# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 11:03:10 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-nitrophenyl beta-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
 147  147  '4-nitrophenyl beta-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_147
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
 147  C1   C  CH1    0   0.260  -1.1510  -0.4600  -0.1602
 147  C2   C  CH1    0  -0.022  -2.4388  -1.2714  -0.0413
 147  O2   O  OH1    0  -0.666  -2.3348  -2.5072  -0.7013
 147  C3   C  CH1    0   0.001  -3.5696  -0.4883  -0.7025
 147  O3   O  OH1    0  -0.671  -4.8172  -1.1027  -0.5045
 147  C4   C  CH1    0   0.003  -3.6511   0.9284  -0.1357
 147  O4   O  OH1    0  -0.670  -4.0460   0.9320   1.2124
 147  C5   C  CH1    0  -0.023  -2.2792   1.5783  -0.2524
 147  C6   C  CH2    0  -0.154  -2.2329   2.9805   0.3113
 147  O6   O  OH1    0  -0.666  -0.9947   3.5533  -0.0354
 147  O5   O  O2     0  -0.490  -1.3043   0.7969   0.4177
 147  O1'  O  O2     0  -0.485  -0.1558  -1.1404   0.5481
 147  C1'  C  CR6    0   0.403   1.1401  -0.8706   0.3105
 147  C2'  C  CR16   0  -0.340   2.0532  -1.8022   0.8091
 147  C3'  C  CR16   0  -0.254   3.4051  -1.6280   0.6105
 147  C4'  C  CR6    0   0.234   3.8500  -0.5152  -0.0949
 147  C5'  C  CR16   0  -0.255   2.9536   0.4227  -0.5858
 147  C6'  C  CR16   0  -0.350   1.5972   0.2534  -0.3784
 147  N1'  N  N      1   0.328   5.2668  -0.3320  -0.3175
 147  O2'  O  O     -1  -0.387   6.0270  -1.1619   0.1276
 147  O3'  O  O      0  -0.387   5.6272   0.6412  -0.9401
 147  H1   H  HCH1   0   0.220  -0.8624  -0.3701  -1.2223
 147  H2   H  HCH1   0   0.238  -2.6671  -1.3995   1.0255
 147  HO2  H  HOH1   0   0.462  -1.8654  -3.1273  -0.1353
 147  H3   H  HCH1   0   0.220  -3.3415  -0.3995  -1.7769
 147  HO3  H  HOH1   0   0.457  -4.7487  -2.0294  -0.7583
 147  H4   H  HCH1   0   0.239  -4.3496   1.5063  -0.7591
 147  HO4  H  HOH1   0   0.454  -4.8470   0.4022   1.2882
 147  H5   H  HCH1   0   0.238  -2.0397   1.6358  -1.3265
 147  H61  H  HCH2   0   0.210  -2.3806   2.9526   1.3967
 147  H62  H  HCH2   0   0.205  -3.0754   3.5399  -0.1154
 147  HO6  H  HOH1   0   0.457  -0.9519   4.4295   0.3575
 147  H2'  H  HCR6   0   0.287   1.6923  -2.6696   1.3454
 147  H3'  H  HCR6   0   0.300   4.0974  -2.3613   0.9973
 147  H5'  H  HCR6   0   0.302   3.2961   1.2958  -1.1216
 147  H6'  H  HCR6   0   0.303   0.9219   1.0162  -0.7380

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
 147  C1   C2   single    1.527  0.020  1.527
 147  C1   O5   single    1.392  0.020  1.392
 147  C1   O1'  single    1.398  0.020  1.398
 147  C1   H1   single    0.970  0.020  1.090
 147  C2   O2   single    1.405  0.020  1.405
 147  C2   C3   single    1.526  0.020  1.526
 147  C2   H2   single    0.970  0.020  1.090
 147  O2   HO2  single    0.850  0.020  0.980
 147  C3   O3   single    1.405  0.020  1.405
 147  C3   C4   single    1.528  0.020  1.528
 147  C3   H3   single    0.970  0.020  1.090
 147  O3   HO3  single    0.850  0.020  0.980
 147  C4   O4   single    1.405  0.020  1.405
 147  C4   C5   single    1.523  0.020  1.523
 147  C4   H4   single    0.970  0.020  1.090
 147  O4   HO4  single    0.850  0.020  0.980
 147  C5   C6   single    1.512  0.020  1.512
 147  C5   O5   single    1.418  0.020  1.418
 147  C5   H5   single    0.970  0.020  1.090
 147  C6   O6   single    1.408  0.020  1.408
 147  C6   H61  single    0.970  0.020  1.090
 147  C6   H62  single    0.970  0.020  1.090
 147  O6   HO6  single    0.850  0.020  0.980
 147  O1'  C1'  single    1.345  0.020  1.345
 147  C1'  C2'  aromatic  1.397  0.020  1.397
 147  C1'  C6'  aromatic  1.395  0.020  1.395
 147  C2'  C3'  aromatic  1.377  0.020  1.377
 147  C2'  H2'  single    0.930  0.020  1.080
 147  C3'  C4'  aromatic  1.391  0.020  1.391
 147  C3'  H3'  single    0.930  0.020  1.080
 147  C4'  C5'  aromatic  1.387  0.020  1.387
 147  C4'  N1'  single    1.446  0.020  1.446
 147  C5'  C6'  aromatic  1.383  0.020  1.383
 147  C5'  H5'  single    0.930  0.020  1.080
 147  C6'  H6'  single    0.930  0.020  1.080
