# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:45:57 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: ~{N}-(2-azanyl-3~{H}-benzimidazol-5-yl)-2-[3-[(2-azanyl-2-oxidanylidene-ethyl)-methylsulfonyl-amino]phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N(CC(N)=O)c1cccc(CC(=O)Nc2ccc3nc(N)[nH]c3c2)c1
#
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
 7ZJ  7ZJ  ~{N}-(2-azanyl-3~{H}-benzimidazol-5-yl)-2-[3-[(2-azanyl-2-oxidanylidene-ethyl)-methylsulfonyl-amino]phenyl]ethanamide  ligand  49  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7ZJ
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
 7ZJ  N3   N  NR15  0  -0.725   5.8508  -2.1711  -0.5820
 7ZJ  C4   C  CR5   0   0.603   7.2126  -2.1051  -0.6158
 7ZJ  C6   C  CR56  0   0.379   5.3919  -0.9140  -0.2693
 7ZJ  C7   C  CH2   0  -0.437  -4.8300   0.3228   1.6582
 7ZJ  C8   C  CR56  0   0.145   6.5550  -0.1409  -0.1289
 7ZJ  C10  C  C     0   0.553   1.5165   1.0900   0.4055
 7ZJ  C17  C  CR16  0  -0.293  -1.7595   0.9405   0.6707
 7ZJ  C21  C  CR6   0   0.146  -0.8603   1.8392   0.1112
 7ZJ  C22  C  CR16  0  -0.335   6.4234   1.2049   0.1902
 7ZJ  C24  C  CH3   0  -0.785  -4.8568  -1.9162  -1.2459
 7ZJ  C26  C  CR16  0  -0.366   5.1502   1.7234   0.3574
 7ZJ  C28  C  CR16  0  -0.240  -2.4112   2.2097  -1.7034
 7ZJ  S1   S  S     0   1.334  -3.8961  -1.7913   0.2422
 7ZJ  N5   N  N     0  -0.520   7.6756  -0.9102  -0.3476
 7ZJ  C9   C  CR6   0   0.320  -2.9809   0.6885   0.0593
 7ZJ  C11  C  C     0   0.524  -6.0437   0.9982   1.0312
 7ZJ  C12  C  CR16  0  -0.401   4.1080  -0.4212  -0.1080
 7ZJ  O13  O  OS    0  -0.665  -4.5874  -2.5313   1.2888
 7ZJ  O14  O  OS    0  -0.656  -2.5263  -2.1429  -0.0952
 7ZJ  C16  C  CR6   0   0.349   3.9984   0.9317   0.2140
 7ZJ  O18  O  O     0  -0.459   1.2340  -0.0706   0.1691
 7ZJ  O19  O  O     0  -0.476  -6.4186   0.7355  -0.1000
 7ZJ  N20  N  NH2   0  -0.849   7.9653  -3.1785  -0.9611
 7ZJ  C23  C  CH2   0  -0.693   0.4557   2.1170   0.7743
 7ZJ  N25  N  NH2   0  -0.796  -6.6693   1.8545   1.8461
 7ZJ  C27  C  CR16  0  -0.278  -3.3140   1.3255  -1.1296
 7ZJ  C29  C  CR16  0  -0.289  -1.1953   2.4648  -1.0865
 7ZJ  H1   H  HNR5  0   0.416   5.2879  -2.9836  -0.7772
 7ZJ  H2   H  HCH2  0   0.311  -5.1885  -0.4812   2.3027
 7ZJ  H3   H  HCH2  0   0.289  -4.2965   1.0154   2.3125
 7ZJ  H4   H  HCR6  0   0.254  -1.5236   0.4443   1.6038
 7ZJ  H5   H  HCR6  0   0.252   7.2913   1.8407   0.3072
 7ZJ  H6   H  HCH3  0   0.298  -4.8458  -2.9609  -1.5529
 7ZJ  H7   H  HCH3  0   0.293  -5.8713  -1.5863  -1.0487
