# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 11:51:34 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-{[(4-nitrophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)NC(=O)c2ccc(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
 NBY  NBY  N-{[(4-nitrophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine  D-saccharide  43  26  .  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_NBY
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
 NBY  O5   O  O2     0  -0.487  -3.2206  -0.7966  -0.4001
 NBY  C1   C  CH1    0   0.206  -2.7273   0.2991   0.3326
 NBY  C2   C  CH1    0  -0.028  -3.3674   1.5978  -0.1656
 NBY  O2   O  OH1    0  -0.662  -2.9791   2.6958   0.6182
 NBY  C3   C  CH1    0  -0.007  -4.8815   1.4749  -0.0690
 NBY  O3   O  OH1    0  -0.671  -5.5379   2.5725  -0.6564
 NBY  C4   C  CH1    0   0.036  -5.3680   0.2170  -0.7792
 NBY  O4   O  OH1    0  -0.672  -6.7416   0.0107  -0.5646
 NBY  C5   C  CH1    0  -0.016  -4.6104  -0.9992  -0.2443
 NBY  C6   C  CH2    0  -0.156  -4.9785  -2.2655  -0.9877
 NBY  O6   O  OH1    0  -0.670  -4.3192  -3.3532  -0.3854
 NBY  N1   N  NH1    0  -0.736  -1.3128   0.3561   0.1665
 NBY  C7   C  C      0   0.772  -0.4520  -0.2561   1.0225
 NBY  O7   O  O      0  -0.466  -0.7824  -0.8015   2.0496
 NBY  N2   N  NH1    0  -0.760   0.8728  -0.1506   0.5937
 NBY  C8   C  C      0   0.560   1.9624  -0.7249   1.1964
 NBY  O8   O  O      0  -0.408   1.9079  -1.4803   2.1376
 NBY  C9   C  CR6    0  -0.040   3.2783  -0.3606   0.5785
 NBY  C10  C  CR16   0  -0.253   4.3193  -1.2784   0.6930
 NBY  C11  C  CR16   0  -0.253   5.5652  -0.9979   0.1643
 NBY  C12  C  CR6    0   0.260   5.7634   0.2229  -0.4630
 NBY  C13  C  CR16   0  -0.250   4.7510   1.1615  -0.5727
 NBY  C14  C  CR16   0  -0.278   3.5044   0.8602  -0.0508
 NBY  N3   N  N      1   0.332   7.0765   0.5298  -1.0202
 NBY  O9   O  O      0  -0.370   7.2294   1.6056  -1.5460
 NBY  O10  O  O     -1  -0.370   7.9397  -0.3088  -0.9273
 NBY  H1   H  HCH1   0   0.238  -2.9498   0.1779   1.4000
 NBY  H2   H  HCH1   0   0.227  -3.0924   1.7377  -1.2230
 NBY  HO2  H  HOH1   0   0.457  -2.0529   2.8918   0.4450
 NBY  H3   H  HCH1   0   0.219  -5.1494   1.3842   0.9960
 NBY  HO3  H  HOH1   0   0.458  -5.3993   3.3464  -0.1017
 NBY  H4   H  HCH1   0   0.213  -5.1451   0.3166  -1.8539
 NBY  HO4  H  HOH1   0   0.455  -7.2137   0.7873  -0.8831
 NBY  H5   H  HCH1   0   0.225  -4.8556  -1.1245   0.8233
 NBY  H16  H  HCH2   0   0.213  -6.0667  -2.3821  -0.9546
 NBY  H26  H  HCH2   0   0.198  -4.6984  -2.1499  -2.0440
 NBY  HO6  H  HOH1   0   0.457  -4.5746  -4.1513  -0.8561
 NBY  HN1  H  HNH1   0   0.411  -0.9730   0.6735  -0.7302
 NBY  HN2  H  HNH1   0   0.432   1.0404   0.3612  -0.2599
 NBY  H10  H  HCR6   0   0.285   4.1581  -2.2249   1.1897
 NBY  H11  H  HCR6   0   0.307   6.3602  -1.7236   0.2498
 NBY  H13  H  HCR6   0   0.308   4.9151   2.1160  -1.0505
 NBY  H14  H  HCR6   0   0.286   2.7281   1.6101  -0.1248

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
 NBY  O9   N3   double    1.207  0.020  1.207
 NBY  O10  N3   single    1.207  0.020  1.207
 NBY  N3   C12  single    1.459  0.020  1.459
 NBY  C12  C13  aromatic  1.385  0.020  1.385
 NBY  C12  C11  aromatic  1.387  0.020  1.387
 NBY  C13  C14  aromatic  1.385  0.020  1.385
 NBY  C11  C10  aromatic  1.382  0.020  1.382
