# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:39:08 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2-deoxy-2-{[methyl(nitroso)carbamoyl]amino}-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(N=O)C(=O)N[C@H]1[C@H](O)O[C@H](CO)[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
 STZ  STZ  2-deoxy-2-{[methyl(nitroso)carbamoyl]amino}-beta-D-glucopyranose  D-saccharide  33  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 OK (reasonable std)
;

data_comp_STZ
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
 STZ  O3    O  OH1   0  -0.662   0.2768   2.2526   0.8400
 STZ  C3    C  CH1   0   0.037   0.8774   1.2529   0.0622
 STZ  C4    C  CH1   0  -0.003   2.3595   1.0887   0.3860
 STZ  O4    O  OH1   0  -0.673   2.9969   2.2904   0.0142
 STZ  C5    C  CH1   0  -0.021   2.9252  -0.1181  -0.3701
 STZ  C6    C  CH2   0  -0.160   4.3706  -0.3888  -0.0166
 STZ  O6    O  OH1   0  -0.669   4.8471  -1.4401  -0.8210
 STZ  O5    O  O2    0  -0.495   2.1726  -1.2663  -0.0362
 STZ  C1    C  CH1   0   0.310   0.8278  -1.1925  -0.4380
 STZ  O1    O  OH1   0  -0.649   0.2045  -2.3751  -0.1138
 STZ  C2    C  CH1   0  -0.157   0.1311  -0.0522   0.3092
 STZ  N2    N  NH1   0  -0.669  -1.2421   0.0717  -0.1086
 STZ  CAM   C  C     0   0.781  -2.2671  -0.3618   0.6326
 STZ  OAG   O  O     0  -0.483  -2.1862  -0.8650   1.7325
 STZ  NAN   N  NT    0  -0.359  -3.5510  -0.1831   0.0418
 STZ  CAH   C  CH3   0  -0.538  -4.7659  -0.6168   0.7069
 STZ  NAO   N  N     0   0.174  -3.5907   0.4126  -1.1294
 STZ  OAP   O  O     0  -0.367  -4.6879   0.5717  -1.5993
 STZ  H3    H  HOH1  0   0.452   0.7536   3.0748   0.6830
 STZ  HA    H  HCH1  0   0.213   0.8027   1.4962  -1.0121
 STZ  H4    H  HCH1  0   0.230   2.4604   0.9047   1.4652
 STZ  H2    H  HCH1  0   0.280   0.1541  -0.2777   1.3784
 STZ  HB    H  HOH1  0   0.464   3.7251   2.4616   0.6172
 STZ  H5    H  HCH1  0   0.223   2.8543   0.0830  -1.4522
 STZ  H61C  H  HCH2  0   0.205   4.9437   0.5315  -0.1771
 STZ  H62C  H  HCH2  0   0.200   4.4386  -0.6281   1.0538
 STZ  H6    H  HOH1  0   0.457   5.7741  -1.5806  -0.6090
 STZ  H1    H  HCH1  0   0.189   0.7829  -0.9943  -1.5239
 STZ  HC    H  HOH1  0   0.467   0.4077  -3.0383  -0.7819
 STZ  HD    H  HNH1  0   0.412  -1.4343   0.4703  -1.0155
 STZ  HAH1  H  HCH3  0   0.267  -5.3936   0.2396   0.9496
 STZ  HAH2  H  HCH3  0   0.267  -5.3220  -1.2961   0.0635
 STZ  HAH3  H  HCH3  0   0.275  -4.4962  -1.1309   1.6202

