# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 15:50:46 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: ~{N}-[3-[[[2-(6-chloranyl-7-fluoranyl-1~{H}-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-~{N}-methyl-methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(c1ncccc1CNc2ccnc(n2)c3[nH]c4c(F)c(Cl)ccc4n3)[S](C)(=O)=O
#
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
 80H  80H  "~{N}-[3-[[[2-(6-chloranyl-7-fluoranyl-1~{H}-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-~{N}-methyl-methanesulfonamide"
  ligand  48  31  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_80H
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
 80H  C18  C   CR16  0  -0.401  22.8970   9.9012  27.9120
 80H  C13  C   CR16  0  -0.346  30.0165  11.9471  26.8239
 80H  C16  C   CR6   0   0.599  30.0316   9.3224  25.7679
 80H  C12  C   CR56  0   0.151  28.8573  11.1678  26.8293
 80H  C8   C   CR6   0   0.567  23.5576  11.1200  28.1760
 80H  C14  C   CR16  0  -0.237  31.1637  11.4006  26.2918
 80H  C7   C   CH2   0  -0.331  23.5511  13.4266  28.9915
 80H  C6   C   CR6   0  -0.005  23.7316  14.3035  27.7742
 80H  C5   C   CR16  0  -0.174  23.1404  14.0260  26.5495
 80H  C4   C   CR16  0  -0.323  23.3609  14.8692  25.4720
 80H  F    F   F     0  -0.286  30.0362   8.0874  25.2693
 80H  C11  C   CR56  0   0.197  28.8737   9.8640  26.3030
 80H  N4   N   NR15  0  -0.692  27.6057   9.3967  26.4588
 80H  C15  C   CR6   0  -0.270  31.1701  10.0972  25.7692
 80H  CL   CL  CL    0  -0.092  32.6218   9.4375  25.1121
 80H  N5   N   N     0  -0.449  27.6035  11.4601  27.2855
 80H  C10  C   CR5   0   0.427  26.8930  10.3919  27.0483
 80H  C9   C   CR6   0   0.319  25.4670  10.2212  27.3574
 80H  N3   N   N     0  -0.468  24.8504  11.2635  27.8879
 80H  N6   N   N     0  -0.463  24.9496   9.0417  27.0653
 80H  C17  C   CR16  0  -0.025  23.6490   8.9025  27.3534
 80H  N2   N   NH1   0  -0.679  22.9154  12.1659  28.7192
 80H  C3   C   CR16  0  -0.067  24.1650  15.9817  25.6561
 80H  N1   N   N     0  -0.391  24.7179  16.2738  26.8257
 80H  C2   C   CR6   0   0.416  24.5104  15.4584  27.8429
 80H  N    N   N     0  -0.658  25.0888  15.8025  29.0970
 80H  C    C   CH3   0  -0.546  24.3225  16.7183  29.9392
 80H  S    S   S     0   1.334  26.7485  15.8706  29.1726
 80H  O    O   OS    0  -0.657  27.1098  15.7662  30.5768
 80H  O1   O   OS    0  -0.656  27.2384  14.8787  28.2299
 80H  C1   C   CH3   0  -0.795  27.2310  17.4843  28.6041
 80H  H1   H   HCR6  0   0.285  21.8485   9.7629  28.1372
 80H  H2   H   HCR6  0   0.270  30.0115  12.9515  27.2252
 80H  H3   H   HCR6  0   0.286  32.0808  11.9729  26.2708
 80H  H4   H   HCH2  0   0.269  24.5209  13.2613  29.4614
 80H  H5   H   HCH2  0   0.286  22.9340  13.9437  29.7281
 80H  H6   H   HCR6  0   0.272  22.5164  13.1498  26.4297
 80H  H7   H   HCR6  0   0.275  22.9174  14.6677  24.5068
 80H  H8   H   HNR5  0   0.428  27.2386   8.4932  26.1980
 80H  H10  H   HCR6  0   0.274  23.2009   7.9433  27.1219
 80H  H11  H   HNH1  0   0.411  21.9316  12.0738  28.9113
 80H  H12  H   HCR6  0   0.269  24.3669  16.6634  24.8384
