# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:18:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2R,3R)-3-[(5-bromo-2-{[4-(S-cyclopropylsulfonimidoyl)phenyl]amino}pyrimidin-4-yl)oxy]butan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C)Oc1nc(Nc2ccc(cc2)[S@](=N)(=O)C3CC3)ncc1Br
#
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
 6AF  6AF  (2R,3R)-3-[(5-bromo-2-{[4-(S-cyclopropylsulfonimidoyl)phenyl]amino}pyrimidin-4-yl)oxy]butan-2-ol  ligand  47  26  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6AF
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
 6AF  C5   C   CR6   0   0.631   0.9036   0.0012   0.6427
 6AF  C7   C   CR16  0   0.029   1.9827  -1.6730   1.6925
 6AF  C10  C   CR16  0  -0.298  -2.0649  -0.7887   1.0396
 6AF  C13  C   CR16  0  -0.221  -3.8326   1.1315   0.0636
 6AF  C20  C   CH2   0  -0.470  -6.6837  -0.0895  -1.9711
 6AF  C22  C   CH1   0  -0.001   4.3372   1.7955  -0.5464
 6AF  C26  C   CH3   0  -0.679   4.1822   1.4837  -2.0220
 6AF  C19  C   CH2   0  -0.468  -7.8735  -0.7234  -1.3294
 6AF  C18  C   CH1   0  -0.404  -6.5045  -0.9640  -0.7745
 6AF  N16  N   N     0  -0.848  -6.8264   1.0607   0.8355
 6AF  O17  O   OS    0  -0.687  -6.2675  -1.3199   1.8066
 6AF  C12  C   CR6   0  -0.162  -4.3171  -0.0259   0.6630
 6AF  C14  C   CR16  0  -0.345  -2.4731   1.3225  -0.0520
 6AF  C11  C   CR16  0  -0.247  -3.4332  -0.9773   1.1480
 6AF  C9   C   CR6   0   0.386  -1.5658   0.3677   0.4312
 6AF  N8   N   NH1   0  -0.767  -0.2259   0.6593   0.2563
 6AF  N4   N   N     0  -0.515   2.0318   0.5943   0.2432
 6AF  N6   N   N     0  -0.479   0.8247  -1.1135   1.3495
 6AF  C2   C   CR6   0  -0.334   3.2001  -1.1422   1.3415
 6AF  BR1  BR  BR    0  -0.010   4.8156  -1.9374   1.8455
 6AF  C3   C   CR6   0   0.637   3.1726   0.0418   0.5791
 6AF  O21  O   O2    0  -0.452   4.3159   0.5725   0.2177
 6AF  C23  C   CH1   0   0.040   5.6313   2.5165  -0.2027
 6AF  C25  C   CH3   0  -0.693   5.7578   2.8155   1.2842
 6AF  O24  O   OH1   0  -0.669   6.7136   1.7520  -0.6834
 6AF  H1   H   HCR6  0   0.292   1.9245  -2.5850   2.2759
 6AF  H2   H   HCR6  0   0.296  -1.3946  -1.5373   1.4273
 6AF  H3   H   HCR6  0   0.277  -4.5122   1.8891  -0.3030
 6AF  H5   H   HCH2  0   0.273  -6.5577   0.9768  -1.8388
 6AF  H6   H   HCH1  0   0.254   3.5136   2.4344  -0.2193
 6AF  H7   H   HCH3  0   0.243   3.1983   1.0646  -2.2300
 6AF  H8   H   HCH3  0   0.238   4.2767   2.4015  -2.6034
 6AF  H9   H   HCH3  0   0.240   4.9400   0.7831  -2.3690
 6AF  H10  H   HCH2  0   0.276  -8.5390  -0.0808  -0.7696
 6AF  H11  H   HCH2  0   0.280  -8.3462  -1.5661  -1.8156
 6AF  H12  H   HCH1  0   0.326  -6.0536  -1.9422  -0.8986
 6AF  H13  H   H     0   0.366  -6.5152   1.6349   1.6122
 6AF  H16  H   HCR6  0   0.282  -2.1028   2.2289  -0.5153
 6AF  H17  H   HCR6  0   0.277  -3.7992  -1.8797   1.6182
