# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:47:28 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-3-methyl-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N[C@@]2(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C1=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
 GL7  GL7  (5S,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-3-methyl-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione  D-saccharide  32  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 GRAND
;

data_comp_GL7
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
 GL7  C1   C  CR5   0   0.352  -0.0099   0.3812   0.4597
 GL7  C2   C  CH1   0  -0.003  -1.3926   0.5295  -0.1823
 GL7  O2   O  OH1   0  -0.664  -2.3124   0.0798   0.7739
 GL7  C3   C  CH1   0  -0.002  -1.4860  -0.2222  -1.5002
 GL7  O3   O  OH1   0  -0.671  -2.7414   0.0914  -2.0525
 GL7  C4   C  CH1   0  -0.006  -0.3396   0.1995  -2.4080
 GL7  O4   O  OH1   0  -0.671  -0.4344  -0.5548  -3.5941
 GL7  C5   C  CH1   0  -0.030   0.9938  -0.0528  -1.6984
 GL7  C6   C  CH2   0  -0.157   2.1625   0.4752  -2.5011
 GL7  O6   O  OH1   0  -0.669   3.3617   0.1335  -1.8501
 GL7  O5   O  O2    0  -0.487   1.0261   0.6216  -0.4439
 GL7  N2   N  NR15  0  -0.705   0.1457   1.2707   1.5653
 GL7  C8   C  CR5   0   0.699   0.2532   0.6407   2.7579
 GL7  O8   O  O     0  -0.463   0.3068   1.1378   3.8568
 GL7  N1   N  NR5   0  -0.542   0.3029  -0.7282   2.4906
 GL7  C7   C  CR5   0   0.556   0.1466  -0.9812   1.1680
 GL7  O7   O  O     0  -0.424   0.1601  -2.0707   0.6485
 GL7  C9   C  CH3   0  -0.530   0.4802  -1.7534   3.4923
 GL7  H2   H  HCH1  0   0.253  -1.5333   1.6010  -0.3996
 GL7  HO2  H  HOH1  0   0.464  -3.2024   0.1859   0.4211
 GL7  H3   H  HCH1  0   0.232  -1.4026  -1.3020  -1.3126
 GL7  HO3  H  HOH1  0   0.457  -2.8804  -0.4699  -2.8220
 GL7  H4   H  HCH1  0   0.231  -0.4359   1.2754  -2.6138
 GL7  HO4  H  HOH1  0   0.464  -0.1367  -0.0182  -4.3336
 GL7  H5   H  HCH1  0   0.240   1.1200  -1.1339  -1.5592
 GL7  H61  H  HCH2  0   0.208   2.1098   0.0362  -3.5038
 GL7  H62  H  HCH2  0   0.200   2.0544   1.5627  -2.6172
 GL7  HO6  H  HOH1  0   0.458   4.0915   0.3810  -2.4247
 GL7  HN2  H  HNR5  0   0.417  -0.0858   2.2515   1.5130
 GL7  H91  H  HCH3  0   0.268   0.5110  -1.2856   4.4711
 GL7  H92  H  HCH3  0   0.262  -0.3502  -2.4557   3.4648
 GL7  H93  H  HCH3  0   0.263   1.4114  -2.2929   3.3305

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
 GL7  C1  C2   single  1.532  0.020  1.532
 GL7  C1  O5   single  1.396  0.020  1.396
 GL7  C1  N2   single  1.427  0.020  1.427
 GL7  C1  C7   single  1.543  0.020  1.543
 GL7  C2  O2   single  1.401  0.020  1.401
 GL7  C2  C3   single  1.520  0.020  1.520
 GL7  C2  H2   single  0.970  0.020  1.090
 GL7  O2  HO2  single  0.850  0.020  0.980
 GL7  C3  O3   single  1.407  0.020  1.407
 GL7  C3  C4   single  1.522  0.020  1.522
 GL7  C3  H3   single  0.970  0.020  1.090
 GL7  O3  HO3  single  0.850  0.020  0.980
 GL7  C4  O4   single  1.409  0.020  1.409
 GL7  C4  C5   single  1.531  0.020  1.531
 GL7  C4  H4   single  0.970  0.020  1.090
 GL7  O4  HO4  single  0.850  0.020  0.980
 GL7  C5  C6   single  1.513  0.020  1.513
 GL7  C5  O5   single  1.425  0.020  1.425
 GL7  C5  H5   single  0.970  0.020  1.090
 GL7  C6  O6   single  1.407  0.020  1.407
 GL7  C6  H61  single  0.970  0.020  1.090
 GL7  C6  H62  single  0.970  0.020  1.090
 GL7  O6  HO6  single  0.850  0.020  0.980
 GL7  N2  C8   single  1.353  0.020  1.353
 GL7  N2  HN2  single  0.860  0.020  1.020
 GL7  C8  O8   double  1.207  0.020  1.207
 GL7  C8  N1   single  1.396  0.020  1.396
 GL7  N1  C7   single  1.356  0.020  1.356
 GL7  N1  C9   single  1.444  0.020  1.444
 GL7  C7  O7   double  1.207  0.020  1.207
 GL7  C9  H91  single  0.970  0.020  1.090
 GL7  C9  H92  single  0.970  0.020  1.090
 GL7  C9  H93  single  0.970  0.020  1.090

