# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 11:08:21 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5'-O-[(2-nitrobenzene-1-carbonyl)sulfamoyl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)c4ccccc4[N+]([O-])=O)[C@@H](O)[C@H]3O
#
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
 B1U  B1U  5'-O-[(2-nitrobenzene-1-carbonyl)sulfamoyl]adenosine  ligand  51  34  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B1U
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
 B1U  O8   O  O     -1  -0.387   1.0097   0.8049  -1.6809
 B1U  N7   N  N      1   0.349   1.3352   1.9593  -1.8554
 B1U  O9   O  O      0  -0.348   0.5941   2.8279  -2.2354
 B1U  C13  C  CR6    0   0.260   2.7231   2.2953  -1.5957
 B1U  C14  C  CR16   0  -0.259   3.3027   3.3234  -2.3163
 B1U  C15  C  CR16   0  -0.249   4.6470   3.6015  -2.1200
 B1U  C16  C  CR16   0  -0.216   5.3852   2.8596  -1.2116
 B1U  C17  C  CR16   0  -0.243   4.7849   1.8365  -0.4883
 B1U  C12  C  CR6    0  -0.058   3.4425   1.5426  -0.6727
 B1U  C11  C  C      0   0.530   2.8017   0.5382   0.2357
 B1U  O7   O  O      0  -0.382   2.0357   0.8453   1.1110
 B1U  N6   N  NC1    0  -0.813   3.2374  -0.7459   0.0219
 B1U  SAT  S  S      0   1.633   2.8623  -2.0298   1.0223
 B1U  O5   O  OS     0  -0.624   3.5073  -3.1635   0.4122
 B1U  O6   O  OS     0  -0.605   3.1038  -1.6726   2.3906
 B1U  O4   O  OC2    0  -0.565   1.2911  -2.1471   0.9102
 B1U  C10  C  CH2    0  -0.204   0.6886  -2.5434  -0.3401
 B1U  C9   C  CH1    0  -0.017  -0.7353  -2.9450  -0.0310
 B1U  O1   O  O2     0  -0.487  -1.4316  -1.8674   0.5905
 B1U  C8   C  CH1    0  -0.053  -1.5057  -3.2953  -1.3070
 B1U  O2   O  OH1    0  -0.662  -2.3749  -4.3556  -1.0173
 B1U  C7   C  CH1    0  -0.034  -2.2798  -1.9963  -1.5639
 B1U  O3   O  OH1    0  -0.651  -3.4559  -2.1477  -2.2956
 B1U  C6   C  CH1    0   0.211  -2.5993  -1.5752  -0.1341
 B1U  N5   N  NR5    0  -0.548  -2.9330  -0.1916   0.0332
 B1U  C5   C  CR15   0   0.115  -2.2092   0.9046  -0.3603
 B1U  N4   N  N      0  -0.447  -2.7575   2.0317  -0.0232
 B1U  C3   C  CR56   0  -0.011  -3.9071   1.6715   0.6334
 B1U  C2   C  CR56   0   0.494  -4.0337   0.2937   0.6846
 B1U  N2   N  N      0  -0.458  -5.0247  -0.3902   1.2488
 B1U  C1   C  CR16   0   0.047  -5.9284   0.4123   1.7850
 B1U  N1   N  N      0  -0.474  -5.9408   1.7417   1.8121
 B1U  C4   C  CR6    0   0.459  -4.9359   2.4153   1.2403
 B1U  N3   N  NH2    0  -0.816  -4.9502   3.7484   1.2581
 B1U  H1   H  HCR6   0   0.309   2.7275   3.8847  -3.0388
 B1U  H2   H  HCR6   0   0.290   5.1154   4.3950  -2.6851
