726   0.2679   3.7378
 GL4  C5   C  CH1   0  -0.031   1.0019   0.0671   1.7536
 GL4  C6   C  CH2   0  -0.157   2.2338  -0.4762   2.4435
 GL4  O6   O  OH1   0  -0.668   3.3786   0.0488   1.8182
 GL4  O5   O  O2    0  -0.484   1.0223  -0.4527   0.4251
 GL4  N2   N  NH1   0  -0.647   0.1006  -0.9241  -1.6146
 GL4  C8   C  C     0   0.387   0.1975  -0.1677  -2.7107
 GL4  S8   S  S1    0  -0.305   0.3431  -0.6704  -4.2715
 GL4  N1   N  NH1   0  -0.658   0.1559   1.1412  -2.3010
 GL4  C7   C  C     0   0.555  -0.0162   1.2645  -0.9541
 GL4  O7   O  O     0  -0.400  -0.0797   2.2871  -0.3240
 GL4  H2   H  HCH1  0   0.258  -1.4699  -1.5927   0.3555
 GL4  HO2  H  HOH1  0   0.466  -3.2569  -0.2080  -0.2455
 GL4  H3   H  HCH1  0   0.235  -1.4932   1.1880   1.5998
 GL4  HO3  H  HOH1  0   0.458  -2.8602   0.1003   3.0351
 GL4  H4   H  HCH1  0   0.234  -0.3032  -1.4447   2.5652
 GL4  HO4  H  HOH1  0   0.463  -0.0244  -0.3282   4.4063
 GL4  H5   H  HCH1  0   0.243   1.0601   1.1629   1.7402
 GL4  H61  H  HCH2  0   0.203   2.2101  -1.5740   2.4052
 GL4  H62  H  HCH2  0   0.207   2.1848  -0.1901   3.5003
 GL4  HO6  H  HOH1  0   0.458   4.1493  -0.2561   2.3052
 GL4  HN2  H  HNH1  0   0.426   0.0311  -1.9295  -1.6630
 GL4  HN1  H  HNH1  0   0.435   0.2458   1.9166  -2.9422

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
 GL4  C1  C2   single  1.531  0.020  1.531
 GL4  C1  O5   single  1.392  0.020  1.392
 GL4  C1  N2   single  1.434  0.020  1.434
 GL4  C1  C7   single  1.547  0.020  1.547
 GL4  C2  O2   single  1.399  0.020  1.399
 GL4  C2  C3   single  1.521  0.020  1.521
 GL4  C2  H2   single  0.970  0.020  1.090
 GL4  O2  HO2  single  0.850  0.020  0.980
 GL4  C3  O3   single  1.406  0.020  1.406
 GL4  C3  C4   single  1.522  0.020  1.522
 GL4  C3  H3   single  0.970  0.020  1.090
 GL4  O3  HO3  single  0.850  0.020  0.980
 GL4  C4  O4   single  1.409  0.020  1.409
 GL4  C4  C5   single  1.531  0.020  1.531
 GL4  C4  H4   single  0.970  0.020  1.090
 GL4  O4  HO4  single  0.850  0.020  0.980
 GL4  C5  C6   single  1.513  0.020  1.513
 GL4  C5  O5   single  1.427  0.020  1.427
 GL4  C5  H5   single  0.970  0.020  1.090
 GL4  C6  O6   single  1.406  0.020  1.406
 GL4  C6  H61  single  0.970  0.020  1.090
 GL4  C6  H62  single  0.970  0.020  1.090
 GL4  O6  HO6  single  0.850  0.020  0.980
 GL4  N2  C8   single  1.335  0.020  1.335
 GL4  N2  HN2  single  0.860  0.020  1.020
 GL4  C8  S8   double  1.646  0.020  1.646
 GL4  C8  N1   single  1.372  0.020  1.372
 GL4  N1  C7   single  1.363  0.020  1.363
 GL4  N1  HN1  single  0.860  0.020  1.020
 GL4  C7  O7   double  1.203  0.020  1.203

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
 GL4  C7   C1  N2   100.29  3.000
