# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 15:38:56 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-azanyl-6-[[(1~{S})-1-[6-fluoranyl-1-(3-methylsulfonylphenyl)benzimidazol-2-yl]ethyl]amino]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1ncnc(N)c1C#N)c2nc3ccc(F)cc3n2c4cccc(c4)[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
 5MT  5MT  4-azanyl-6-[[(1~{S})-1-[6-fluoranyl-1-(3-methylsulfonylphenyl)benzimidazol-2-yl]ethyl]amino]pyrimidine-5-carbonitrile  ligand  50  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5MT
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
 5MT  C20  C  CH3   0  -0.791  -3.7167  -3.4516   2.0126
 5MT  S1   S  S     0   1.219  -4.5459  -2.4307   0.8182
 5MT  O1   O  OS    0  -0.661  -5.4020  -3.2794  -0.0058
 5MT  O2   O  OS    0  -0.661  -5.1375  -1.2880   1.5084
 5MT  C18  C  CR6   0  -0.203  -3.2187  -1.8319  -0.2045
 5MT  C19  C  CR16  0  -0.245  -2.5343  -0.6914   0.1862
 5MT  C17  C  CR16  0  -0.221  -2.8875  -2.5221  -1.3610
 5MT  C16  C  CR16  0  -0.245  -1.8471  -2.0523  -2.1483
 5MT  C15  C  CR16  0  -0.241  -1.1546  -0.9089  -1.7815
 5MT  C14  C  CR6   0   0.272  -1.4926  -0.2421  -0.6108
 5MT  N5   N  NR5   0  -0.657  -0.7764   0.9153  -0.2260
 5MT  C9   C  CR56  0   0.336  -1.2608   2.2035  -0.2292
 5MT  C10  C  CR16  0  -0.458  -2.5021   2.7226  -0.5702
 5MT  C11  C  CR6   0   0.519  -2.6092   4.0920  -0.4568
 5MT  F1   F  F     0  -0.318  -3.7838   4.6657  -0.7671
 5MT  C12  C  CR16  0  -0.423  -1.5681   4.9216  -0.0393
 5MT  C13  C  CR16  0  -0.311  -0.3398   4.3768   0.2877
 5MT  C8   C  CR56  0   0.157  -0.1852   2.9971   0.1916
 5MT  N6   N  N     0  -0.487   0.9089   2.2013   0.4434
 5MT  C7   C  CR5   0   0.486   0.5285   0.9887   0.1869
 5MT  C6   C  CH1   0  -0.179   1.3821  -0.2255   0.3971
 5MT  C21  C  CH3   0  -0.647   0.9759  -0.9613   1.6765
 5MT  N4   N  NH1   0  -0.681   2.7548   0.2250   0.4385
 5MT  C2   C  CR6   0   0.608   3.7991  -0.5636   0.1764
 5MT  N2   N  N     0  -0.495   3.5615  -1.8287  -0.1838
 5MT  C1   C  CR16  0   0.085   4.6188  -2.5760  -0.4460
 5MT  N1   N  N     0  -0.475   5.8920  -2.2444  -0.3940
 5MT  C4   C  CR6   0   0.538   6.1678  -0.9822  -0.0321
 5MT  N3   N  NH2   0  -0.819   7.4499  -0.6315   0.0223
 5MT  C3   C  CR6   0  -0.243   5.1254  -0.0802   0.2690
 5MT  C5   C  CSP   0   0.013   5.3930   1.2498   0.6457
 5MT  N7   N  NS    0  -0.253   5.6079   2.3427   0.9556
 5MT  H1   H  HCH3  0   0.296  -3.0440  -2.8381   2.6079
 5MT  H2   H  HCH3  0   0.316  -4.4808  -3.8941   2.6511
 5MT  H3   H  HCH3  0   0.300  -3.1633  -4.2326   1.4965
 5MT  H4   H  HCR6  0   0.310  -2.7918  -0.1626   1.0954
 5MT  H5   H  HCR6  0   0.295  -3.4297  -3.4106  -1.6539
