# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 13:23:41 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-nitrophenyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1Oc2ccc(cc2)[N+]([O-])=O
#
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
 LEC  LEC  '4-nitrophenyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranoside'  D-saccharide  42  24  .  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_LEC
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
 LEC  C8   C  CH3    0  -0.788  -2.1347   4.3565   0.7498
 LEC  C7   C  C      0   0.512  -2.1594   3.1446  -0.1493
 LEC  O7   O  O      0  -0.492  -2.1359   3.2230  -1.3672
 LEC  N2   N  NH1    0  -0.624  -2.2177   1.9698   0.5143
 LEC  C2   C  CH1    0  -0.154  -2.2518   0.6828  -0.1216
 LEC  C3   C  CH1    0   0.036  -3.3695  -0.1864   0.4487
 LEC  O3   O  OH1    0  -0.660  -4.5879   0.4498   0.1793
 LEC  C4   C  CH1    0   0.005  -3.3145  -1.5917  -0.1469
 LEC  O4   O  OH1    0  -0.671  -4.2909  -2.3588   0.5185
 LEC  C5   C  CH1    0  -0.029  -1.9104  -2.1774   0.0364
 LEC  C6   C  CH2    0  -0.159  -1.7513  -3.5333  -0.6118
 LEC  O6   O  OH1    0  -0.665  -0.4667  -4.0239  -0.3163
 LEC  O5   O  O2     0  -0.491  -0.9688  -1.3021  -0.5612
 LEC  C1   C  CH1    0   0.306  -0.9234  -0.0530   0.0508
 LEC  O1   O  O2     0  -0.474   0.0611   0.6995  -0.5879
 LEC  C1'  C  CR6    0   0.405   1.3579   0.4888  -0.3053
 LEC  C2'  C  CR16   0  -0.341   2.2423   1.4607  -0.7789
 LEC  C3'  C  CR16   0  -0.254   3.5940   1.3492  -0.5397
 LEC  C4'  C  CR6    0   0.233   4.0679   0.2595   0.1830
 LEC  N1'  N  N      1   0.328   5.4849   0.1390   0.4445
 LEC  O2'  O  O     -1  -0.387   6.2201   0.9995   0.0156
 LEC  O1'  O  O      0  -0.387   5.8706  -0.8151   1.0813
 LEC  C5'  C  CR16   0  -0.255   3.2007  -0.7153   0.6534
 LEC  C6'  C  CR16   0  -0.350   1.8448  -0.6093   0.4049
 LEC  H8   H  HCH3   0   0.261  -2.0864   5.2665   0.1579
 LEC  H8A  H  HCH3   0   0.266  -3.0288   4.3920   1.3737
 LEC  H8B  H  HCH3   0   0.266  -1.2723   4.3264   1.4169
 LEC  HN2  H  HNH1   0   0.403  -2.2507   1.9944   1.5219
 LEC  H2   H  HCH1   0   0.282  -2.4239   0.8310  -1.1908
 LEC  H3   H  HCH1   0   0.215  -3.2109  -0.2849   1.5369
 LEC  HO3  H  HOH1   0   0.453  -5.2917  -0.0877   0.5581
 LEC  H4   H  HCH1   0   0.233  -3.5279  -1.5203  -1.2229
 LEC  HO4  H  HOH1   0   0.465  -4.6505  -3.0117  -0.0887
 LEC  H5   H  HCH1   0   0.232  -1.7048  -2.2749   1.1149
 LEC  H6   H  HCH2   0   0.208  -2.5346  -4.1930  -0.2226
 LEC  H6A  H  HCH2   0   0.202  -1.9178  -3.4345  -1.6934
 LEC  HO6  H  HOH1   0   0.458  -0.4069  -4.9228  -0.6520
 LEC  H1   H  HCH1   0   0.219  -0.6873  -0.1547   1.1245
 LEC  H2'  H  HCR6   0   0.287   1.8582   2.3084  -1.3305
 LEC  H3'  H  HCR6   0   0.300   4.2631   2.1118  -0.9100
 LEC  H5'  H  HCR6   0   0.301   3.5665  -1.5694   1.2043
 LEC  H6'  H  HCR6   0   0.303   1.1958  -1.3998   0.7520

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
 LEC  C8   C7   single    1.509  0.020  1.509
 LEC  C7   O7   double    1.221  0.020  1.221
 LEC  C7   N2   single    1.351  0.020  1.351
 LEC  N2   C2   single    1.436  0.020  1.436
 LEC  C2   C3   single    1.526  0.020  1.526
