# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 06:34:11 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-nitrophenyl alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(cc2)[N+]([O-])=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
 PNG  PNG  '4-nitrophenyl alpha-D-glucopyranoside'  D-saccharide  36  21  .  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_PNG
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
 PNG  C1   C  CH1    0   0.200  -1.2218  -0.6966   0.8702
 PNG  C2   C  CH1    0  -0.014  -2.5920  -1.3058   0.5686
 PNG  C3   C  CH1    0  -0.007  -3.2927  -0.5124  -0.5265
 PNG  C4   C  CH1    0   0.028  -3.3312   0.9650  -0.1517
 PNG  C5   C  CH1    0  -0.019  -1.9260   1.4704   0.1711
 PNG  C6   C  CH2    0  -0.160  -1.9477   2.8819   0.7184
 PNG  C7   C  CR6    0   0.424   0.9211  -0.7717  -0.1898
 PNG  C8   C  CR16   0  -0.357   1.5980  -0.2116   0.8953
 PNG  C9   C  CR16   0  -0.254   2.9766  -0.1128   0.8667
 PNG  C10  C  CR6    0   0.229   3.6795  -0.5564  -0.2437
 PNG  C11  C  CR16   0  -0.252   3.0147  -1.1032  -1.3367
 PNG  C12  C  CR16   0  -0.347   1.6425  -1.2082  -1.3054
 PNG  N1   N  N      1   0.328   5.1198  -0.4452  -0.2680
 PNG  O1   O  O2     0  -0.481  -0.4069  -0.9335  -0.2611
 PNG  O2   O  OH1    0  -0.662  -2.5012  -2.6447   0.1637
 PNG  O3   O  OH1    0  -0.672  -4.6259  -0.9328  -0.6947
 PNG  O4   O  OH1    0  -0.670  -3.8355   1.7501  -1.2026
 PNG  O5   O  O2     0  -0.489  -1.3262   0.6507   1.1672
 PNG  O6   O  OH1    0  -0.666  -0.6223   3.3157   0.9036
 PNG  O7   O  O      0  -0.388   5.6746   0.0304   0.6972
 PNG  O8   O  O     -1  -0.388   5.7064  -0.8330  -1.2533
 PNG  H1   H  HCH1   0   0.272  -0.7782  -1.1723   1.7525
 PNG  H2   H  HCH1   0   0.242  -3.1811  -1.2081   1.4910
 PNG  H3   H  HCH1   0   0.224  -2.7325  -0.6176  -1.4674
 PNG  H4   H  HCH1   0   0.216  -3.9522   1.0686   0.7525
 PNG  H5   H  HCH1   0   0.237  -1.3236   1.4573  -0.7475
 PNG  H61  H  HCH2   0   0.198  -2.5183   2.8901   1.6578
 PNG  H62  H  HCH2   0   0.214  -2.4873   3.5168   0.0082
 PNG  H8   H  HCR6   0   0.301   1.0762   0.1684   1.7604
 PNG  H9   H  HCR6   0   0.300   3.4870   0.3213   1.7137
 PNG  H11  H  HCR6   0   0.299   3.5539  -1.4519  -2.2051
 PNG  H12  H  HCR6   0   0.285   1.1142  -1.6374  -2.1462
 PNG  HO2  H  HOH1   0   0.462  -2.3864  -3.1991   0.9414
 PNG  HO3  H  HOH1   0   0.457  -4.6226  -1.8083  -1.0938
 PNG  HO4  H  HOH1   0   0.456  -4.7327   1.4576  -1.3940
 PNG  HO6  H  HOH1   0   0.456  -0.6514   4.2219   1.2228

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
 PNG  C1   C2   single    1.530  0.020  1.530
 PNG  C1   O1   single    1.414  0.020  1.414
 PNG  C1   O5   single    1.384  0.020  1.384
 PNG  C1   H1   single    0.970  0.020  1.090
