# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 04:41:31 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-2,5-dichloro-3-(hydroxymethyl)benzene-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(cn1)C#Cc2c(F)ccc(N[S](=O)(=O)c3cc(Cl)cc(CO)c3Cl)c2F
#
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
 KA4  KA4  N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-2,5-dichloro-3-(hydroxymethyl)benzene-1-sulfonamide  ligand  43  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KA4
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
 KA4  N1   N   NH2   0  -0.809   9.8762   0.0502  -1.1545
 KA4  N3   N   N     0  -0.443   7.7843  -0.8730  -1.1974
 KA4  C4   C   CR16  0  -0.031   6.5184  -0.7812  -0.8608
 KA4  C5   C   CR6   0  -0.288   5.9988   0.2959  -0.1356
 KA4  C6   C   CR16  0  -0.031   6.9299   1.2806   0.2101
 KA4  C8   C   CSP   0   0.162   4.6346   0.3823   0.2198
 KA4  C10  C   CR6   0  -0.513   2.0999   0.5340   0.8698
 KA4  C13  C   CR16  0  -0.441   0.1842   1.8320   1.6272
 KA4  C15  C   CR6   0   0.095  -0.0765  -0.5218   1.1507
 KA4  C20  C   CR6   0  -0.131  -3.0141  -0.8567  -0.3241
 KA4  C21  C   CR16  0  -0.230  -3.0555   0.1127  -1.3141
 KA4  C22  C   CR6   0   0.002  -4.1003   1.0178  -1.3083
 KA4  C24  C   CR16  0  -0.263  -5.0883   0.9719  -0.3405
 KA4  C28  C   CR6   0  -0.080  -4.0073  -0.9178   0.6498
 KA4  C2   C   CR6   0   0.572   8.5892   0.1304  -0.8123
 KA4  N7   N   N     0  -0.443   8.2003   1.2102  -0.1155
 KA4  C9   C   CSP   0   0.182   3.4680   0.4526   0.5213
 KA4  C11  C   CR6   0   0.549   1.5146   1.7308   1.2847
 KA4  F12  F   F     0  -0.282   2.2960   2.8063   1.3486
 KA4  C14  C   CR16  0  -0.240  -0.6058   0.6947   1.5637
 KA4  N16  N   NC1   0  -0.824  -0.8961  -1.6680   1.0762
 KA4  S17  S   S     0   1.377  -1.6498  -2.0031  -0.3568
 KA4  O18  O   OS    0  -0.634  -2.1388  -3.3635  -0.2686
 KA4  O19  O   OS    0  -0.624  -0.8109  -1.6125  -1.4749
 KA4  CL1  CL  CL    0  -0.100  -4.1671   2.2350  -2.5306
 KA4  C25  C   CR6   0   0.121  -5.0529   0.0031   0.6543
 KA4  O27  O   OH1   0  -0.661  -7.0433   0.9733   1.5086
 KA4  CL2  CL  CL    0  -0.076  -3.9584  -2.1082   1.8940
 KA4  C30  C   CR6   0   0.575   1.2649  -0.5769   0.8035
 KA4  F31  F   F     0  -0.270   1.7877  -1.7314   0.4098
 KA4  H1   H   HNH2  0   0.408  10.2234  -0.7554  -1.6441
 KA4  H2   H   HNH2  0   0.408  10.5289   0.7534  -0.8565
 KA4  H3   H   HCR6  0   0.275   5.8679  -1.5914  -1.1736
 KA4  H4   H   HCR6  0   0.276   6.6158   2.1529   0.7738
 KA4  H5   H   HCR6  0   0.299  -0.2276   2.7791   1.9466
 KA4  H6   H   HCR6  0   0.314  -2.2859   0.1665  -2.0702
 KA4  H7   H   HCR6  0   0.301  -5.8898   1.6959  -0.3561
 KA4  H8   H   HCH2  0   0.234  -6.5869  -1.0428   1.6923
 KA4  H9   H   HCH2  0   0.236  -5.6284   0.0340   2.6995
 KA4  H10  H   HCR6  0   0.293  -1.6487   0.7470   1.8453
