# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:37:31 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N~4~-1H-indazol-4-yl-N~2~-[3-(methylsulfonyl)phenyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc(Nc2nccc(Nc3cccc4[nH]ncc34)n2)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
 X9F  X9F  N~4~-1H-indazol-4-yl-N~2~-[3-(methylsulfonyl)phenyl]pyrimidine-2,4-diamine  ligand  43  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X9F
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
 X9F  C7    C  CR6   0   0.627  -0.0311  -1.4693  -0.0351
 X9F  N2    N  N     0  -0.494  -0.2505  -2.7723  -0.0352
 X9F  C8    C  CR16  0   0.007   0.8450  -3.5381  -0.0586
 X9F  C9    C  CR16  0  -0.469   2.1187  -3.0392  -0.0800
 X9F  C10   C  CR6   0   0.580   2.2322  -1.6334  -0.0738
 X9F  N3    N  NH1   0  -0.781   3.4754  -1.0837  -0.0842
 X9F  C11   C  CR6   0   0.323   3.8921   0.2387  -0.0277
 X9F  C12   C  CR16  0  -0.347   3.0755   1.3572  -0.0202
 X9F  C13   C  CR16  0  -0.260   3.6268   2.6526   0.0462
 X9F  C14   C  CR16  0  -0.313   4.9776   2.8967   0.1062
 X9F  C15   C  CR56  0   0.424   5.7996   1.7633   0.0961
 X9F  N4    N  NR15  0  -0.547   7.1439   1.6266   0.1446
 X9F  N5    N  N     0  -0.227   7.5317   0.3513   0.1162
 X9F  C16   C  CR15  0  -0.125   6.4416  -0.3708   0.0480
 X9F  C17   C  CR56  0  -0.194   5.2877   0.4582   0.0301
 X9F  N6    N  N     0  -0.530   1.1600  -0.8630  -0.0547
 X9F  C1    C  CH3   0  -0.790  -5.7370   2.1243   1.8165
 X9F  O1    O  OS    0  -0.668  -6.9636   1.3174  -0.3687
 X9F  O2    O  OS    0  -0.668  -4.9003   2.7351  -0.6036
 X9F  C2    C  CR6   0  -0.189  -4.6291   0.2094   0.1090
 X9F  C3    C  CR16  0  -0.261  -5.2532  -1.0253   0.2169
 X9F  C4    C  CR16  0  -0.233  -4.4459  -2.1506   0.2407
 X9F  C5    C  CR16  0  -0.298  -3.0644  -2.0576   0.1617
 X9F  C6    C  CR6   0   0.394  -2.4476  -0.8063   0.0556
 X9F  N1    N  NH1   0  -0.777  -1.0811  -0.5953  -0.0170
 X9F  C18   C  CR16  0  -0.343  -3.2552   0.3363   0.0238
 X9F  H1    H  HNH1  0   0.415  -0.7914   0.3707  -0.0479
 X9F  H8    H  HCR6  0   0.274   0.6792  -4.6092  -0.0593
 X9F  H9    H  HCR6  0   0.283   2.9832  -3.6871  -0.0956
 X9F  H3    H  HNH1  0   0.422   4.2191  -1.7636  -0.1048
 X9F  H12   H  HCR6  0   0.288   2.0053   1.2499  -0.0624
 X9F  H13   H  HCR6  0   0.260   2.9399   3.4889   0.0498
 X9F  H14   H  HCR6  0   0.267   5.3785   3.8995   0.1588
 X9F  H4    H  HNR5  0   0.418   7.8341   2.3571   0.2026
 X9F  H16   H  HCR5  0   0.267   6.5119  -1.4481   0.0142
 X9F  H11C  H  HCH3  0   0.296  -6.1886   1.3071   2.3740
 X9F  H12C  H  HCH3  0   0.296  -4.7423   2.3395   2.1994
 X9F  H13C  H  HCH3  0   0.311  -6.3637   3.0134   1.8810
 X9F  HA    H  HCR6  0   0.281  -6.3286  -1.1135   0.2771
 X9F  H18   H  HCR6  0   0.294  -2.7983   1.3143  -0.0715
 X9F  HB    H  HCR6  0   0.272  -4.8985  -3.1299   0.3213
 X9F  H5    H  HCR6  0   0.300  -2.4632  -2.9518   0.1796
 X9F  S1    S  S     0   1.216  -5.6269   1.6791   0.0986

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
 X9F  C7   N2    aromatic  1.321  0.020  1.321