 6AF  H18  H   HNH1  0   0.418  -0.0315   1.5070  -0.2559
 6AF  H19  H   HCH1  0   0.212   5.5654   3.4758  -0.7374
 6AF  H20  H   HCH3  0   0.236   6.6405   3.4288   1.4736
 6AF  H21  H   HCH3  0   0.227   4.8929   3.3744   1.6449
 6AF  H22  H   HCH3  0   0.234   5.8467   1.9021   1.8725
 6AF  H23  H   HOH1  0   0.453   7.5213   2.2534  -0.5370
 6AF  S15  S   S     0   1.050  -6.0725  -0.2713   0.7873
 6AF  H4   H   HCH2  0   0.277  -6.3222  -0.4823  -2.9117

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
 6AF  C7   N6   aromatic  1.331  0.020  1.331
 6AF  C7   C2   aromatic  1.374  0.020  1.374
 6AF  BR1  C2   single    1.870  0.020  1.870
 6AF  N6   C5   aromatic  1.322  0.020  1.322
 6AF  C2   C3   aromatic  1.408  0.020  1.408
 6AF  C5   N8   single    1.363  0.020  1.363
 6AF  C5   N4   aromatic  1.336  0.020  1.336
 6AF  C3   N4   aromatic  1.311  0.020  1.311
 6AF  C3   O21  single    1.311  0.020  1.311
 6AF  N8   C9   single    1.382  0.020  1.382
 6AF  O21  C22  single    1.442  0.020  1.442
 6AF  C25  C23  single    1.522  0.020  1.522
 6AF  C9   C10  aromatic  1.399  0.020  1.399
 6AF  C9   C14  aromatic  1.403  0.020  1.403
 6AF  C10  C11  aromatic  1.385  0.020  1.385
 6AF  C22  C23  single    1.521  0.020  1.521
 6AF  C22  C26  single    1.516  0.020  1.516
 6AF  C23  O24  single    1.410  0.020  1.410
 6AF  C14  C13  aromatic  1.378  0.020  1.378
 6AF  C11  C12  aromatic  1.386  0.020  1.386
 6AF  C13  C12  aromatic  1.391  0.020  1.391
 6AF  C12  S15  single    1.777  0.020  1.777
 6AF  N16  S15  double    1.531  0.020  1.531
 6AF  S15  O17  double    1.475  0.020  1.475
 6AF  S15  C18  single    1.762  0.020  1.762
 6AF  C18  C19  single    1.497  0.020  1.497
 6AF  C18  C20  single    1.493  0.020  1.493
 6AF  C19  C20  single    1.493  0.020  1.493
 6AF  C7   H1   single    0.930  0.020  1.080
 6AF  C10  H2   single    0.930  0.020  1.080
 6AF  C13  H3   single    0.930  0.020  1.080
 6AF  C20  H4   single    0.970  0.020  1.090
 6AF  C20  H5   single    0.970  0.020  1.090
 6AF  C22  H6   single    0.970  0.020  1.090
 6AF  C26  H7   single    0.970  0.020  1.090
 6AF  C26  H8   single    0.970  0.020  1.090
 6AF  C26  H9   single    0.970  0.020  1.090
 6AF  C19  H10  single    0.970  0.020  1.090
 6AF  C19  H11  single    0.970  0.020  1.090
 6AF  C18  H12  single    0.970  0.020  1.090
 6AF  N16  H13  single    0.890  0.020  1.040
 6AF  C14  H16  single    0.930  0.020  1.080
 6AF  C11  H17  single    0.930  0.020  1.080
 6AF  N8   H18  single    0.860  0.020  1.020
 6AF  C23  H19  single    0.970  0.020  1.090
 6AF  C25  H20  single    0.970  0.020  1.090
 6AF  C25  H21  single    0.970  0.020  1.090
 6AF  C25  H22  single    0.970  0.020  1.090
 6AF  O24  H23  single    0.850  0.020  0.980

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