 LEC  C2   C1   single    1.528  0.020  1.528
 LEC  C3   O3   single    1.401  0.020  1.401
 LEC  C3   C4   single    1.527  0.020  1.527
 LEC  C4   O4   single    1.409  0.020  1.409
 LEC  C4   C5   single    1.532  0.020  1.532
 LEC  C5   C6   single    1.511  0.020  1.511
 LEC  C5   O5   single    1.418  0.020  1.418
 LEC  C6   O6   single    1.406  0.020  1.406
 LEC  O5   C1   single    1.392  0.020  1.392
 LEC  C1   O1   single    1.394  0.020  1.394
 LEC  O1   C1'  single    1.344  0.020  1.344
 LEC  C1'  C2'  aromatic  1.397  0.020  1.397
 LEC  C1'  C6'  aromatic  1.395  0.020  1.395
 LEC  C2'  C3'  aromatic  1.377  0.020  1.377
 LEC  C3'  C4'  aromatic  1.391  0.020  1.391
 LEC  C4'  N1'  single    1.446  0.020  1.446
 LEC  C4'  C5'  aromatic  1.387  0.020  1.387
 LEC  N1'  O2'  single    1.210  0.020  1.210
 LEC  N1'  O1'  double    1.210  0.020  1.210
 LEC  C5'  C6'  aromatic  1.383  0.020  1.383
 LEC  C8   H8   single    0.970  0.020  1.090
 LEC  C8   H8A  single    0.970  0.020  1.090
 LEC  C8   H8B  single    0.970  0.020  1.090
 LEC  N2   HN2  single    0.860  0.020  1.020
 LEC  C2   H2   single    0.970  0.020  1.090
 LEC  C3   H3   single    0.970  0.020  1.090
 LEC  O3   HO3  single    0.850  0.020  0.980
 LEC  C4   H4   single    0.970  0.020  1.090
 LEC  O4   HO4  single    0.850  0.020  0.980
 LEC  C5   H5   single    0.970  0.020  1.090
 LEC  C6   H6   single    0.970  0.020  1.090
 LEC  C6   H6A  single    0.970  0.020  1.090
 LEC  O6   HO6  single    0.850  0.020  0.980
 LEC  C1   H1   single    0.970  0.020  1.090
 LEC  C2'  H2'  single    0.930  0.020  1.080
 LEC  C3'  H3'  single    0.930  0.020  1.080
 LEC  C5'  H5'  single    0.930  0.020  1.080
 LEC  C6'  H6'  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
 LEC  H8B  C8   H8A  107.41  3.000
 LEC  H8B  C8   H8   108.73  3.000
 LEC  H8A  C8   H8   108.70  3.000
 LEC  H8B  C8   C7   110.80  3.000
 LEC  H8A  C8   C7   110.70  3.000
 LEC  H8   C8   C7   110.40  3.000
 LEC  N2   C7   O7   123.16  3.000
 LEC  N2   C7   C8   113.99  3.000
 LEC  O7   C7   C8   122.86  3.000
 LEC  HN2  N2   C2   117.62  3.000
 LEC  HN2  N2   C7   118.10  3.000
 LEC  C2   N2   C7   124.27  3.000
 LEC  H2   C2   C1   108.20  3.000
 LEC  H2   C2   C3   109.11  3.000
 LEC  C1   C2   C3   108.67  3.000
 LEC  H2   C2   N2   108.39  3.000
 LEC  C1   C2   N2   111.16  3.000
 LEC  C3   C2   N2   111.24  3.000
 LEC  H3   C3   C4   107.29  3.000
 LEC  H3   C3   O3   110.79  3.000
 LEC  C4   C3   O3   111.98  3.000
 LEC  H3   C3   C2   108.29  3.000
 LEC  C4   C3   C2   110.61  3.000
 LEC  O3   C3   C2   107.84  3.000
 LEC  HO3  O3   C3   107.85  3.000
 LEC  H4   C4   C5   108.65  3.000
 LEC  H4   C4   O4   111.29  3.000
 LEC  C5   C4   O4   111.74  3.000
 LEC  H4   C4   C3   108.36  3.000
 LEC  C5   C4   C3   109.76  3.000
 LEC  O4   C4   C3   106.97  3.000
 LEC  HO4  O4   C4   109.31  3.000
 LEC  H5   C5   O5   110.07  3.000
 LEC  H5   C5   C6   108.70  3.000
 LEC  O5   C5   C6   107.65  3.000
 LEC  H5   C5   C4   108.77  3.000
 LEC  O5   C5   C4   108.79  3.000
 LEC  C6   C5   C4   112.84  3.000
 LEC  H6A  C6   H6   107.18  3.000
 LEC  H6A  C6   O6   112.12  3.000
 LEC  H6   C6   O6   111.61  3.000
 LEC  H6A  C6   C5   109.00  3.000
