# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 16:20:23 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]-5-chloranyl-phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N(CC(N)=O)c1cc(Cl)cc(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
 7LR  7LR  ~{N}-(2-azanyl-3~{H}-benzimidazol-5-yl)-2-[3-[(2-azanyl-2-oxidanylidene-ethyl)-methylsulfonyl-amino]-5-chloranyl-phenyl]ethanamide  ligand  49  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7LR
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
 7LR  N3   N   NR15  0  -0.725   6.2654  -0.3785   1.4048
 7LR  C4   C   CR5   0   0.602   7.4132   0.3430   1.2565
 7LR  C6   C   CR6   0   0.303  -3.0473  -0.5103   0.0579
 7LR  C7   C   CR56  0   0.379   5.4300  -0.0282   0.3717
 7LR  C8   C   CH2   0  -0.432  -3.6134   1.3303   1.6388
 7LR  C10  C   C     0   0.557   1.3627  -1.0023  -1.0336
 7LR  C13  C   CR16  0  -0.400   4.1536  -0.4498   0.0407
 7LR  C17  C   CR16  0  -0.279  -1.9159  -0.3083  -0.7222
 7LR  C20  C   CR6   0  -0.030  -2.5650  -2.8464   0.1433
 7LR  C22  C   CH2   0  -0.695   0.1220  -1.1570  -1.9016
 7LR  C26  C   CR16  0  -0.253  -1.4363  -2.6602  -0.6364
 7LR  S1   S   S     0   1.333  -4.9715   1.1628  -0.6628
 7LR  N2   N   N     0  -0.693  -3.8826   0.5753   0.4370
 7LR  N5   N   N     0  -0.520   7.3929   1.1312   0.2113
 7LR  C9   C   CR56  0   0.145   6.1592   0.9211  -0.3617
 7LR  C11  C   CR16  0  -0.232  -3.3810  -1.7849   0.4980
 7LR  C12  C   C     0   0.524  -2.8158   2.6048   1.3797
 7LR  O14  O   OS    0  -0.658  -5.4266   2.4463  -0.1490
 7LR  O15  O   OS    0  -0.652  -4.4105   1.0829  -2.0015
 7LR  C16  C   CR6   0   0.141  -1.1087  -1.3818  -1.0757
 7LR  C19  C   CR6   0   0.348   3.5857   0.1234  -1.0976
 7LR  O21  O   O     0  -0.465   1.4795  -1.5894   0.0275
 7LR  O23  O   O     0  -0.477  -2.2869   2.8318   0.3055
 7LR  N24  N   NH2   0  -0.849   8.4190   0.2646   2.1629
 7LR  C25  C   CR16  0  -0.335   5.5763   1.4774  -1.4935
 7LR  C27  C   CH3   0  -0.782  -6.3213   0.0111  -0.5810
 7LR  N28  N   NH2   0  -0.800  -2.7351   3.4154   2.4413
 7LR  C29  C   CR16  0  -0.365   4.2998   1.0730  -1.8468
 7LR  H1   H   HNR5  0   0.416   6.0642  -1.0278   2.1485
 7LR  H2   H   HCH2  0   0.293  -4.5366   1.5623   2.1727
 7LR  H3   H   HCH2  0   0.312  -3.0343   0.6876   2.3047
 7LR  H4   H   HCR6  0   0.285   3.6327  -1.1808   0.6373
 7LR  H5   H   HCR6  0   0.267  -1.6655   0.6930  -1.0436
 7LR  H6   H   HCH2  0   0.290  -0.0112  -0.2913  -2.5527
 7LR  H7   H   HCH2  0   0.310   0.3018  -2.0112  -2.5602