 5MT  H6   H  HCR6  0   0.288  -1.5817  -2.5722  -3.0580
 5MT  H7   H  HCR6  0   0.298  -0.3556  -0.5298  -2.4054
 5MT  H8   H  HCR6  0   0.293  -3.3324   2.1134  -0.9022
 5MT  H9   H  HCR6  0   0.281  -1.7330   5.9890   0.0235
 5MT  H10  H  HCR6  0   0.273   0.4783   5.0084   0.6075
 5MT  H11  H  HCH1  0   0.289   1.2682  -0.9062  -0.4491
 5MT  H12  H  HCH3  0   0.236  -0.0495  -1.3252   1.6133
 5MT  H13  H  HCH3  0   0.259   1.6261  -1.8216   1.8233
 5MT  H14  H  HCH3  0   0.243   1.0546  -0.3038   2.5417
 5MT  H15  H  HNH1  0   0.413   2.9023   1.1827   0.7247
 5MT  H16  H  HCR6  0   0.265   4.4086  -3.5991  -0.7408
 5MT  H17  H  HNH2  0   0.412   8.1570  -1.3150  -0.1892
 5MT  H18  H  HNH2  0   0.417   7.7540   0.2849   0.3018

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
 5MT  F1   C11  single    1.344  0.020  1.344
 5MT  C12  C11  aromatic  1.395  0.020  1.395
 5MT  C12  C13  aromatic  1.383  0.020  1.383
 5MT  C11  C10  aromatic  1.378  0.020  1.378
 5MT  C13  C8   aromatic  1.392  0.020  1.392
 5MT  C10  C9   aromatic  1.388  0.020  1.388
 5MT  C8   C9   aromatic  1.401  0.020  1.401
 5MT  C8   N6   aromatic  1.376  0.020  1.376
 5MT  C9   N5   aromatic  1.376  0.020  1.376
 5MT  O1   S1   double    1.460  0.020  1.460
 5MT  N6   C7   aromatic  1.297  0.020  1.297
 5MT  N5   C7   aromatic  1.371  0.020  1.371
 5MT  N5   C14  single    1.414  0.020  1.414
 5MT  C20  S1   single    1.777  0.020  1.777
 5MT  C19  C14  aromatic  1.387  0.020  1.387
 5MT  C19  C18  aromatic  1.386  0.020  1.386
 5MT  C7   C6   single    1.499  0.020  1.499
 5MT  S1   C18  single    1.779  0.020  1.779
 5MT  S1   O2   double    1.460  0.020  1.460
 5MT  C14  C15  aromatic  1.389  0.020  1.389
 5MT  C18  C17  aromatic  1.387  0.020  1.387
 5MT  C15  C16  aromatic  1.386  0.020  1.386
 5MT  C21  C6   single    1.531  0.020  1.531
 5MT  C17  C16  aromatic  1.387  0.020  1.387
 5MT  C6   N4   single    1.445  0.020  1.445
 5MT  N4   C2   single    1.335  0.020  1.335
 5MT  N2   C2   aromatic  1.337  0.020  1.337
 5MT  N2   C1   aromatic  1.321  0.020  1.321
 5MT  C2   C3   aromatic  1.415  0.020  1.415
 5MT  C1   N1   aromatic  1.317  0.020  1.317
 5MT  C3   C5   single    1.408  0.020  1.408
 5MT  C3   C4   aromatic  1.411  0.020  1.411
 5MT  C5   N7   triple    1.156  0.020  1.156
 5MT  N1   C4   aromatic  1.342  0.020  1.342
 5MT  C4   N3   single    1.330  0.020  1.330
 5MT  C20  H1   single    0.970  0.020  1.090
 5MT  C20  H2   single    0.970  0.020  1.090
 5MT  C20  H3   single    0.970  0.020  1.090
 5MT  C19  H4   single    0.930  0.020  1.080
 5MT  C17  H5   single    0.930  0.020  1.080
 5MT  C16  H6   single    0.930  0.020  1.080
 5MT  C15  H7   single    0.930  0.020  1.080
