# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 00:38:35 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-{[(4-aminophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1)C(=O)NC(=O)N[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
#
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
 NBX  NBX  N-{[(4-aminophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine  D-saccharide  43  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_NBX
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
 NBX  O5    O  O2    0  -0.488   2.5816   0.8826  -0.3765
 NBX  C1    C  CH1   0   0.209   2.0022  -0.2470   0.2334
 NBX  C2    C  CH1   0  -0.028   2.6444  -1.5248  -0.3132
 NBX  O2    O  OH1   0  -0.663   2.1628  -2.6656   0.3490
 NBX  C3    C  CH1   0  -0.007   4.1484  -1.4617  -0.0884
 NBX  O3    O  OH1   0  -0.672   4.8195  -2.5336  -0.7064
 NBX  C4    C  CH1   0   0.036   4.7252  -0.1713  -0.6589
 NBX  O4    O  OH1   0  -0.672   6.0814  -0.0254  -0.3195
 NBX  C5    C  CH1   0  -0.014   3.9587   1.0271  -0.0971
 NBX  C6    C  CH2   0  -0.157   4.4220   2.3318  -0.7093
 NBX  O6    O  OH1   0  -0.670   3.7449   3.3929  -0.0797
 NBX  N1    N  NH1   0  -0.739   0.6037  -0.2485  -0.0326
 NBX  C7    C  C     0   0.762  -0.3051   0.3048   0.8196
 NBX  O7    O  O     0  -0.476  -0.0161   0.7870   1.8922
 NBX  N2    N  NH1   0  -0.770  -1.6020   0.2089   0.3312
 NBX  C8    C  C     0   0.548  -2.7355   0.7523   0.9071
 NBX  O8    O  O     0  -0.436  -2.6876   1.5575   1.8136
 NBX  C9    C  CR6   0  -0.093  -4.0161   0.3001   0.3231
 NBX  C10   C  CR16  0  -0.251  -5.1672   1.0445   0.6021
 NBX  C11   C  CR16  0  -0.319  -6.4000   0.6774   0.1123
 NBX  C12   C  CR6   0   0.343  -6.5438  -0.4774  -0.6771
 NBX  C13   C  CR16  0  -0.317  -5.3921  -1.2340  -0.9507
 NBX  C14   C  CR16  0  -0.283  -4.1624  -0.8490  -0.4604
 NBX  N3    N  NH2   0  -0.854  -7.7634  -0.8733  -1.1223
 NBX  H1    H  HCH1  0   0.235   2.1477  -0.2114   1.3200
 NBX  H2    H  HCH1  0   0.226   2.4523  -1.5766  -1.3967
 NBX  HO2   H  HOH1  0   0.456   1.2492  -2.8171   0.0871
 NBX  H3    H  HCH1  0   0.219   4.3307  -1.4625   0.9983
 NBX  HO3   H  HOH1  0   0.458   4.6181  -3.3418  -0.2246
 NBX  H4    H  HCH1  0   0.213   4.5898  -0.1842  -1.7527
 NBX  HO4   H  HOH1  0   0.455   6.5598  -0.7865  -0.6647
 NBX  H5    H  HCH1  0   0.224   4.1200   1.0674   0.9930
 NBX  H6    H  HCH2  0   0.213   5.5063   2.4085  -0.5788
 NBX  H6A   H  HCH2  0   0.197   4.2284   2.3065  -1.7908
 NBX  HO6   H  HOH1  0   0.457   4.0885   4.2172  -0.4353
 NBX  HN1   H  HNH1  0   0.408   0.3150  -0.4971  -0.9678
 NBX  HN2   H  HNH1  0   0.423  -1.7277  -0.3071  -0.5255
 NBX  H10   H  HCR6  0   0.258  -5.0927   1.9372   1.2091
 NBX  H11   H  HCR6  0   0.264  -7.2698   1.2827   0.3379
 NBX  H13   H  HCR6  0   0.266  -5.4718  -2.1350  -1.5462
 NBX  H14   H  HCR6  0   0.252  -3.3191  -1.4904  -0.6866
 NBX  HN3   H  HNH2  0   0.393  -8.5208  -0.2118  -1.1052
 NBX  HN3A  H  HNH2  0   0.393  -7.8104  -1.5441  -1.8702

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
 NBX  O5   C1    single    1.408  0.020  1.408
 NBX  O5   C5    single    1.413  0.020  1.413
 NBX  C1   C2    single    1.531  0.020  1.531
 NBX  C1   N1    single    1.424  0.020  1.424
 NBX  C2   O2    single    1.404  0.020  1.404
 NBX  C2   C3    single    1.522  0.020  1.522