 PNG  C2   C3   single    1.523  0.020  1.523
 PNG  C2   O2   single    1.402  0.020  1.402
 PNG  C2   H2   single    0.970  0.020  1.090
 PNG  C3   C4   single    1.525  0.020  1.525
 PNG  C3   O3   single    1.408  0.020  1.408
 PNG  C3   H3   single    0.970  0.020  1.090
 PNG  C4   C5   single    1.528  0.020  1.528
 PNG  C4   O4   single    1.405  0.020  1.405
 PNG  C4   H4   single    0.970  0.020  1.090
 PNG  C5   C6   single    1.514  0.020  1.514
 PNG  C5   O5   single    1.423  0.020  1.423
 PNG  C5   H5   single    0.970  0.020  1.090
 PNG  C6   O6   single    1.407  0.020  1.407
 PNG  C6   H61  single    0.970  0.020  1.090
 PNG  C6   H62  single    0.970  0.020  1.090
 PNG  C7   C8   aromatic  1.396  0.020  1.396
 PNG  C7   C12  aromatic  1.398  0.020  1.398
 PNG  C7   O1   single    1.340  0.020  1.340
 PNG  C8   C9   aromatic  1.382  0.020  1.382
 PNG  C8   H8   single    0.930  0.020  1.080
 PNG  C9   C10  aromatic  1.387  0.020  1.387
 PNG  C9   H9   single    0.930  0.020  1.080
 PNG  C10  C11  aromatic  1.391  0.020  1.391
 PNG  C10  N1   single    1.445  0.020  1.445
 PNG  C11  C12  aromatic  1.377  0.020  1.377
 PNG  C11  H11  single    0.930  0.020  1.080
 PNG  C12  H12  single    0.930  0.020  1.080
 PNG  N1   O7   double    1.211  0.020  1.211
 PNG  N1   O8   single    1.211  0.020  1.211
 PNG  O2   HO2  single    0.850  0.020  0.980
 PNG  O3   HO3  single    0.850  0.020  0.980
 PNG  O4   HO4  single    0.850  0.020  0.980
 PNG  O6   HO6  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
 PNG  H1   C1   O5   106.28  3.000
 PNG  H1   C1   O1   109.75  3.000
 PNG  O5   C1   O1   112.23  3.000
 PNG  H1   C1   C2   110.39  3.000
 PNG  O5   C1   C2   111.26  3.000
 PNG  O1   C1   C2   106.96  3.000
 PNG  H2   C2   O2   111.24  3.000
 PNG  H2   C2   C3   108.09  3.000
 PNG  O2   C2   C3   108.64  3.000
 PNG  H2   C2   C1   106.22  3.000
 PNG  O2   C2   C1   112.30  3.000
 PNG  C3   C2   C1   110.27  3.000
 PNG  H3   C3   O3   110.58  3.000
 PNG  H3   C3   C4   108.40  3.000
 PNG  O3   C3   C4   107.14  3.000
 PNG  H3   C3   C2   109.32  3.000
 PNG  O3   C3   C2   111.47  3.000
 PNG  C4   C3   C2   109.85  3.000
 PNG  H4   C4   O4   111.03  3.000
 PNG  H4   C4   C5   108.29  3.000
 PNG  O4   C4   C5   107.65  3.000
 PNG  H4   C4   C3   107.88  3.000
 PNG  O4   C4   C3   111.50  3.000
 PNG  C5   C4   C3   110.44  3.000
 PNG  H5   C5   O5   110.32  3.000
 PNG  H5   C5   C6   108.74  3.000
 PNG  O5   C5   C6   106.86  3.000
 PNG  H5   C5   C4   108.89  3.000
 PNG  O5   C5   C4   110.19  3.000
 PNG  C6   C5   C4   111.82  3.000
 PNG  H62  C6   H61  107.11  3.000
 PNG  H62  C6   O6   111.77  3.000
 PNG  H61  C6   O6   111.98  3.000
 PNG  H62  C6   C5   108.25  3.000
