# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:46:11 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-5-chloro-2-methoxypyridine-3-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(Cl)cc1[S](=O)(=O)Nc2ccc(F)c(C#Cc3cnc(N)nc3)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
 KA7  KA7  N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-5-chloro-2-methoxypyridine-3-sulfonamide  ligand  42  30  .  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_KA7
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
 KA7  C4   C   CR16  0  -0.440    0.1182   2.0189  -1.3799
 KA7  C5   C   CR16  0  -0.059    3.6564   0.1828   1.2474
 KA7  C6   C   CR16  0  -0.032   -6.6116   1.2678  -0.0540
 KA7  C7   C   CR16  0  -0.031   -6.2074  -0.8975   0.7921
 KA7  C8   C   CR16  0   0.000    5.6884   0.7588   0.1388
 KA7  C10  C   CR6   0  -0.512   -1.7690   0.6378  -0.7039
 KA7  C13  C   CR6   0   0.570   -0.9072  -0.4543  -0.6894
 KA7  C15  C   CR6   0  -0.132    4.7849   0.9842   1.1609
 KA7  C17  C   CR6   0   0.571   -8.2861  -0.0024   0.7849
 KA7  C1   C   CSP   0   0.161   -4.3092   0.3915  -0.1067
 KA7  C2   C   CSP   0   0.183   -3.1387   0.5053  -0.3784
 KA7  C3   C   CR16  0  -0.245    0.9338   0.8978  -1.3762
 KA7  C9   C   CR6   0  -0.287   -5.6799   0.2577   0.2064
 KA7  C11  C   CR6   0   0.104    0.4326  -0.3512  -1.0312
 KA7  C12  C   CR6   0   0.548   -1.2109   1.8686  -1.0513
 KA7  C14  C   CR6   0  -0.377    3.4881  -0.8105   0.3046
 KA7  C16  C   CR6   0   0.604    4.4611  -0.9725  -0.6993
 KA7  C18  C   CH3   0  -0.419    5.2302  -2.0670  -2.6433
 KA7  N19  N   N     0  -0.451    5.5213  -0.1969  -0.7648
 KA7  N20  N   N     0  -0.442   -7.8896   1.1517   0.2249
 KA7  N21  N   N     0  -0.442   -7.4812  -1.0358   1.0800
 KA7  N23  N   NC1   0  -0.825    1.2747  -1.4826  -1.0213
 KA7  O26  O   O2    0  -0.449    4.2758  -1.9236  -1.5918
 KA7  F27  F   F     0  -0.283   -2.0183   2.9268  -1.0642
 KA7  F28  F   F     0  -0.271   -1.4019  -1.6395  -0.3523
 KA7  S29  S   S     0   1.375    2.0678  -1.8599   0.3830
 KA7  CL   CL  CL    0  -0.101    5.0577   2.2459   2.3016
 KA7  H1   H   HCR6  0   0.299    0.5088   2.9909  -1.6467
 KA7  H2   H   HCR6  0   0.321    2.9258   0.3356   2.0300
 KA7  H3   H   HCR6  0   0.277   -6.2907   2.2001  -0.5070
 KA7  H4   H   HCR6  0   0.275   -5.5574  -1.7331   1.0301
 KA7  H5   H   HCR6  0   0.303    6.5772   1.3712   0.0449
 KA7  H6   H   HCR6  0   0.292    1.9755   0.9900  -1.6516
 KA7  H7   H   HCH3  0   0.242    5.2721  -1.1720  -3.2631
 KA7  H8   H   HCH3  0   0.243    6.2243  -2.2801  -2.2526
 KA7  H9   H   HCH3  0   0.257    4.8831  -2.9069  -3.2375
 KA7  H10  H   HNH2  0   0.407  -10.2353   0.5874   0.8182
 KA7  H11  H   HNH2  0   0.407   -9.9365  -0.9955   1.4440
 KA7  H12  H   HNC1  0   0.434    0.9984  -2.2961  -1.5606
