# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:30:43 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-nitrophenyl beta-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
 PNW  PNW  '4-nitrophenyl beta-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_PNW
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
 PNW  C1   C  CH1    0   0.260   1.1248   0.5870  -0.0251
 PNW  N1   N  N      1   0.329  -5.2549  -0.0655  -0.3809
 PNW  O1   O  O2     0  -0.487   0.0533   1.2054   0.6253
 PNW  C2   C  CH1    0  -0.023   2.3446   1.4913   0.1269
 PNW  O2   O  OH1    0  -0.664   2.1833   2.7028  -0.5619
 PNW  C3   C  CH1    0  -0.013   3.5541   0.7729  -0.4630
 PNW  O3   O  OH1    0  -0.670   4.7498   1.4676  -0.2082
 PNW  C4   C  CH1    0   0.042   3.7007  -0.6260   0.1309
 PNW  O4   O  OH1    0  -0.670   4.7077  -1.3543  -0.5230
 PNW  C5   C  CH1    0  -0.026   2.3828  -1.3833  -0.0282
 PNW  O5   O  O2     0  -0.492   1.3508  -0.6390   0.5951
 PNW  C6   C  CH2    0  -0.154   2.4120  -2.7537   0.6108
 PNW  O6   O  OH1    0  -0.666   1.1873  -3.3937   0.3458
 PNW  C7   C  CR6    0   0.402  -1.2082   0.8255   0.3539
 PNW  O7   O  O      0  -0.387  -6.0935   0.7126   0.0141
 PNW  C8   C  CR16   0  -0.340  -2.2089   1.6931   0.7968
 PNW  O8   O  O     -1  -0.386  -5.5151  -1.0842  -0.9801
 PNW  C9   C  CR16   0  -0.254  -3.5351   1.4043   0.5620
 PNW  C10  C  CR6    0   0.234  -3.8651   0.2401  -0.1232
 PNW  C11  C  CR16   0  -0.256  -2.8807  -0.6347  -0.5592
 PNW  C12  C  CR16   0  -0.349  -1.5498  -0.3501  -0.3157
 PNW  H1   H  HCH1   0   0.223   0.8894   0.4480  -1.0946
 PNW  H2   H  HCH1   0   0.235   2.5168   1.6520   1.2012
 PNW  HO2  H  HOH1   0   0.461   1.6145   3.2831  -0.0466
 PNW  H3   H  HCH1   0   0.223   3.3918   0.6605  -1.5470
 PNW  HO3  H  HOH1   0   0.459   4.7647   2.2647  -0.7469
 PNW  H4   H  HCH1   0   0.217   3.9149  -0.5288   1.2071
 PNW  HO4  H  HOH1   0   0.456   5.5334  -0.8659  -0.4400
 PNW  H5   H  HCH1   0   0.233   2.1672  -1.4967  -1.1033
 PNW  H6   H  HCH2   0   0.216   3.2600  -3.3085   0.1966
 PNW  H6A  H  HCH2   0   0.199   2.5945  -2.6422   1.6888
 PNW  HO6  H  HOH1   0   0.458   1.2425  -4.2920   0.6834
 PNW  H8   H  HCR6   0   0.287  -1.9358   2.5996   1.3202
 PNW  H9   H  HCR6   0   0.300  -4.2973   2.0881   0.9056
 PNW  H11  H  HCR6   0   0.302  -3.1356  -1.5461  -1.0800
 PNW  H12  H  HCR6   0   0.304  -0.8027  -1.0644  -0.6298

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
 PNW  C1   O1   single    1.398  0.020  1.398
 PNW  C1   C2   single    1.526  0.020  1.526
 PNW  C1   O5   single    1.392  0.020  1.392
 PNW  N1   O7   double    1.210  0.020  1.210
 PNW  N1   O8   single    1.210  0.020  1.210
 PNW  N1   C10  single    1.446  0.020  1.446
 PNW  O1   C7   single    1.345  0.020  1.345
 PNW  C2   O2   single    1.403  0.020  1.403
 PNW  C2   C3   single    1.525  0.020  1.525
 PNW  C3   O3   single    1.406  0.020  1.406
 PNW  C3   C4   single    1.527  0.020  1.527
 PNW  C4   O4   single    1.404  0.020  1.404
 PNW  C4   C5   single    1.528  0.020  1.528
 PNW  C5   O5   single    1.417  0.020  1.417
 PNW  C5   C6   single    1.512  0.020  1.512
 PNW  C6   O6   single    1.407  0.020  1.407
 PNW  C7   C8   aromatic  1.396  0.020  1.396
 PNW  C7   C12  aromatic  1.395  0.020  1.395
 PNW  C8   C9   aromatic  1.377  0.020  1.377
 PNW  C9   C10  aromatic  1.391  0.020  1.391
 PNW  C10  C11  aromatic  1.387  0.020  1.387
 PNW  C11  C12  aromatic  1.383  0.020  1.383
 PNW  C1   H1   single    0.970  0.020  1.090
 PNW  C2   H2   single    0.970  0.020  1.090
 PNW  O2   HO2  single    0.850  0.020  0.980
 PNW  C3   H3   single    0.970  0.020  1.090
 PNW  O3   HO3  single    0.850  0.020  0.980
 PNW  C4   H4   single    0.970  0.020  1.090
 PNW  O4   HO4  single    0.850  0.020  0.980
 PNW  C5   H5   single    0.970  0.020  1.090
 PNW  C6   H6   single    0.970  0.020  1.090
 PNW  C6   H6A  single    0.970  0.020  1.090
 PNW  O6   HO6  single    0.850  0.020  0.980
 PNW  C8   H8   single    0.930  0.020  1.080
 PNW  C9   H9   single    0.930  0.020  1.080