 7LR  H8   H   HCR6  0   0.280  -0.8192  -3.5060  -0.9099
 7LR  H10  H   HCR6  0   0.288  -4.2623  -1.9367   1.1070
 7LR  H11  H   HNH1  0   0.417   2.0591   0.2449  -2.4458
 7LR  H12  H   HNH2  0   0.398   8.5220  -0.6038   2.6631
 7LR  H13  H   HNH2  0   0.397   9.2963   0.6539   1.8578
 7LR  H14  H   HCR6  0   0.252   6.1025   2.2109  -2.0906
 7LR  H15  H   HCH3  0   0.290  -5.9716  -0.9782  -0.8679
 7LR  H16  H   HCH3  0   0.292  -6.7158  -0.0061   0.4320
 7LR  H17  H   HCH3  0   0.305  -7.0898   0.3444  -1.2768
 7LR  H18  H   HNH2  0   0.411  -3.2107   3.2139   3.3045
 7LR  H19  H   HNH2  0   0.405  -2.2079   4.2720   2.3928
 7LR  H20  H   HCR6  0   0.262   3.8376   1.5032  -2.7275
 7LR  N18  N   NH1   0  -0.742   2.3036  -0.1975  -1.5731
 7LR  CL1  CL  CL    0  -0.122  -2.9732  -4.4416   0.6807

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
 7LR  N28  C12  single    1.338  0.020  1.338
 7LR  O23  C12  double    1.219  0.020  1.219
 7LR  C12  C8   single    1.526  0.020  1.526
 7LR  C8   N2   single    1.445  0.020  1.445
 7LR  N2   C6   single    1.421  0.020  1.421
 7LR  N2   S1   single    1.655  0.020  1.655
 7LR  O14  S1   double    1.456  0.020  1.456
 7LR  C11  C6   aromatic  1.389  0.020  1.389
 7LR  C11  C20  aromatic  1.385  0.020  1.385
 7LR  CL1  C20  single    1.732  0.020  1.732
 7LR  C6   C17  aromatic  1.389  0.020  1.389
 7LR  C20  C26  aromatic  1.384  0.020  1.384
 7LR  S1   O15  double    1.454  0.020  1.454
 7LR  S1   C27  single    1.776  0.020  1.776
 7LR  C17  C16  aromatic  1.389  0.020  1.389
 7LR  C26  C16  aromatic  1.391  0.020  1.391
 7LR  C16  C22  single    1.499  0.020  1.499
 7LR  C22  C10  single    1.522  0.020  1.522
 7LR  N18  C10  single    1.351  0.020  1.351
 7LR  N18  C19  single    1.405  0.020  1.405
 7LR  C10  O21  double    1.218  0.020  1.218
 7LR  C29  C19  aromatic  1.405  0.020  1.405
 7LR  C29  C25  aromatic  1.385  0.020  1.385
 7LR  C19  C13  aromatic  1.395  0.020  1.395
 7LR  C25  C9   aromatic  1.389  0.020  1.389
 7LR  C13  C7   aromatic  1.384  0.020  1.384
 7LR  C9   C7   aromatic  1.404  0.020  1.404
 7LR  C9   N5   aromatic  1.376  0.020  1.376
 7LR  C7   N3   aromatic  1.374  0.020  1.374
 7LR  N5   C4   aromatic  1.309  0.020  1.309
 7LR  N3   C4   aromatic  1.364  0.020  1.364
 7LR  C4   N24  single    1.356  0.020  1.356
 7LR  N3   H1   single    0.860  0.020  1.020
 7LR  C8   H2   single    0.970  0.020  1.090
 7LR  C8   H3   single    0.970  0.020  1.090
 7LR  C13  H4   single    0.930  0.020  1.080
 7LR  C17  H5   single    0.930  0.020  1.080
 7LR  C22  H6   single    0.970  0.020  1.090