 6AF  N6   C5   N4   125.78  3.000
 6AF  N4   C5   N8   113.62  3.000
 6AF  N6   C5   N8   120.60  3.000
 6AF  H1   C7   C2   120.67  3.000
 6AF  H1   C7   N6   116.46  3.000
 6AF  C2   C7   N6   122.87  3.000
 6AF  H2   C10  C9   120.60  3.000
 6AF  H2   C10  C11  119.46  3.000
 6AF  C9   C10  C11  119.93  3.000
 6AF  H3   C13  C14  119.64  3.000
 6AF  H3   C13  C12  120.67  3.000
 6AF  C14  C13  C12  119.69  3.000
 6AF  H5   C20  H4   115.17  3.000
 6AF  H5   C20  C18  117.73  3.000
 6AF  H4   C20  C18  116.37  3.000
 6AF  H5   C20  C19  117.31  3.000
 6AF  H4   C20  C19  119.08  3.000
 6AF  C18  C20  C19   60.16  3.000
 6AF  H6   C22  C23  107.25  3.000
 6AF  H6   C22  O21  109.04  3.000
 6AF  C23  C22  O21  107.15  3.000
 6AF  H6   C22  C26  109.55  3.000
 6AF  C23  C22  C26  113.86  3.000
 6AF  O21  C22  C26  109.86  3.000
 6AF  H9   C26  H8   108.13  3.000
 6AF  H9   C26  H7   108.67  3.000
 6AF  H8   C26  H7   107.47  3.000
 6AF  H9   C26  C22  111.80  3.000
 6AF  H8   C26  C22  109.69  3.000
 6AF  H7   C26  C22  110.93  3.000
 6AF  H11  C19  H10  115.26  3.000
 6AF  H11  C19  C18  116.18  3.000
 6AF  H10  C19  C18  117.81  3.000
 6AF  H11  C19  C20  119.06  3.000
 6AF  H10  C19  C20  117.43  3.000
 6AF  C18  C19  C20   59.91  3.000
 6AF  H12  C18  S15  110.74  3.000
 6AF  H12  C18  C19  118.88  3.000
 6AF  S15  C18  C19  119.32  3.000
 6AF  H12  C18  C20  119.12  3.000
 6AF  C19  C18  C20   59.93  3.000
 6AF  S15  C18  C20  120.63  3.000
 6AF  H13  N16  S15  111.43  3.000
 6AF  C11  C12  S15  120.71  3.000
 6AF  S15  C12  C13  119.30  3.000
 6AF  C11  C12  C13  119.99  3.000
 6AF  H16  C14  C9   119.72  3.000
 6AF  H16  C14  C13  119.29  3.000
 6AF  C9   C14  C13  120.99  3.000
 6AF  H17  C11  C12  120.60  3.000
 6AF  H17  C11  C10  118.81  3.000
 6AF  C12  C11  C10  120.59  3.000
 6AF  N8   C9   C14  116.09  3.000
 6AF  C14  C9   C10  118.79  3.000
 6AF  N8   C9   C10  125.12  3.000
 6AF  H18  N8   C9   115.34  3.000
 6AF  H18  N8   C5   112.94  3.000
 6AF  C9   N8   C5   131.72  3.000
 6AF  C3   N4   C5   118.10  3.000
 6AF  C7   N6   C5   116.12  3.000
 6AF  C3   C2   BR1  121.35  3.000
 6AF  C3   C2   C7   116.48  3.000
 6AF  BR1  C2   C7   122.17  3.000
 6AF  O21  C3   C2   118.19  3.000
 6AF  O21  C3   N4   121.16  3.000
 6AF  C2   C3   N4   120.65  3.000
 6AF  C3   O21  C22  120.14  3.000
 6AF  H19  C23  O24  110.68  3.000
 6AF  H19  C23  C25  107.97  3.000
 6AF  O24  C23  C25  112.08  3.000
 6AF  H19  C23  C22  104.63  3.000
 6AF  O24  C23  C22  108.61  3.000
 6AF  C25  C23  C22  112.62  3.000
 6AF  H22  C25  H21  108.39  3.000
 6AF  H22  C25  H20  108.14  3.000
 6AF  H21  C25  H20  107.21  3.000
 6AF  H22  C25  C23  111.68  3.000
 6AF  H21  C25  C23  110.96  3.000
 6AF  H20  C25  C23  110.31  3.000
 6AF  H23  O24  C23  108.07  3.000
