# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 00:46:32 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: N-(acetylcarbamoyl)-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC(=O)N[C@@H]1O[C@H](CO)[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
 AZC  AZC  N-(acetylcarbamoyl)-beta-D-glucopyranosylamine  D-saccharide  34  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_AZC
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
 AZC  C1   C  CH1   0   0.208   0.4142   0.2361  -0.2558
 AZC  C2   C  CH1   0  -0.028   1.5908  -0.1780  -1.1427
 AZC  O2   O  OH1   0  -0.663   2.7838   0.4451  -0.7406
 AZC  C3   C  CH1   0  -0.004   1.3077   0.2492  -2.5761
 AZC  O3   O  OH1   0  -0.672   2.2813  -0.2306  -3.4713
 AZC  C4   C  CH1   0   0.035  -0.0448  -0.2773  -3.0407
 AZC  O4   O  OH1   0  -0.672  -0.3895   0.2435  -4.3002
 AZC  C5   C  CH1   0  -0.014  -1.1248   0.1384  -2.0407
 AZC  O5   O  O2    0  -0.487  -0.7802  -0.3227  -0.7509
 AZC  C6   C  CH2   0  -0.156  -2.4773  -0.4419  -2.3968
 AZC  O6   O  OH1   0  -0.670  -3.4349   0.0447  -1.4873
 AZC  N1   N  NH1   0  -0.730   0.6163  -0.2224   1.0771
 AZC  C7   C  C     0   0.762   0.1026   0.4378   2.1542
 AZC  O7   O  O     0  -0.474  -0.4328   1.5216   2.0886
 AZC  N2   N  NH1   0  -0.731   0.2931  -0.2637   3.3384
 AZC  C8   C  C     0   0.517  -0.1487   0.1003   4.5947
 AZC  C9   C  CH3   0  -0.796   0.2640  -0.8818   5.6587
 AZC  O8   O  O     0  -0.427  -0.7945   1.0966   4.8185
 AZC  H1   H  HCH1  0   0.235   0.3464   1.3310  -0.2410
 AZC  H2   H  HCH1  0   0.227   1.6812  -1.2754  -1.1117
 AZC  HO2  H  HOH1  0   0.457   3.0826   0.0434   0.0813
 AZC  H3   H  HCH1  0   0.217   1.2623   1.3505  -2.6004
 AZC  HO3  H  HOH1  0   0.457   3.1152   0.2108  -3.2820
 AZC  H4   H  HCH1  0   0.213  -0.0022  -1.3780  -3.0661
 AZC  HO4  H  HOH1  0   0.455   0.2832  -0.0281  -4.9334
 AZC  H5   H  HCH1  0   0.223  -1.1957   1.2387  -2.0411
 AZC  H61  H  HCH2  0   0.214  -2.7146  -0.1566  -3.4266
 AZC  H62  H  HCH2  0   0.195  -2.4111  -1.5388  -2.3719
 AZC  HO6  H  HOH1  0   0.457  -4.2988  -0.2645  -1.7740
 AZC  HN1  H  HNH1  0   0.406   0.8990  -1.1858   1.1868
 AZC  HN2  H  HNH1  0   0.425   0.8111  -1.1297   3.2883
 AZC  H91  H  HCH3  0   0.271  -0.1517  -0.5918   6.6194
 AZC  H92  H  HCH3  0   0.273  -0.0754  -1.8889   5.4136
 AZC  H93  H  HCH3  0   0.277   1.3516  -0.9155   5.7414

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
 AZC  C1  C2   single  1.531  0.020  1.531
 AZC  C1  O5   single  1.409  0.020  1.409
 AZC  C1  N1   single  1.424  0.020  1.424
 AZC  C1  H1   single  0.970  0.020  1.090
 AZC  C2  O2   single  1.405  0.020  1.405
 AZC  C2  C3   single  1.522  0.020  1.522
 AZC  C2  H2   single  0.970  0.020  1.090
 AZC  O2  HO2  single  0.850  0.020  0.980
 AZC  C3  O3   single  1.407  0.020  1.407
 AZC  C3  C4   single  1.524  0.020  1.524
 AZC  C3  H3   single  0.970  0.020  1.090
 AZC  O3  HO3  single  0.850  0.020  0.980
 AZC  C4  O4   single  1.406  0.020  1.406
 AZC  C4  C5   single  1.529  0.020  1.529
 AZC  C4  H4   single  0.970  0.020  1.090
 AZC  O4  HO4  single  0.850  0.020  0.980
 AZC  C5  O5   single  1.412  0.020  1.412
 AZC  C5  C6   single  1.514  0.020  1.514
 AZC  C5  H5   single  0.970  0.020  1.090
 AZC  C6  O6   single  1.408  0.020  1.408
 AZC  C6  H61  single  0.970  0.020  1.090
 AZC  C6  H62  single  0.970  0.020  1.090
 AZC  O6  HO6  single  0.850  0.020  0.980
 AZC  N1  C7   single  1.364  0.020  1.364