 KA4  H11  H   HNC1  0   0.436  -0.6219  -2.4953   1.5957
 KA4  H12  H   HOH1  0   0.471  -7.6460   0.9885   2.2575
 KA4  C26  C   CH2   0  -0.172  -6.1146  -0.0518   1.7192

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
 KA4  CL1  C22  single    1.726  0.020  1.726
 KA4  C22  C21  aromatic  1.382  0.020  1.382
 KA4  C22  C24  aromatic  1.384  0.020  1.384
 KA4  C21  C20  aromatic  1.386  0.020  1.386
 KA4  C24  C25  aromatic  1.389  0.020  1.389
 KA4  O19  S17  double    1.451  0.020  1.451
 KA4  O27  C26  single    1.399  0.020  1.399
 KA4  O18  S17  double    1.448  0.020  1.448
 KA4  C25  C26  single    1.505  0.020  1.505
 KA4  C25  C28  aromatic  1.393  0.020  1.393
 KA4  C20  C28  aromatic  1.392  0.020  1.392
 KA4  C20  S17  single    1.782  0.020  1.782
 KA4  C28  CL2  single    1.723  0.020  1.723
 KA4  S17  N16  single    1.653  0.020  1.653
 KA4  N16  C15  single    1.411  0.020  1.411
 KA4  C14  C15  aromatic  1.389  0.020  1.389
 KA4  C14  C13  aromatic  1.386  0.020  1.386
 KA4  C15  C30  aromatic  1.387  0.020  1.387
 KA4  C13  C11  aromatic  1.378  0.020  1.378
 KA4  C30  F31  single    1.327  0.020  1.327
 KA4  C30  C10  aromatic  1.391  0.020  1.391
 KA4  C11  C10  aromatic  1.395  0.020  1.395
 KA4  C11  F12  single    1.331  0.020  1.331
 KA4  C10  C9   single    1.414  0.020  1.414
 KA4  C9   C8   triple    1.207  0.020  1.207
 KA4  C8   C5   single    1.412  0.020  1.412
 KA4  C5   C4   aromatic  1.399  0.020  1.399
 KA4  C5   C6   aromatic  1.399  0.020  1.399
 KA4  C4   N3   aromatic  1.313  0.020  1.313
 KA4  C6   N7   aromatic  1.313  0.020  1.313
 KA4  N3   C2   aromatic  1.343  0.020  1.343
 KA4  N7   C2   aromatic  1.343  0.020  1.343
 KA4  C2   N1   single    1.334  0.020  1.334
 KA4  N1   H1   single    0.860  0.020  1.020
 KA4  N1   H2   single    0.860  0.020  1.020
 KA4  C4   H3   single    0.930  0.020  1.080
 KA4  C6   H4   single    0.930  0.020  1.080
 KA4  C13  H5   single    0.930  0.020  1.080
 KA4  C21  H6   single    0.930  0.020  1.080
 KA4  C24  H7   single    0.930  0.020  1.080
 KA4  C26  H8   single    0.970  0.020  1.090
 KA4  C26  H9   single    0.970  0.020  1.090
 KA4  C14  H10  single    0.930  0.020  1.080
 KA4  N16  H11  single    0.890  0.020  1.040
 KA4  O27  H12  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
 KA4  H2   N1   H1   118.77  3.000
 KA4  H2   N1   C2   120.57  3.000
 KA4  H1   N1   C2   120.44  3.000
 KA4  C2   N3   C4   116.88  3.000
 KA4  H3   C4   C5   120.12  3.000
 KA4  H3   C4   N3   116.86  3.000
 KA4  C5   C4   N3   123.02  3.000
 KA4  C8   C5   C6   122.53  3.000
 KA4  C6   C5   C4   115.03  3.000
 KA4  C8   C5   C4   122.44  3.000
 KA4  H4   C6   N7   116.86  3.000
 KA4  H4   C6   C5   120.11  3.000
 KA4  N7   C6   C5   123.02  3.000
 KA4  C9   C8   C5   180.00  3.000
 KA4  C30  C10  C11  116.57  3.000