 80H  H13  H   HCH3  0   0.267  24.7243  16.7244  30.9491
 80H  H14  H   HCH3  0   0.250  24.3119  17.7375  29.5463
 80H  H15  H   HCH3  0   0.273  23.2956  16.3618  29.9949
 80H  H16  H   HCH3  0   0.290  26.7872  18.2452  29.2428
 80H  H17  H   HCH3  0   0.303  28.3167  17.5437  28.6652
 80H  H18  H   HCH3  0   0.292  26.8975  17.6107  27.5780

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
 80H  C4   C3   aromatic  1.385  0.020  1.385
 80H  C4   C5   aromatic  1.386  0.020  1.386
 80H  C3   N1   aromatic  1.326  0.020  1.326
 80H  F    C16  single    1.332  0.020  1.332
 80H  CL   C15  single    1.725  0.020  1.725
 80H  C16  C15  aromatic  1.377  0.020  1.377
 80H  C16  C11  aromatic  1.386  0.020  1.386
 80H  C15  C14  aromatic  1.404  0.020  1.404
 80H  C11  N4   aromatic  1.360  0.020  1.360
 80H  C11  C12  aromatic  1.406  0.020  1.406
 80H  N4   C10  aromatic  1.359  0.020  1.359
 80H  C5   C6   aromatic  1.388  0.020  1.388
 80H  C14  C13  aromatic  1.378  0.020  1.378
 80H  N1   C2   aromatic  1.320  0.020  1.320
 80H  C12  C13  aromatic  1.397  0.020  1.397
 80H  C12  N5   aromatic  1.366  0.020  1.366
 80H  C10  N5   aromatic  1.305  0.020  1.305
 80H  C10  C9   single    1.469  0.020  1.469
 80H  N6   C17  aromatic  1.339  0.020  1.339
 80H  N6   C9   aromatic  1.321  0.020  1.321
 80H  C17  C18  aromatic  1.369  0.020  1.369
 80H  C9   N3   aromatic  1.322  0.020  1.322
 80H  O1   S    double    1.453  0.020  1.453
 80H  C18  C8   aromatic  1.411  0.020  1.411
 80H  C2   C6   aromatic  1.395  0.020  1.395
 80H  C2   N    single    1.423  0.020  1.423
 80H  C6   C7   single    1.511  0.020  1.511
 80H  N3   C8   aromatic  1.332  0.020  1.332
 80H  C8   N2   single    1.342  0.020  1.342
 80H  C1   S    single    1.778  0.020  1.778
 80H  N2   C7   single    1.438  0.020  1.438
 80H  S    N    single    1.663  0.020  1.663
 80H  S    O    double    1.454  0.020  1.454
 80H  N    C    single    1.461  0.020  1.461
 80H  C18  H1   single    0.930  0.020  1.080
 80H  C13  H2   single    0.930  0.020  1.080
 80H  C14  H3   single    0.930  0.020  1.080
 80H  C7   H4   single    0.970  0.020  1.090
 80H  C7   H5   single    0.970  0.020  1.090
 80H  C5   H6   single    0.930  0.020  1.080
 80H  C4   H7   single    0.930  0.020  1.080
 80H  N4   H8   single    0.860  0.020  1.020
 80H  C17  H10  single    0.930  0.020  1.080
 80H  N2   H11  single    0.860  0.020  1.020
 80H  C3   H12  single    0.930  0.020  1.080
 80H  C    H13  single    0.970  0.020  1.090
 80H  C    H14  single    0.970  0.020  1.090
 80H  C    H15  single    0.970  0.020  1.090
 80H  C1   H16  single    0.970  0.020  1.090
 80H  C1   H17  single    0.970  0.020  1.090
 80H  C1   H18  single    0.970  0.020  1.090

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
 80H  H1   C18  C17  121.62  3.000
 80H  H1   C18  C8   121.69  3.000
 80H  C17  C18  C8   116.69  3.000
 80H  H2   C13  C14  121.04  3.000
 80H  H2   C13  C12  120.85  3.000
 80H  C14  C13  C12  118.11  3.000
 80H  C15  C16  C11  118.07  3.000
 80H  C11  C16  F    120.65  3.000