 7ZJ  H8   H  HCH3  0   0.284  -4.4054  -1.3009  -2.0205
 7ZJ  H9   H  HCR6  0   0.262   5.0383   2.7729   0.6040
 7ZJ  H10  H  HCR6  0   0.262  -2.6621   2.7075  -2.6307
 7ZJ  H12  H  HCR6  0   0.285   3.2446  -1.0545  -0.2299
 7ZJ  H13  H  HNH1  0   0.415   2.8563   2.5746   0.6064
 7ZJ  H14  H  HNH2  0   0.398   7.5833  -4.0919  -0.7762
 7ZJ  H15  H  HNH2  0   0.397   8.9430  -3.1022  -0.7324
 7ZJ  H16  H  HCH2  0   0.304   0.3445   2.0773   1.8624
 7ZJ  H17  H  HCH2  0   0.284   0.7954   3.1271   0.5370
 7ZJ  H18  H  HNH2  0   0.412  -6.3251   2.0623   2.7681
 7ZJ  H19  H  HNH2  0   0.406  -7.5307   2.2941   1.5649
 7ZJ  H20  H  HCR6  0   0.267  -4.2756   1.1432  -1.5888
 7ZJ  H21  H  HCR6  0   0.257  -0.5027   3.1650  -1.5379
 7ZJ  N15  N  NH1   0  -0.743   2.7732   1.5891   0.4089
 7ZJ  N2   N  N     0  -0.692  -3.8952  -0.2026   0.6921

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
 7ZJ  N25  C11  single    1.337  0.020  1.337
 7ZJ  O19  C11  double    1.220  0.020  1.220
 7ZJ  C11  C7   single    1.524  0.020  1.524
 7ZJ  C7   N2   single    1.443  0.020  1.443
 7ZJ  O13  S1   double    1.456  0.020  1.456
 7ZJ  N2   C9   single    1.425  0.020  1.425
 7ZJ  N2   S1   single    1.651  0.020  1.651
 7ZJ  C27  C9   aromatic  1.389  0.020  1.389
 7ZJ  C27  C28  aromatic  1.388  0.020  1.388
 7ZJ  C9   C17  aromatic  1.389  0.020  1.389
 7ZJ  S1   O14  double    1.454  0.020  1.454
 7ZJ  S1   C24  single    1.776  0.020  1.776
 7ZJ  C28  C29  aromatic  1.387  0.020  1.387
 7ZJ  C17  C21  aromatic  1.389  0.020  1.389
 7ZJ  C29  C21  aromatic  1.392  0.020  1.392
 7ZJ  C21  C23  single    1.500  0.020  1.500
 7ZJ  C23  C10  single    1.522  0.020  1.522
 7ZJ  N15  C10  single    1.352  0.020  1.352
 7ZJ  N15  C16  single    1.404  0.020  1.404
 7ZJ  C10  O18  double    1.218  0.020  1.218
 7ZJ  C26  C16  aromatic  1.405  0.020  1.405
 7ZJ  C26  C22  aromatic  1.385  0.020  1.385
 7ZJ  C16  C12  aromatic  1.395  0.020  1.395
 7ZJ  C22  C8   aromatic  1.389  0.020  1.389
 7ZJ  C12  C6   aromatic  1.385  0.020  1.385
 7ZJ  C8   C6   aromatic  1.404  0.020  1.404
 7ZJ  C8   N5   aromatic  1.377  0.020  1.377
 7ZJ  C6   N3   aromatic  1.374  0.020  1.374
 7ZJ  N5   C4   aromatic  1.309  0.020  1.309
 7ZJ  N3   C4   aromatic  1.364  0.020  1.364
 7ZJ  C4   N20  single    1.356  0.020  1.356
 7ZJ  N3   H1   single    0.860  0.020  1.020
 7ZJ  C7   H2   single    0.970  0.020  1.090
 7ZJ  C7   H3   single    0.970  0.020  1.090
 7ZJ  C17  H4   single    0.930  0.020  1.080
 7ZJ  C22  H5   single    0.930  0.020  1.080
 7ZJ  C24  H6   single    0.970  0.020  1.090