 147  N1'  O2'  single    1.210  0.020  1.210
 147  N1'  O3'  double    1.210  0.020  1.210

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
 147  H1   C1   O1'  109.92  3.000
 147  H1   C1   O5   110.77  3.000
 147  O1'  C1   O5   107.91  3.000
 147  H1   C1   C2   109.79  3.000
 147  O1'  C1   C2   107.60  3.000
 147  O5   C1   C2   110.77  3.000
 147  H2   C2   C3   109.07  3.000
 147  H2   C2   O2   111.66  3.000
 147  C3   C2   O2   107.62  3.000
 147  H2   C2   C1   108.24  3.000
 147  C3   C2   C1   108.58  3.000
 147  O2   C2   C1   111.62  3.000
 147  HO2  O2   C2   109.07  3.000
 147  H3   C3   C4   107.34  3.000
 147  H3   C3   O3   110.89  3.000
 147  C4   C3   O3   107.81  3.000
 147  H3   C3   C2   108.08  3.000
 147  C4   C3   C2   110.76  3.000
 147  O3   C3   C2   111.87  3.000
 147  HO3  O3   C3   108.69  3.000
 147  H4   C4   C5   107.73  3.000
 147  H4   C4   O4   111.34  3.000
 147  C5   C4   O4   109.01  3.000
 147  H4   C4   C3   108.10  3.000
 147  C5   C4   C3   108.62  3.000
 147  O4   C4   C3   111.92  3.000
 147  HO4  O4   C4   107.93  3.000
 147  H5   C5   O5   109.87  3.000
 147  H5   C5   C6   107.96  3.000
 147  O5   C5   C6   108.29  3.000
 147  H5   C5   C4   107.03  3.000
 147  O5   C5   C4   110.37  3.000
 147  C6   C5   C4   113.26  3.000
 147  H62  C6   H61  107.13  3.000
 147  H62  C6   O6   111.85  3.000
 147  H61  C6   O6   111.90  3.000
 147  H62  C6   C5   107.71  3.000
 147  H61  C6   C5   109.97  3.000
 147  O6   C6   C5   108.21  3.000
 147  HO6  O6   C6   108.02  3.000
 147  C5   O5   C1   112.16  3.000
 147  C1'  O1'  C1   119.92  3.000
 147  C6'  C1'  C2'  119.96  3.000
 147  C6'  C1'  O1'  124.37  3.000
 147  C2'  C1'  O1'  115.67  3.000
 147  H2'  C2'  C3'  120.02  3.000
 147  H2'  C2'  C1'  119.58  3.000
 147  C3'  C2'  C1'  120.39  3.000
 147  H3'  C3'  C4'  121.32  3.000
 147  H3'  C3'  C2'  119.45  3.000
 147  C4'  C3'  C2'  119.23  3.000
 147  N1'  C4'  C5'  119.54  3.000
 147  N1'  C4'  C3'  119.54  3.000
 147  C5'  C4'  C3'  120.92  3.000
 147  H5'  C5'  C6'  118.98  3.000
 147  H5'  C5'  C4'  121.15  3.000
 147  C6'  C5'  C4'  119.87  3.000
 147  H6'  C6'  C5'  118.48  3.000
 147  H6'  C6'  C1'  121.90  3.000
 147  C5'  C6'  C1'  119.61  3.000
 147  O3'  N1'  O2'  123.61  3.000
 147  O3'  N1'  C4'  118.23  3.000
 147  O2'  N1'  C4'  118.16  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
 147  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 147  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 147  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 147  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 147  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 147  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 147  CONST_07  C3'  C2'  C1'  O1'   180.00   0.0  0
 147  CONST_08  C5'  C6'  C1'  O1'   180.00   0.0  0
 147  CONST_09  N1'  C4'  C3'  C2'   180.00   0.0  0
 147  CONST_10  N1'  C4'  C5'  C6'   180.00   0.0  0
 147  CONST_11  H3'  C3'  C2'  C1'   180.00   0.0  0
 147  CONST_12  H5'  C5'  C6'  C1'   180.00   0.0  0
 147  CONST_13  H6'  C6'  C1'  C2'   180.00   0.0  0
 147  CONST_14  H2'  C2'  C3'  C4'   180.00   0.0  0
 147  CONST_15  O2'  N1'  C4'  C3'     0.00   0.0  0
 147  CONST_16  O3'  N1'  C4'  C3'   180.00   0.0  0
 147  CONST_17  O2'  N1'  C4'  C5'   180.00   0.0  0
 147  CONST_18  O3'  N1'  C4'  C5'     0.00   0.0  0
 147  Var_01    C2'  C1'  O1'  C1   -165.07  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
 147  chir_01  C1  C2  O5  O1'  negativ
 147  chir_02  C2  O2  C1  C3   negativ
 147  chir_03  C3  O3  C2  C4   positiv
 147  chir_04  C4  O4  C5  C3   negativ
 147  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
 147  plan-1  O1'  0.020
 147  plan-1  C1'  0.020
 147  plan-1  C2'  0.020
 147  plan-1  C3'  0.020
 147  plan-1  C4'  0.020
 147  plan-1  C5'  0.020
 147  plan-1  C6'  0.020
 147  plan-1  N1'  0.020
 147  plan-1  H2'  0.020
 147  plan-1  H3'  0.020
 147  plan-1  H5'  0.020
 147  plan-1  H6'  0.020
 147  plan-2  C4'  0.020
 147  plan-2  N1'  0.020
 147  plan-2  O2'  0.020
 147  plan-2  O3'  0.020