 80H  C15  C16  F    121.27  3.000
 80H  N5   C12  C11  109.52  3.000
 80H  N5   C12  C13  130.07  3.000
 80H  C11  C12  C13  120.41  3.000
 80H  N2   C8   N3   117.90  3.000
 80H  N2   C8   C18  121.65  3.000
 80H  N3   C8   C18  120.45  3.000
 80H  H3   C14  C15  118.70  3.000
 80H  H3   C14  C13  120.25  3.000
 80H  C15  C14  C13  121.05  3.000
 80H  H5   C7   H4   106.50  3.000
 80H  H5   C7   N2   107.05  3.000
 80H  H4   C7   N2   109.99  3.000
 80H  H5   C7   C6   109.65  3.000
 80H  H4   C7   C6   109.21  3.000
 80H  N2   C7   C6   114.14  3.000
 80H  C2   C6   C5   116.55  3.000
 80H  C2   C6   C7   120.50  3.000
 80H  C5   C6   C7   122.95  3.000
 80H  H6   C5   C4   119.89  3.000
 80H  H6   C5   C6   120.34  3.000
 80H  C4   C5   C6   119.78  3.000
 80H  H7   C4   C3   120.43  3.000
 80H  H7   C4   C5   121.03  3.000
 80H  C3   C4   C5   118.54  3.000
 80H  N4   C11  C12  105.36  3.000
 80H  C12  C11  C16  121.10  3.000
 80H  N4   C11  C16  133.54  3.000
 80H  H8   N4   C10  125.23  3.000
 80H  H8   N4   C11  128.09  3.000
 80H  C10  N4   C11  106.68  3.000
 80H  CL   C15  C14  120.04  3.000
 80H  C14  C15  C16  121.25  3.000
 80H  CL   C15  C16  118.71  3.000
 80H  C10  N5   C12  105.31  3.000
 80H  C9   C10  N5   125.84  3.000
 80H  C9   C10  N4   121.02  3.000
 80H  N5   C10  N4   113.13  3.000
 80H  N6   C9   N3   127.59  3.000
 80H  N3   C9   C10  116.46  3.000
 80H  N6   C9   C10  115.95  3.000
 80H  C9   N3   C8   117.03  3.000
 80H  C17  N6   C9   115.20  3.000
 80H  H10  C17  N6   116.59  3.000
 80H  H10  C17  C18  120.37  3.000
 80H  N6   C17  C18  123.04  3.000
 80H  H11  N2   C7   118.44  3.000
 80H  H11  N2   C8   118.26  3.000
 80H  C7   N2   C8   123.25  3.000
 80H  H12  C3   N1   116.70  3.000
 80H  H12  C3   C4   120.88  3.000
 80H  N1   C3   C4   122.42  3.000
 80H  C2   N1   C3   118.55  3.000
 80H  N    C2   N1   117.76  3.000
 80H  N    C2   C6   118.07  3.000
 80H  N1   C2   C6   124.14  3.000
 80H  S    N    C    118.14  3.000
 80H  C    N    C2   116.50  3.000
 80H  S    N    C2   117.10  3.000
 80H  H15  C    H14  108.35  3.000
 80H  H15  C    H13  107.65  3.000
 80H  H14  C    H13  109.42  3.000
 80H  H15  C    N    108.60  3.000
 80H  H14  C    N    112.49  3.000
 80H  H13  C    N    110.19  3.000
 80H  C1   S    O1   108.70  3.000
 80H  C1   S    O    107.86  3.000
 80H  O1   S    O    119.59  3.000
 80H  O    S    N    106.80  3.000
 80H  C1   S    N    107.07  3.000
 80H  O1   S    N    106.20  3.000
 80H  H18  C1   H17  110.65  3.000
 80H  H18  C1   H16  110.36  3.000
 80H  H17  C1   H16  109.61  3.000
 80H  H18  C1   S    108.93  3.000
 80H  H17  C1   S    107.59  3.000
 80H  H16  C1   S    109.66  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
 80H  CONST_01  C9   N6   C17  C18     0.00   0.0  0
 80H  CONST_02  C9   N3   C8   C18     0.00   0.0  0
 80H  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 80H  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 80H  CONST_05  N4   C11  C12  C13   180.00   0.0  0
 80H  CONST_06  C10  N5   C12  C13   180.00   0.0  0
 80H  CONST_07  C10  N4   C11  C16   180.00   0.0  0