 X9F  C7   N6    aromatic  1.337  0.020  1.337
 X9F  C7   N1    single    1.366  0.020  1.366
 X9F  N2   C8    aromatic  1.337  0.020  1.337
 X9F  C8   C9    aromatic  1.368  0.020  1.368
 X9F  C9   C10   aromatic  1.410  0.020  1.410
 X9F  C10  N3    single    1.359  0.020  1.359
 X9F  C10  N6    aromatic  1.320  0.020  1.320
 X9F  N3   C11   single    1.388  0.020  1.388
 X9F  C11  C12   aromatic  1.385  0.020  1.385
 X9F  C11  C17   aromatic  1.414  0.020  1.414
 X9F  C12  C13   aromatic  1.409  0.020  1.409
 X9F  C13  C14   aromatic  1.374  0.020  1.374
 X9F  C14  C15   aromatic  1.400  0.020  1.400
 X9F  C15  N4    aromatic  1.352  0.020  1.352
 X9F  C15  C17   aromatic  1.403  0.020  1.403
 X9F  N4   N5    aromatic  1.333  0.020  1.333
 X9F  N5   C16   aromatic  1.309  0.020  1.309
 X9F  C16  C17   aromatic  1.421  0.020  1.421
 X9F  C1   S1    single    1.778  0.020  1.778
 X9F  S1   O1    double    1.461  0.020  1.461
 X9F  S1   O2    double    1.462  0.020  1.462
 X9F  S1   C2    single    1.776  0.020  1.776
 X9F  C2   C3    aromatic  1.388  0.020  1.388
 X9F  C2   C18   aromatic  1.382  0.020  1.382
 X9F  C3   C4    aromatic  1.385  0.020  1.385
 X9F  C4   C5    aromatic  1.387  0.020  1.387
 X9F  C5   C6    aromatic  1.399  0.020  1.399
 X9F  C6   N1    single    1.385  0.020  1.385
 X9F  C6   C18   aromatic  1.400  0.020  1.400
 X9F  N1   H1    single    0.860  0.020  1.020
 X9F  C8   H8    single    0.930  0.020  1.080
 X9F  C9   H9    single    0.930  0.020  1.080
 X9F  N3   H3    single    0.860  0.020  1.020
 X9F  C12  H12   single    0.930  0.020  1.080
 X9F  C13  H13   single    0.930  0.020  1.080
 X9F  C14  H14   single    0.930  0.020  1.080
 X9F  N4   H4    single    0.860  0.020  1.020
 X9F  C16  H16   single    0.930  0.020  1.080
 X9F  C1   H11C  single    0.970  0.020  1.090
 X9F  C1   H12C  single    0.970  0.020  1.090
 X9F  C1   H13C  single    0.970  0.020  1.090
 X9F  C3   HA    single    0.930  0.020  1.080
 X9F  C18  H18   single    0.930  0.020  1.080
 X9F  C4   HB    single    0.930  0.020  1.080
 X9F  C5   H5    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
 X9F  N1    C7   N6    113.26  3.000
 X9F  N1    C7   N2    120.21  3.000
 X9F  N6    C7   N2    126.53  3.000
 X9F  C8    N2   C7    115.39  3.000
 X9F  H8    C8   C9    120.19  3.000
 X9F  H8    C8   N2    116.15  3.000
 X9F  C9    C8   N2    123.66  3.000
 X9F  H9    C9   C10   122.24  3.000
 X9F  H9    C9   C8    121.77  3.000
 X9F  C10   C9   C8    116.00  3.000
 X9F  N6    C10  N3    120.45  3.000
 X9F  N6    C10  C9    121.08  3.000
 X9F  N3    C10  C9    118.46  3.000
 X9F  H3    N3   C11   114.97  3.000
 X9F  H3    N3   C10   113.72  3.000
 X9F  C11   N3   C10   131.27  3.000
 X9F  C17   C11  C12   117.16  3.000
 X9F  C17   C11  N3    116.48  3.000
 X9F  C12   C11  N3    126.36  3.000
 X9F  H12   C12  C13   118.84  3.000
 X9F  H12   C12  C11   120.36  3.000
 X9F  C13   C12  C11   120.79  3.000
 X9F  H13   C13  C14   119.12  3.000
 X9F  H13   C13  C12   117.52  3.000
 X9F  C14   C13  C12   123.36  3.000