 5MT  C10  H8   single    0.930  0.020  1.080
 5MT  C12  H9   single    0.930  0.020  1.080
 5MT  C13  H10  single    0.930  0.020  1.080
 5MT  C6   H11  single    0.970  0.020  1.090
 5MT  C21  H12  single    0.970  0.020  1.090
 5MT  C21  H13  single    0.970  0.020  1.090
 5MT  C21  H14  single    0.970  0.020  1.090
 5MT  N4   H15  single    0.860  0.020  1.020
 5MT  C1   H16  single    0.930  0.020  1.080
 5MT  N3   H17  single    0.860  0.020  1.020
 5MT  N3   H18  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
 5MT  H3   C20  H2   110.08  3.000
 5MT  H3   C20  H1   110.49  3.000
 5MT  H2   C20  H1   110.00  3.000
 5MT  H3   C20  S1   109.34  3.000
 5MT  H2   C20  S1   107.46  3.000
 5MT  H1   C20  S1   109.42  3.000
 5MT  C18  S1   O2   108.09  3.000
 5MT  O2   S1   O1   118.95  3.000
 5MT  C18  S1   O1   107.97  3.000
 5MT  O2   S1   C20  108.72  3.000
 5MT  C18  S1   C20  103.40  3.000
 5MT  O1   S1   C20  108.61  3.000
 5MT  C17  C18  C19  121.77  3.000
 5MT  C17  C18  S1   119.33  3.000
 5MT  C19  C18  S1   118.89  3.000
 5MT  H4   C19  C14  120.20  3.000
 5MT  H4   C19  C18  121.40  3.000
 5MT  C14  C19  C18  118.39  3.000
 5MT  H5   C17  C16  120.06  3.000
 5MT  H5   C17  C18  120.99  3.000
 5MT  C16  C17  C18  118.94  3.000
 5MT  H6   C16  C15  119.79  3.000
 5MT  H6   C16  C17  119.94  3.000
 5MT  C15  C16  C17  120.27  3.000
 5MT  H7   C15  C14  119.83  3.000
 5MT  H7   C15  C16  120.34  3.000
 5MT  C14  C15  C16  119.83  3.000
 5MT  N5   C14  C15  119.93  3.000
 5MT  C15  C14  C19  120.78  3.000
 5MT  N5   C14  C19  119.29  3.000
 5MT  C7   N5   C9   106.60  3.000
 5MT  C7   N5   C14  127.43  3.000
 5MT  C9   N5   C14  125.95  3.000
 5MT  C8   C9   C10  123.26  3.000
 5MT  C8   C9   N5   105.02  3.000
 5MT  C10  C9   N5   131.71  3.000
 5MT  H8   C10  C11  121.67  3.000
 5MT  H8   C10  C9   123.44  3.000
 5MT  C11  C10  C9   114.89  3.000
 5MT  C12  C11  F1   117.88  3.000
 5MT  C12  C11  C10  123.88  3.000
 5MT  F1   C11  C10  118.24  3.000
 5MT  H9   C12  C13  120.68  3.000
 5MT  H9   C12  C11  119.36  3.000
 5MT  C13  C12  C11  119.96  3.000
 5MT  H10  C13  C8   121.01  3.000
 5MT  H10  C13  C12  120.77  3.000
 5MT  C8   C13  C12  118.22  3.000
 5MT  N6   C8   C13  130.47  3.000
 5MT  N6   C8   C9   109.74  3.000
 5MT  C13  C8   C9   119.80  3.000
 5MT  C7   N6   C8   105.75  3.000
 5MT  C6   C7   N6   124.24  3.000
 5MT  C6   C7   N5   122.75  3.000
 5MT  N6   C7   N5   112.89  3.000
 5MT  H11  C6   N4   108.39  3.000
 5MT  H11  C6   C21  108.68  3.000
 5MT  N4   C6   C21  112.21  3.000
 5MT  H11  C6   C7   109.68  3.000
 5MT  N4   C6   C7   107.00  3.000
 5MT  C21  C6   C7   110.82  3.000
 5MT  H14  C21  H13  109.07  3.000
 5MT  H14  C21  H12  108.39  3.000