 NBY  C14  C9   aromatic  1.392  0.020  1.392
 NBY  C10  C9   aromatic  1.393  0.020  1.393
 NBY  C9   C8   single    1.499  0.020  1.499
 NBY  C8   N2   single    1.371  0.020  1.371
 NBY  C8   O8   double    1.208  0.020  1.208
 NBY  N2   C7   single    1.396  0.020  1.396
 NBY  C7   O7   double    1.209  0.020  1.209
 NBY  C7   N1   single    1.360  0.020  1.360
 NBY  N1   C1   single    1.425  0.020  1.425
 NBY  O2   C2   single    1.404  0.020  1.404
 NBY  C1   C2   single    1.531  0.020  1.531
 NBY  C1   O5   single    1.407  0.020  1.407
 NBY  C2   C3   single    1.522  0.020  1.522
 NBY  O5   C5   single    1.413  0.020  1.413
 NBY  C3   O3   single    1.407  0.020  1.407
 NBY  C3   C4   single    1.524  0.020  1.524
 NBY  C5   C4   single    1.529  0.020  1.529
 NBY  C5   C6   single    1.514  0.020  1.514
 NBY  C4   O4   single    1.406  0.020  1.406
 NBY  C6   O6   single    1.407  0.020  1.407
 NBY  C1   H1   single    0.970  0.020  1.090
 NBY  C2   H2   single    0.970  0.020  1.090
 NBY  O2   HO2  single    0.850  0.020  0.980
 NBY  C3   H3   single    0.970  0.020  1.090
 NBY  O3   HO3  single    0.850  0.020  0.980
 NBY  C4   H4   single    0.970  0.020  1.090
 NBY  O4   HO4  single    0.850  0.020  0.980
 NBY  C5   H5   single    0.970  0.020  1.090
 NBY  C6   H16  single    0.970  0.020  1.090
 NBY  C6   H26  single    0.970  0.020  1.090
 NBY  O6   HO6  single    0.850  0.020  0.980
 NBY  N1   HN1  single    0.860  0.020  1.020
 NBY  N2   HN2  single    0.860  0.020  1.020
 NBY  C10  H10  single    0.930  0.020  1.080
 NBY  C11  H11  single    0.930  0.020  1.080
 NBY  C13  H13  single    0.930  0.020  1.080
 NBY  C14  H14  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
 NBY  C5   O5   C1   113.51  3.000
 NBY  H1   C1   N1   108.61  3.000
 NBY  H1   C1   C2   108.99  3.000
 NBY  N1   C1   C2   110.06  3.000
 NBY  H1   C1   O5   110.46  3.000
 NBY  C2   C1   O5   110.14  3.000
 NBY  N1   C1   O5   108.56  3.000
 NBY  H2   C2   C3   108.64  3.000
 NBY  H2   C2   O2   111.57  3.000
 NBY  C3   C2   O2   107.63  3.000
 NBY  H2   C2   C1   108.40  3.000
 NBY  C3   C2   C1   109.07  3.000
 NBY  O2   C2   C1   111.48  3.000
 NBY  HO2  O2   C2   108.97  3.000
 NBY  H3   C3   C4   107.75  3.000
 NBY  H3   C3   O3   110.75  3.000
 NBY  C4   C3   O3   107.47  3.000
 NBY  H3   C3   C2   108.05  3.000
 NBY  C4   C3   C2   110.76  3.000
 NBY  O3   C3   C2   111.99  3.000
 NBY  HO3  O3   C3   108.63  3.000
 NBY  H4   C4   C5   108.22  3.000
 NBY  H4   C4   O4   111.09  3.000
 NBY  C5   C4   O4   108.30  3.000
 NBY  H4   C4   C3   108.38  3.000
 NBY  O4   C4   C3   111.22  3.000
 NBY  C5   C4   C3   109.58  3.000
 NBY  HO4  O4   C4   108.07  3.000
 NBY  H5   C5   C6   109.05  3.000
 NBY  H5   C5   C4   108.59  3.000
 NBY  C6   C5   C4   111.90  3.000
 NBY  H5   C5   O5   109.99  3.000
 NBY  C6   C5   O5   107.76  3.000
 NBY  C4   C5   O5   109.54  3.000
 NBY  H26  C6   H16  107.07  3.000
 NBY  H26  C6   O6   111.92  3.000
 NBY  H16  C6   O6   111.74  3.000
 NBY  H26  C6   C5   108.79  3.000
 NBY  H16  C6   C5   108.42  3.000
 NBY  O6   C6   C5   108.81  3.000
 NBY  HO6  O6   C6   107.92  3.000
 NBY  HN1  N1   C7   119.17  3.000
 NBY  HN1  N1   C1   116.73  3.000
 NBY  C7   N1   C1   122.48  3.000
 NBY  N2   C7   O7   123.66  3.000
 NBY  O7   C7   N1   124.40  3.000