 PNG  H61  C6   C5   108.86  3.000
 PNG  O6   C6   C5   108.76  3.000
 PNG  O1   C7   C12  115.55  3.000
 PNG  O1   C7   C8   124.77  3.000
 PNG  C12  C7   C8   119.68  3.000
 PNG  H8   C8   C9   118.26  3.000
 PNG  H8   C8   C7   122.00  3.000
 PNG  C9   C8   C7   119.73  3.000
 PNG  H9   C9   C10  121.13  3.000
 PNG  H9   C9   C8   118.93  3.000
 PNG  C10  C9   C8   119.94  3.000
 PNG  N1   C10  C11  119.57  3.000
 PNG  N1   C10  C9   119.61  3.000
 PNG  C11  C10  C9   120.83  3.000
 PNG  H11  C11  C12  119.42  3.000
 PNG  H11  C11  C10  121.33  3.000
 PNG  C12  C11  C10  119.24  3.000
 PNG  H12  C12  C11  119.96  3.000
 PNG  H12  C12  C7   119.47  3.000
 PNG  C11  C12  C7   120.57  3.000
 PNG  O8   N1   O7   123.56  3.000
 PNG  O8   N1   C10  118.17  3.000
 PNG  O7   N1   C10  118.27  3.000
 PNG  C7   O1   C1   120.56  3.000
 PNG  HO2  O2   C2   108.94  3.000
 PNG  HO3  O3   C3   108.54  3.000
 PNG  HO4  O4   C4   108.25  3.000
 PNG  C5   O5   C1   116.27  3.000
 PNG  HO6  O6   C6   107.82  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
 PNG  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 PNG  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 PNG  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 PNG  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 PNG  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 PNG  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 PNG  CONST_07  N1   C10  C9   C8   180.00   0.0  0
 PNG  CONST_08  O1   C7   C8   C9   180.00   0.0  0
 PNG  CONST_09  O1   C7   C12  C11  180.00   0.0  0
 PNG  CONST_10  N1   C10  C11  C12  180.00   0.0  0
 PNG  CONST_11  H9   C9   C8   C7   180.00   0.0  0
 PNG  CONST_12  H11  C11  C12  C7   180.00   0.0  0
 PNG  CONST_13  H12  C12  C7   C8   180.00   0.0  0
 PNG  CONST_14  H8   C8   C9   C10  180.00   0.0  0
 PNG  CONST_15  O7   N1   C10  C9     0.00   0.0  0
 PNG  CONST_16  O8   N1   C10  C9   180.00   0.0  0
 PNG  CONST_17  O7   N1   C10  C11  180.00   0.0  0
 PNG  CONST_18  O8   N1   C10  C11    0.00   0.0  0
 PNG  Var_01    C8   C7   O1   C1    -8.52  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
 PNG  chir_01  C1  C2  O1  O5  negativ
 PNG  chir_02  C2  O2  C1  C3  negativ
 PNG  chir_03  C3  O3  C2  C4  positiv
 PNG  chir_04  C4  O4  C3  C5  negativ
 PNG  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
 PNG  plan-1  C7   0.020
 PNG  plan-1  C8   0.020
 PNG  plan-1  C9   0.020
 PNG  plan-1  C10  0.020
 PNG  plan-1  C11  0.020
 PNG  plan-1  C12  0.020
 PNG  plan-1  N1   0.020
 PNG  plan-1  O1   0.020
 PNG  plan-1  H8   0.020
 PNG  plan-1  H9   0.020
 PNG  plan-1  H11  0.020
 PNG  plan-1  H12  0.020
 PNG  plan-2  C10  0.020
 PNG  plan-2  N1   0.020
 PNG  plan-2  O7   0.020
 PNG  plan-2  O8   0.020

