# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:27:29 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (5S,7R,8S,9S,10R)-3,8,9,10-tetrahydroxy-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)N(O)C2=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
 GL5  GL5  (5S,7R,8S,9S,10R)-3,8,9,10-tetrahydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione  D-saccharide  30  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 PERFECT
;

data_comp_GL5
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
 GL5  C1   C  CR5   0   0.336   0.0071  -0.4630  -0.4692
 GL5  C2   C  CH1   0  -0.002  -1.3817  -0.5550   0.1685
 GL5  O2   O  OH1   0  -0.663  -2.2856  -0.1274  -0.8119
 GL5  C3   C  CH1   0  -0.003  -1.4672   0.2543   1.4528
 GL5  O3   O  OH1   0  -0.671  -2.7309  -0.0140   2.0088
 GL5  C4   C  CH1   0  -0.006  -0.3334  -0.1476   2.3846
 GL5  O4   O  OH1   0  -0.670  -0.4189   0.6622   3.5340
 GL5  C5   C  CH1   0  -0.032   1.0072   0.0511   1.6724
 GL5  C6   C  CH2   0  -0.157   2.1638  -0.4624   2.5017
 GL5  O6   O  OH1   0  -0.668   3.3690  -0.1754   1.8366
 GL5  O5   O  O2    0  -0.485   1.0346  -0.6770   0.4467
 GL5  N2   N  NR15  0  -0.704   0.1515  -1.4195  -1.5256
 GL5  C8   C  CR5   0   0.684   0.2825  -0.8691  -2.7515
 GL5  O8   O  O     0  -0.444   0.3560  -1.4034  -3.8271
 GL5  N1   N  NR5   0  -0.259   0.3192   0.5144  -2.5359
 GL5  C7   C  CR5   0   0.543   0.1893   0.8674  -1.2329
 GL5  O7   O  O     0  -0.403   0.2362   1.9799  -0.7761
 GL5  O9   O  OH1   0  -0.532   0.6240   1.3780  -3.5200
 GL5  H2   H  HCH1  0   0.256  -1.5450  -1.6131   0.4305
 GL5  HO2  H  HOH1  0   0.465  -3.1781  -0.1768  -0.4524
 GL5  H3   H  HCH1  0   0.233  -1.3638   1.3241   1.2210
 GL5  HO3  H  HOH1  0   0.458  -2.8640   0.5789   2.7552
 GL5  H4   H  HCH1  0   0.233  -0.4500  -1.2109   2.6390
 GL5  HO4  H  HOH1  0   0.464  -0.1334   0.1560   4.2993
 GL5  H5   H  HCH1  0   0.243   1.1533   1.1227   1.4876
 GL5  H61  H  HCH2  0   0.200   2.0338  -1.5410   2.6683
 GL5  H62  H  HCH2  0   0.209   2.1186   0.0251   3.4819
 GL5  HO6  H  HOH1  0   0.458   4.0943  -0.4116   2.4216
 GL5  HN2  H  HNR5  0   0.422  -0.0831  -2.3946  -1.4112
 GL5  HO9  H  HOH1  0   0.493  -0.2154   1.6602  -3.9124

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
 GL5  C1  C2   single  1.531  0.020  1.531
 GL5  C1  O5   single  1.393  0.020  1.393
 GL5  C1  N2   single  1.432  0.020  1.432
 GL5  C1  C7   single  1.545  0.020  1.545
 GL5  C2  O2   single  1.400  0.020  1.400
 GL5  C2  C3   single  1.520  0.020  1.520
 GL5  C2  H2   single  0.970  0.020  1.090
 GL5  O2  HO2  single  0.850  0.020  0.980
 GL5  C3  O3   single  1.406  0.020  1.406
 GL5  C3  C4   single  1.522  0.020  1.522
 GL5  C3  H3   single  0.970  0.020  1.090
 GL5  O3  HO3  single  0.850  0.020  0.980
 GL5  C4  O4   single  1.409  0.020  1.409
 GL5  C4  C5   single  1.531  0.020  1.531
 GL5  C4  H4   single  0.970  0.020  1.090
 GL5  O4  HO4  single  0.850  0.020  0.980
 GL5  C5  C6   single  1.513  0.020  1.513
 GL5  C5  O5   single  1.426  0.020  1.426
 GL5  C5  H5   single  0.970  0.020  1.090
 GL5  C6  O6   single  1.406  0.020  1.406
 GL5  C6  H61  single  0.970  0.020  1.090
 GL5  C6  H62  single  0.970  0.020  1.090
 GL5  O6  HO6  single  0.850  0.020  0.980