 7LR  C22  H7   single    0.970  0.020  1.090
 7LR  C26  H8   single    0.930  0.020  1.080
 7LR  C11  H10  single    0.930  0.020  1.080
 7LR  N18  H11  single    0.860  0.020  1.020
 7LR  N24  H12  single    0.890  0.020  1.040
 7LR  N24  H13  single    0.890  0.020  1.040
 7LR  C25  H14  single    0.930  0.020  1.080
 7LR  C27  H15  single    0.970  0.020  1.090
 7LR  C27  H16  single    0.970  0.020  1.090
 7LR  C27  H17  single    0.970  0.020  1.090
 7LR  N28  H18  single    0.860  0.020  1.020
 7LR  N28  H19  single    0.860  0.020  1.020
 7LR  C29  H20  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
 7LR  H1   N3   C7   126.71  3.000
 7LR  H1   N3   C4   126.11  3.000
 7LR  C7   N3   C4   107.16  3.000
 7LR  N24  C4   N5   125.44  3.000
 7LR  N24  C4   N3   121.39  3.000
 7LR  N5   C4   N3   113.10  3.000
 7LR  C11  C6   N2   118.37  3.000
 7LR  C11  C6   C17  120.47  3.000
 7LR  N2   C6   C17  121.16  3.000
 7LR  C9   C7   C13  124.05  3.000
 7LR  C9   C7   N3   104.44  3.000
 7LR  C13  C7   N3   131.51  3.000
 7LR  H3   C8   H2   105.98  3.000
 7LR  H3   C8   C12  108.54  3.000
 7LR  H2   C8   C12  110.35  3.000
 7LR  H3   C8   N2   107.38  3.000
 7LR  H2   C8   N2   111.13  3.000
 7LR  C12  C8   N2   113.13  3.000
 7LR  O21  C10  N18  124.64  3.000
 7LR  O21  C10  C22  121.72  3.000
 7LR  N18  C10  C22  113.62  3.000
 7LR  H4   C13  C19  122.24  3.000
 7LR  H4   C13  C7   121.32  3.000
 7LR  C19  C13  C7   116.44  3.000
 7LR  H5   C17  C16  120.37  3.000
 7LR  H5   C17  C6   119.36  3.000
 7LR  C16  C17  C6   120.26  3.000
 7LR  CL1  C20  C11  119.18  3.000
 7LR  CL1  C20  C26  119.39  3.000
 7LR  C11  C20  C26  121.43  3.000
 7LR  H7   C22  H6   106.29  3.000
 7LR  H7   C22  C16  110.47  3.000
 7LR  H6   C22  C16  110.33  3.000
 7LR  H7   C22  C10  106.79  3.000
 7LR  H6   C22  C10  111.04  3.000
 7LR  C16  C22  C10  111.73  3.000
 7LR  H8   C26  C16  120.28  3.000
 7LR  H8   C26  C20  120.14  3.000
 7LR  C16  C26  C20  119.58  3.000
 7LR  C27  S1   O15  107.46  3.000
 7LR  C27  S1   O14  108.54  3.000
 7LR  O15  S1   O14  119.62  3.000
 7LR  C27  S1   N2   103.83  3.000
 7LR  O15  S1   N2   109.78  3.000
 7LR  O14  S1   N2   106.51  3.000
 7LR  S1   N2   C8   119.33  3.000
 7LR  S1   N2   C6   118.71  3.000
 7LR  C8   N2   C6   120.77  3.000
 7LR  C9   N5   C4   104.73  3.000
 7LR  C25  C9   N5   130.85  3.000
 7LR  N5   C9   C7   110.57  3.000
 7LR  C25  C9   C7   118.59  3.000
 7LR  H10  C11  C20  121.10  3.000
 7LR  H10  C11  C6   120.19  3.000
 7LR  C20  C11  C6   118.72  3.000
 7LR  N28  C12  O23  124.08  3.000