 PNW  C11  H11  single    0.930  0.020  1.080
 PNW  C12  H12  single    0.930  0.020  1.080

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
 PNW  H1   C1   O5   110.81  3.000
 PNW  H1   C1   C2   109.97  3.000
 PNW  O5   C1   C2   110.34  3.000
 PNW  H1   C1   O1   110.07  3.000
 PNW  O5   C1   O1   107.86  3.000
 PNW  C2   C1   O1   107.71  3.000
 PNW  C10  N1   O8   118.22  3.000
 PNW  C10  N1   O7   118.16  3.000
 PNW  O8   N1   O7   123.63  3.000
 PNW  C7   O1   C1   120.01  3.000
 PNW  H2   C2   C3   108.81  3.000
 PNW  H2   C2   O2   111.80  3.000
 PNW  C3   C2   O2   107.94  3.000
 PNW  H2   C2   C1   108.00  3.000
 PNW  C3   C2   C1   108.43  3.000
 PNW  O2   C2   C1   111.77  3.000
 PNW  HO2  O2   C2   109.02  3.000
 PNW  H3   C3   C4   107.66  3.000
 PNW  H3   C3   O3   110.73  3.000
 PNW  C4   C3   O3   107.49  3.000
 PNW  H3   C3   C2   108.16  3.000
 PNW  C4   C3   C2   110.93  3.000
 PNW  O3   C3   C2   111.80  3.000
 PNW  HO3  O3   C3   108.73  3.000
 PNW  H4   C4   C5   108.25  3.000
 PNW  H4   C4   O4   111.18  3.000
 PNW  C5   C4   O4   108.23  3.000
 PNW  H4   C4   C3   108.53  3.000
 PNW  C5   C4   C3   109.31  3.000
 PNW  O4   C4   C3   111.27  3.000
 PNW  HO4  O4   C4   108.16  3.000
 PNW  H5   C5   C6   108.83  3.000
 PNW  H5   C5   O5   109.91  3.000
 PNW  C6   C5   O5   107.71  3.000
 PNW  H5   C5   C4   108.73  3.000
 PNW  C6   C5   C4   112.85  3.000
 PNW  O5   C5   C4   108.78  3.000
 PNW  C5   O5   C1   112.63  3.000
 PNW  H6A  C6   H6   107.10  3.000
 PNW  H6A  C6   O6   112.05  3.000
 PNW  H6   C6   O6   111.87  3.000
 PNW  H6A  C6   C5   109.01  3.000
 PNW  H6   C6   C5   108.32  3.000
 PNW  O6   C6   C5   108.41  3.000
 PNW  HO6  O6   C6   108.00  3.000
 PNW  C12  C7   C8   120.01  3.000
 PNW  C12  C7   O1   124.36  3.000
 PNW  C8   C7   O1   115.63  3.000
 PNW  H8   C8   C9   120.08  3.000
 PNW  H8   C8   C7   119.55  3.000
 PNW  C9   C8   C7   120.37  3.000
 PNW  H9   C9   C10  121.29  3.000
 PNW  H9   C9   C8   119.50  3.000
 PNW  C10  C9   C8   119.21  3.000
 PNW  C11  C10  C9   120.96  3.000
 PNW  C11  C10  N1   119.52  3.000
 PNW  C9   C10  N1   119.52  3.000
 PNW  H11  C11  C12  119.06  3.000
 PNW  H11  C11  C10  121.07  3.000
 PNW  C12  C11  C10  119.86  3.000
 PNW  H12  C12  C11  118.58  3.000
 PNW  H12  C12  C7   121.82  3.000
 PNW  C11  C12  C7   119.58  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
 PNW  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 PNW  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 PNW  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 PNW  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 PNW  CONST_05  C12  C7   C8   C9      0.00   0.0  0
 PNW  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 PNW  CONST_07  C8   C9   C10  N1    180.00   0.0  0
 PNW  CONST_08  C12  C11  C10  N1    180.00   0.0  0
 PNW  CONST_09  C9   C8   C7   O1    180.00   0.0  0
 PNW  CONST_10  C11  C12  C7   O1    180.00   0.0  0
 PNW  CONST_11  H9   C9   C8   C7    180.00   0.0  0
 PNW  CONST_12  H11  C11  C12  C7    180.00   0.0  0
 PNW  CONST_13  H12  C12  C7   C8    180.00   0.0  0
 PNW  CONST_14  H8   C8   C9   C10   180.00   0.0  0
 PNW  CONST_15  C9   C10  N1   O7      0.00   0.0  0
 PNW  CONST_16  C11  C10  N1   O7    180.00   0.0  0
 PNW  CONST_17  C9   C10  N1   O8    180.00   0.0  0
 PNW  CONST_18  C11  C10  N1   O8      0.00   0.0  0
 PNW  Var_01    C8   C7   O1   C1   -165.37  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
 PNW  chir_01  C1  O1  C2  O5  negativ
 PNW  chir_02  C2  O2  C1  C3  negativ
 PNW  chir_03  C3  O3  C2  C4  positiv
 PNW  chir_04  C4  O4  C3  C5  negativ
 PNW  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
 PNW  plan-1  N1   0.020
 PNW  plan-1  O1   0.020
 PNW  plan-1  C7   0.020
 PNW  plan-1  C8   0.020
 PNW  plan-1  C9   0.020
 PNW  plan-1  C10  0.020
 PNW  plan-1  C11  0.020
 PNW  plan-1  C12  0.020
 PNW  plan-1  H8   0.020
 PNW  plan-1  H9   0.020
 PNW  plan-1  H11  0.020
 PNW  plan-1  H12  0.020
 PNW  plan-2  N1   0.020
 PNW  plan-2  O7   0.020
 PNW  plan-2  O8   0.020
 PNW  plan-2  C10  0.020

