# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:32:02 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-nitrophenyl alpha-D-galactopyranoside
#   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
 9PG  9PG  '4-nitrophenyl alpha-D-galactopyranoside'  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_9PG
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
 9PG  C6   C  CH2    0  -0.159   2.0874   2.8326   0.2206
 9PG  C5   C  CH1    0  -0.019   2.0212   1.3276   0.3625
 9PG  C4   C  CH1    0  -0.009   3.3864   0.7035   0.6085
 9PG  C3   C  CH1    0   0.004   3.2462  -0.8169   0.6446
 9PG  C2   C  CH1    0  -0.012   2.5691  -1.3029  -0.6308
 9PG  C1   C  CH1    0   0.203   1.2484  -0.5616  -0.8515
 9PG  O8   O  O     -1  -0.389  -5.6032   0.5171  -0.8703
 9PG  O7   O  O      0  -0.389  -5.7835  -0.6382   0.9139
 9PG  C9   C  CR6    0   0.228  -3.6959  -0.3410   0.0439
 9PG  C14  C  CR16   0  -0.253  -3.1197  -1.0967   1.0603
 9PG  C13  C  CR16   0  -0.348  -1.7568  -1.2898   1.0645
 9PG  C12  C  CR6    0   0.428  -0.9558  -0.7351   0.0610
 9PG  C11  C  CR16   0  -0.357  -1.5434   0.0362  -0.9442
 9PG  C10  C  CR16   0  -0.255  -2.9131   0.2224  -0.9531
 9PG  O1   O  O2     0  -0.481   0.3524  -1.0053   0.1515
 9PG  O2   O  OH1    0  -0.665   2.3878  -2.6913  -0.5347
 9PG  O3   O  OH1    0  -0.674   4.5368  -1.3587   0.7851
 9PG  O4   O  OH1    0  -0.671   4.2696   1.1208  -0.4030
 9PG  O5   O  O2     0  -0.486   1.4186   0.8100  -0.8202
 9PG  O6   O  OH1    0  -0.667   0.7742   3.3400   0.2310
 9PG  H1   H  HCH2   0   0.205   2.6794   3.2210   1.0597
 9PG  H2   H  HCH2   0   0.208   2.6185   3.0974  -0.7006
 9PG  H3   H  HCH1   0   0.243   1.3978   1.0995   1.2372
 9PG  H4   H  HCH1   0   0.240   3.7293   1.0405   1.5984
 9PG  H5   H  HCH1   0   0.224   2.6180  -1.0801   1.5085
 9PG  H6   H  HCH1   0   0.243   3.2126  -1.0448  -1.4812
 9PG  H7   H  HCH1   0   0.270   0.8443  -0.8033  -1.8413
 9PG  H9   H  HCR6   0   0.285  -1.2964  -1.8792   1.8464
 9PG  H10  H  HCR6   0   0.300  -0.9598   0.5060  -1.7210
 9PG  H11  H  HCR6   0   0.300  -3.3560   0.8145  -1.7405
 9PG  H12  H  HOH1   0   0.462   2.3086  -3.0593  -1.4199
 9PG  H13  H  HOH1   0   0.456   4.4804  -2.3153   0.6867
 9PG  H14  H  HOH1   0   0.453   5.0926   0.6306  -0.3013
 9PG  H15  H  HOH1   0   0.456   0.8243   4.2925   0.1124
 9PG  H8   H  HCR6   0   0.298  -3.7202  -1.5369   1.8427
 9PG  N    N  N      1   0.328  -5.1260  -0.1394   0.0281

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
 9PG  O3   C3   single    1.407  0.020  1.407
 9PG  O2   C2   single    1.403  0.020  1.403
 9PG  C3   C2   single    1.524  0.020  1.524
 9PG  C3   C4   single    1.527  0.020  1.527
 9PG  C2   C1   single    1.531  0.020  1.531