 LEC  H6   C6   C5   108.21  3.000
 LEC  O6   C6   C5   108.61  3.000
 LEC  HO6  O6   C6   108.04  3.000
 LEC  C1   O5   C5   112.99  3.000
 LEC  H1   C1   O1   110.14  3.000
 LEC  H1   C1   O5   110.61  3.000
 LEC  O1   C1   O5   107.82  3.000
 LEC  H1   C1   C2   109.87  3.000
 LEC  O1   C1   C2   107.59  3.000
 LEC  O5   C1   C2   110.74  3.000
 LEC  C1'  O1   C1   120.03  3.000
 LEC  C6'  C1'  C2'  119.94  3.000
 LEC  C6'  C1'  O1   124.55  3.000
 LEC  C2'  C1'  O1   115.51  3.000
 LEC  H2'  C2'  C3'  120.03  3.000
 LEC  H2'  C2'  C1'  119.56  3.000
 LEC  C3'  C2'  C1'  120.41  3.000
 LEC  H3'  C3'  C4'  121.35  3.000
 LEC  H3'  C3'  C2'  119.43  3.000
 LEC  C4'  C3'  C2'  119.22  3.000
 LEC  C5'  C4'  N1'  119.53  3.000
 LEC  C5'  C4'  C3'  120.92  3.000
 LEC  N1'  C4'  C3'  119.55  3.000
 LEC  O1'  N1'  O2'  123.60  3.000
 LEC  O1'  N1'  C4'  118.24  3.000
 LEC  O2'  N1'  C4'  118.16  3.000
 LEC  H5'  C5'  C6'  118.97  3.000
 LEC  H5'  C5'  C4'  121.13  3.000
 LEC  C6'  C5'  C4'  119.89  3.000
 LEC  H6'  C6'  C5'  118.38  3.000
 LEC  H6'  C6'  C1'  121.99  3.000
 LEC  C5'  C6'  C1'  119.61  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
 LEC  CONST_01  C4'  C3'  C2'  C1'     0.00   0.0  0
 LEC  CONST_02  C4'  C5'  C6'  C1'     0.00   0.0  0
 LEC  CONST_03  C5'  C6'  C1'  C2'     0.00   0.0  0
 LEC  CONST_04  C5'  C4'  C3'  C2'     0.00   0.0  0
 LEC  CONST_05  C6'  C1'  C2'  C3'     0.00   0.0  0
 LEC  CONST_06  C6'  C5'  C4'  C3'     0.00   0.0  0
 LEC  CONST_07  C3'  C2'  C1'  O1    180.00   0.0  0
 LEC  CONST_08  C5'  C6'  C1'  O1    180.00   0.0  0
 LEC  CONST_09  N1'  C4'  C3'  C2'   180.00   0.0  0
 LEC  CONST_10  C6'  C5'  C4'  N1'   180.00   0.0  0
 LEC  CONST_11  H3'  C3'  C2'  C1'   180.00   0.0  0
 LEC  CONST_12  H5'  C5'  C6'  C1'   180.00   0.0  0
 LEC  CONST_13  H6'  C6'  C1'  C2'   180.00   0.0  0
 LEC  CONST_14  H2'  C2'  C3'  C4'   180.00   0.0  0
 LEC  CONST_15  O2'  N1'  C4'  C3'     0.00   0.0  0
 LEC  CONST_16  O1'  N1'  C4'  C3'   180.00   0.0  0
 LEC  CONST_17  C5'  C4'  N1'  O2'   180.00   0.0  0
 LEC  CONST_18  C5'  C4'  N1'  O1'     0.00   0.0  0
 LEC  CONST_19  C2   N2   C7   C8    180.00   0.0  0
 LEC  CONST_20  C2   N2   C7   O7      0.00   0.0  0
 LEC  CONST_21  HN2  N2   C7   C8      0.00   0.0  0
 LEC  Var_01    C2'  C1'  O1   C1   -167.40  30.0  2
 LEC  Var_02    H8   C8   C7   O7     -0.45  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
 LEC  chir_01  C2  N2  C3  C1  positiv
 LEC  chir_02  C3  O3  C2  C4  positiv
 LEC  chir_03  C4  O4  C5  C3  positiv
 LEC  chir_04  C5  O5  C4  C6  negativ
 LEC  chir_05  C1  O5  O1  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
 LEC  plan-1  O1   0.020
 LEC  plan-1  C1'  0.020
 LEC  plan-1  C2'  0.020
 LEC  plan-1  C3'  0.020
 LEC  plan-1  C4'  0.020
 LEC  plan-1  N1'  0.020
 LEC  plan-1  C5'  0.020
 LEC  plan-1  C6'  0.020
 LEC  plan-1  H2'  0.020
 LEC  plan-1  H3'  0.020
 LEC  plan-1  H5'  0.020
 LEC  plan-1  H6'  0.020
 LEC  plan-2  C4'  0.020
 LEC  plan-2  N1'  0.020
 LEC  plan-2  O2'  0.020
 LEC  plan-2  O1'  0.020
 LEC  plan-3  C8   0.020
 LEC  plan-3  C7   0.020
 LEC  plan-3  O7   0.020
 LEC  plan-3  N2   0.020
 LEC  plan-3  C2   0.020
 LEC  plan-3  HN2  0.020