 7ZJ  C24  H7   single    0.970  0.020  1.090
 7ZJ  C24  H8   single    0.970  0.020  1.090
 7ZJ  C26  H9   single    0.930  0.020  1.080
 7ZJ  C28  H10  single    0.930  0.020  1.080
 7ZJ  C12  H12  single    0.930  0.020  1.080
 7ZJ  N15  H13  single    0.860  0.020  1.020
 7ZJ  N20  H14  single    0.890  0.020  1.040
 7ZJ  N20  H15  single    0.890  0.020  1.040
 7ZJ  C23  H16  single    0.970  0.020  1.090
 7ZJ  C23  H17  single    0.970  0.020  1.090
 7ZJ  N25  H18  single    0.860  0.020  1.020
 7ZJ  N25  H19  single    0.860  0.020  1.020
 7ZJ  C27  H20  single    0.930  0.020  1.080
 7ZJ  C29  H21  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
 7ZJ  H1   N3   C6   126.53  3.000
 7ZJ  H1   N3   C4   126.30  3.000
 7ZJ  C6   N3   C4   107.15  3.000
 7ZJ  N20  C4   N5   125.34  3.000
 7ZJ  N20  C4   N3   121.50  3.000
 7ZJ  N5   C4   N3   113.09  3.000
 7ZJ  C12  C6   C8   124.10  3.000
 7ZJ  C8   C6   N3   104.47  3.000
 7ZJ  C12  C6   N3   131.43  3.000
 7ZJ  H3   C7   H2   105.90  3.000
 7ZJ  H3   C7   C11  110.76  3.000
 7ZJ  H2   C7   C11  107.93  3.000
 7ZJ  H3   C7   N2   108.39  3.000
 7ZJ  H2   C7   N2   109.88  3.000
 7ZJ  C11  C7   N2   113.69  3.000
 7ZJ  N5   C8   C22  130.91  3.000
 7ZJ  N5   C8   C6   110.54  3.000
 7ZJ  C22  C8   C6   118.55  3.000
 7ZJ  C23  C10  O18  121.90  3.000
 7ZJ  O18  C10  N15  124.61  3.000
 7ZJ  C23  C10  N15  113.46  3.000
 7ZJ  H4   C17  C9   119.19  3.000
 7ZJ  H4   C17  C21  120.17  3.000
 7ZJ  C9   C17  C21  120.62  3.000
 7ZJ  C29  C21  C23  120.55  3.000
 7ZJ  C23  C21  C17  120.66  3.000
 7ZJ  C29  C21  C17  118.78  3.000
 7ZJ  H5   C22  C26  120.28  3.000
 7ZJ  H5   C22  C8   121.19  3.000
 7ZJ  C26  C22  C8   118.52  3.000
 7ZJ  H8   C24  H7   110.22  3.000
 7ZJ  H8   C24  H6   109.74  3.000
 7ZJ  H7   C24  H6   110.64  3.000
 7ZJ  H8   C24  S1   109.43  3.000
 7ZJ  H7   C24  S1   109.41  3.000
 7ZJ  H6   C24  S1   107.36  3.000
 7ZJ  H9   C26  C16  118.96  3.000
 7ZJ  H9   C26  C22  119.01  3.000
 7ZJ  C16  C26  C22  122.03  3.000
 7ZJ  H10  C28  C29  119.98  3.000
 7ZJ  H10  C28  C27  119.78  3.000
 7ZJ  C29  C28  C27  120.24  3.000
 7ZJ  O14  S1   O13  119.41  3.000
 7ZJ  O14  S1   N2   107.18  3.000
 7ZJ  O13  S1   N2   107.06  3.000
 7ZJ  O14  S1   C24  107.35  3.000
 7ZJ  N2   S1   C24  107.24  3.000
 7ZJ  O13  S1   C24  108.04  3.000
 7ZJ  C8   N5   C4   104.75  3.000
 7ZJ  C27  C9   N2   120.86  3.000
 7ZJ  C27  C9   C17  120.29  3.000
 7ZJ  N2   C9   C17  118.83  3.000
 7ZJ  N25  C11  O19  123.98  3.000
 7ZJ  O19  C11  C7   122.05  3.000