 7LR  O23  C12  C8   122.15  3.000
 7LR  N28  C12  C8   113.76  3.000
 7LR  C26  C16  C22  120.35  3.000
 7LR  C22  C16  C17  120.09  3.000
 7LR  C26  C16  C17  119.55  3.000
 7LR  C29  C19  N18  115.97  3.000
 7LR  C29  C19  C13  120.40  3.000
 7LR  N18  C19  C13  123.63  3.000
 7LR  H13  N24  H12  113.24  3.000
 7LR  H13  N24  C4   114.91  3.000
 7LR  H12  N24  C4   117.23  3.000
 7LR  H14  C25  C29  120.35  3.000
 7LR  H14  C25  C9   121.12  3.000
 7LR  C29  C25  C9   118.53  3.000
 7LR  H17  C27  H16  110.12  3.000
 7LR  H17  C27  H15  109.67  3.000
 7LR  H16  C27  H15  110.37  3.000
 7LR  H17  C27  S1   107.96  3.000
 7LR  H16  C27  S1   109.20  3.000
 7LR  H15  C27  S1   109.47  3.000
 7LR  H19  N28  H18  117.34  3.000
 7LR  H19  N28  C12  120.57  3.000
 7LR  H18  N28  C12  122.07  3.000
 7LR  H20  C29  C25  118.98  3.000
 7LR  H20  C29  C19  119.02  3.000
 7LR  C25  C29  C19  122.00  3.000
 7LR  H11  N18  C19  114.46  3.000
 7LR  H11  N18  C10  115.98  3.000
 7LR  C19  N18  C10  129.55  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
 7LR  CONST_01  C19  C13  C7   N3    180.00   0.0  0
 7LR  CONST_02  C25  C9   C7   N3    180.00   0.0  0
 7LR  CONST_03  N5   C9   C7   N3      0.00   0.0  0
 7LR  CONST_04  C9   N5   C4   N3      0.00   0.0  0
 7LR  CONST_05  C25  C9   N5   C4    180.00   0.0  0
 7LR  CONST_06  C7   C9   N5   C4      0.00   0.0  0
 7LR  CONST_07  C13  C7   N3   C4    180.00   0.0  0
 7LR  CONST_08  C9   C7   N3   C4      0.00   0.0  0
 7LR  CONST_09  C26  C20  C11  C6      0.00   0.0  0
 7LR  CONST_10  C26  C16  C17  C6      0.00   0.0  0
 7LR  CONST_11  C29  C19  C13  C7      0.00   0.0  0
 7LR  CONST_12  C29  C25  C9   C7      0.00   0.0  0
 7LR  CONST_13  N5   C4   N3   C7      0.00   0.0  0
 7LR  CONST_14  C25  C29  C19  C13     0.00   0.0  0
 7LR  CONST_15  C25  C9   C7   C13     0.00   0.0  0
 7LR  CONST_16  N5   C9   C7   C13   180.00   0.0  0
 7LR  CONST_17  C20  C11  C6   C17     0.00   0.0  0
 7LR  CONST_18  C20  C26  C16  C17     0.00   0.0  0
 7LR  CONST_19  C29  C25  C9   N5    180.00   0.0  0
 7LR  CONST_20  C19  C29  C25  C9      0.00   0.0  0
 7LR  CONST_21  C19  C13  C7   C9      0.00   0.0  0
 7LR  CONST_22  C16  C17  C6   C11     0.00   0.0  0
 7LR  CONST_23  C16  C26  C20  C11     0.00   0.0  0
 7LR  CONST_24  CL1  C20  C11  C6    180.00   0.0  0
 7LR  CONST_25  C22  C16  C17  C6    180.00   0.0  0
 7LR  CONST_26  N18  C19  C13  C7    180.00   0.0  0
 7LR  CONST_27  N24  C4   N3   C7    180.00   0.0  0
 7LR  CONST_28  N2   C6   C11  C20   180.00   0.0  0