 GL4  C7   C1  O5   111.79  3.000
 GL4  N2   C1  O5   108.06  3.000
 GL4  C7   C1  C2   112.07  3.000
 GL4  N2   C1  C2   111.06  3.000
 GL4  O5   C1  C2   112.82  3.000
 GL4  H2   C2  C3   107.57  3.000
 GL4  H2   C2  O2   111.47  3.000
 GL4  C3   C2  O2   113.27  3.000
 GL4  H2   C2  C1   107.01  3.000
 GL4  C3   C2  C1   111.53  3.000
 GL4  O2   C2  C1   105.86  3.000
 GL4  HO2  O2  C2   108.85  3.000
 GL4  H3   C3  C4   108.57  3.000
 GL4  H3   C3  O3   110.63  3.000
 GL4  C4   C3  O3   112.10  3.000
 GL4  H3   C3  C2   109.51  3.000
 GL4  C4   C3  C2   109.64  3.000
 GL4  O3   C3  C2   106.36  3.000
 GL4  HO3  O3  C3   108.34  3.000
 GL4  H4   C4  C5   108.93  3.000
 GL4  H4   C4  O4   111.19  3.000
 GL4  C5   C4  O4   110.87  3.000
 GL4  H4   C4  C3   108.52  3.000
 GL4  C5   C4  C3   109.68  3.000
 GL4  O4   C4  C3   107.60  3.000
 GL4  HO4  O4  C4   109.22  3.000
 GL4  H5   C5  O5   110.58  3.000
 GL4  H5   C5  C6   108.72  3.000
 GL4  O5   C5  C6   106.39  3.000
 GL4  H5   C5  C4   108.76  3.000
 GL4  O5   C5  C4   110.58  3.000
 GL4  C6   C5  C4   111.79  3.000
 GL4  H62  C6  H61  107.06  3.000
 GL4  H62  C6  O6   111.58  3.000
 GL4  H61  C6  O6   112.03  3.000
 GL4  H62  C6  C5   108.04  3.000
 GL4  H61  C6  C5   108.99  3.000
 GL4  O6   C6  C5   109.03  3.000
 GL4  HO6  O6  C6   108.00  3.000
 GL4  C5   O5  C1   118.01  3.000
 GL4  HN2  N2  C8   122.02  3.000
 GL4  HN2  N2  C1   123.40  3.000
 GL4  C8   N2  C1   114.13  3.000
 GL4  N1   C8  S8   125.24  3.000
 GL4  N1   C8  N2   107.04  3.000
 GL4  S8   C8  N2   127.71  3.000
 GL4  HN1  N1  C7   124.67  3.000
 GL4  HN1  N1  C8   122.68  3.000
 GL4  C7   N1  C8   112.65  3.000
 GL4  O7   C7  N1   126.94  3.000
 GL4  O7   C7  C1   127.19  3.000
 GL4  N1   C7  C1   105.84  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
 GL4  CONST_01  N1   C8  N2  C1    0.00  0.0  0
 GL4  CONST_02  C8   N1  C7  C1    0.00  0.0  0
 GL4  CONST_03  C7   N1  C8  N2    0.00  0.0  0
 GL4  CONST_04  S8   C8  N2  C1  180.00  0.0  0
 GL4  CONST_05  O7   C7  N1  C8  180.00  0.0  0
 GL4  CONST_06  C7   N1  C8  S8  180.00  0.0  0
 GL4  CONST_07  HN1  N1  C7  C1  180.00  0.0  0
 GL4  CONST_08  HN2  N2  C8  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
 GL4  chir_01  C1  O5  N2  C7  positiv
 GL4  chir_02  C2  O2  C1  C3  negativ
 GL4  chir_03  C3  O3  C2  C4  positiv
 GL4  chir_04  C4  O4  C5  C3  positiv
 GL4  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
 GL4  plan-1  C1   0.020
 GL4  plan-1  N2   0.020
 GL4  plan-1  C8   0.020
 GL4  plan-1  S8   0.020
 GL4  plan-1  N1   0.020
 GL4  plan-1  C7   0.020
 GL4  plan-1  O7   0.020
 GL4  plan-1  HN2  0.020
 GL4  plan-1  HN1  0.020