 7ZJ  N25  C11  C7   113.93  3.000
 7ZJ  H12  C12  C16  122.21  3.000
 7ZJ  H12  C12  C6   121.37  3.000
 7ZJ  C16  C12  C6   116.42  3.000
 7ZJ  N15  C16  C12  123.69  3.000
 7ZJ  C12  C16  C26  120.37  3.000
 7ZJ  N15  C16  C26  115.94  3.000
 7ZJ  H15  N20  H14  113.28  3.000
 7ZJ  H15  N20  C4   114.91  3.000
 7ZJ  H14  N20  C4   117.43  3.000
 7ZJ  H17  C23  H16  106.33  3.000
 7ZJ  H17  C23  C21  110.39  3.000
 7ZJ  H16  C23  C21  110.11  3.000
 7ZJ  H17  C23  C10  110.78  3.000
 7ZJ  H16  C23  C10  106.69  3.000
 7ZJ  C21  C23  C10  112.31  3.000
 7ZJ  H19  N25  H18  117.29  3.000
 7ZJ  H19  N25  C11  120.63  3.000
 7ZJ  H18  N25  C11  122.05  3.000
 7ZJ  H20  C27  C9   119.96  3.000
 7ZJ  H20  C27  C28  120.70  3.000
 7ZJ  C9   C27  C28  119.34  3.000
 7ZJ  H21  C29  C28  119.60  3.000
 7ZJ  H21  C29  C21  119.68  3.000
 7ZJ  C28  C29  C21  120.72  3.000
 7ZJ  H13  N15  C16  114.38  3.000
 7ZJ  H13  N15  C10  115.96  3.000
 7ZJ  C16  N15  C10  129.63  3.000
 7ZJ  C9   N2   S1   118.75  3.000
 7ZJ  S1   N2   C7   122.15  3.000
 7ZJ  C9   N2   C7   119.03  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
 7ZJ  CONST_01  C16  C12  C6   N3    180.00   0.0  0
 7ZJ  CONST_02  C22  C8   C6   N3    180.00   0.0  0
 7ZJ  CONST_03  N5   C8   C6   N3      0.00   0.0  0
 7ZJ  CONST_04  C8   N5   C4   N3      0.00   0.0  0
 7ZJ  CONST_05  C22  C8   N5   C4    180.00   0.0  0
 7ZJ  CONST_06  C6   C8   N5   C4      0.00   0.0  0
 7ZJ  CONST_07  C12  C6   N3   C4    180.00   0.0  0
 7ZJ  CONST_08  C8   C6   N3   C4      0.00   0.0  0
 7ZJ  CONST_09  C26  C16  C12  C6      0.00   0.0  0
 7ZJ  CONST_10  C26  C22  C8   C6      0.00   0.0  0
 7ZJ  CONST_11  N5   C4   N3   C6      0.00   0.0  0
 7ZJ  CONST_12  C16  C26  C22  C8      0.00   0.0  0
 7ZJ  CONST_13  C16  C12  C6   C8      0.00   0.0  0
 7ZJ  CONST_14  C28  C27  C9   C17     0.00   0.0  0
 7ZJ  CONST_15  C28  C29  C21  C17     0.00   0.0  0
 7ZJ  CONST_16  C27  C9   C17  C21     0.00   0.0  0
 7ZJ  CONST_17  C27  C28  C29  C21     0.00   0.0  0
 7ZJ  CONST_18  C12  C16  C26  C22     0.00   0.0  0
 7ZJ  CONST_19  C12  C6   C8   C22     0.00   0.0  0
 7ZJ  CONST_20  N5   C8   C22  C26   180.00   0.0  0
 7ZJ  CONST_21  C12  C6   C8   N5    180.00   0.0  0
 7ZJ  CONST_22  C29  C28  C27  C9      0.00   0.0  0
 7ZJ  CONST_23  C29  C21  C17  C9      0.00   0.0  0
 7ZJ  CONST_24  N15  C16  C12  C6    180.00   0.0  0
 7ZJ  CONST_25  N20  C4   N3   C6    180.00   0.0  0
 7ZJ  CONST_26  N20  C4   N5   C8    180.00   0.0  0
 7ZJ  CONST_27  N2   C9   C17  C21   180.00   0.0  0
 7ZJ  CONST_28  N15  C16  C26  C22   180.00   0.0  0