 7LR  CONST_29  C22  C16  C26  C20   180.00   0.0  0
 7LR  CONST_30  C16  C17  C6   N2    180.00   0.0  0
 7LR  CONST_31  N24  C4   N5   C9    180.00   0.0  0
 7LR  CONST_32  CL1  C20  C26  C16   180.00   0.0  0
 7LR  CONST_33  C25  C29  C19  N18   180.00   0.0  0
 7LR  CONST_34  H4   C13  C7   N3      0.00   0.0  0
 7LR  CONST_35  H14  C25  C9   C7    180.00   0.0  0
 7LR  CONST_36  H20  C29  C19  C13   180.00   0.0  0
 7LR  CONST_37  H1   N3   C7   C13     0.00   0.0  0
 7LR  CONST_38  H10  C11  C6   C17   180.00   0.0  0
 7LR  CONST_39  H8   C26  C16  C17   180.00   0.0  0
 7LR  CONST_40  H5   C17  C16  C26   180.00   0.0  0
 7LR  CONST_43  C29  C19  N18  C10   180.00   0.0  0
 7LR  CONST_44  C13  C19  N18  C10     0.00   0.0  0
 7LR  CONST_48  H13  N24  C4   N3    180.00   0.0  0
 7LR  CONST_49  H11  N18  C19  C13   180.00   0.0  0
 7LR  CONST_50  C19  N18  C10  C22   180.00   0.0  0
 7LR  CONST_51  O21  C10  N18  C19     0.00   0.0  0
 7LR  CONST_52  H18  N28  C12  C8      0.00   0.0  0
 7LR  CONST_53  H19  N28  C12  C8    180.00   0.0  0
 7LR  Var_01    C17  C16  C22  C10    94.60  30.0  2
 7LR  Var_02    C12  C8   N2   C6     96.14  30.0  3
 7LR  Var_03    O14  S1   N2   C6   -165.74  30.0  3
 7LR  Var_04    N18  C10  C22  C16  -149.46  30.0  3
 7LR  Var_05    N28  C12  C8   N2    170.28  30.0  1
 7LR  Var_06    H15  C27  S1   N2    -61.37  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
 7LR  plan-1  C6   0.020
 7LR  plan-1  C17  0.020
 7LR  plan-1  C20  0.020
 7LR  plan-1  C22  0.020
 7LR  plan-1  C26  0.020
 7LR  plan-1  N2   0.020
 7LR  plan-1  C11  0.020
 7LR  plan-1  C16  0.020
 7LR  plan-1  H5   0.020
 7LR  plan-1  H8   0.020
 7LR  plan-1  H10  0.020
 7LR  plan-1  CL1  0.020
 7LR  plan-2  N3   0.020
 7LR  plan-2  C4   0.020
 7LR  plan-2  C7   0.020
 7LR  plan-2  C13  0.020
 7LR  plan-2  N5   0.020
 7LR  plan-2  C9   0.020
 7LR  plan-2  C19  0.020
 7LR  plan-2  N24  0.020
 7LR  plan-2  C25  0.020
 7LR  plan-2  C29  0.020
 7LR  plan-2  H1   0.020
 7LR  plan-2  H4   0.020
 7LR  plan-2  H14  0.020
 7LR  plan-2  H20  0.020
 7LR  plan-2  N18  0.020
 7LR  plan-3  C10  0.020
 7LR  plan-3  C22  0.020
 7LR  plan-3  C19  0.020
 7LR  plan-3  O21  0.020
 7LR  plan-3  H11  0.020
 7LR  plan-3  N18  0.020
 7LR  plan-4  C8   0.020
 7LR  plan-4  C12  0.020
 7LR  plan-4  O23  0.020
 7LR  plan-4  N28  0.020
 7LR  plan-4  H18  0.020
 7LR  plan-4  H19  0.020
 7LR  plan-5  C6   0.020
 7LR  plan-5  C8   0.020
 7LR  plan-5  S1   0.020
 7LR  plan-5  N2   0.020
 7LR  plan-6  C4   0.020
 7LR  plan-6  N24  0.020
 7LR  plan-6  H12  0.020
 7LR  plan-6  H13  0.020