 NBX  C3   O3    single    1.408  0.020  1.408
 NBX  C3   C4    single    1.524  0.020  1.524
 NBX  C4   O4    single    1.406  0.020  1.406
 NBX  C4   C5    single    1.530  0.020  1.530
 NBX  C5   C6    single    1.514  0.020  1.514
 NBX  C6   O6    single    1.407  0.020  1.407
 NBX  N1   C7    single    1.363  0.020  1.363
 NBX  C7   O7    double    1.211  0.020  1.211
 NBX  C7   N2    single    1.389  0.020  1.389
 NBX  N2   C8    single    1.383  0.020  1.383
 NBX  C8   O8    double    1.213  0.020  1.213
 NBX  C8   C9    single    1.478  0.020  1.478
 NBX  C9   C10   aromatic  1.399  0.020  1.399
 NBX  C9   C14   aromatic  1.398  0.020  1.398
 NBX  C10  C11   aromatic  1.376  0.020  1.376
 NBX  C11  C12   aromatic  1.406  0.020  1.406
 NBX  C12  C13   aromatic  1.405  0.020  1.405
 NBX  C12  N3    single    1.357  0.020  1.357
 NBX  C13  C14   aromatic  1.379  0.020  1.379
 NBX  C1   H1    single    0.970  0.020  1.090
 NBX  C2   H2    single    0.970  0.020  1.090
 NBX  O2   HO2   single    0.850  0.020  0.980
 NBX  C3   H3    single    0.970  0.020  1.090
 NBX  O3   HO3   single    0.850  0.020  0.980
 NBX  C4   H4    single    0.970  0.020  1.090
 NBX  O4   HO4   single    0.850  0.020  0.980
 NBX  C5   H5    single    0.970  0.020  1.090
 NBX  C6   H6    single    0.970  0.020  1.090
 NBX  C6   H6A   single    0.970  0.020  1.090
 NBX  O6   HO6   single    0.850  0.020  0.980
 NBX  N1   HN1   single    0.860  0.020  1.020
 NBX  N2   HN2   single    0.860  0.020  1.020
 NBX  C10  H10   single    0.930  0.020  1.080
 NBX  C11  H11   single    0.930  0.020  1.080
 NBX  C13  H13   single    0.930  0.020  1.080
 NBX  C14  H14   single    0.930  0.020  1.080
 NBX  N3   HN3   single    0.890  0.020  1.040
 NBX  N3   HN3A  single    0.890  0.020  1.040

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
 NBX  C5    O5   C1   113.42  3.000
 NBX  H1    C1   N1   108.39  3.000
 NBX  H1    C1   C2   108.97  3.000
 NBX  N1    C1   C2   110.15  3.000
 NBX  H1    C1   O5   110.39  3.000
 NBX  N1    C1   O5   108.91  3.000
 NBX  C2    C1   O5   110.01  3.000
 NBX  H2    C2   C3   108.64  3.000
 NBX  H2    C2   O2   111.46  3.000
 NBX  C3    C2   O2   107.63  3.000
 NBX  H2    C2   C1   108.50  3.000
 NBX  C3    C2   C1   109.09  3.000
 NBX  O2    C2   C1   111.46  3.000
 NBX  HO2   O2   C2   108.96  3.000
 NBX  H3    C3   C4   107.89  3.000
 NBX  H3    C3   O3   110.71  3.000
 NBX  C4    C3   O3   107.46  3.000
 NBX  H3    C3   C2   108.00  3.000
 NBX  C4    C3   C2   110.71  3.000
 NBX  O3    C3   C2   112.01  3.000
 NBX  HO3   O3   C3   108.66  3.000
 NBX  H4    C4   C5   108.19  3.000
 NBX  H4    C4   O4   111.06  3.000
 NBX  C5    C4   O4   108.27  3.000
 NBX  H4    C4   C3   108.37  3.000
 NBX  C5    C4   C3   109.65  3.000
 NBX  O4    C4   C3   111.26  3.000
 NBX  HO4   O4   C4   108.10  3.000
 NBX  H5    C5   C6   108.88  3.000
 NBX  H5    C5   C4   108.57  3.000
 NBX  C6    C5   C4   111.92  3.000
 NBX  H5    C5   O5   109.99  3.000
 NBX  C6    C5   O5   107.85  3.000
 NBX  C4    C5   O5   109.62  3.000
 NBX  H6A   C6   H6   107.07  3.000
 NBX  H6A   C6   O6   111.89  3.000
 NBX  H6    C6   O6   111.73  3.000
 NBX  H6A   C6   C5   108.91  3.000
 NBX  H6    C6   C5   108.38  3.000
 NBX  O6    C6   C5   108.76  3.000
 NBX  HO6   O6   C6   108.00  3.000
 NBX  HN1   N1   C7   119.23  3.000
 NBX  HN1   N1   C1   117.01  3.000
