# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:52:25 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (5S,7R,8S,9S,10R)-3-amino-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: NN1C(=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
 GL2  GL2  (5S,7R,8S,9S,10R)-3-amino-8,9,10-trihydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione  D-saccharide  31  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_GL2
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
 GL2  C1    C  CR5   0   0.343  -0.0630   0.3762   0.4575
 GL2  C2    C  CH1   0  -0.001  -1.4326   0.5242  -0.2113
 GL2  O2    O  OH1   0  -0.664  -2.3707   0.0703   0.7244
 GL2  C3    C  CH1   0  -0.004  -1.4990  -0.2215  -1.5345
 GL2  O3    O  OH1   0  -0.671  -2.7433   0.0959  -2.1096
 GL2  C4    C  CH1   0  -0.006  -0.3347   0.2038  -2.4176
 GL2  O4    O  OH1   0  -0.671  -0.4037  -0.5505  -3.6055
 GL2  C5    C  CH1   0  -0.030   0.9848  -0.0458  -1.6816
 GL2  C6    C  CH2   0  -0.157   2.1680   0.4886  -2.4584
 GL2  O6    O  OH1   0  -0.669   3.3548   0.1458  -1.7859
 GL2  O5    O  O2    0  -0.487   0.9893   0.6255  -0.4243
 GL2  N2    N  NR15  0  -0.702   0.0665   1.2698   1.5662
 GL2  C8    C  CR5   0   0.685   0.1642   0.6454   2.7586
 GL2  O8    O  O     0  -0.455   0.2058   1.1246   3.8646
 GL2  N1    N  NR5   0  -0.425   0.2217  -0.7282   2.4848
 GL2  C7    C  CR5   0   0.554   0.0839  -0.9928   1.1576
 GL2  O7    O  O     0  -0.408   0.1039  -2.0744   0.6301
 GL2  N3    N  NH2   0  -0.635   0.3820  -1.7129   3.4295
 GL2  H2    H  HCH1  0   0.253  -1.5687   1.5968  -0.4268
 GL2  HO2   H  HOH1  0   0.464  -3.2525   0.1587   0.3467
 GL2  H3    H  HCH1  0   0.233  -1.4205  -1.3020  -1.3507
 GL2  HO3   H  HOH1  0   0.458  -2.8775  -0.4748  -2.8729
 GL2  H4    H  HCH1  0   0.231  -0.4299   1.2796  -2.6247
 GL2  HO4   H  HOH1  0   0.464  -0.0802  -0.0178  -4.3370
 GL2  H5    H  HCH1  0   0.241   1.1128  -1.1266  -1.5427
 GL2  H61   H  HCH2  0   0.208   2.1356   0.0546  -3.4641
 GL2  H62   H  HCH2  0   0.200   2.0603   1.5765  -2.5714
 GL2  HO6   H  HOH1  0   0.458   4.0952   0.3927  -2.3471
 GL2  HN2   H  HNR5  0   0.418  -0.1535   2.2529   1.5028
 GL2  HN31  H  HNH2  0   0.388   1.2536  -1.5716   3.9242
 GL2  HN32  H  HNH2  0   0.388  -0.3777  -1.6692   4.0968

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
 GL2  C1  C2    single  1.531  0.020  1.531
 GL2  C1  O5    single  1.395  0.020  1.395
 GL2  C1  N2    single  1.430  0.020  1.430
 GL2  C1  C7    single  1.545  0.020  1.545
 GL2  C2  O2    single  1.401  0.020  1.401
 GL2  C2  C3    single  1.520  0.020  1.520
 GL2  C2  H2    single  0.970  0.020  1.090
 GL2  O2  HO2   single  0.850  0.020  0.980
 GL2  C3  O3    single  1.407  0.020  1.407
 GL2  C3  C4    single  1.522  0.020  1.522
 GL2  C3  H3    single  0.970  0.020  1.090
 GL2  O3  HO3   single  0.850  0.020  0.980
 GL2  C4  O4    single  1.409  0.020  1.409
 GL2  C4  C5    single  1.531  0.020  1.531
 GL2  C4  H4    single  0.970  0.020  1.090
 GL2  O4  HO4   single  0.850  0.020  0.980
 GL2  C5  C6    single  1.513  0.020  1.513
 GL2  C5  O5    single  1.425  0.020  1.425
 GL2  C5  H5    single  0.970  0.020  1.090
 GL2  C6  O6    single  1.407  0.020  1.407
 GL2  C6  H61   single  0.970  0.020  1.090
 GL2  C6  H62   single  0.970  0.020  1.090
 GL2  O6  HO6   single  0.850  0.020  0.980
 GL2  N2  C8    single  1.350  0.020  1.350
 GL2  N2  HN2   single  0.860  0.020  1.020
 GL2  C8  O8    double  1.206  0.020  1.206
 GL2  C8  N1    single  1.402  0.020  1.402
 GL2  N1  C7    single  1.360  0.020  1.360
 GL2  N1  N3    single  1.374  0.020  1.374
 GL2  C7  O7    double  1.204  0.020  1.204
 GL2  N3  HN31  single  0.890  0.020  1.040
 GL2  N3  HN32  single  0.890  0.020  1.040