 80H  CONST_08  N5   C12  C11  C16   180.00   0.0  0
 80H  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 80H  CONST_10  C10  N4   C11  C12     0.00   0.0  0
 80H  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 80H  CONST_12  N4   C10  N5   C12     0.00   0.0  0
 80H  CONST_13  C9   C10  N5   C12   180.00   0.0  0
 80H  CONST_14  N6   C17  C18  C8      0.00   0.0  0
 80H  CONST_15  C10  C9   N3   C8    180.00   0.0  0
 80H  CONST_16  N6   C9   N3   C8      0.00   0.0  0
 80H  CONST_17  C11  C16  C15  C14     0.00   0.0  0
 80H  CONST_18  C11  C12  C13  C14     0.00   0.0  0
 80H  CONST_19  N5   C12  C13  C14   180.00   0.0  0
 80H  CONST_20  C3   C4   C5   C6      0.00   0.0  0
 80H  CONST_21  C3   N1   C2   C6      0.00   0.0  0
 80H  CONST_22  N1   C3   C4   C5      0.00   0.0  0
 80H  CONST_23  N1   C2   C6   C5      0.00   0.0  0
 80H  CONST_24  C2   N1   C3   C4      0.00   0.0  0
 80H  CONST_25  C2   C6   C5   C4      0.00   0.0  0
 80H  CONST_26  N5   C10  N4   C11     0.00   0.0  0
 80H  CONST_27  C9   C10  N4   C11   180.00   0.0  0
 80H  CONST_28  C10  N5   C12  C11     0.00   0.0  0
 80H  CONST_29  C15  C16  C11  N4    180.00   0.0  0
 80H  CONST_30  N5   C12  C11  N4      0.00   0.0  0
 80H  CONST_31  N6   C9   C10  N4      0.00   0.0  0
 80H  CONST_32  N3   C9   C10  N4    180.00   0.0  0
 80H  CONST_33  N6   C9   C10  N5    180.00   0.0  0
 80H  CONST_34  N3   C9   C10  N5      0.00   0.0  0
 80H  CONST_35  C17  N6   C9   C10   180.00   0.0  0
 80H  CONST_36  C17  N6   C9   N3      0.00   0.0  0
 80H  CONST_37  C17  C18  C8   N3      0.00   0.0  0
 80H  CONST_38  CL   C15  C14  C13   180.00   0.0  0
 80H  CONST_39  F    C16  C11  C12   180.00   0.0  0
 80H  CONST_40  F    C16  C15  C14   180.00   0.0  0
 80H  CONST_41  C4   C5   C6   C7    180.00   0.0  0
 80H  CONST_42  N1   C2   C6   C7    180.00   0.0  0
 80H  CONST_43  N    C2   C6   C5    180.00   0.0  0
 80H  CONST_44  N4   C11  C16  F       0.00   0.0  0
 80H  CONST_45  CL   C15  C16  C11   180.00   0.0  0
 80H  CONST_46  N2   C8   N3   C9    180.00   0.0  0
 80H  CONST_47  N2   C8   C18  C17   180.00   0.0  0
 80H  CONST_48  N    C2   N1   C3    180.00   0.0  0
 80H  CONST_49  H3   C14  C15  C16   180.00   0.0  0
 80H  CONST_50  H8   N4   C11  C16     0.00   0.0  0
 80H  CONST_51  H8   N4   C11  C12   180.00   0.0  0
 80H  CONST_52  H3   C14  C13  C12   180.00   0.0  0
 80H  CONST_53  H10  C17  C18  C8    180.00   0.0  0
 80H  CONST_54  H7   C4   C5   C6    180.00   0.0  0
 80H  CONST_55  H12  C3   C4   C5    180.00   0.0  0
 80H  CONST_56  H2   C13  C12  C11   180.00   0.0  0
 80H  CONST_57  H2   C13  C14  C15   180.00   0.0  0
 80H  CONST_58  H2   C13  C12  N5      0.00   0.0  0
 80H  CONST_59  H8   N4   C10  N5    180.00   0.0  0
 80H  CONST_60  H8   N4   C10  C9      0.00   0.0  0
 80H  CONST_61  H10  C17  N6   C9    180.00   0.0  0
 80H  CONST_62  H1   C18  C8   N3    180.00   0.0  0
 80H  CONST_63  H1   C18  C17  N6    180.00   0.0  0
 80H  CONST_64  H6   C5   C4   C3    180.00   0.0  0
 80H  CONST_65  H7   C4   C3   N1    180.00   0.0  0
