# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:31:09 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc(N[C@@H](c2cccc(Cl)c2)c3ccccn3)c(Nc4ncccn4)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
 N4W  N4W  ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine  ligand  52  32  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N4W
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
 N4W  C1   C   CR6   0   0.412   0.6128  -0.4080  -0.2739
 N4W  C2   C   CR16  0  -0.352   0.6919  -1.6398  -0.9465
 N4W  C3   C   CR16  0  -0.223   1.7899  -2.4609  -0.7973
 N4W  C11  C   CH3   0  -0.786   5.3568  -2.5851  -1.0867
 N4W  C12  C   CH1   0  -0.237  -1.6076   0.1536  -1.1884
 N4W  C13  C   CR6   0   0.283  -2.4260   1.4294  -1.2862
 N4W  C15  C   CR16  0  -0.059  -2.9519   3.4563  -0.3788
 N4W  C16  C   CR16  0  -0.333  -3.8989   3.7135  -1.3552
 N4W  C17  C   CR16  0  -0.145  -4.0990   2.7579  -2.3428
 N4W  C18  C   CR16  0  -0.320  -3.3515   1.5936  -2.3097
 N4W  C19  C   CR6   0   0.144  -2.4884  -0.9540  -0.6285
 N4W  C20  C   CR16  0  -0.300  -3.0822  -1.8786  -1.4775
 N4W  C21  C   CR16  0  -0.246  -3.9133  -2.8659  -0.9657
 N4W  C22  C   CR16  0  -0.224  -4.1586  -2.9425   0.3966
 N4W  C23  C   CR6   0  -0.024  -3.5567  -2.0136   1.2331
 N4W  C24  C   CR16  0  -0.252  -2.7266  -1.0222   0.7394
 N4W  C27  C   CR6   0   0.559   1.9074   2.3971   0.6789
 N4W  C29  C   CR16  0  -0.010   2.3297   3.6169  -1.1703
 N4W  C30  C   CR16  0  -0.380   2.3880   4.7780  -0.4184
 N4W  C4   C   CR6   0  -0.257   2.8391  -2.0775   0.0286
 N4W  C5   C   CR16  0  -0.249   2.7898  -0.8570   0.6972
 N4W  C6   C   CR6   0   0.238   1.6983  -0.0295   0.5538
 N4W  N7   N   NH1   0  -0.698  -0.4467   0.4154  -0.3923
 N4W  S8   S   S     0   1.212   4.2465  -3.1150   0.1999
 N4W  O9   O   OS    0  -0.677   3.8480  -4.4915  -0.0959
 N4W  O10  O   OS    0  -0.676   4.8837  -2.8323   1.4865
 N4W  N14  N   N     0  -0.444  -2.2331   2.3391  -0.3447
 N4W  CL1  CL  CL    0  -0.128  -3.8498  -2.0970   2.9407
 N4W  N26  N   NH1   0  -0.757   1.6346   1.1932   1.2538
 N4W  N28  N   N     0  -0.435   2.0958   2.4267  -0.6385
 N4W  C31  C   CR16  0  -0.018   2.1847   4.6217   0.9441
 N4W  N32  N   N     0  -0.449   1.9432   3.4472   1.5023
 N4W  H1   H   HCR6  0   0.280  -0.1186  -1.9720  -1.5794
 N4W  H2   H   HCR6  0   0.280   1.8146  -3.4059  -1.3235
 N4W  H3   H   HCH3  0   0.291   5.6236  -1.5427  -0.9293
 N4W  H4   H   HCH3  0   0.304   6.2466  -3.2118  -1.0312
 N4W  H5   H   HCH3  0   0.291   4.8737  -2.7090  -2.0532
 N4W  H6   H   HCH1  0   0.293  -1.3098  -0.1299  -2.2043
 N4W  H7   H   HCR6  0   0.269  -2.7608   4.1773   0.4073
 N4W  H8   H   HCR6  0   0.275  -4.4587   4.6382  -1.3438