 B1U  H3   H  HCR6   0   0.290   6.4331   3.0766  -1.0577
 B1U  H4   H  HCR6   0   0.296   5.3646   1.2777   0.2345
 B1U  H5   H  HNC1   0   0.464   3.8246  -0.9623  -0.7763
 B1U  H6   H  HCH2   0   0.263   0.7409  -1.7109  -1.0439
 B1U  H7   H  HCH2   0   0.278   1.2150  -3.4007  -0.7626
 B1U  H8   H  HCH1   0   0.277  -0.7197  -3.8069   0.6439
 B1U  H9   H  HCH1   0   0.261  -0.8331  -3.5378  -2.1405
 B1U  H10  H  HOH1   0   0.453  -3.0363  -4.4014  -1.7176
 B1U  H11  H  HCH1   0   0.248  -1.6021  -1.2667  -2.0268
 B1U  H12  H  HOH1   0   0.471  -3.2480  -2.1099  -3.2345
 B1U  H13  H  HCH1   0   0.262  -3.4600  -2.1428   0.2372
 B1U  H14  H  HCR5   0   0.281  -1.2773   0.8103  -0.8956
 B1U  H15  H  HCR6   0   0.253  -6.7706  -0.0718   2.2673
 B1U  H16  H  HNH2   0   0.412  -4.1809   4.2816   0.8926
 B1U  H17  H  HNH2   0   0.404  -5.6819   4.2391   1.7426

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
 B1U  O9   N7   double    1.203  0.020  1.203
 B1U  C14  C15  aromatic  1.387  0.020  1.387
 B1U  C14  C13  aromatic  1.383  0.020  1.383
 B1U  C15  C16  aromatic  1.386  0.020  1.386
 B1U  N7   C13  single    1.451  0.020  1.451
 B1U  N7   O8   single    1.212  0.020  1.212
 B1U  C13  C12  aromatic  1.391  0.020  1.391
 B1U  C16  C17  aromatic  1.389  0.020  1.389
 B1U  N3   C4   single    1.333  0.020  1.333
 B1U  C17  C12  aromatic  1.386  0.020  1.386
 B1U  C12  C11  single    1.498  0.020  1.498
 B1U  N4   C3   aromatic  1.372  0.020  1.372
 B1U  N4   C5   aromatic  1.298  0.020  1.298
 B1U  C4   C3   aromatic  1.407  0.020  1.407
 B1U  C4   N1   aromatic  1.338  0.020  1.338
 B1U  C3   C2   aromatic  1.385  0.020  1.385
 B1U  O2   C8   single    1.401  0.020  1.401
 B1U  C11  N6   single    1.373  0.020  1.373
 B1U  C11  O7   double    1.203  0.020  1.203
 B1U  N6   SAT  single    1.670  0.020  1.670
 B1U  C5   N5   aromatic  1.371  0.020  1.371
 B1U  N1   C1   aromatic  1.330  0.020  1.330
 B1U  C8   C7   single    1.534  0.020  1.534
 B1U  C8   C9   single    1.531  0.020  1.531
 B1U  C10  C9   single    1.511  0.020  1.511
 B1U  C10  O4   single    1.443  0.020  1.443
 B1U  C2   N5   aromatic  1.368  0.020  1.368
 B1U  C2   N2   aromatic  1.330  0.020  1.330
 B1U  N5   C6   single    1.433  0.020  1.433
 B1U  O6   SAT  deloc     1.435  0.020  1.435
 B1U  C7   C6   single    1.524  0.020  1.524
 B1U  C7   O3   single    1.393  0.020  1.393
 B1U  C1   N2   aromatic  1.322  0.020  1.322
 B1U  C9   O1   single    1.426  0.020  1.426
 B1U  SAT  O4   single    1.580  0.020  1.580
 B1U  SAT  O5   deloc     1.440  0.020  1.440