 5MT  H13  C21  H12  107.81  3.000
 5MT  H14  C21  C6   110.76  3.000
 5MT  H13  C21  C6   109.53  3.000
 5MT  H12  C21  C6   111.20  3.000
 5MT  H15  N4   C2   120.10  3.000
 5MT  H15  N4   C6   116.24  3.000
 5MT  C2   N4   C6   123.60  3.000
 5MT  C3   C2   N2   120.51  3.000
 5MT  C3   C2   N4   121.25  3.000
 5MT  N2   C2   N4   118.24  3.000
 5MT  C1   N2   C2   116.52  3.000
 5MT  H16  C1   N1   115.81  3.000
 5MT  H16  C1   N2   115.60  3.000
 5MT  N1   C1   N2   128.59  3.000
 5MT  C4   N1   C1   116.51  3.000
 5MT  C3   C4   N3   122.33  3.000
 5MT  N3   C4   N1   117.20  3.000
 5MT  C3   C4   N1   120.47  3.000
 5MT  H18  N3   H17  117.73  3.000
 5MT  H18  N3   C4   122.90  3.000
 5MT  H17  N3   C4   119.33  3.000
 5MT  C5   C3   C4   121.37  3.000
 5MT  C4   C3   C2   117.40  3.000
 5MT  C5   C3   C2   121.23  3.000
 5MT  N7   C5   C3   180.00  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
 5MT  CONST_01  N5   C14  C19  C18  180.00   0.0  0
 5MT  CONST_02  C15  C14  C19  C18    0.00   0.0  0
 5MT  CONST_03  C15  C16  C17  C18    0.00   0.0  0
 5MT  CONST_06  C16  C15  C14  C19    0.00   0.0  0
 5MT  CONST_07  C16  C17  C18  C19    0.00   0.0  0
 5MT  CONST_08  C14  C19  C18  C17    0.00   0.0  0
 5MT  CONST_09  C14  C15  C16  C17    0.00   0.0  0
 5MT  CONST_10  N5   C14  C15  C16  180.00   0.0  0
 5MT  CONST_13  C10  C9   N5   C14    0.00   0.0  0
 5MT  CONST_14  C8   C9   N5   C14  180.00   0.0  0
 5MT  CONST_15  N6   C7   N5   C14  180.00   0.0  0
 5MT  CONST_16  C11  C10  C9   N5   180.00   0.0  0
 5MT  CONST_17  C13  C8   C9   N5   180.00   0.0  0
 5MT  CONST_18  N6   C8   C9   N5     0.00   0.0  0
 5MT  CONST_19  C8   N6   C7   N5     0.00   0.0  0
 5MT  CONST_20  C12  C11  C10  C9     0.00   0.0  0
 5MT  CONST_21  C12  C13  C8   C9     0.00   0.0  0
 5MT  CONST_22  C7   N6   C8   C9     0.00   0.0  0
 5MT  CONST_23  N6   C7   N5   C9     0.00   0.0  0
 5MT  CONST_24  C13  C12  C11  C10    0.00   0.0  0
 5MT  CONST_25  C13  C8   C9   C10    0.00   0.0  0
 5MT  CONST_26  N6   C8   C9   C10  180.00   0.0  0
 5MT  CONST_27  C7   N5   C9   C10  180.00   0.0  0
 5MT  CONST_28  C8   C13  C12  C11    0.00   0.0  0
 5MT  CONST_29  C8   C9   C10  C11    0.00   0.0  0
 5MT  CONST_30  N6   C8   C13  C12  180.00   0.0  0
 5MT  CONST_31  C7   N6   C8   C13  180.00   0.0  0
 5MT  CONST_32  C7   N5   C9   C8     0.00   0.0  0
 5MT  CONST_33  N1   C1   N2   C2     0.00   0.0  0
 5MT  CONST_34  N1   C4   C3   C2     0.00   0.0  0
 5MT  CONST_35  C4   C3   C2   N2     0.00   0.0  0
 5MT  CONST_36  C4   N1   C1   N2     0.00   0.0  0
 5MT  CONST_37  C3   C2   N2   C1     0.00   0.0  0
 5MT  CONST_38  C3   C4   N1   C1     0.00   0.0  0
