# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:37:28 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-nitrophenyl alpha-D-mannopyranoside
#   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
 PNA  PNA  '4-nitrophenyl alpha-D-mannopyranoside'  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_PNA
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
 PNA  C1   C  CH1    0   0.198  -1.2189  -0.8933   0.6977
 PNA  C2   C  CH1    0  -0.025  -2.5699  -1.4969   0.2992
 PNA  C3   C  CH1    0   0.003  -3.2451  -0.5896  -0.7272
 PNA  C4   C  CH1    0   0.030  -3.3221   0.8433  -0.2101
 PNA  C5   C  CH1    0  -0.019  -1.9238   1.3232   0.1816
 PNA  C6   C  CH2    0  -0.159  -1.9571   2.6815   0.8480
 PNA  C7   C  CR6    0   0.421   0.9473  -0.8284  -0.3248
 PNA  C8   C  CR16   0  -0.354   1.5892  -0.3463   0.8175
 PNA  C9   C  CR16   0  -0.255   2.9635  -0.1956   0.8183
 PNA  C10  C  CR6    0   0.230   3.6958  -0.5088  -0.3172
 PNA  C11  C  CR16   0  -0.252   3.0654  -0.9779  -1.4650
 PNA  C12  C  CR16   0  -0.347   1.6978  -1.1358  -1.4639
 PNA  N1   N  N      1   0.328   5.1307  -0.3396  -0.3100
 PNA  O1   O  O2     0  -0.489  -0.3733  -1.0338  -0.4311
 PNA  O2   O  OH1    0  -0.663  -3.3948  -1.5865   1.4300
 PNA  O3   O  OH1    0  -0.670  -4.5545  -1.0036  -1.0295
 PNA  O4   O  OH1    0  -0.674  -3.8032   1.7165  -1.2027
 PNA  O5   O  O2     0  -0.484  -1.3317   0.4205   1.1076
 PNA  O6   O  OH1    0  -0.666  -0.6357   3.1011   1.0879
 PNA  O7   O  O      0  -0.388   5.6569   0.0499   0.7082
 PNA  O8   O  O     -1  -0.388   5.7413  -0.5942  -1.3238
 PNA  H1   H  HCH1   0   0.272  -0.7941  -1.4447   1.5449
 PNA  H2   H  HCH1   0   0.245  -2.3917  -2.4854  -0.1458
 PNA  H3   H  HCH1   0   0.232  -2.6221  -0.5840  -1.6322
 PNA  H4   H  HCH1   0   0.218  -3.9655   0.8687   0.6816
 PNA  H5   H  HCH1   0   0.234  -1.3100   1.3905  -0.7274
 PNA  H61  H  HCH2   0   0.198  -2.5400   2.6092   1.7772
 PNA  H62  H  HCH2   0   0.213  -2.4897   3.3741   0.1880
 PNA  H8   H  HCR6   0   0.301   1.0443  -0.0670   1.7063
 PNA  H9   H  HCR6   0   0.300   3.4470   0.1784   1.7087
 PNA  H11  H  HCR6   0   0.299   3.6281  -1.2260  -2.3530
 PNA  H12  H  HCR6   0   0.285   1.1965  -1.5066  -2.3479
 PNA  HO2  H  HOH1   0   0.459  -3.0724  -2.2993   1.9902
 PNA  HO3  H  HOH1   0   0.458  -4.5127  -1.7458  -1.6400
 PNA  HO4  H  HOH1   0   0.454  -4.6708   1.4036  -1.4798
 PNA  HO6  H  HOH1   0   0.456  -0.6717   3.9787   1.4784

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
 PNA  C1   C2   single    1.532  0.020  1.532
 PNA  C1   O1   single    1.417  0.020  1.417
 PNA  C1   O5   single    1.381  0.020  1.381
 PNA  C1   H1   single    0.970  0.020  1.090
 PNA  C2   C3   single    1.527  0.020  1.527
 PNA  C2   O2   single    1.403  0.020  1.403
 PNA  C2   H2   single    0.970  0.020  1.090
 PNA  C3   C4   single    1.525  0.020  1.525
 PNA  C3   O3   single    1.406  0.020  1.406
 PNA  C3   H3   single    0.970  0.020  1.090
 PNA  C4   C5   single    1.529  0.020  1.529
 PNA  C4   O4   single    1.407  0.020  1.407
 PNA  C4   H4   single    0.970  0.020  1.090
 PNA  C5   C6   single    1.513  0.020  1.513
 PNA  C5   O5   single    1.422  0.020  1.422
 PNA  C5   H5   single    0.970  0.020  1.090
 PNA  C6   O6   single    1.407  0.020  1.407
 PNA  C6   H61  single    0.970  0.020  1.090
 PNA  C6   H62  single    0.970  0.020  1.090
 PNA  C7   C8   aromatic  1.396  0.020  1.396
 PNA  C7   C12  aromatic  1.398  0.020  1.398
 PNA  C7   O1   single    1.341  0.020  1.341
 PNA  C8   C9   aromatic  1.383  0.020  1.383
 PNA  C8   H8   single    0.930  0.020  1.080
 PNA  C9   C10  aromatic  1.387  0.020  1.387
 PNA  C9   H9   single    0.930  0.020  1.080
 PNA  C10  C11  aromatic  1.391  0.020  1.391
 PNA  C10  N1   single    1.445  0.020  1.445
 PNA  C11  C12  aromatic  1.377  0.020  1.377
 PNA  C11  H11  single    0.930  0.020  1.080
 PNA  C12  H12  single    0.930  0.020  1.080
 PNA  N1   O7   double    1.211  0.020  1.211
 PNA  N1   O8   single    1.211  0.020  1.211
 PNA  O2   HO2  single    0.850  0.020  0.980