 N4W  H9   H   HCR6  0   0.279  -4.8232   2.9203  -3.1299
 N4W  H10  H   HCR6  0   0.271  -3.4776   0.8295  -3.0657
 N4W  H11  H   HCR6  0   0.264  -2.8886  -1.8367  -2.5429
 N4W  H12  H   HCR6  0   0.271  -4.3697  -3.5881  -1.6294
 N4W  H13  H   HCR6  0   0.281  -4.8004  -3.7137   0.8001
 N4W  H14  H   HCR6  0   0.272  -2.2645  -0.3120   1.4136
 N4W  H15  H   HCR6  0   0.272   2.4803   3.6432  -2.2440
 N4W  H16  H   HCR6  0   0.274   2.5838   5.7417  -0.8629
 N4W  H17  H   HCR6  0   0.281   3.6023  -0.5408   1.3393
 N4W  H18  H   HNH1  0   0.403  -0.4973   1.2437   0.1841
 N4W  H19  H   HNH1  0   0.403   1.6385   1.1712   2.2622
 N4W  H20  H   HCR6  0   0.274   2.2180   5.4751   1.6124

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
 N4W  CL1  C23  single    1.735  0.020  1.735
 N4W  C23  C22  aromatic  1.387  0.020  1.387
 N4W  C23  C24  aromatic  1.384  0.020  1.384
 N4W  C22  C21  aromatic  1.386  0.020  1.386
 N4W  C24  C19  aromatic  1.390  0.020  1.390
 N4W  C21  C20  aromatic  1.388  0.020  1.388
 N4W  O10  S8   double    1.463  0.020  1.463
 N4W  C19  C20  aromatic  1.389  0.020  1.389
 N4W  C19  C12  single    1.522  0.020  1.522
 N4W  C11  S8   single    1.780  0.020  1.780
 N4W  C3   C2   aromatic  1.379  0.020  1.379
 N4W  C3   C4   aromatic  1.389  0.020  1.389
 N4W  C2   C1   aromatic  1.406  0.020  1.406
 N4W  S8   C4   single    1.757  0.020  1.757
 N4W  S8   O9   double    1.463  0.020  1.463
 N4W  C12  C13  single    1.519  0.020  1.519
 N4W  C12  N7   single    1.432  0.020  1.432
 N4W  C18  C13  aromatic  1.390  0.020  1.390
 N4W  C18  C17  aromatic  1.384  0.020  1.384
 N4W  C4   C5   aromatic  1.392  0.020  1.392
 N4W  C13  N14  aromatic  1.323  0.020  1.323
 N4W  C1   N7   single    1.347  0.020  1.347
 N4W  C1   C6   aromatic  1.417  0.020  1.417
 N4W  C17  C16  aromatic  1.389  0.020  1.389
 N4W  C5   C6   aromatic  1.377  0.020  1.377
 N4W  C6   N26  single    1.410  0.020  1.410
 N4W  N14  C15  aromatic  1.329  0.020  1.329
 N4W  C16  C15  aromatic  1.384  0.020  1.384
 N4W  N26  C27  single    1.362  0.020  1.362
 N4W  C27  N32  aromatic  1.335  0.020  1.335
 N4W  C27  N28  aromatic  1.331  0.020  1.331
 N4W  N32  C31  aromatic  1.323  0.020  1.323
 N4W  N28  C29  aromatic  1.324  0.020  1.324
 N4W  C31  C30  aromatic  1.386  0.020  1.386
 N4W  C29  C30  aromatic  1.384  0.020  1.384
 N4W  C2   H1   single    0.930  0.020  1.080
 N4W  C3   H2   single    0.930  0.020  1.080
 N4W  C11  H3   single    0.970  0.020  1.090
 N4W  C11  H4   single    0.970  0.020  1.090
 N4W  C11  H5   single    0.970  0.020  1.090
 N4W  C12  H6   single    0.970  0.020  1.090
 N4W  C15  H7   single    0.930  0.020  1.080
 N4W  C16  H8   single    0.930  0.020  1.080
 N4W  C17  H9   single    0.930  0.020  1.080