 KA4  C11  C10  C9   121.91  3.000
 KA4  C30  C10  C9   121.53  3.000
 KA4  H5   C13  C14  121.02  3.000
 KA4  H5   C13  C11  120.38  3.000
 KA4  C14  C13  C11  118.60  3.000
 KA4  C30  C15  N16  121.09  3.000
 KA4  C30  C15  C14  118.53  3.000
 KA4  N16  C15  C14  120.37  3.000
 KA4  S17  C20  C28  122.05  3.000
 KA4  S17  C20  C21  117.36  3.000
 KA4  C28  C20  C21  120.59  3.000
 KA4  H6   C21  C22  120.59  3.000
 KA4  H6   C21  C20  120.89  3.000
 KA4  C22  C21  C20  118.52  3.000
 KA4  CL1  C22  C24  119.40  3.000
 KA4  C24  C22  C21  121.39  3.000
 KA4  CL1  C22  C21  119.21  3.000
 KA4  H7   C24  C25  119.78  3.000
 KA4  H7   C24  C22  119.83  3.000
 KA4  C25  C24  C22  120.39  3.000
 KA4  CL2  C28  C25  118.40  3.000
 KA4  CL2  C28  C20  121.01  3.000
 KA4  C25  C28  C20  120.57  3.000
 KA4  N7   C2   N3   125.18  3.000
 KA4  N7   C2   N1   117.45  3.000
 KA4  N3   C2   N1   117.37  3.000
 KA4  C2   N7   C6   116.87  3.000
 KA4  C10  C9   C8   180.00  3.000
 KA4  F12  C11  C13  119.72  3.000
 KA4  F12  C11  C10  117.46  3.000
 KA4  C13  C11  C10  122.82  3.000
 KA4  H10  C14  C15  119.15  3.000
 KA4  H10  C14  C13  119.86  3.000
 KA4  C15  C14  C13  120.99  3.000
 KA4  H11  N16  S17  113.68  3.000
 KA4  H11  N16  C15  118.58  3.000
 KA4  S17  N16  C15  118.37  3.000
 KA4  O19  S17  O18  119.66  3.000
 KA4  O18  S17  N16  106.95  3.000
 KA4  O19  S17  N16  110.47  3.000
 KA4  N16  S17  C20  101.69  3.000
 KA4  O18  S17  C20  110.16  3.000
 KA4  O19  S17  C20  106.47  3.000
 KA4  C28  C25  C26  120.51  3.000
 KA4  C28  C25  C24  118.54  3.000
 KA4  C26  C25  C24  120.95  3.000
 KA4  H12  O27  C26  108.08  3.000
 KA4  F31  C30  C15  119.34  3.000
 KA4  F31  C30  C10  118.18  3.000
 KA4  C15  C30  C10  122.48  3.000
 KA4  H9   C26  H8   106.43  3.000
 KA4  H9   C26  O27  111.79  3.000
 KA4  H8   C26  O27  111.84  3.000
 KA4  H9   C26  C25  108.46  3.000
 KA4  H8   C26  C25  108.61  3.000
 KA4  O27  C26  C25  109.58  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
 KA4  CONST_01  C6   C5   C4   N3     0.00   0.0  0
 KA4  CONST_02  C6   N7   C2   N3     0.00   0.0  0
 KA4  CONST_03  N7   C6   C5   C4     0.00   0.0  0
 KA4  CONST_04  N7   C2   N3   C4     0.00   0.0  0
 KA4  CONST_05  C2   N3   C4   C5     0.00   0.0  0
 KA4  CONST_06  C2   N7   C6   C5     0.00   0.0  0
 KA4  CONST_07  C14  C15  C30  C10    0.00   0.0  0
 KA4  CONST_08  C14  C13  C11  C10    0.00   0.0  0
 KA4  CONST_09  C30  C15  C14  C13    0.00   0.0  0
 KA4  CONST_10  C30  C10  C11  C13    0.00   0.0  0
 KA4  CONST_11  C11  C13  C14  C15    0.00   0.0  0
 KA4  CONST_12  C11  C10  C30  C15    0.00   0.0  0
 KA4  CONST_13  C24  C22  C21  C20    0.00   0.0  0
 KA4  CONST_14  C24  C25  C28  C20    0.00   0.0  0
 KA4  CONST_15  C25  C24  C22  C21    0.00   0.0  0
 KA4  CONST_16  C25  C28  C20  C21    0.00   0.0  0