 KA7  N22  N   NH2   0  -0.809   -9.5813  -0.1289   1.0803
 KA7  O24  O   OS    0  -0.637    2.4669  -3.2483   0.2766
 KA7  O25  O   OS    0  -0.630    1.2920  -1.4154   1.5277

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
 KA7  CL   C15  single    1.723  0.020  1.723
 KA7  C15  C8   aromatic  1.383  0.020  1.383
 KA7  C15  C5   aromatic  1.387  0.020  1.387
 KA7  C8   N19  aromatic  1.326  0.020  1.326
 KA7  C5   C14  aromatic  1.380  0.020  1.380
 KA7  O25  S29  double    1.452  0.020  1.452
 KA7  N19  C16  aromatic  1.315  0.020  1.315
 KA7  O24  S29  double    1.449  0.020  1.449
 KA7  C14  C16  aromatic  1.407  0.020  1.407
 KA7  C14  S29  single    1.768  0.020  1.768
 KA7  C16  O26  single    1.317  0.020  1.317
 KA7  S29  N23  single    1.656  0.020  1.656
 KA7  O26  C18  single    1.427  0.020  1.427
 KA7  N23  C11  single    1.410  0.020  1.410
 KA7  C3   C11  aromatic  1.389  0.020  1.389
 KA7  C3   C4   aromatic  1.386  0.020  1.386
 KA7  C11  C13  aromatic  1.387  0.020  1.387
 KA7  C4   C12  aromatic  1.377  0.020  1.377
 KA7  C13  F28  single    1.328  0.020  1.328
 KA7  C13  C10  aromatic  1.391  0.020  1.391
 KA7  C12  C10  aromatic  1.395  0.020  1.395
 KA7  C12  F27  single    1.331  0.020  1.331
 KA7  C10  C2   single    1.414  0.020  1.414
 KA7  C2   C1   triple    1.207  0.020  1.207
 KA7  C1   C9   single    1.412  0.020  1.412
 KA7  C9   C6   aromatic  1.399  0.020  1.399
 KA7  C9   C7   aromatic  1.399  0.020  1.399
 KA7  C6   N20  aromatic  1.313  0.020  1.313
 KA7  C7   N21  aromatic  1.313  0.020  1.313
 KA7  N20  C17  aromatic  1.343  0.020  1.343
 KA7  N21  C17  aromatic  1.343  0.020  1.343
 KA7  C17  N22  single    1.334  0.020  1.334
 KA7  C4   H1   single    0.930  0.020  1.080
 KA7  C5   H2   single    0.930  0.020  1.080
 KA7  C6   H3   single    0.930  0.020  1.080
 KA7  C7   H4   single    0.930  0.020  1.080
 KA7  C8   H5   single    0.930  0.020  1.080
 KA7  C3   H6   single    0.930  0.020  1.080
 KA7  C18  H7   single    0.970  0.020  1.090
 KA7  C18  H8   single    0.970  0.020  1.090
 KA7  C18  H9   single    0.970  0.020  1.090
 KA7  N22  H10  single    0.860  0.020  1.020
 KA7  N22  H11  single    0.860  0.020  1.020
 KA7  N23  H12  single    0.890  0.020  1.040

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
 KA7  H1   C4   C12  120.38  3.000
 KA7  H1   C4   C3   121.01  3.000
 KA7  C12  C4   C3   118.61  3.000
 KA7  H2   C5   C14  120.92  3.000
 KA7  H2   C5   C15  120.88  3.000
 KA7  C14  C5   C15  118.21  3.000
 KA7  H3   C6   N20  116.90  3.000
 KA7  H3   C6   C9   120.08  3.000
 KA7  N20  C6   C9   123.02  3.000
 KA7  H4   C7   N21  116.87  3.000
 KA7  H4   C7   C9   120.13  3.000
 KA7  N21  C7   C9   123.00  3.000
 KA7  H5   C8   N19  116.86  3.000