 N4W  C18  H10  single    0.930  0.020  1.080
 N4W  C20  H11  single    0.930  0.020  1.080
 N4W  C21  H12  single    0.930  0.020  1.080
 N4W  C22  H13  single    0.930  0.020  1.080
 N4W  C24  H14  single    0.930  0.020  1.080
 N4W  C29  H15  single    0.930  0.020  1.080
 N4W  C30  H16  single    0.930  0.020  1.080
 N4W  C5   H17  single    0.930  0.020  1.080
 N4W  N7   H18  single    0.860  0.020  1.020
 N4W  N26  H19  single    0.860  0.020  1.020
 N4W  C31  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
 N4W  N7   C1   C6   119.39  3.000
 N4W  C6   C1   C2   118.07  3.000
 N4W  N7   C1   C2   122.54  3.000
 N4W  H1   C2   C3   118.52  3.000
 N4W  H1   C2   C1   120.49  3.000
 N4W  C3   C2   C1   120.98  3.000
 N4W  H2   C3   C4   120.87  3.000
 N4W  H2   C3   C2   119.04  3.000
 N4W  C4   C3   C2   120.08  3.000
 N4W  H5   C11  H4   110.03  3.000
 N4W  H5   C11  H3   110.29  3.000
 N4W  H4   C11  H3   110.09  3.000
 N4W  H5   C11  S8   109.35  3.000
 N4W  H4   C11  S8   107.53  3.000
 N4W  H3   C11  S8   109.50  3.000
 N4W  H6   C12  N7   110.02  3.000
 N4W  H6   C12  C19  108.06  3.000
 N4W  N7   C12  C19  113.44  3.000
 N4W  H6   C12  C13  107.70  3.000
 N4W  N7   C12  C13  108.61  3.000
 N4W  C19  C12  C13  108.85  3.000
 N4W  N14  C13  C18  122.68  3.000
 N4W  N14  C13  C12  116.94  3.000
 N4W  C18  C13  C12  120.36  3.000
 N4W  H7   C15  N14  116.45  3.000
 N4W  H7   C15  C16  120.57  3.000
 N4W  N14  C15  C16  122.98  3.000
 N4W  H8   C16  C17  121.44  3.000
 N4W  H8   C16  C15  120.38  3.000
 N4W  C17  C16  C15  118.18  3.000
 N4W  H9   C17  C18  120.34  3.000
 N4W  H9   C17  C16  120.70  3.000
 N4W  C18  C17  C16  118.95  3.000
 N4W  H10  C18  C17  120.95  3.000
 N4W  H10  C18  C13  120.58  3.000
 N4W  C17  C18  C13  118.47  3.000
 N4W  C24  C19  C20  119.71  3.000
 N4W  C20  C19  C12  120.47  3.000
 N4W  C24  C19  C12  119.79  3.000
 N4W  H11  C20  C21  119.79  3.000
 N4W  H11  C20  C19  119.93  3.000
 N4W  C21  C20  C19  120.27  3.000
 N4W  H12  C21  C22  119.43  3.000
 N4W  H12  C21  C20  120.07  3.000
 N4W  C22  C21  C20  120.49  3.000
 N4W  H13  C22  C23  120.66  3.000
 N4W  H13  C22  C21  120.73  3.000
 N4W  C23  C22  C21  118.60  3.000
 N4W  CL1  C23  C24  119.14  3.000
 N4W  C24  C23  C22  121.65  3.000
 N4W  CL1  C23  C22  119.21  3.000
 N4W  H14  C24  C23  120.25  3.000
 N4W  H14  C24  C19  120.49  3.000
 N4W  C23  C24  C19  119.26  3.000
 N4W  N32  C27  N28  126.10  3.000
 N4W  N28  C27  N26  117.77  3.000
 N4W  N32  C27  N26  116.13  3.000
 N4W  H15  C29  N28  116.34  3.000
 N4W  H15  C29  C30  120.77  3.000
 N4W  N28  C29  C30  122.89  3.000
 N4W  H16  C30  C31  122.14  3.000
 N4W  H16  C30  C29  122.20  3.000
 N4W  C31  C30  C29  115.66  3.000
 N4W  S8   C4   C5   119.94  3.000