 B1U  C6   O1   single    1.405  0.020  1.405
 B1U  C14  H1   single    0.930  0.020  1.080
 B1U  C15  H2   single    0.930  0.020  1.080
 B1U  C16  H3   single    0.930  0.020  1.080
 B1U  C17  H4   single    0.930  0.020  1.080
 B1U  N6   H5   single    0.860  0.020  1.020
 B1U  C10  H6   single    0.970  0.020  1.090
 B1U  C10  H7   single    0.970  0.020  1.090
 B1U  C9   H8   single    0.970  0.020  1.090
 B1U  C8   H9   single    0.970  0.020  1.090
 B1U  O2   H10  single    0.850  0.020  0.980
 B1U  C7   H11  single    0.970  0.020  1.090
 B1U  O3   H12  single    0.850  0.020  0.980
 B1U  C6   H13  single    0.970  0.020  1.090
 B1U  C5   H14  single    0.930  0.020  1.080
 B1U  C1   H15  single    0.930  0.020  1.080
 B1U  N3   H16  single    0.860  0.020  1.020
 B1U  N3   H17  single    0.860  0.020  1.020

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
 B1U  C13  N7   O9   118.58  3.000
 B1U  C13  N7   O8   116.84  3.000
 B1U  O9   N7   O8   124.58  3.000
 B1U  C12  C13  C14  122.08  3.000
 B1U  C12  C13  N7   119.21  3.000
 B1U  C14  C13  N7   118.66  3.000
 B1U  H1   C14  C15  120.43  3.000
 B1U  H1   C14  C13  120.76  3.000
 B1U  C15  C14  C13  118.79  3.000
 B1U  H2   C15  C16  120.32  3.000
 B1U  H2   C15  C14  119.56  3.000
 B1U  C16  C15  C14  120.12  3.000
 B1U  H3   C16  C17  119.50  3.000
 B1U  H3   C16  C15  120.14  3.000
 B1U  C17  C16  C15  120.35  3.000
 B1U  H4   C17  C12  119.87  3.000
 B1U  H4   C17  C16  119.78  3.000
 B1U  C12  C17  C16  120.35  3.000
 B1U  C11  C12  C17  118.40  3.000
 B1U  C11  C12  C13  122.93  3.000
 B1U  C17  C12  C13  118.30  3.000
 B1U  N6   C11  O7   123.65  3.000
 B1U  O7   C11  C12  122.84  3.000
 B1U  N6   C11  C12  113.39  3.000
 B1U  H5   N6   SAT  115.94  3.000
 B1U  H5   N6   C11  120.39  3.000
 B1U  SAT  N6   C11  123.67  3.000
 B1U  O4   SAT  O6   104.69  3.000
 B1U  O4   SAT  O5   110.92  3.000
 B1U  O6   SAT  O5   121.65  3.000
 B1U  O5   SAT  N6   104.52  3.000
 B1U  O4   SAT  N6   103.76  3.000
 B1U  O6   SAT  N6   110.00  3.000
 B1U  C10  O4   SAT  119.81  3.000
 B1U  H7   C10  H6   109.06  3.000
 B1U  H7   C10  C9   108.96  3.000
 B1U  H6   C10  C9   112.32  3.000
 B1U  H7   C10  O4   110.47  3.000
 B1U  H6   C10  O4   109.22  3.000
 B1U  C9   C10  O4   106.80  3.000
 B1U  H8   C9   C8   109.92  3.000
 B1U  H8   C9   O1   109.47  3.000
 B1U  C8   C9   O1   106.89  3.000
 B1U  H8   C9   C10  108.78  3.000
 B1U  O1   C9   C10  110.39  3.000
 B1U  C8   C9   C10  111.37  3.000
 B1U  C6   O1   C9   109.77  3.000
 B1U  H9   C8   C7   111.66  3.000
 B1U  H9   C8   O2   111.69  3.000