 7ZJ  CONST_29  N2   C9   C27  C28   180.00   0.0  0
 7ZJ  CONST_30  C23  C21  C29  C28   180.00   0.0  0
 7ZJ  CONST_31  C23  C21  C17  C9    180.00   0.0  0
 7ZJ  CONST_32  H12  C12  C6   N3      0.00   0.0  0
 7ZJ  CONST_33  H5   C22  C8   C6    180.00   0.0  0
 7ZJ  CONST_34  H9   C26  C22  C8    180.00   0.0  0
 7ZJ  CONST_35  H1   N3   C6   C8    180.00   0.0  0
 7ZJ  CONST_36  H20  C27  C9   C17   180.00   0.0  0
 7ZJ  CONST_37  H21  C29  C21  C17   180.00   0.0  0
 7ZJ  CONST_38  H10  C28  C29  C21   180.00   0.0  0
 7ZJ  CONST_39  H4   C17  C9   C27   180.00   0.0  0
 7ZJ  CONST_42  C26  C16  N15  C10   180.00   0.0  0
 7ZJ  CONST_43  C12  C16  N15  C10     0.00   0.0  0
 7ZJ  CONST_47  H15  N20  C4   N3    180.00   0.0  0
 7ZJ  CONST_48  H13  N15  C16  C26     0.00   0.0  0
 7ZJ  CONST_49  C23  C10  N15  C16   180.00   0.0  0
 7ZJ  CONST_50  O18  C10  N15  C16     0.00   0.0  0
 7ZJ  CONST_51  H18  N25  C11  C7      0.00   0.0  0
 7ZJ  CONST_52  H19  N25  C11  C7    180.00   0.0  0
 7ZJ  Var_01    C17  C21  C23  C10    84.14  30.0  2
 7ZJ  Var_02    N15  C10  C23  C21   149.86  30.0  3
 7ZJ  Var_03    C9   N2   S1   C24   -81.51  30.0  3
 7ZJ  Var_04    C11  C7   N2   C9     79.66  30.0  3
 7ZJ  Var_05    N25  C11  C7   N2   -158.90  30.0  1
 7ZJ  Var_06    H6   C24  S1   N2    179.13  30.0  3

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
 7ZJ  plan-1  C17  0.020
 7ZJ  plan-1  C21  0.020
 7ZJ  plan-1  C28  0.020
 7ZJ  plan-1  C9   0.020
 7ZJ  plan-1  C23  0.020
 7ZJ  plan-1  C27  0.020
 7ZJ  plan-1  C29  0.020
 7ZJ  plan-1  H4   0.020
 7ZJ  plan-1  H10  0.020
 7ZJ  plan-1  H20  0.020
 7ZJ  plan-1  H21  0.020
 7ZJ  plan-1  N2   0.020
 7ZJ  plan-2  N3   0.020
 7ZJ  plan-2  C4   0.020
 7ZJ  plan-2  C6   0.020
 7ZJ  plan-2  C8   0.020
 7ZJ  plan-2  C22  0.020
 7ZJ  plan-2  C26  0.020
 7ZJ  plan-2  N5   0.020
 7ZJ  plan-2  C12  0.020
 7ZJ  plan-2  C16  0.020
 7ZJ  plan-2  N20  0.020
 7ZJ  plan-2  H1   0.020
 7ZJ  plan-2  H5   0.020
 7ZJ  plan-2  H9   0.020
 7ZJ  plan-2  H12  0.020
 7ZJ  plan-2  N15  0.020
 7ZJ  plan-3  C10  0.020
 7ZJ  plan-3  C16  0.020
 7ZJ  plan-3  O18  0.020
 7ZJ  plan-3  C23  0.020
 7ZJ  plan-3  H13  0.020
 7ZJ  plan-3  N15  0.020
 7ZJ  plan-4  C7   0.020
 7ZJ  plan-4  C11  0.020
 7ZJ  plan-4  O19  0.020
 7ZJ  plan-4  N25  0.020
 7ZJ  plan-4  H18  0.020
 7ZJ  plan-4  H19  0.020
 7ZJ  plan-5  C4   0.020
 7ZJ  plan-5  N20  0.020
 7ZJ  plan-5  H14  0.020
 7ZJ  plan-5  H15  0.020
 7ZJ  plan-6  C7   0.020
 7ZJ  plan-6  S1   0.020
 7ZJ  plan-6  C9   0.020
 7ZJ  plan-6  N2   0.020

