# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:07:36 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(NC(=O)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
 GLS  GLS  (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione  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_GLS
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
 GLS  C1   C  CR5   0   0.344   0.0313  -0.2271  -0.7122
 GLS  C2   C  CH1   0  -0.002  -1.3652  -0.4919  -0.1430
 GLS  O2   O  OH1   0  -0.664  -2.2704  -0.0148  -1.0995
 GLS  C3   C  CH1   0  -0.003  -1.5494   0.1474   1.2239
 GLS  O3   O  OH1   0  -0.672  -2.8065  -0.2742   1.6951
 GLS  C4   C  CH1   0  -0.008  -0.4188  -0.2841   2.1472
 GLS  O4   O  OH1   0  -0.671  -0.5979   0.3777   3.3781
 GLS  C5   C  CH1   0  -0.029   0.9268   0.0840   1.5155
 GLS  C6   C  CH2   0  -0.158   2.0904  -0.4494   2.3224
 GLS  O6   O  OH1   0  -0.669   3.2916   0.0234   1.7643
 GLS  O5   O  O2    0  -0.487   1.0413  -0.4883   0.2158
 GLS  N2   N  NR15  0  -0.697   0.2774  -1.0202  -1.8739
 GLS  C8   C  CR5   0   0.672   0.4445  -0.2971  -3.0058
 GLS  O8   O  O     0  -0.460   0.5972  -0.7007  -4.1331
 GLS  N1   N  NR15  0  -0.699   0.4122   1.0407  -2.6240
 GLS  C7   C  CR5   0   0.555   0.1541   1.1987  -1.3026
 GLS  O7   O  O     0  -0.414   0.0707   2.2377  -0.6973
 GLS  H2   H  HCH1  0   0.253  -1.4566  -1.5828  -0.0137
 GLS  HO2  H  HOH1  0   0.464  -3.1663  -0.1897  -0.7923
 GLS  H3   H  HCH1  0   0.233  -1.5197   1.2411   1.1233
 GLS  HO3  H  HOH1  0   0.457  -3.0109   0.2201   2.4953
 GLS  H4   H  HCH1  0   0.231  -0.4682  -1.3755   2.2729
 GLS  HO4  H  HOH1  0   0.464  -0.3053  -0.1973   4.0903
 GLS  H5   H  HCH1  0   0.240   1.0045   1.1775   1.4659
 GLS  H61  H  HCH2  0   0.201   2.0451  -1.5472   2.3320
 GLS  H62  H  HCH2  0   0.208   1.9682  -0.1131   3.3582
 GLS  HO6  H  HOH1  0   0.458   4.0131  -0.2489   2.3379
 GLS  HN2  H  HNR5  0   0.418   0.1106  -2.0148  -1.9042
 GLS  HN1  H  HNR5  0   0.431   0.5606   1.8004  -3.2738

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
 GLS  C1  C2   single  1.531  0.020  1.531
 GLS  C1  O5   single  1.396  0.020  1.396
 GLS  C1  N2   single  1.428  0.020  1.428
 GLS  C1  C7   single  1.548  0.020  1.548
 GLS  C2  O2   single  1.401  0.020  1.401
 GLS  C2  C3   single  1.520  0.020  1.520
 GLS  C2  H2   single  0.970  0.020  1.090
 GLS  O2  HO2  single  0.850  0.020  0.980
 GLS  C3  O3   single  1.407  0.020  1.407
 GLS  C3  C4   single  1.522  0.020  1.522
 GLS  C3  H3   single  0.970  0.020  1.090
 GLS  O3  HO3  single  0.850  0.020  0.980
 GLS  C4  O4   single  1.409  0.020  1.409
 GLS  C4  C5   single  1.531  0.020  1.531
 GLS  C4  H4   single  0.970  0.020  1.090
 GLS  O4  HO4  single  0.850  0.020  0.980
 GLS  C5  C6   single  1.513  0.020  1.513
 GLS  C5  O5   single  1.425  0.020  1.425
 GLS  C5  H5   single  0.970  0.020  1.090
 GLS  C6  O6   single  1.406  0.020  1.406
 GLS  C6  H61  single  0.970  0.020  1.090
 GLS  C6  H62  single  0.970  0.020  1.090
 GLS  O6  HO6  single  0.850  0.020  0.980