 9PG  C4   O4   single    1.406  0.020  1.406
 9PG  C4   C5   single    1.521  0.020  1.521
 9PG  O1   C1   single    1.416  0.020  1.416
 9PG  O1   C12  single    1.339  0.020  1.339
 9PG  C1   O5   single    1.382  0.020  1.382
 9PG  C11  C12  aromatic  1.397  0.020  1.397
 9PG  C11  C10  aromatic  1.382  0.020  1.382
 9PG  C5   O5   single    1.425  0.020  1.425
 9PG  C5   C6   single    1.513  0.020  1.513
 9PG  C12  C13  aromatic  1.399  0.020  1.399
 9PG  C10  C9   aromatic  1.387  0.020  1.387
 9PG  C13  C14  aromatic  1.377  0.020  1.377
 9PG  O6   C6   single    1.408  0.020  1.408
 9PG  C9   C14  aromatic  1.391  0.020  1.391
 9PG  C9   N    single    1.444  0.020  1.444
 9PG  N    O7   double    1.211  0.020  1.211
 9PG  N    O8   single    1.211  0.020  1.211
 9PG  C6   H1   single    0.970  0.020  1.090
 9PG  C6   H2   single    0.970  0.020  1.090
 9PG  C5   H3   single    0.970  0.020  1.090
 9PG  C4   H4   single    0.970  0.020  1.090
 9PG  C3   H5   single    0.970  0.020  1.090
 9PG  C2   H6   single    0.970  0.020  1.090
 9PG  C1   H7   single    0.970  0.020  1.090
 9PG  C14  H8   single    0.930  0.020  1.080
 9PG  C13  H9   single    0.930  0.020  1.080
 9PG  C11  H10  single    0.930  0.020  1.080
 9PG  C10  H11  single    0.930  0.020  1.080
 9PG  O2   H12  single    0.850  0.020  0.980
 9PG  O3   H13  single    0.850  0.020  0.980
 9PG  O4   H14  single    0.850  0.020  0.980
 9PG  O6   H15  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
 9PG  H2   C6   H1   107.20  3.000
 9PG  H2   C6   O6   111.80  3.000
 9PG  H1   C6   O6   111.71  3.000
 9PG  H2   C6   C5   109.89  3.000
 9PG  H1   C6   C5   107.68  3.000
 9PG  O6   C6   C5   108.48  3.000
 9PG  H3   C5   O5   110.22  3.000
 9PG  H3   C5   C4   107.19  3.000
 9PG  O5   C5   C4   111.40  3.000
 9PG  H3   C5   C6   107.82  3.000
 9PG  O5   C5   C6   107.58  3.000
 9PG  C4   C5   C6   112.58  3.000
 9PG  H4   C4   O4   111.13  3.000
 9PG  H4   C4   C3   108.19  3.000
 9PG  O4   C4   C3   111.72  3.000
 9PG  H4   C4   C5   107.43  3.000
 9PG  O4   C4   C5   109.00  3.000
 9PG  C3   C4   C5   109.26  3.000
 9PG  H5   C3   O3   110.69  3.000
 9PG  H5   C3   C2   109.10  3.000
 9PG  O3   C3   C2   111.62  3.000
 9PG  H5   C3   C4   108.01  3.000
 9PG  C2   C3   C4   109.79  3.000
 9PG  O3   C3   C4   107.55  3.000
 9PG  H6   C2   O2   111.20  3.000
 9PG  H6   C2   C1   106.28  3.000
 9PG  O2   C2   C1   112.18  3.000
 9PG  H6   C2   C3   108.25  3.000
 9PG  C1   C2   C3   110.47  3.000
 9PG  O2   C2   C3   108.40  3.000
 9PG  H7   C1   O5   106.53  3.000
 9PG  H7   C1   O1   109.70  3.000
 9PG  O5   C1   O1   111.88  3.000
 9PG  H7   C1   C2   109.98  3.000
 9PG  O5   C1   C2   111.78  3.000