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
 GL7  C7   C1  N2   100.58  3.000
 GL7  C7   C1  O5   111.96  3.000
 GL7  N2   C1  O5   108.25  3.000
 GL7  C7   C1  C2   111.68  3.000
 GL7  N2   C1  C2   111.26  3.000
 GL7  O5   C1  C2   112.46  3.000
 GL7  H2   C2  C3   107.57  3.000
 GL7  H2   C2  O2   111.27  3.000
 GL7  C3   C2  O2   113.12  3.000
 GL7  H2   C2  C1   106.98  3.000
 GL7  C3   C2  C1   111.78  3.000
 GL7  O2   C2  C1   105.99  3.000
 GL7  HO2  O2  C2   108.74  3.000
 GL7  H3   C3  C4   108.48  3.000
 GL7  H3   C3  O3   110.71  3.000
 GL7  C4   C3  O3   112.10  3.000
 GL7  H3   C3  C2   109.46  3.000
 GL7  C4   C3  C2   109.50  3.000
 GL7  O3   C3  C2   106.55  3.000
 GL7  HO3  O3  C3   108.22  3.000
 GL7  H4   C4  C5   108.91  3.000
 GL7  H4   C4  O4   111.13  3.000
 GL7  C5   C4  O4   111.13  3.000
 GL7  H4   C4  C3   108.47  3.000
 GL7  C5   C4  C3   109.50  3.000
 GL7  O4   C4  C3   107.65  3.000
 GL7  HO4  O4  C4   109.15  3.000
 GL7  H5   C5  O5   110.62  3.000
 GL7  H5   C5  C6   108.80  3.000
 GL7  O5   C5  C6   106.53  3.000
 GL7  H5   C5  C4   108.73  3.000
 GL7  O5   C5  C4   110.48  3.000
 GL7  C6   C5  C4   111.67  3.000
 GL7  H62  C6  H61  107.16  3.000
 GL7  H62  C6  O6   111.91  3.000
 GL7  H61  C6  O6   111.54  3.000
 GL7  H62  C6  C5   108.99  3.000
 GL7  H61  C6  C5   107.97  3.000
 GL7  O6   C6  C5   109.16  3.000
 GL7  HO6  O6  C6   107.94  3.000
 GL7  C5   O5  C1   118.15  3.000
 GL7  HN2  N2  C8   121.09  3.000
 GL7  HN2  N2  C1   122.72  3.000
 GL7  C8   N2  C1   113.65  3.000
 GL7  N1   C8  O8   125.21  3.000
 GL7  N1   C8  N2   106.90  3.000
 GL7  O8   C8  N2   127.89  3.000
 GL7  C9   N1  C7   123.94  3.000
 GL7  C9   N1  C8   124.60  3.000
 GL7  C7   N1  C8   111.46  3.000
 GL7  O7   C7  N1   125.95  3.000
 GL7  O7   C7  C1   126.90  3.000
 GL7  N1   C7  C1   107.14  3.000
 GL7  H93  C9  H92  109.23  3.000
 GL7  H93  C9  H91  108.87  3.000
 GL7  H92  C9  H91  108.83  3.000
 GL7  H93  C9  N1   110.72  3.000
 GL7  H92  C9  N1   110.31  3.000
 GL7  H91  C9  N1   108.85  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
 GL7  CONST_01  N1   C8  N2  C1    0.00   0.0  0
 GL7  CONST_02  C8   N1  C7  C1    0.00   0.0  0
 GL7  CONST_03  C7   N1  C8  N2    0.00   0.0  0
 GL7  CONST_04  O8   C8  N2  C1  180.00   0.0  0
 GL7  CONST_05  C9   N1  C7  C1  180.00   0.0  0
 GL7  CONST_06  C9   N1  C8  N2  180.00   0.0  0
 GL7  CONST_07  O7   C7  N1  C8  180.00   0.0  0
 GL7  CONST_08  C7   N1  C8  O8  180.00   0.0  0
 GL7  CONST_09  HN2  N2  C8  N1  180.00   0.0  0
 GL7  CONST_10  C9   N1  C8  O8    0.00   0.0  0
 GL7  CONST_11  C9   N1  C7  O7    0.00   0.0  0
 GL7  Var_01    H91  C9  N1  C8    3.07  30.0  3

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
 GL7  chir_01  C1  O5  N2  C7  positiv
 GL7  chir_02  C2  O2  C1  C3  negativ
 GL7  chir_03  C3  O3  C2  C4  positiv
 GL7  chir_04  C4  O4  C5  C3  positiv
 GL7  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
 GL7  plan-1  C1   0.020
 GL7  plan-1  N2   0.020
 GL7  plan-1  C8   0.020
 GL7  plan-1  O8   0.020
 GL7  plan-1  N1   0.020
 GL7  plan-1  C7   0.020
 GL7  plan-1  O7   0.020
 GL7  plan-1  C9   0.020
 GL7  plan-1  HN2  0.020