 GLS  N2  C8   single  1.354  0.020  1.354
 GLS  N2  HN2  single  0.860  0.020  1.020
 GLS  C8  O8   double  1.207  0.020  1.207
 GLS  C8  N1   single  1.392  0.020  1.392
 GLS  N1  C7   single  1.356  0.020  1.356
 GLS  N1  HN1  single  0.860  0.020  1.020
 GLS  C7  O7   double  1.205  0.020  1.205

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
 GLS  C7   C1  N2   100.81  3.000
 GLS  C7   C1  O5   111.62  3.000
 GLS  N2   C1  O5   108.19  3.000
 GLS  C7   C1  C2   111.92  3.000
 GLS  N2   C1  C2   111.32  3.000
 GLS  O5   C1  C2   112.35  3.000
 GLS  H2   C2  C3   107.50  3.000
 GLS  H2   C2  O2   111.32  3.000
 GLS  C3   C2  O2   113.11  3.000
 GLS  H2   C2  C1   106.88  3.000
 GLS  C3   C2  C1   111.84  3.000
 GLS  O2   C2  C1   106.06  3.000
 GLS  HO2  O2  C2   108.75  3.000
 GLS  H3   C3  C4   108.52  3.000
 GLS  H3   C3  O3   110.67  3.000
 GLS  C4   C3  O3   112.06  3.000
 GLS  H3   C3  C2   109.45  3.000
 GLS  C4   C3  C2   109.65  3.000
 GLS  O3   C3  C2   106.46  3.000
 GLS  HO3  O3  C3   108.31  3.000
 GLS  H4   C4  C5   108.97  3.000
 GLS  H4   C4  O4   111.14  3.000
 GLS  C5   C4  O4   111.05  3.000
 GLS  H4   C4  C3   108.50  3.000
 GLS  C5   C4  C3   109.53  3.000
 GLS  O4   C4  C3   107.60  3.000
 GLS  HO4  O4  C4   109.14  3.000
 GLS  H5   C5  O5   110.69  3.000
 GLS  H5   C5  C6   108.72  3.000
 GLS  O5   C5  C6   106.44  3.000
 GLS  H5   C5  C4   108.68  3.000
 GLS  O5   C5  C4   110.51  3.000
 GLS  C6   C5  C4   111.78  3.000
 GLS  H62  C6  H61  107.08  3.000
 GLS  H62  C6  O6   111.54  3.000
 GLS  H61  C6  O6   112.00  3.000
 GLS  H62  C6  C5   108.07  3.000
 GLS  H61  C6  C5   108.98  3.000
 GLS  O6   C6  C5   109.07  3.000
 GLS  HO6  O6  C6   108.00  3.000
 GLS  C5   O5  C1   118.24  3.000
 GLS  HN2  N2  C8   121.46  3.000
 GLS  HN2  N2  C1   122.92  3.000
 GLS  C8   N2  C1   113.89  3.000
 GLS  N1   C8  O8   125.50  3.000
 GLS  N1   C8  N2   106.33  3.000
 GLS  O8   C8  N2   128.17  3.000
 GLS  HN1  N1  C7   124.55  3.000
 GLS  HN1  N1  C8   122.87  3.000
 GLS  C7   N1  C8   112.58  3.000
 GLS  O7   C7  N1   127.09  3.000
 GLS  O7   C7  C1   126.65  3.000
 GLS  N1   C7  C1   106.23  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
 GLS  CONST_01  N1   C8  N2  C1    0.00  0.0  0
 GLS  CONST_02  C8   N1  C7  C1    0.00  0.0  0
 GLS  CONST_03  C7   N1  C8  N2    0.00  0.0  0
 GLS  CONST_04  O8   C8  N2  C1  180.00  0.0  0
 GLS  CONST_05  O7   C7  N1  C8  180.00  0.0  0
 GLS  CONST_06  C7   N1  C8  O8  180.00  0.0  0
 GLS  CONST_07  HN1  N1  C7  C1  180.00  0.0  0
 GLS  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
 GLS  chir_01  C1  O5  N2  C7  positiv
 GLS  chir_02  C2  O2  C1  C3  negativ
 GLS  chir_03  C3  O3  C2  C4  positiv
 GLS  chir_04  C4  O4  C5  C3  positiv
 GLS  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
 GLS  plan-1  C1   0.020
 GLS  plan-1  N2   0.020
 GLS  plan-1  C8   0.020
 GLS  plan-1  O8   0.020
 GLS  plan-1  N1   0.020
 GLS  plan-1  C7   0.020
 GLS  plan-1  O7   0.020
 GLS  plan-1  HN2  0.020
 GLS  plan-1  HN1  0.020