 6AF  C12  S15  O17  106.09  3.000
 6AF  O17  S15  N16  122.10  3.000
 6AF  C12  S15  N16  111.62  3.000
 6AF  O17  S15  C18  107.49  3.000
 6AF  N16  S15  C18  104.42  3.000
 6AF  C12  S15  C18  103.56  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
 6AF  CONST_01  C2   C7   N6   C5      0.00   0.0  0
 6AF  CONST_02  C2   C3   N4   C5      0.00   0.0  0
 6AF  CONST_03  N4   C5   N6   C7      0.00   0.0  0
 6AF  CONST_04  N4   C3   C2   C7      0.00   0.0  0
 6AF  CONST_05  C13  C14  C9   C10     0.00   0.0  0
 6AF  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 6AF  CONST_07  C9   C10  C11  C12     0.00   0.0  0
 6AF  CONST_08  C9   C14  C13  C12     0.00   0.0  0
 6AF  CONST_09  C11  C10  C9   C14     0.00   0.0  0
 6AF  CONST_10  C11  C12  C13  C14     0.00   0.0  0
 6AF  CONST_11  C3   C2   C7   N6      0.00   0.0  0
 6AF  CONST_12  C3   N4   C5   N6      0.00   0.0  0
 6AF  CONST_13  O21  C3   N4   C5    180.00   0.0  0
 6AF  CONST_14  N8   C5   N6   C7    180.00   0.0  0
 6AF  CONST_15  O21  C3   C2   C7    180.00   0.0  0
 6AF  CONST_16  S15  C12  C11  C10   180.00   0.0  0
 6AF  CONST_17  N8   C9   C14  C13   180.00   0.0  0
 6AF  CONST_18  C14  C13  C12  S15   180.00   0.0  0
 6AF  CONST_19  N8   C9   C10  C11   180.00   0.0  0
 6AF  CONST_20  C3   N4   C5   N8    180.00   0.0  0
 6AF  CONST_21  BR1  C2   C3   N4    180.00   0.0  0
 6AF  CONST_22  BR1  C2   C7   N6    180.00   0.0  0
 6AF  CONST_23  H1   C7   N6   C5    180.00   0.0  0
 6AF  CONST_24  H16  C14  C9   C10   180.00   0.0  0
 6AF  CONST_25  H17  C11  C12  C13   180.00   0.0  0
 6AF  CONST_26  H2   C10  C11  C12   180.00   0.0  0
 6AF  CONST_27  H3   C13  C12  C11   180.00   0.0  0
 6AF  Var_01    C10  C9   N8   C5     -3.26  30.0  2
 6AF  Var_02    C18  S15  C12  C13    84.30  30.0  2
 6AF  Var_03    C12  S15  C18  C20   -80.51  30.0  3
 6AF  Var_04    S15  C18  C19  C20   110.49  30.0  1
 6AF  Var_05    N6   C5   N8   C9     -2.10  30.0  1
 6AF  Var_06    C2   C3   O21  C22  -179.06  30.0  2

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
 6AF  chir_01  C22  O21  C23  C26  negativ
 6AF  chir_04  C23  O24  C22  C25  negativ
 6AF  chir_05  S15  N16  O17  C18  both
 6AF  chir_06  C18  S15  C19  C20  both

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
 6AF  plan-1  C5   0.020
 6AF  plan-1  C7   0.020
 6AF  plan-1  N8   0.020
 6AF  plan-1  N4   0.020
 6AF  plan-1  N6   0.020
 6AF  plan-1  C2   0.020
 6AF  plan-1  BR1  0.020
 6AF  plan-1  C3   0.020
 6AF  plan-1  O21  0.020
 6AF  plan-1  H1   0.020
 6AF  plan-2  C10  0.020
 6AF  plan-2  C13  0.020
 6AF  plan-2  C12  0.020
 6AF  plan-2  C14  0.020
 6AF  plan-2  C11  0.020
 6AF  plan-2  C9   0.020
 6AF  plan-2  N8   0.020
 6AF  plan-2  H2   0.020
 6AF  plan-2  H3   0.020
 6AF  plan-2  H16  0.020
 6AF  plan-2  H17  0.020
 6AF  plan-2  S15  0.020