 KA7  H5   C8   C15  120.53  3.000
 KA7  N19  C8   C15  122.61  3.000
 KA7  C12  C10  C2   121.83  3.000
 KA7  C2   C10  C13  121.61  3.000
 KA7  C12  C10  C13  116.56  3.000
 KA7  F28  C13  C11  119.27  3.000
 KA7  F28  C13  C10  118.19  3.000
 KA7  C11  C13  C10  122.53  3.000
 KA7  CL   C15  C8   120.36  3.000
 KA7  C8   C15  C5   118.92  3.000
 KA7  CL   C15  C5   120.72  3.000
 KA7  N22  C17  N21  117.39  3.000
 KA7  N22  C17  N20  117.42  3.000
 KA7  N21  C17  N20  125.18  3.000
 KA7  C9   C1   C2   180.00  3.000
 KA7  C1   C2   C10  180.00  3.000
 KA7  H6   C3   C11  119.17  3.000
 KA7  H6   C3   C4   119.80  3.000
 KA7  C11  C3   C4   121.03  3.000
 KA7  C1   C9   C7   122.49  3.000
 KA7  C7   C9   C6   115.04  3.000
 KA7  C1   C9   C6   122.47  3.000
 KA7  N23  C11  C3   120.50  3.000
 KA7  C3   C11  C13  118.46  3.000
 KA7  N23  C11  C13  121.04  3.000
 KA7  F27  C12  C10  117.45  3.000
 KA7  F27  C12  C4   119.75  3.000
 KA7  C10  C12  C4   122.79  3.000
 KA7  S29  C14  C16  121.26  3.000
 KA7  S29  C14  C5   119.67  3.000
 KA7  C16  C14  C5   119.07  3.000
 KA7  O26  C16  N19  120.36  3.000
 KA7  O26  C16  C14  117.98  3.000
 KA7  N19  C16  C14  121.67  3.000
 KA7  H9   C18  H8   109.68  3.000
 KA7  H9   C18  H7   109.66  3.000
 KA7  H8   C18  H7   109.25  3.000
 KA7  H9   C18  O26  105.50  3.000
 KA7  H8   C18  O26  111.45  3.000
 KA7  H7   C18  O26  111.24  3.000
 KA7  C16  N19  C8   119.52  3.000
 KA7  C17  N20  C6   116.87  3.000
 KA7  C17  N21  C7   116.88  3.000
 KA7  H12  N23  S29  113.48  3.000
 KA7  H12  N23  C11  118.49  3.000
 KA7  S29  N23  C11  118.33  3.000
 KA7  C18  O26  C16  118.53  3.000
 KA7  O25  S29  O24  119.89  3.000
 KA7  O24  S29  N23  106.74  3.000
 KA7  O25  S29  N23  110.05  3.000
 KA7  N23  S29  C14  102.23  3.000
 KA7  O24  S29  C14  110.14  3.000
 KA7  O25  S29  C14  106.41  3.000
 KA7  H11  N22  H10  118.63  3.000
 KA7  H11  N22  C17  120.34  3.000
 KA7  H10  N22  C17  120.42  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
 KA7  CONST_01  C13  C11  C3   C4     0.00   0.0  0
 KA7  CONST_02  C13  C10  C12  C4     0.00   0.0  0
 KA7  CONST_03  N19  C8   C15  C5     0.00   0.0  0
 KA7  CONST_04  N19  C16  C14  C5     0.00   0.0  0
 KA7  CONST_05  N21  C7   C9   C6     0.00   0.0  0
 KA7  CONST_06  N21  C17  N20  C6     0.00   0.0  0
 KA7  CONST_07  N20  C6   C9   C7     0.00   0.0  0
 KA7  CONST_08  N20  C17  N21  C7     0.00   0.0  0
 KA7  CONST_09  C14  C5   C15  C8     0.00   0.0  0
 KA7  CONST_10  C14  C16  N19  C8     0.00   0.0  0
 KA7  CONST_11  C3   C11  C13  C10    0.00   0.0  0
 KA7  CONST_12  C3   C4   C12  C10    0.00   0.0  0
 KA7  CONST_13  C16  N19  C8   C15    0.00   0.0  0
 KA7  CONST_14  C16  C14  C5   C15    0.00   0.0  0
 KA7  CONST_15  C9   C6   N20  C17    0.00   0.0  0
 KA7  CONST_16  C9   C7   N21  C17    0.00   0.0  0