 9PG  O1   C1   C2   106.98  3.000
 9PG  C10  C9   C14  120.79  3.000
 9PG  C14  C9   N    119.59  3.000
 9PG  C10  C9   N    119.61  3.000
 9PG  H8   C14  C13  119.41  3.000
 9PG  H8   C14  C9   121.35  3.000
 9PG  C13  C14  C9   119.24  3.000
 9PG  H9   C13  C12  119.40  3.000
 9PG  H9   C13  C14  119.99  3.000
 9PG  C12  C13  C14  120.61  3.000
 9PG  O1   C12  C11  124.83  3.000
 9PG  C11  C12  C13  119.63  3.000
 9PG  O1   C12  C13  115.53  3.000
 9PG  H10  C11  C10  118.20  3.000
 9PG  H10  C11  C12  122.06  3.000
 9PG  C10  C11  C12  119.73  3.000
 9PG  H11  C10  C11  119.00  3.000
 9PG  H11  C10  C9   121.01  3.000
 9PG  C11  C10  C9   119.99  3.000
 9PG  C12  O1   C1   120.47  3.000
 9PG  H12  O2   C2   109.03  3.000
 9PG  H13  O3   C3   108.58  3.000
 9PG  H14  O4   C4   108.04  3.000
 9PG  C1   O5   C5   115.55  3.000
 9PG  H15  O6   C6   107.92  3.000
 9PG  C9   N    O7   118.18  3.000
 9PG  O7   N    O8   123.52  3.000
 9PG  C9   N    O8   118.30  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
 9PG  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 9PG  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 9PG  CONST_03  C11  C12  C13  C14    0.00   0.0  0
 9PG  CONST_04  C11  C10  C9   C14    0.00   0.0  0
 9PG  CONST_05  C10  C11  C12  C13    0.00   0.0  0
 9PG  CONST_06  C10  C9   C14  C13    0.00   0.0  0
 9PG  CONST_07  C11  C10  C9   N    180.00   0.0  0
 9PG  CONST_08  C13  C14  C9   N    180.00   0.0  0
 9PG  CONST_09  O1   C12  C13  C14  180.00   0.0  0
 9PG  CONST_10  O1   C12  C11  C10  180.00   0.0  0
 9PG  CONST_11  H10  C11  C10  C9   180.00   0.0  0
 9PG  CONST_12  H9   C13  C14  C9   180.00   0.0  0
 9PG  CONST_13  H11  C10  C9   C14  180.00   0.0  0
 9PG  CONST_14  H8   C14  C13  C12  180.00   0.0  0
 9PG  CONST_15  C10  C9   N    O8     0.00   0.0  0
 9PG  CONST_16  C14  C9   N    O8   180.00   0.0  0
 9PG  CONST_17  C10  C9   N    O7   180.00   0.0  0
 9PG  CONST_18  C14  C9   N    O7     0.00   0.0  0
 9PG  Var_01    C11  C12  O1   C1    -3.43  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
 9PG  chir_01  C5  C4  O5  C6  positiv
 9PG  chir_02  C4  O4  C5  C3  negativ
 9PG  chir_03  C3  O3  C2  C4  positiv
 9PG  chir_04  C2  O2  C1  C3  negativ
 9PG  chir_05  C1  O1  O5  C2  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
 9PG  plan-1  C9   0.020
 9PG  plan-1  C14  0.020
 9PG  plan-1  C13  0.020
 9PG  plan-1  C12  0.020
 9PG  plan-1  C11  0.020
 9PG  plan-1  C10  0.020
 9PG  plan-1  O1   0.020
 9PG  plan-1  H9   0.020
 9PG  plan-1  H10  0.020
 9PG  plan-1  H11  0.020
 9PG  plan-1  H8   0.020
 9PG  plan-1  N    0.020
 9PG  plan-2  O8   0.020
 9PG  plan-2  O7   0.020
 9PG  plan-2  C9   0.020
 9PG  plan-2  N    0.020