 KA4  CONST_17  C28  C20  C21  C22    0.00   0.0  0
 KA4  CONST_18  C28  C25  C24  C22    0.00   0.0  0
 KA4  CONST_19  C4   N3   C2   N1   180.00   0.0  0
 KA4  CONST_20  C6   N7   C2   N1   180.00   0.0  0
 KA4  CONST_21  C8   C5   C4   N3   180.00   0.0  0
 KA4  CONST_22  N7   C6   C5   C8   180.00   0.0  0
 KA4  CONST_23  N16  C15  C30  C10  180.00   0.0  0
 KA4  CONST_24  N16  C15  C14  C13  180.00   0.0  0
 KA4  CONST_25  C9   C10  C11  C13  180.00   0.0  0
 KA4  CONST_26  C9   C10  C30  C15  180.00   0.0  0
 KA4  CONST_27  CL1  C22  C21  C20  180.00   0.0  0
 KA4  CONST_28  C26  C25  C28  C20  180.00   0.0  0
 KA4  CONST_29  CL2  C28  C20  C21  180.00   0.0  0
 KA4  CONST_30  S17  C20  C21  C22  180.00   0.0  0
 KA4  CONST_31  C26  C25  C24  C22  180.00   0.0  0
 KA4  CONST_32  CL2  C28  C25  C24  180.00   0.0  0
 KA4  CONST_33  F31  C30  C10  C11  180.00   0.0  0
 KA4  CONST_34  C14  C13  C11  F12  180.00   0.0  0
 KA4  CONST_35  C30  C10  C11  F12  180.00   0.0  0
 KA4  CONST_36  F31  C30  C15  C14  180.00   0.0  0
 KA4  CONST_37  C25  C28  C20  S17  180.00   0.0  0
 KA4  CONST_38  C25  C24  C22  CL1  180.00   0.0  0
 KA4  CONST_39  H4   C6   C5   C4   180.00   0.0  0
 KA4  CONST_40  H3   C4   C5   C6   180.00   0.0  0
 KA4  CONST_41  H5   C13  C11  C10  180.00   0.0  0
 KA4  CONST_42  H7   C24  C22  C21  180.00   0.0  0
 KA4  CONST_43  H6   C21  C22  C24  180.00   0.0  0
 KA4  CONST_44  H10  C14  C13  C11  180.00   0.0  0
 KA4  CONST_47  H1   N1   C2   N3     0.00   0.0  0
 KA4  CONST_48  H2   N1   C2   N3   180.00   0.0  0
 KA4  Var_01    C20  S17  N16  C15  -78.28  30.0  1
 KA4  Var_02    O19  S17  C20  C21    1.52  30.0  2
 KA4  Var_03    O27  C26  C25  C24    0.07  30.0  2

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
 KA4  plan-1  N1   0.020
 KA4  plan-1  N3   0.020
 KA4  plan-1  C4   0.020
 KA4  plan-1  C5   0.020
 KA4  plan-1  C6   0.020
 KA4  plan-1  C8   0.020
 KA4  plan-1  C2   0.020
 KA4  plan-1  N7   0.020
 KA4  plan-1  C9   0.020
 KA4  plan-1  H3   0.020
 KA4  plan-1  H4   0.020
 KA4  plan-2  C20  0.020
 KA4  plan-2  C21  0.020
 KA4  plan-2  C22  0.020
 KA4  plan-2  C24  0.020
 KA4  plan-2  C28  0.020
 KA4  plan-2  S17  0.020
 KA4  plan-2  CL1  0.020
 KA4  plan-2  C25  0.020
 KA4  plan-2  CL2  0.020
 KA4  plan-2  H6   0.020
 KA4  plan-2  H7   0.020
 KA4  plan-2  C26  0.020
 KA4  plan-3  C8   0.020
 KA4  plan-3  C10  0.020
 KA4  plan-3  C13  0.020
 KA4  plan-3  C15  0.020
 KA4  plan-3  C9   0.020
 KA4  plan-3  C11  0.020
 KA4  plan-3  F12  0.020
 KA4  plan-3  C14  0.020
 KA4  plan-3  N16  0.020
 KA4  plan-3  C30  0.020
 KA4  plan-3  F31  0.020
 KA4  plan-3  H5   0.020
 KA4  plan-3  H10  0.020
 KA4  plan-4  N1   0.020
 KA4  plan-4  C2   0.020
 KA4  plan-4  H1   0.020
 KA4  plan-4  H2   0.020
 KA4  plan-5  C15  0.020
 KA4  plan-5  N16  0.020
 KA4  plan-5  S17  0.020
 KA4  plan-5  H11  0.020