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
 STZ  O3   C3    single  1.402  0.020  1.402
 STZ  C3   C4    single  1.526  0.020  1.526
 STZ  C3   C2    single  1.524  0.020  1.524
 STZ  C4   O4    single  1.410  0.020  1.410
 STZ  C4   C5    single  1.532  0.020  1.532
 STZ  C5   C6    single  1.512  0.020  1.512
 STZ  C5   O5    single  1.413  0.020  1.413
 STZ  C6   O6    single  1.407  0.020  1.407
 STZ  O5   C1    single  1.405  0.020  1.405
 STZ  C1   O1    single  1.376  0.020  1.376
 STZ  C1   C2    single  1.531  0.020  1.531
 STZ  C2   N2    single  1.441  0.020  1.441
 STZ  N2   CAM   single  1.337  0.020  1.337
 STZ  CAM  OAG   double  1.212  0.020  1.212
 STZ  CAM  NAN   single  1.425  0.020  1.425
 STZ  NAN  CAH   single  1.451  0.020  1.451
 STZ  NAN  NAO   single  1.315  0.020  1.315
 STZ  NAO  OAP   double  1.204  0.020  1.204
 STZ  O3   H3    single  0.850  0.020  0.980
 STZ  C3   HA    single  0.970  0.020  1.090
 STZ  C4   H4    single  0.970  0.020  1.090
 STZ  C2   H2    single  0.970  0.020  1.090
 STZ  O4   HB    single  0.850  0.020  0.980
 STZ  C5   H5    single  0.970  0.020  1.090
 STZ  C6   H61C  single  0.970  0.020  1.090
 STZ  C6   H62C  single  0.970  0.020  1.090
 STZ  O6   H6    single  0.850  0.020  0.980
 STZ  C1   H1    single  0.970  0.020  1.090
 STZ  O1   HC    single  0.850  0.020  0.980
 STZ  N2   HD    single  0.860  0.020  1.020
 STZ  CAH  HAH1  single  0.970  0.020  1.090
 STZ  CAH  HAH2  single  0.970  0.020  1.090
 STZ  CAH  HAH3  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
 STZ  H3    O3   C3    107.83  3.000
 STZ  HA    C3   C2    108.26  3.000
 STZ  HA    C3   C4    107.21  3.000
 STZ  C2    C3   C4    110.43  3.000
 STZ  HA    C3   O3    110.72  3.000
 STZ  C2    C3   O3    108.12  3.000
 STZ  C4    C3   O3    112.03  3.000
 STZ  H4    C4   C5    108.59  3.000
 STZ  H4    C4   O4    111.10  3.000
 STZ  C5    C4   O4    111.97  3.000
 STZ  H4    C4   C3    108.39  3.000
 STZ  C5    C4   C3    109.79  3.000
 STZ  O4    C4   C3    106.93  3.000
 STZ  HB    O4   C4    109.20  3.000
 STZ  H5    C5   O5    110.23  3.000
 STZ  H5    C5   C6    108.86  3.000
 STZ  O5    C5   C6    107.96  3.000
 STZ  H5    C5   C4    108.48  3.000
 STZ  O5    C5   C4    109.07  3.000
 STZ  C6    C5   C4    112.23  3.000
 STZ  H62C  C6   H61C  107.05  3.000
 STZ  H62C  C6   O6    111.91  3.000
 STZ  H61C  C6   O6    111.51  3.000
 STZ  H62C  C6   C5    109.01  3.000
 STZ  H61C  C6   C5    108.37  3.000
 STZ  O6    C6   C5    108.89  3.000
 STZ  H6    O6   C6    108.05  3.000
 STZ  C1    O5   C5    113.54  3.000
 STZ  H1    C1   C2    109.12  3.000
 STZ  H1    C1   O1    111.56  3.000
 STZ  C2    C1   O1    108.61  3.000
 STZ  H1    C1   O5    109.23  3.000
 STZ  C2    C1   O5    109.57  3.000
 STZ  O1    C1   O5    108.73  3.000
 STZ  HC    O1   C1    109.45  3.000
 STZ  H2    C2   N2    108.76  3.000
 STZ  H2    C2   C1    108.31  3.000
 STZ  N2    C2   C1    110.87  3.000
 STZ  H2    C2   C3    108.97  3.000
 STZ  N2    C2   C3    110.25  3.000
 STZ  C1    C2   C3    109.63  3.000
 STZ  HD    N2   CAM   118.70  3.000
 STZ  HD    N2   C2    118.44  3.000
 STZ  CAM   N2   C2    122.82  3.000
 STZ  NAN   CAM  OAG   119.24  3.000
 STZ  NAN   CAM  N2    114.85  3.000
 STZ  OAG   CAM  N2    125.90  3.000
 STZ  NAO   NAN  CAH   121.22  3.000
 STZ  NAO   NAN  CAM   116.97  3.000
 STZ  CAH   NAN  CAM   121.79  3.000
 STZ  HAH3  CAH  HAH2  109.25  3.000
 STZ  HAH3  CAH  HAH1  109.22  3.000
 STZ  HAH2  CAH  HAH1  109.14  3.000
 STZ  HAH3  CAH  NAN   108.67  3.000
 STZ  HAH2  CAH  NAN   110.08  3.000
 STZ  HAH1  CAH  NAN   110.46  3.000
 STZ  OAP   NAO  NAN   115.79  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
 STZ  CONST_01  OAG   CAM  N2   C2     0.00   0.0  0
 STZ  CONST_02  NAN   CAM  N2   C2   180.00   0.0  0
 STZ  CONST_03  CAH   NAN  CAM  OAG    0.00   0.0  0
 STZ  CONST_04  NAO   NAN  CAM  OAG  180.00   0.0  0
 STZ  CONST_05  CAH   NAN  CAM  N2   180.00   0.0  0
 STZ  CONST_06  NAO   NAN  CAM  N2     0.00   0.0  0
 STZ  CONST_07  HD    N2   CAM  OAG  180.00   0.0  0
 STZ  Var_01    HAH1  CAH  NAN  CAM  115.39  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
 STZ  chir_01  C3  O3  C4  C2  negativ
 STZ  chir_02  C4  O4  C3  C5  negativ
 STZ  chir_03  C5  O5  C4  C6  negativ
 STZ  chir_04  C1  O5  O1  C2  negativ
 STZ  chir_05  C2  N2  C3  C1  positiv

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
 STZ  plan-1  C2   0.020
 STZ  plan-1  N2   0.020
 STZ  plan-1  CAM  0.020
 STZ  plan-1  OAG  0.020
 STZ  plan-1  NAN  0.020
 STZ  plan-1  CAH  0.020
 STZ  plan-1  NAO  0.020
 STZ  plan-1  HD   0.020
 STZ  plan-2  NAN  0.020
 STZ  plan-2  NAO  0.020
 STZ  plan-2  OAP  0.020