 N4W  C5   C4   C3   120.04  3.000
 N4W  S8   C4   C3   120.00  3.000
 N4W  H17  C5   C6   118.75  3.000
 N4W  H17  C5   C4   120.94  3.000
 N4W  C6   C5   C4   120.31  3.000
 N4W  N26  C6   C5   120.33  3.000
 N4W  N26  C6   C1   119.15  3.000
 N4W  C5   C6   C1   120.50  3.000
 N4W  H18  N7   C12  115.25  3.000
 N4W  H18  N7   C1   119.36  3.000
 N4W  C12  N7   C1   125.09  3.000
 N4W  O10  S8   O9   118.56  3.000
 N4W  O9   S8   C4   108.52  3.000
 N4W  O10  S8   C4   108.69  3.000
 N4W  O9   S8   C11  107.69  3.000
 N4W  C4   S8   C11  104.68  3.000
 N4W  O10  S8   C11  107.84  3.000
 N4W  C15  N14  C13  118.74  3.000
 N4W  H19  N26  C6   118.50  3.000
 N4W  H19  N26  C27  116.14  3.000
 N4W  C6   N26  C27  123.22  3.000
 N4W  C29  N28  C27  116.25  3.000
 N4W  H20  C31  N32  116.38  3.000
 N4W  H20  C31  C30  120.82  3.000
 N4W  N32  C31  C30  122.79  3.000
 N4W  C31  N32  C27  116.30  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
 N4W  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 N4W  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 N4W  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 N4W  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 N4W  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 N4W  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 N4W  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 N4W  CONST_08  C16  C15  N14  C13     0.00   0.0  0
 N4W  CONST_09  C18  C13  N14  C15     0.00   0.0  0
 N4W  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 N4W  CONST_11  N14  C13  C18  C17     0.00   0.0  0
 N4W  CONST_12  N14  C15  C16  C17     0.00   0.0  0
 N4W  CONST_13  C22  C23  C24  C19     0.00   0.0  0
 N4W  CONST_14  C22  C21  C20  C19     0.00   0.0  0
 N4W  CONST_15  C23  C22  C21  C20     0.00   0.0  0
 N4W  CONST_16  C23  C24  C19  C20     0.00   0.0  0
 N4W  CONST_17  C24  C23  C22  C21     0.00   0.0  0
 N4W  CONST_18  C24  C19  C20  C21     0.00   0.0  0
 N4W  CONST_19  C30  C31  N32  C27     0.00   0.0  0
 N4W  CONST_20  C30  C29  N28  C27     0.00   0.0  0
 N4W  CONST_21  N32  C27  N28  C29     0.00   0.0  0
 N4W  CONST_22  N32  C31  C30  C29     0.00   0.0  0
 N4W  CONST_23  C31  N32  C27  N28     0.00   0.0  0
 N4W  CONST_24  C31  C30  C29  N28     0.00   0.0  0
 N4W  CONST_25  S8   C4   C3   C2    180.00   0.0  0
 N4W  CONST_26  N26  C6   C1   C2    180.00   0.0  0
 N4W  CONST_27  N7   C1   C2   C3    180.00   0.0  0
 N4W  CONST_28  C23  C24  C19  C12   180.00   0.0  0
 N4W  CONST_29  C21  C20  C19  C12   180.00   0.0  0
 N4W  CONST_30  C17  C18  C13  C12   180.00   0.0  0
 N4W  CONST_31  C15  N14  C13  C12   180.00   0.0  0
 N4W  CONST_32  CL1  C23  C24  C19   180.00   0.0  0
 N4W  CONST_33  CL1  C23  C22  C21   180.00   0.0  0