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
 GL2  C7    C1  N2    101.18  3.000
 GL2  C7    C1  O5    111.91  3.000
 GL2  N2    C1  O5    108.06  3.000
 GL2  C7    C1  C2    111.63  3.000
 GL2  N2    C1  C2    111.05  3.000
 GL2  O5    C1  C2    112.41  3.000
 GL2  H2    C2  C3    107.56  3.000
 GL2  H2    C2  O2    111.30  3.000
 GL2  C3    C2  O2    113.16  3.000
 GL2  H2    C2  C1    106.85  3.000
 GL2  C3    C2  C1    111.82  3.000
 GL2  O2    C2  C1    106.02  3.000
 GL2  HO2   O2  C2    108.75  3.000
 GL2  H3    C3  C4    108.49  3.000
 GL2  H3    C3  O3    110.69  3.000
 GL2  C4    C3  O3    112.11  3.000
 GL2  H3    C3  C2    109.49  3.000
 GL2  C4    C3  C2    109.55  3.000
 GL2  O3    C3  C2    106.48  3.000
 GL2  HO3   O3  C3    108.28  3.000
 GL2  H4    C4  C5    108.94  3.000
 GL2  H4    C4  O4    111.15  3.000
 GL2  C5    C4  O4    111.11  3.000
 GL2  H4    C4  C3    108.44  3.000
 GL2  C5    C4  C3    109.56  3.000
 GL2  O4    C4  C3    107.59  3.000
 GL2  HO4   O4  C4    109.18  3.000
 GL2  H5    C5  O5    110.61  3.000
 GL2  H5    C5  C6    108.77  3.000
 GL2  O5    C5  C6    106.50  3.000
 GL2  H5    C5  C4    108.78  3.000
 GL2  O5    C5  C4    110.48  3.000
 GL2  C6    C5  C4    111.69  3.000
 GL2  H62   C6  H61   107.14  3.000
 GL2  H62   C6  O6    111.91  3.000
 GL2  H61   C6  O6    111.54  3.000
 GL2  H62   C6  C5    109.01  3.000
 GL2  H61   C6  C5    107.95  3.000
 GL2  O6    C6  C5    109.17  3.000
 GL2  HO6   O6  C6    107.95  3.000
 GL2  C5    O5  C1    118.10  3.000
 GL2  HN2   N2  C8    121.46  3.000
 GL2  HN2   N2  C1    122.70  3.000
 GL2  C8    N2  C1    113.73  3.000
 GL2  N1    C8  O8    124.55  3.000
 GL2  N1    C8  N2    106.49  3.000
 GL2  O8    C8  N2    128.97  3.000
 GL2  N3    N1  C7    122.91  3.000
 GL2  N3    N1  C8    124.94  3.000
 GL2  C7    N1  C8    112.15  3.000
 GL2  O7    C7  N1    126.92  3.000
 GL2  O7    C7  C1    126.83  3.000
 GL2  N1    C7  C1    106.23  3.000
 GL2  HN32  N3  HN31  108.55  3.000
 GL2  HN32  N3  N1    109.56  3.000
 GL2  HN31  N3  N1    109.66  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
 GL2  CONST_01  N1    C8  N2  C1    0.00   0.0  0
 GL2  CONST_02  C8    N1  C7  C1    0.00   0.0  0
 GL2  CONST_03  C7    N1  C8  N2    0.00   0.0  0
 GL2  CONST_04  O8    C8  N2  C1  180.00   0.0  0
 GL2  CONST_05  N3    N1  C7  C1  180.00   0.0  0
 GL2  CONST_06  N3    N1  C8  N2  180.00   0.0  0
 GL2  CONST_07  O7    C7  N1  C8  180.00   0.0  0
 GL2  CONST_08  C7    N1  C8  O8  180.00   0.0  0
 GL2  CONST_09  HN2   N2  C8  N1  180.00   0.0  0
 GL2  CONST_10  N3    N1  C8  O8    0.00   0.0  0
 GL2  CONST_11  N3    N1  C7  O7    0.00   0.0  0
 GL2  Var_01    HN31  N3  N1  C8  -59.69  30.0  2

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
 GL2  chir_01  C1  O5  N2  C7  positiv
 GL2  chir_02  C2  O2  C1  C3  negativ
 GL2  chir_03  C3  O3  C2  C4  positiv
 GL2  chir_04  C4  O4  C5  C3  positiv
 GL2  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
 GL2  plan-1  C1   0.020
 GL2  plan-1  N2   0.020
 GL2  plan-1  C8   0.020
 GL2  plan-1  O8   0.020
 GL2  plan-1  N1   0.020
 GL2  plan-1  C7   0.020
 GL2  plan-1  O7   0.020
 GL2  plan-1  N3   0.020
 GL2  plan-1  HN2  0.020