 NBX  C7    N1   C1   122.53  3.000
 NBX  N2    C7   O7   124.17  3.000
 NBX  N2    C7   N1   112.00  3.000
 NBX  O7    C7   N1   123.80  3.000
 NBX  HN2   N2   C8   116.93  3.000
 NBX  HN2   N2   C7   116.79  3.000
 NBX  C8    N2   C7   126.28  3.000
 NBX  C9    C8   O8   122.16  3.000
 NBX  C9    C8   N2   115.18  3.000
 NBX  O8    C8   N2   122.66  3.000
 NBX  C14   C9   C10  117.57  3.000
 NBX  C14   C9   C8   124.28  3.000
 NBX  C10   C9   C8   118.11  3.000
 NBX  H10   C10  C11  118.77  3.000
 NBX  H10   C10  C9   119.62  3.000
 NBX  C11   C10  C9   121.61  3.000
 NBX  H11   C11  C12  119.58  3.000
 NBX  H11   C11  C10  119.73  3.000
 NBX  C12   C11  C10  120.69  3.000
 NBX  N3    C12  C13  121.04  3.000
 NBX  N3    C12  C11  121.03  3.000
 NBX  C13   C12  C11  117.89  3.000
 NBX  H13   C13  C14  119.57  3.000
 NBX  H13   C13  C12  119.66  3.000
 NBX  C14   C13  C12  120.77  3.000
 NBX  H14   C14  C13  117.05  3.000
 NBX  H14   C14  C9   121.47  3.000
 NBX  C13   C14  C9   121.47  3.000
 NBX  HN3A  N3   HN3  114.59  3.000
 NBX  HN3A  N3   C12  118.71  3.000
 NBX  HN3   N3   C12  118.64  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
 NBX  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 NBX  CONST_02  C12  C13  C14  C9      0.00   0.0  0
 NBX  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 NBX  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 NBX  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 NBX  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 NBX  CONST_07  C11  C10  C9   C8    180.00   0.0  0
 NBX  CONST_08  C13  C14  C9   C8    180.00   0.0  0
 NBX  CONST_09  N3   C12  C11  C10   180.00   0.0  0
 NBX  CONST_10  N3   C12  C13  C14   180.00   0.0  0
 NBX  CONST_11  H11  C11  C10  C9    180.00   0.0  0
 NBX  CONST_12  H13  C13  C14  C9    180.00   0.0  0
 NBX  CONST_13  H14  C14  C9   C10   180.00   0.0  0
 NBX  CONST_14  H10  C10  C11  C12   180.00   0.0  0
 NBX  CONST_17  O7   C7   N1   C1      0.00   0.0  0
 NBX  CONST_18  C9   C8   N2   C7    180.00   0.0  0
 NBX  CONST_19  N2   C7   N1   C1    180.00   0.0  0
 NBX  CONST_20  HN2  N2   C8   C9      0.00   0.0  0
 NBX  CONST_21  O8   C8   N2   C7      0.00   0.0  0
 NBX  CONST_22  C8   N2   C7   O7      0.00   0.0  0
 NBX  CONST_23  C8   N2   C7   N1    180.00   0.0  0
 NBX  CONST_24  HN1  N1   C7   O7    180.00   0.0  0
 NBX  Var_01    C10  C9   C8   N2   -163.74  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
 NBX  chir_01  C1  O5  C2  N1  positiv
 NBX  chir_02  C2  O2  C1  C3  negativ
 NBX  chir_03  C3  O3  C2  C4  positiv
 NBX  chir_04  C4  O4  C5  C3  positiv
 NBX  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
 NBX  plan-1  C8    0.020
 NBX  plan-1  C9    0.020
 NBX  plan-1  C10   0.020
 NBX  plan-1  C11   0.020
 NBX  plan-1  C12   0.020
 NBX  plan-1  C13   0.020
 NBX  plan-1  C14   0.020
 NBX  plan-1  N3    0.020
 NBX  plan-1  H10   0.020
 NBX  plan-1  H11   0.020
 NBX  plan-1  H13   0.020
 NBX  plan-1  H14   0.020
 NBX  plan-2  C1    0.020
 NBX  plan-2  N1    0.020
 NBX  plan-2  C7    0.020
 NBX  plan-2  O7    0.020
 NBX  plan-2  N2    0.020
 NBX  plan-2  C8    0.020
 NBX  plan-2  O8    0.020
 NBX  plan-2  C9    0.020
 NBX  plan-2  HN1   0.020
 NBX  plan-2  HN2   0.020
 NBX  plan-3  C12   0.020
 NBX  plan-3  N3    0.020
 NBX  plan-3  HN3   0.020
 NBX  plan-3  HN3A  0.020