 GL5  N2  C8   single  1.350  0.020  1.350
 GL5  N2  HN2  single  0.860  0.020  1.020
 GL5  C8  O8   double  1.203  0.020  1.203
 GL5  C8  N1   single  1.401  0.020  1.401
 GL5  N1  C7   single  1.356  0.020  1.356
 GL5  N1  O9   single  1.344  0.020  1.344
 GL5  C7  O7   double  1.204  0.020  1.204
 GL5  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
 GL5  C7   C1  N2   101.46  3.000
 GL5  C7   C1  O5   111.74  3.000
 GL5  N2   C1  O5   107.94  3.000
 GL5  C7   C1  C2   111.39  3.000
 GL5  N2   C1  C2   111.01  3.000
 GL5  O5   C1  C2   112.70  3.000
 GL5  H2   C2  C3   107.57  3.000
 GL5  H2   C2  O2   111.34  3.000
 GL5  C3   C2  O2   113.12  3.000
 GL5  H2   C2  C1   106.92  3.000
 GL5  C3   C2  C1   111.77  3.000
 GL5  O2   C2  C1   105.99  3.000
 GL5  HO2  O2  C2   108.73  3.000
 GL5  H3   C3  C4   108.42  3.000
 GL5  H3   C3  O3   110.70  3.000
 GL5  C4   C3  O3   112.15  3.000
 GL5  H3   C3  C2   109.54  3.000
 GL5  C4   C3  C2   109.56  3.000
 GL5  O3   C3  C2   106.43  3.000
 GL5  HO3  O3  C3   108.26  3.000
 GL5  H4   C4  C5   109.03  3.000
 GL5  H4   C4  O4   111.15  3.000
 GL5  C5   C4  O4   110.99  3.000
 GL5  H4   C4  C3   108.54  3.000
 GL5  C5   C4  C3   109.47  3.000
 GL5  O4   C4  C3   107.61  3.000
 GL5  HO4  O4  C4   109.20  3.000
 GL5  H5   C5  O5   110.57  3.000
 GL5  H5   C5  C6   108.79  3.000
 GL5  O5   C5  C6   106.45  3.000
 GL5  H5   C5  C4   108.77  3.000
 GL5  O5   C5  C4   110.51  3.000
 GL5  C6   C5  C4   111.74  3.000
 GL5  H62  C6  H61  107.22  3.000
 GL5  H62  C6  O6   111.57  3.000
 GL5  H61  C6  O6   111.93  3.000
 GL5  H62  C6  C5   107.92  3.000
 GL5  H61  C6  C5   109.01  3.000
 GL5  O6   C6  C5   109.07  3.000
 GL5  HO6  O6  C6   107.98  3.000
 GL5  C5   O5  C1   118.21  3.000
 GL5  HN2  N2  C8   121.28  3.000
 GL5  HN2  N2  C1   122.55  3.000
 GL5  C8   N2  C1   114.03  3.000
 GL5  N1   C8  O8   125.07  3.000
 GL5  N1   C8  N2   105.39  3.000
 GL5  O8   C8  N2   129.53  3.000
 GL5  O9   N1  C7   123.90  3.000
 GL5  O9   N1  C8   121.86  3.000
 GL5  C7   N1  C8   113.74  3.000
 GL5  O7   C7  N1   126.98  3.000
 GL5  O7   C7  C1   127.81  3.000
 GL5  N1   C7  C1   105.19  3.000
 GL5  HO9  O9  N1   106.69  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
 GL5  CONST_01  N1   C8  N2  C1    0.00  0.0  0
 GL5  CONST_02  C8   N1  C7  C1    0.00  0.0  0
 GL5  CONST_03  C7   N1  C8  N2    0.00  0.0  0
 GL5  CONST_04  O8   C8  N2  C1  180.00  0.0  0
 GL5  CONST_05  O9   N1  C7  C1  180.00  0.0  0
 GL5  CONST_06  O9   N1  C8  N2  180.00  0.0  0
 GL5  CONST_07  O7   C7  N1  C8  180.00  0.0  0
 GL5  CONST_08  C7   N1  C8  O8  180.00  0.0  0
 GL5  CONST_09  HN2  N2  C8  N1  180.00  0.0  0
 GL5  CONST_10  O9   N1  C8  O8    0.00  0.0  0
 GL5  CONST_11  O9   N1  C7  O7    0.00  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
 GL5  chir_01  C1  O5  N2  C7  positiv
 GL5  chir_02  C2  O2  C1  C3  negativ
 GL5  chir_03  C3  O3  C2  C4  positiv
 GL5  chir_04  C4  O4  C5  C3  positiv
 GL5  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
 GL5  plan-1  C1   0.020
 GL5  plan-1  N2   0.020
 GL5  plan-1  C8   0.020
 GL5  plan-1  O8   0.020
 GL5  plan-1  N1   0.020
 GL5  plan-1  C7   0.020
 GL5  plan-1  O7   0.020
 GL5  plan-1  O9   0.020
 GL5  plan-1  HN2  0.020