 80H  CONST_66  H12  C3   N1   C2    180.00   0.0  0
 80H  CONST_67  H6   C5   C6   C2    180.00   0.0  0
 80H  CONST_68  C7   N2   C8   C18   180.00   0.0  0
 80H  CONST_69  N3   C8   N2   C7      0.00   0.0  0
 80H  CONST_74  H11  N2   C8   C18     0.00   0.0  0
 80H  CONST_75  H11  N2   C8   N3    180.00   0.0  0
 80H  Var_01    C6   C7   N2   C8     78.26  30.0  3
 80H  Var_02    N2   C7   C6   C5     10.38  30.0  2
 80H  Var_03    C2   C6   C7   N2   -170.14  30.0  1
 80H  Var_04    H4   C7   C6   C5    133.95  30.0  2
 80H  Var_05    H5   C7   C6   C5   -109.71  30.0  2
 80H  Var_06    H4   C7   C6   C2    -46.57  30.0  2
 80H  Var_07    H5   C7   C6   C2     69.77  30.0  2
 80H  Var_08    O1   S    N    C2    -31.79  30.0  2
 80H  Var_09    C1   S    N    C2     84.22  30.0  2
 80H  Var_10    O    S    N    C2   -160.46  30.0  2
 80H  Var_11    H4   C7   N2   C8    -44.88  30.0  3
 80H  Var_12    H5   C7   N2   C8   -160.20  30.0  3
 80H  Var_13    H11  N2   C7   C6    -99.24  30.0  1
 80H  Var_14    H13  C    N    C2    166.37  30.0  3
 80H  Var_15    H14  C    N    C2    -71.23  30.0  3
 80H  Var_16    H15  C    N    C2     48.69  30.0  3
 80H  Var_17    O1   S    N    C    -179.16  30.0  2
 80H  Var_18    C1   S    N    C     -63.15  30.0  2
 80H  Var_19    O    S    N    C      52.17  30.0  2
 80H  Var_20    H16  C1   S    N      59.97  30.0  3
 80H  Var_21    H17  C1   S    N     179.11  30.0  3
 80H  Var_22    H18  C1   S    N     -60.90  30.0  3
 80H  Var_23    H13  C    N    S     -46.06  30.0  3
 80H  Var_24    H14  C    N    S      76.33  30.0  3
 80H  Var_25    H15  C    N    S    -163.75  30.0  3
 80H  Var_26    H16  C1   S    O     -54.65  30.0  3
 80H  Var_27    H17  C1   S    O      64.49  30.0  3
 80H  Var_28    H18  C1   S    O    -175.52  30.0  3
 80H  Var_29    H16  C1   S    O1    174.30  30.0  3
 80H  Var_30    H17  C1   S    O1    -66.55  30.0  3
 80H  Var_31    H18  C1   S    O1     53.44  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
 80H  plan-1  C7   0.020
 80H  plan-1  C6   0.020
 80H  plan-1  C5   0.020
 80H  plan-1  C4   0.020
 80H  plan-1  C3   0.020
 80H  plan-1  N1   0.020
 80H  plan-1  C2   0.020
 80H  plan-1  N    0.020
 80H  plan-1  H6   0.020
 80H  plan-1  H7   0.020
 80H  plan-1  H12  0.020
 80H  plan-2  C18  0.020
 80H  plan-2  C8   0.020
 80H  plan-2  C10  0.020
 80H  plan-2  C9   0.020
 80H  plan-2  N3   0.020
 80H  plan-2  N6   0.020
 80H  plan-2  C17  0.020
 80H  plan-2  N2   0.020
 80H  plan-2  H1   0.020
 80H  plan-2  H10  0.020
 80H  plan-3  C13  0.020
 80H  plan-3  C16  0.020
 80H  plan-3  C12  0.020
 80H  plan-3  C14  0.020
 80H  plan-3  F    0.020
 80H  plan-3  C11  0.020
 80H  plan-3  N4   0.020
 80H  plan-3  C15  0.020
 80H  plan-3  CL   0.020
 80H  plan-3  N5   0.020
 80H  plan-3  C10  0.020
 80H  plan-3  C9   0.020
 80H  plan-3  H2   0.020
 80H  plan-3  H3   0.020
 80H  plan-3  H8   0.020
 80H  plan-4  C8   0.020
 80H  plan-4  C7   0.020
 80H  plan-4  N2   0.020
 80H  plan-4  H11  0.020
 80H  plan-5  C2   0.020
 80H  plan-5  N    0.020
 80H  plan-5  C    0.020
 80H  plan-5  S    0.020