 KA7  CONST_17  C12  C4   C3   C11    0.00   0.0  0
 KA7  CONST_18  C12  C10  C13  C11    0.00   0.0  0
 KA7  CONST_19  N23  C11  C3   C4   180.00   0.0  0
 KA7  CONST_20  C2   C10  C12  C4   180.00   0.0  0
 KA7  CONST_21  O26  C16  C14  C5   180.00   0.0  0
 KA7  CONST_22  N22  C17  N20  C6   180.00   0.0  0
 KA7  CONST_23  N22  C17  N21  C7   180.00   0.0  0
 KA7  CONST_24  O26  C16  N19  C8   180.00   0.0  0
 KA7  CONST_25  N23  C11  C13  C10  180.00   0.0  0
 KA7  CONST_26  F27  C12  C10  C13  180.00   0.0  0
 KA7  CONST_27  S29  C14  C5   C15  180.00   0.0  0
 KA7  CONST_28  N20  C6   C9   C1   180.00   0.0  0
 KA7  CONST_29  N21  C7   C9   C1   180.00   0.0  0
 KA7  CONST_30  C11  C13  C10  C2   180.00   0.0  0
 KA7  CONST_31  F28  C13  C11  C3   180.00   0.0  0
 KA7  CONST_32  F27  C12  C4   C3   180.00   0.0  0
 KA7  CONST_33  F28  C13  C10  C12  180.00   0.0  0
 KA7  CONST_34  CL   C15  C5   C14  180.00   0.0  0
 KA7  CONST_35  CL   C15  C8   N19  180.00   0.0  0
 KA7  CONST_36  S29  C14  C16  N19  180.00   0.0  0
 KA7  CONST_37  H5   C8   C15  C5   180.00   0.0  0
 KA7  CONST_38  H4   C7   C9   C6   180.00   0.0  0
 KA7  CONST_39  H3   C6   C9   C7   180.00   0.0  0
 KA7  CONST_40  H2   C5   C15  C8   180.00   0.0  0
 KA7  CONST_41  H1   C4   C12  C10  180.00   0.0  0
 KA7  CONST_42  H6   C3   C11  C13  180.00   0.0  0
 KA7  CONST_46  H10  N22  C17  N20    0.00   0.0  0
 KA7  CONST_47  H11  N22  C17  N20  180.00   0.0  0
 KA7  Var_01    O25  S29  C14  C5     0.31  30.0  2
 KA7  Var_02    C14  S29  N23  C11  -83.51  30.0  3
 KA7  Var_03    N19  C16  O26  C18   -1.58  30.0  1
 KA7  Var_04    H7   C18  O26  C16  -61.87  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
 KA7  plan-1  C5   0.020
 KA7  plan-1  C8   0.020
 KA7  plan-1  C15  0.020
 KA7  plan-1  C14  0.020
 KA7  plan-1  C16  0.020
 KA7  plan-1  N19  0.020
 KA7  plan-1  O26  0.020
 KA7  plan-1  S29  0.020
 KA7  plan-1  CL   0.020
 KA7  plan-1  H2   0.020
 KA7  plan-1  H5   0.020
 KA7  plan-2  C4   0.020
 KA7  plan-2  C10  0.020
 KA7  plan-2  C13  0.020
 KA7  plan-2  C1   0.020
 KA7  plan-2  C2   0.020
 KA7  plan-2  C3   0.020
 KA7  plan-2  C11  0.020
 KA7  plan-2  C12  0.020
 KA7  plan-2  N23  0.020
 KA7  plan-2  F27  0.020
 KA7  plan-2  F28  0.020
 KA7  plan-2  H1   0.020
 KA7  plan-2  H6   0.020
 KA7  plan-3  C6   0.020
 KA7  plan-3  C7   0.020
 KA7  plan-3  C17  0.020
 KA7  plan-3  C1   0.020
 KA7  plan-3  C2   0.020
 KA7  plan-3  C9   0.020
 KA7  plan-3  N20  0.020
 KA7  plan-3  N21  0.020
 KA7  plan-3  H3   0.020
 KA7  plan-3  H4   0.020
 KA7  plan-3  N22  0.020
 KA7  plan-4  C11  0.020
 KA7  plan-4  N23  0.020
 KA7  plan-4  S29  0.020
 KA7  plan-4  H12  0.020
 KA7  plan-5  C17  0.020
 KA7  plan-5  H10  0.020
 KA7  plan-5  H11  0.020
 KA7  plan-5  N22  0.020