 AZC  N1  HN1  single  0.860  0.020  1.020
 AZC  C7  O7   double  1.211  0.020  1.211
 AZC  C7  N2   single  1.390  0.020  1.390
 AZC  N2  C8   single  1.381  0.020  1.381
 AZC  N2  HN2  single  0.860  0.020  1.020
 AZC  C8  C9   single  1.506  0.020  1.506
 AZC  C8  O8   double  1.208  0.020  1.208
 AZC  C9  H91  single  0.970  0.020  1.090
 AZC  C9  H92  single  0.970  0.020  1.090
 AZC  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
 AZC  H1   C1  N1   108.52  3.000
 AZC  H1   C1  O5   110.38  3.000
 AZC  N1   C1  O5   108.76  3.000
 AZC  H1   C1  C2   108.99  3.000
 AZC  N1   C1  C2   110.25  3.000
 AZC  O5   C1  C2   109.93  3.000
 AZC  H2   C2  C3   108.74  3.000
 AZC  H2   C2  O2   111.36  3.000
 AZC  C3   C2  O2   107.64  3.000
 AZC  H2   C2  C1   108.44  3.000
 AZC  C3   C2  C1   109.07  3.000
 AZC  O2   C2  C1   111.53  3.000
 AZC  HO2  O2  C2   108.84  3.000
 AZC  H3   C3  C4   107.57  3.000
 AZC  H3   C3  O3   110.80  3.000
 AZC  C4   C3  O3   107.60  3.000
 AZC  H3   C3  C2   107.98  3.000
 AZC  C4   C3  C2   110.80  3.000
 AZC  O3   C3  C2   112.01  3.000
 AZC  HO3  O3  C3   108.55  3.000
 AZC  H4   C4  C5   108.29  3.000
 AZC  H4   C4  O4   111.03  3.000
 AZC  C5   C4  O4   108.18  3.000
 AZC  H4   C4  C3   108.54  3.000
 AZC  C5   C4  C3   109.48  3.000
 AZC  O4   C4  C3   111.27  3.000
 AZC  HO4  O4  C4   108.26  3.000
 AZC  H5   C5  C6   108.96  3.000
 AZC  H5   C5  O5   109.99  3.000
 AZC  C6   C5  O5   107.92  3.000
 AZC  H5   C5  C4   108.44  3.000
 AZC  C6   C5  C4   111.89  3.000
 AZC  O5   C5  C4   109.64  3.000
 AZC  C5   O5  C1   113.48  3.000
 AZC  H62  C6  H61  107.13  3.000
 AZC  H62  C6  O6   111.79  3.000
 AZC  H61  C6  O6   111.73  3.000
 AZC  H62  C6  C5   108.86  3.000
 AZC  H61  C6  C5   108.36  3.000
 AZC  O6   C6  C5   108.86  3.000
 AZC  HO6  O6  C6   107.91  3.000
 AZC  HN1  N1  C7   118.78  3.000
 AZC  HN1  N1  C1   116.65  3.000
 AZC  C7   N1  C1   122.00  3.000
 AZC  N2   C7  O7   123.97  3.000
 AZC  N2   C7  N1   112.15  3.000
 AZC  O7   C7  N1   123.87  3.000
 AZC  HN2  N2  C8   115.80  3.000
 AZC  HN2  N2  C7   117.44  3.000
 AZC  C8   N2  C7   126.76  3.000
 AZC  O8   C8  C9   123.61  3.000
 AZC  O8   C8  N2   123.85  3.000
 AZC  C9   C8  N2   112.54  3.000
 AZC  H93  C9  H92  107.38  3.000
 AZC  H93  C9  H91  108.83  3.000
 AZC  H92  C9  H91  109.04  3.000
 AZC  H93  C9  C8   110.30  3.000
 AZC  H92  C9  C8   110.99  3.000
 AZC  H91  C9  C8   110.24  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
 AZC  CONST_01  O7   C7  N1  C1     0.00   0.0  0
 AZC  CONST_02  N2   C7  N1  C1   180.00   0.0  0
 AZC  CONST_03  C9   C8  N2  C7   180.00   0.0  0
 AZC  CONST_04  O8   C8  N2  C7     0.00   0.0  0
 AZC  CONST_05  C8   N2  C7  O7     0.00   0.0  0
 AZC  CONST_06  C8   N2  C7  N1   180.00   0.0  0
 AZC  CONST_07  HN1  N1  C7  O7   180.00   0.0  0
 AZC  CONST_08  HN2  N2  C7  O7   180.00   0.0  0
 AZC  Var_01    H91  C9  C8  N2  -176.64  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
 AZC  chir_01  C1  C2  O5  N1  negativ
 AZC  chir_02  C2  O2  C1  C3  negativ
 AZC  chir_03  C3  O3  C2  C4  positiv
 AZC  chir_04  C4  O4  C5  C3  positiv
 AZC  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
 AZC  plan-1  C1   0.020
 AZC  plan-1  N1   0.020
 AZC  plan-1  C7   0.020
 AZC  plan-1  O7   0.020
 AZC  plan-1  N2   0.020
 AZC  plan-1  C8   0.020
 AZC  plan-1  C9   0.020
 AZC  plan-1  O8   0.020
 AZC  plan-1  HN1  0.020
 AZC  plan-1  HN2  0.020