 N4W  CONST_34  N26  C27  N28  C29   180.00   0.0  0
 N4W  CONST_35  N26  C6   C5   C4    180.00   0.0  0
 N4W  CONST_36  N7   C1   C6   C5    180.00   0.0  0
 N4W  CONST_37  S8   C4   C5   C6    180.00   0.0  0
 N4W  CONST_38  C31  N32  C27  N26   180.00   0.0  0
 N4W  CONST_39  H2   C3   C2   C1    180.00   0.0  0
 N4W  CONST_40  H17  C5   C6   C1    180.00   0.0  0
 N4W  CONST_41  H9   C17  C18  C13   180.00   0.0  0
 N4W  CONST_42  H7   C15  N14  C13   180.00   0.0  0
 N4W  CONST_43  H10  C18  C17  C16   180.00   0.0  0
 N4W  CONST_44  H8   C16  C17  C18   180.00   0.0  0
 N4W  CONST_45  H12  C21  C20  C19   180.00   0.0  0
 N4W  CONST_46  H13  C22  C21  C20   180.00   0.0  0
 N4W  CONST_47  H14  C24  C19  C20   180.00   0.0  0
 N4W  CONST_48  H11  C20  C21  C22   180.00   0.0  0
 N4W  CONST_49  H20  C31  N32  C27   180.00   0.0  0
 N4W  CONST_50  H15  C29  N28  C27   180.00   0.0  0
 N4W  CONST_51  H1   C2   C3   C4    180.00   0.0  0
 N4W  CONST_52  H16  C30  C29  N28   180.00   0.0  0
 N4W  CONST_53  C12  N7   C1   C2      0.00   0.0  0
 N4W  CONST_54  C6   C1   N7   C12   180.00   0.0  0
 N4W  CONST_55  H18  N7   C1   C2    180.00   0.0  0
 N4W  Var_01    C27  N26  C6   C1    -80.24  30.0  2
 N4W  Var_02    N32  C27  N26  C6   -173.11  30.0  2
 N4W  Var_03    O10  S8   C4   C3   -155.20  30.0  2
 N4W  Var_04    H3   C11  S8   C4     61.15  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
 N4W  chir_01  C12  C19  C13  N7  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
 N4W  plan-1  C1   0.020
 N4W  plan-1  C2   0.020
 N4W  plan-1  C3   0.020
 N4W  plan-1  C4   0.020
 N4W  plan-1  C5   0.020
 N4W  plan-1  C6   0.020
 N4W  plan-1  N7   0.020
 N4W  plan-1  S8   0.020
 N4W  plan-1  N26  0.020
 N4W  plan-1  H1   0.020
 N4W  plan-1  H2   0.020
 N4W  plan-1  H17  0.020
 N4W  plan-2  C12  0.020
 N4W  plan-2  C13  0.020
 N4W  plan-2  C15  0.020
 N4W  plan-2  C16  0.020
 N4W  plan-2  C17  0.020
 N4W  plan-2  C18  0.020
 N4W  plan-2  N14  0.020
 N4W  plan-2  H7   0.020
 N4W  plan-2  H8   0.020
 N4W  plan-2  H9   0.020
 N4W  plan-2  H10  0.020
 N4W  plan-3  C12  0.020
 N4W  plan-3  C19  0.020
 N4W  plan-3  C20  0.020
 N4W  plan-3  C21  0.020
 N4W  plan-3  C22  0.020
 N4W  plan-3  C23  0.020
 N4W  plan-3  C24  0.020
 N4W  plan-3  CL1  0.020
 N4W  plan-3  H11  0.020
 N4W  plan-3  H12  0.020
 N4W  plan-3  H13  0.020
 N4W  plan-3  H14  0.020
 N4W  plan-4  C27  0.020
 N4W  plan-4  C29  0.020
 N4W  plan-4  C30  0.020
 N4W  plan-4  N26  0.020
 N4W  plan-4  N28  0.020
 N4W  plan-4  C31  0.020
 N4W  plan-4  N32  0.020
 N4W  plan-4  H15  0.020
 N4W  plan-4  H16  0.020
 N4W  plan-4  H20  0.020
 N4W  plan-5  C1   0.020
 N4W  plan-5  C12  0.020
 N4W  plan-5  N7   0.020
 N4W  plan-5  H18  0.020