 B1U  C7   C8   O2   111.24  3.000
 B1U  H9   C8   C9   112.02  3.000
 B1U  C7   C8   C9   101.53  3.000
 B1U  O2   C8   C9   108.24  3.000
 B1U  H10  O2   C8   108.13  3.000
 B1U  H11  C7   C6   109.95  3.000
 B1U  H11  C7   O3   111.82  3.000
 B1U  C6   C7   O3   110.22  3.000
 B1U  H11  C7   C8   108.77  3.000
 B1U  O3   C7   C8   114.96  3.000
 B1U  C6   C7   C8   100.52  3.000
 B1U  H12  O3   C7   109.02  3.000
 B1U  H13  C6   N5   106.12  3.000
 B1U  H13  C6   C7   109.84  3.000
 B1U  N5   C6   C7   115.15  3.000
 B1U  H13  C6   O1   111.74  3.000
 B1U  C7   C6   O1   104.60  3.000
 B1U  N5   C6   O1   109.52  3.000
 B1U  C2   N5   C5   106.13  3.000
 B1U  C2   N5   C6   125.84  3.000
 B1U  C5   N5   C6   127.98  3.000
 B1U  H14  C5   N4   124.72  3.000
 B1U  H14  C5   N5   121.90  3.000
 B1U  N4   C5   N5   113.38  3.000
 B1U  C3   N4   C5   104.49  3.000
 B1U  C4   C3   C2   116.31  3.000
 B1U  C2   C3   N4   110.82  3.000
 B1U  C4   C3   N4   132.86  3.000
 B1U  N2   C2   C3   126.56  3.000
 B1U  N2   C2   N5   128.26  3.000
 B1U  C3   C2   N5   105.18  3.000
 B1U  C1   N2   C2   111.67  3.000
 B1U  H15  C1   N1   115.46  3.000
 B1U  H15  C1   N2   116.12  3.000
 B1U  N1   C1   N2   128.43  3.000
 B1U  C4   N1   C1   119.17  3.000
 B1U  N3   C4   N1   119.31  3.000
 B1U  N1   C4   C3   117.86  3.000
 B1U  N3   C4   C3   122.83  3.000
 B1U  H17  N3   H16  118.26  3.000
 B1U  H17  N3   C4   120.15  3.000
 B1U  H16  N3   C4   121.16  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
 B1U  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 B1U  CONST_02  C16  C17  C12  C13    0.00   0.0  0
 B1U  CONST_03  C17  C16  C15  C14    0.00   0.0  0
 B1U  CONST_04  C17  C12  C13  C14    0.00   0.0  0
 B1U  CONST_05  C12  C13  C14  C15    0.00   0.0  0
 B1U  CONST_06  C12  C17  C16  C15    0.00   0.0  0
 B1U  CONST_07  C3   N4   C5   N5     0.00   0.0  0
 B1U  CONST_08  N4   C3   C2   N5     0.00   0.0  0
 B1U  CONST_09  C4   C3   C2   N5   180.00   0.0  0
 B1U  CONST_10  C1   N2   C2   N5   180.00   0.0  0
 B1U  CONST_11  C4   C3   N4   C5   180.00   0.0  0
 B1U  CONST_12  C2   C3   N4   C5     0.00   0.0  0
 B1U  CONST_13  C3   C2   N5   C5     0.00   0.0  0
 B1U  CONST_14  N2   C2   N5   C5   180.00   0.0  0
 B1U  CONST_15  N1   C4   C3   N4   180.00   0.0  0
 B1U  CONST_16  N2   C2   C3   N4   180.00   0.0  0
 B1U  CONST_17  C2   N5   C5   N4     0.00   0.0  0
 B1U  CONST_18  C1   N1   C4   C3     0.00   0.0  0
 B1U  CONST_19  C1   N2   C2   C3     0.00   0.0  0
 B1U  CONST_20  N1   C4   C3   C2     0.00   0.0  0
 B1U  CONST_21  N1   C1   N2   C2     0.00   0.0  0