 PNA  O3   HO3  single    0.850  0.020  0.980
 PNA  O4   HO4  single    0.850  0.020  0.980
 PNA  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
 PNA  H1   C1   O5   106.31  3.000
 PNA  H1   C1   O1   109.53  3.000
 PNA  O5   C1   O1   112.30  3.000
 PNA  H1   C1   C2   110.14  3.000
 PNA  O5   C1   C2   112.33  3.000
 PNA  O1   C1   C2   106.25  3.000
 PNA  H2   C2   O2   111.38  3.000
 PNA  H2   C2   C3   109.51  3.000
 PNA  O2   C2   C3   108.65  3.000
 PNA  H2   C2   C1   108.47  3.000
 PNA  O2   C2   C1   109.51  3.000
 PNA  C3   C2   C1   109.30  3.000
 PNA  H3   C3   O3   110.63  3.000
 PNA  H3   C3   C4   107.64  3.000
 PNA  O3   C3   C4   107.60  3.000
 PNA  H3   C3   C2   107.82  3.000
 PNA  O3   C3   C2   112.41  3.000
 PNA  C4   C3   C2   110.64  3.000
 PNA  H4   C4   O4   110.95  3.000
 PNA  H4   C4   C5   108.66  3.000
 PNA  O4   C4   C5   107.38  3.000
 PNA  H4   C4   C3   109.03  3.000
 PNA  O4   C4   C3   111.17  3.000
 PNA  C5   C4   C3   109.60  3.000
 PNA  H5   C5   O5   110.18  3.000
 PNA  H5   C5   C6   108.76  3.000
 PNA  O5   C5   C6   106.99  3.000
 PNA  H5   C5   C4   108.54  3.000
 PNA  O5   C5   C4   110.38  3.000
 PNA  C6   C5   C4   111.98  3.000
 PNA  H62  C6   H61  107.05  3.000
 PNA  H62  C6   O6   111.77  3.000
 PNA  H61  C6   O6   111.93  3.000
 PNA  H62  C6   C5   108.24  3.000
 PNA  H61  C6   C5   108.96  3.000
 PNA  O6   C6   C5   108.79  3.000
 PNA  O1   C7   C12  115.49  3.000
 PNA  O1   C7   C8   124.79  3.000
 PNA  C12  C7   C8   119.71  3.000
 PNA  H8   C8   C9   118.24  3.000
 PNA  H8   C8   C7   122.08  3.000
 PNA  C9   C8   C7   119.68  3.000
 PNA  H9   C9   C10  121.12  3.000
 PNA  H9   C9   C8   118.90  3.000
 PNA  C10  C9   C8   119.98  3.000
 PNA  N1   C10  C11  119.58  3.000
 PNA  N1   C10  C9   119.59  3.000
 PNA  C11  C10  C9   120.83  3.000
 PNA  H11  C11  C12  119.46  3.000
 PNA  H11  C11  C10  121.32  3.000
 PNA  C12  C11  C10  119.22  3.000
 PNA  H12  C12  C11  119.93  3.000
 PNA  H12  C12  C7   119.49  3.000
 PNA  C11  C12  C7   120.57  3.000
 PNA  O8   N1   O7   123.56  3.000
 PNA  O8   N1   C10  118.17  3.000
 PNA  O7   N1   C10  118.27  3.000
 PNA  C7   O1   C1   120.62  3.000
 PNA  HO2  O2   C2   108.64  3.000
 PNA  HO3  O3   C3   108.85  3.000
 PNA  HO4  O4   C4   108.03  3.000
 PNA  C5   O5   C1   116.40  3.000
 PNA  HO6  O6   C6   107.84  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
 PNA  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 PNA  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 PNA  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 PNA  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 PNA  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 PNA  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 PNA  CONST_07  N1   C10  C9   C8   180.00   0.0  0
 PNA  CONST_08  O1   C7   C8   C9   180.00   0.0  0
 PNA  CONST_09  O1   C7   C12  C11  180.00   0.0  0
 PNA  CONST_10  N1   C10  C11  C12  180.00   0.0  0
 PNA  CONST_11  H9   C9   C8   C7   180.00   0.0  0
 PNA  CONST_12  H11  C11  C12  C7   180.00   0.0  0
 PNA  CONST_13  H12  C12  C7   C8   180.00   0.0  0
 PNA  CONST_14  H8   C8   C9   C10  180.00   0.0  0
 PNA  CONST_15  O7   N1   C10  C9     0.00   0.0  0
 PNA  CONST_16  O8   N1   C10  C9   180.00   0.0  0
 PNA  CONST_17  O7   N1   C10  C11  180.00   0.0  0
 PNA  CONST_18  O8   N1   C10  C11    0.00   0.0  0
 PNA  Var_01    C8   C7   O1   C1    -6.50  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
 PNA  chir_01  C1  C2  O1  O5  negativ
 PNA  chir_02  C2  O2  C1  C3  positiv
 PNA  chir_03  C3  O3  C2  C4  positiv
 PNA  chir_04  C4  O4  C3  C5  negativ
 PNA  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
 PNA  plan-1  C7   0.020
 PNA  plan-1  C8   0.020
 PNA  plan-1  C9   0.020
 PNA  plan-1  C10  0.020
 PNA  plan-1  C11  0.020
 PNA  plan-1  C12  0.020
 PNA  plan-1  N1   0.020
 PNA  plan-1  O1   0.020
 PNA  plan-1  H8   0.020
 PNA  plan-1  H9   0.020
 PNA  plan-1  H11  0.020
 PNA  plan-1  H12  0.020
 PNA  plan-2  C10  0.020
 PNA  plan-2  N1   0.020
 PNA  plan-2  O7   0.020
 PNA  plan-2  O8   0.020