 NBY  N2   C7   N1   111.92  3.000
 NBY  HN2  N2   C8   116.88  3.000
 NBY  HN2  N2   C7   117.10  3.000
 NBY  C8   N2   C7   125.96  3.000
 NBY  C9   C8   O8   120.85  3.000
 NBY  O8   C8   N2   124.65  3.000
 NBY  C9   C8   N2   114.50  3.000
 NBY  C14  C9   C10  119.59  3.000
 NBY  C10  C9   C8   117.53  3.000
 NBY  C14  C9   C8   122.83  3.000
 NBY  H10  C10  C11  119.20  3.000
 NBY  H10  C10  C9   120.22  3.000
 NBY  C11  C10  C9   120.57  3.000
 NBY  H11  C11  C12  121.48  3.000
 NBY  H11  C11  C10  119.80  3.000
 NBY  C12  C11  C10  118.72  3.000
 NBY  N3   C12  C13  119.02  3.000
 NBY  C13  C12  C11  121.87  3.000
 NBY  N3   C12  C11  119.11  3.000
 NBY  H13  C13  C14  119.73  3.000
 NBY  H13  C13  C12  121.53  3.000
 NBY  C14  C13  C12  118.74  3.000
 NBY  H14  C14  C13  118.00  3.000
 NBY  H14  C14  C9   121.48  3.000
 NBY  C13  C14  C9   120.50  3.000
 NBY  O10  N3   O9   124.20  3.000
 NBY  O10  N3   C12  117.91  3.000
 NBY  O9   N3   C12  117.89  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
 NBY  CONST_01  C12  C13  C14  C9     0.00   0.0  0
 NBY  CONST_02  C12  C11  C10  C9     0.00   0.0  0
 NBY  CONST_03  C13  C12  C11  C10    0.00   0.0  0
 NBY  CONST_04  C13  C14  C9   C10    0.00   0.0  0
 NBY  CONST_05  C14  C13  C12  C11    0.00   0.0  0
 NBY  CONST_06  C14  C9   C10  C11    0.00   0.0  0
 NBY  CONST_07  C13  C14  C9   C8   180.00   0.0  0
 NBY  CONST_08  C11  C10  C9   C8   180.00   0.0  0
 NBY  CONST_09  N3   C12  C11  C10  180.00   0.0  0
 NBY  CONST_10  N3   C12  C13  C14  180.00   0.0  0
 NBY  CONST_11  H13  C13  C14  C9   180.00   0.0  0
 NBY  CONST_12  H11  C11  C10  C9   180.00   0.0  0
 NBY  CONST_13  H14  C14  C9   C10  180.00   0.0  0
 NBY  CONST_14  H10  C10  C11  C12  180.00   0.0  0
 NBY  CONST_15  O9   N3   C12  C11  180.00   0.0  0
 NBY  CONST_16  O10  N3   C12  C11    0.00   0.0  0
 NBY  CONST_17  O9   N3   C12  C13    0.00   0.0  0
 NBY  CONST_18  O10  N3   C12  C13  180.00   0.0  0
 NBY  CONST_19  O7   C7   N1   C1     0.00   0.0  0
 NBY  CONST_20  C9   C8   N2   C7   180.00   0.0  0
 NBY  CONST_21  N2   C7   N1   C1   180.00   0.0  0
 NBY  CONST_22  HN2  N2   C8   C9     0.00   0.0  0
 NBY  CONST_23  O8   C8   N2   C7     0.00   0.0  0
 NBY  CONST_24  C8   N2   C7   O7     0.00   0.0  0
 NBY  CONST_25  C8   N2   C7   N1   180.00   0.0  0
 NBY  CONST_26  HN1  N1   C7   O7   180.00   0.0  0
 NBY  Var_01    C14  C9   C8   N2    30.05  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
 NBY  chir_01  C1  N1  C2  O5  negativ
 NBY  chir_02  C2  O2  C1  C3  negativ
 NBY  chir_03  C3  O3  C2  C4  positiv
 NBY  chir_04  C4  O4  C5  C3  positiv
 NBY  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
 NBY  plan-1  C8   0.020
 NBY  plan-1  C9   0.020
 NBY  plan-1  C10  0.020
 NBY  plan-1  C11  0.020
 NBY  plan-1  C12  0.020
 NBY  plan-1  C13  0.020
 NBY  plan-1  C14  0.020
 NBY  plan-1  N3   0.020
 NBY  plan-1  H10  0.020
 NBY  plan-1  H11  0.020
 NBY  plan-1  H13  0.020
 NBY  plan-1  H14  0.020
 NBY  plan-2  C12  0.020
 NBY  plan-2  N3   0.020
 NBY  plan-2  O9   0.020
 NBY  plan-2  O10  0.020
 NBY  plan-3  C1   0.020
 NBY  plan-3  N1   0.020
 NBY  plan-3  C7   0.020
 NBY  plan-3  O7   0.020
 NBY  plan-3  N2   0.020
 NBY  plan-3  C8   0.020
 NBY  plan-3  O8   0.020
 NBY  plan-3  C9   0.020
 NBY  plan-3  HN1  0.020
 NBY  plan-3  HN2  0.020