 5MT  CONST_39  C14  C19  C18  S1   180.00   0.0  0
 5MT  CONST_40  C16  C17  C18  S1   180.00   0.0  0
 5MT  CONST_41  C6   C7   N5   C14    0.00   0.0  0
 5MT  CONST_42  F1   C11  C10  C9   180.00   0.0  0
 5MT  CONST_43  C6   C7   N5   C9   180.00   0.0  0
 5MT  CONST_44  C13  C12  C11  F1   180.00   0.0  0
 5MT  CONST_45  C6   C7   N6   C8   180.00   0.0  0
 5MT  CONST_46  C1   N2   C2   N4   180.00   0.0  0
 5MT  CONST_47  C4   C3   C2   N4   180.00   0.0  0
 5MT  CONST_48  N3   C4   C3   C2   180.00   0.0  0
 5MT  CONST_49  C5   C3   C2   N2   180.00   0.0  0
 5MT  CONST_50  N3   C4   N1   C1   180.00   0.0  0
 5MT  CONST_51  C5   C3   C4   N1   180.00   0.0  0
 5MT  CONST_52  H6   C16  C17  C18  180.00   0.0  0
 5MT  CONST_53  H7   C15  C14  C19  180.00   0.0  0
 5MT  CONST_54  H5   C17  C18  C19  180.00   0.0  0
 5MT  CONST_55  H4   C19  C18  C17  180.00   0.0  0
 5MT  CONST_56  H8   C10  C9   N5     0.00   0.0  0
 5MT  CONST_57  H10  C13  C8   C9   180.00   0.0  0
 5MT  CONST_58  H9   C12  C11  C10  180.00   0.0  0
 5MT  CONST_59  H16  C1   N2   C2   180.00   0.0  0
 5MT  CONST_60  N2   C2   N4   C6     0.00   0.0  0
 5MT  CONST_61  C3   C2   N4   C6   180.00   0.0  0
 5MT  CONST_62  H15  N4   C2   N2   180.00   0.0  0
 5MT  CONST_63  H17  N3   C4   N1     0.00   0.0  0
 5MT  CONST_64  H18  N3   C4   N1   180.00   0.0  0
 5MT  Var_01    C19  C18  S1   C20  -86.02  30.0  2
 5MT  Var_02    H1   C20  S1   C18   63.20  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
 5MT  chir_01  C6  C7  C21  N4  positiv

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
 5MT  plan-1  S1   0.020
 5MT  plan-1  C18  0.020
 5MT  plan-1  C19  0.020
 5MT  plan-1  C17  0.020
 5MT  plan-1  C16  0.020
 5MT  plan-1  C15  0.020
 5MT  plan-1  C14  0.020
 5MT  plan-1  N5   0.020
 5MT  plan-1  H4   0.020
 5MT  plan-1  H5   0.020
 5MT  plan-1  H6   0.020
 5MT  plan-1  H7   0.020
 5MT  plan-2  N4   0.020
 5MT  plan-2  C2   0.020
 5MT  plan-2  N2   0.020
 5MT  plan-2  C1   0.020
 5MT  plan-2  N1   0.020
 5MT  plan-2  C4   0.020
 5MT  plan-2  N3   0.020
 5MT  plan-2  C3   0.020
 5MT  plan-2  C5   0.020
 5MT  plan-2  N7   0.020
 5MT  plan-2  H16  0.020
 5MT  plan-3  C14  0.020
 5MT  plan-3  N5   0.020
 5MT  plan-3  C9   0.020
 5MT  plan-3  C10  0.020
 5MT  plan-3  C11  0.020
 5MT  plan-3  F1   0.020
 5MT  plan-3  C12  0.020
 5MT  plan-3  C13  0.020
 5MT  plan-3  C8   0.020
 5MT  plan-3  N6   0.020
 5MT  plan-3  C7   0.020
 5MT  plan-3  C6   0.020
 5MT  plan-3  H8   0.020
 5MT  plan-3  H9   0.020
 5MT  plan-3  H10  0.020
 5MT  plan-4  C6   0.020
 5MT  plan-4  N4   0.020
 5MT  plan-4  C2   0.020
 5MT  plan-4  H15  0.020
 5MT  plan-5  C4   0.020
 5MT  plan-5  N3   0.020
 5MT  plan-5  H17  0.020
 5MT  plan-5  H18  0.020