 B1U  CONST_22  C4   C3   C2   N2     0.00   0.0  0
 B1U  CONST_23  C4   N1   C1   N2     0.00   0.0  0
 B1U  CONST_24  N4   C5   N5   C6   180.00   0.0  0
 B1U  CONST_25  C3   C2   N5   C6   180.00   0.0  0
 B1U  CONST_26  N2   C2   N5   C6     0.00   0.0  0
 B1U  CONST_27  C15  C14  C13  N7   180.00   0.0  0
 B1U  CONST_28  C17  C12  C13  N7   180.00   0.0  0
 B1U  CONST_29  C11  C12  C13  C14  180.00   0.0  0
 B1U  CONST_30  C11  C12  C17  C16  180.00   0.0  0
 B1U  CONST_31  N3   C4   C3   N4     0.00   0.0  0
 B1U  CONST_32  N3   C4   C3   C2   180.00   0.0  0
 B1U  CONST_33  N3   C4   N1   C1   180.00   0.0  0
 B1U  CONST_34  H2   C15  C14  C13  180.00   0.0  0
 B1U  CONST_35  H4   C17  C12  C13  180.00   0.0  0
 B1U  CONST_36  H3   C16  C15  C14  180.00   0.0  0
 B1U  CONST_37  H1   C14  C15  C16  180.00   0.0  0
 B1U  CONST_38  H14  C5   N5   C6     0.00   0.0  0
 B1U  CONST_39  H15  C1   N2   C2   180.00   0.0  0
 B1U  CONST_44  H16  N3   C4   C3     0.00   0.0  0
 B1U  CONST_45  H17  N3   C4   C3   180.00   0.0  0
 B1U  CONST_46  SAT  N6   C11  C12  180.00   0.0  0
 B1U  CONST_47  H5   N6   C11  C12    0.00   0.0  0
 B1U  CONST_48  SAT  N6   C11  O7     0.00   0.0  0
 B1U  Var_01    N6   C11  C12  C13  117.10  30.0  2
 B1U  Var_02    C9   C10  O4   SAT  164.04  30.0  2
 B1U  Var_03    O6   SAT  N6   C11  -48.55  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
 B1U  chir_01  C9  C8  C10  O1  negativ
 B1U  chir_02  C8  O2  C9   C7  positiv
 B1U  chir_03  C7  O3  C8   C6  positiv
 B1U  chir_04  C6  O1  N5   C7  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
 B1U  plan-1  N7   0.020
 B1U  plan-1  C13  0.020
 B1U  plan-1  C14  0.020
 B1U  plan-1  C15  0.020
 B1U  plan-1  C16  0.020
 B1U  plan-1  C17  0.020
 B1U  plan-1  C12  0.020
 B1U  plan-1  C11  0.020
 B1U  plan-1  H1   0.020
 B1U  plan-1  H2   0.020
 B1U  plan-1  H3   0.020
 B1U  plan-1  H4   0.020
 B1U  plan-2  C6   0.020
 B1U  plan-2  N5   0.020
 B1U  plan-2  C5   0.020
 B1U  plan-2  N4   0.020
 B1U  plan-2  C3   0.020
 B1U  plan-2  C2   0.020
 B1U  plan-2  N2   0.020
 B1U  plan-2  C1   0.020
 B1U  plan-2  N1   0.020
 B1U  plan-2  C4   0.020
 B1U  plan-2  N3   0.020
 B1U  plan-2  H14  0.020
 B1U  plan-2  H15  0.020
 B1U  plan-3  O8   0.020
 B1U  plan-3  N7   0.020
 B1U  plan-3  O9   0.020
 B1U  plan-3  C13  0.020
 B1U  plan-4  C4   0.020
 B1U  plan-4  N3   0.020
 B1U  plan-4  H16  0.020
 B1U  plan-4  H17  0.020
 B1U  plan-5  C12  0.020
 B1U  plan-5  C11  0.020
 B1U  plan-5  O7   0.020
 B1U  plan-5  N6   0.020
 B1U  plan-5  SAT  0.020
 B1U  plan-5  H5   0.020