 X9F  H14   C14  C15   122.24  3.000
 X9F  H14   C14  C13   122.10  3.000
 X9F  C15   C14  C13   115.66  3.000
 X9F  C17   C15  N4    105.68  3.000
 X9F  C17   C15  C14   122.61  3.000
 X9F  N4    C15  C14   131.70  3.000
 X9F  H4    N4   N5    119.73  3.000
 X9F  H4    N4   C15   127.62  3.000
 X9F  N5    N4   C15   112.65  3.000
 X9F  C16   N5   N4    106.64  3.000
 X9F  H16   C16  C17   129.37  3.000
 X9F  H16   C16  N5    119.84  3.000
 X9F  C17   C16  N5    110.80  3.000
 X9F  C16   C17  C15   104.22  3.000
 X9F  C16   C17  C11   135.36  3.000
 X9F  C15   C17  C11   120.42  3.000
 X9F  C10   N6   C7    117.33  3.000
 X9F  H13C  C1   H12C  110.11  3.000
 X9F  H13C  C1   H11C  110.12  3.000
 X9F  H12C  C1   H11C  110.37  3.000
 X9F  H13C  C1   S1    107.28  3.000
 X9F  H12C  C1   S1    109.46  3.000
 X9F  H11C  C1   S1    109.44  3.000
 X9F  C18   C2   C3    122.24  3.000
 X9F  C18   C2   S1    118.81  3.000
 X9F  C3    C2   S1    118.94  3.000
 X9F  HA    C3   C4    120.85  3.000
 X9F  HA    C3   C2    121.63  3.000
 X9F  C4    C3   C2    117.52  3.000
 X9F  HB    C4   C5    118.79  3.000
 X9F  HB    C4   C3    119.53  3.000
 X9F  C5    C4   C3    121.68  3.000
 X9F  H5    C5   C6    119.83  3.000
 X9F  H5    C5   C4    119.95  3.000
 X9F  C6    C5   C4    120.23  3.000
 X9F  C18   C6   N1    116.35  3.000
 X9F  C18   C6   C5    118.52  3.000
 X9F  N1    C6   C5    125.12  3.000
 X9F  H1    N1   C6    115.52  3.000
 X9F  H1    N1   C7    113.04  3.000
 X9F  C6    N1   C7    131.43  3.000
 X9F  H18   C18  C6    119.70  3.000
 X9F  H18   C18  C2    120.49  3.000
 X9F  C6    C18  C2    119.81  3.000
 X9F  C2    S1   O2    108.74  3.000
 X9F  C2    S1   O1    108.11  3.000
 X9F  O2    S1   O1    118.68  3.000
 X9F  C2    S1   C1    103.67  3.000
 X9F  O2    S1   C1    108.30  3.000
 X9F  O1    S1   C1    108.32  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
 X9F  CONST_01  C9    C8   N2   C7      0.00   0.0  0
 X9F  CONST_02  C9    C10  N6   C7      0.00   0.0  0
 X9F  CONST_03  C10   N6   C7   N2      0.00   0.0  0
 X9F  CONST_04  C10   C9   C8   N2      0.00   0.0  0
 X9F  CONST_05  N6    C7   N2   C8      0.00   0.0  0
 X9F  CONST_06  N6    C10  C9   C8      0.00   0.0  0
 X9F  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 X9F  CONST_08  C14   C15  C17  C11     0.00   0.0  0
 X9F  CONST_09  N4    C15  C17  C11   180.00   0.0  0
 X9F  CONST_10  N5    C16  C17  C11   180.00   0.0  0
 X9F  CONST_11  C15   C17  C11  C12     0.00   0.0  0
 X9F  CONST_12  C16   C17  C11  C12   180.00   0.0  0
 X9F  CONST_13  C15   C14  C13  C12     0.00   0.0  0
 X9F  CONST_14  C17   C11  C12  C13     0.00   0.0  0
 X9F  CONST_15  N4    C15  C14  C13   180.00   0.0  0
 X9F  CONST_16  C17   C15  C14  C13     0.00   0.0  0
 X9F  CONST_17  N5    N4   C15  C14   180.00   0.0  0
 X9F  CONST_18  C16   C17  C15  C14   180.00   0.0  0
 X9F  CONST_19  C16   N5   N4   C15     0.00   0.0  0
 X9F  CONST_20  N5    C16  C17  C15     0.00   0.0  0
 X9F  CONST_21  C16   C17  C15  N4      0.00   0.0  0
 X9F  CONST_22  C17   C16  N5   N4      0.00   0.0  0
 X9F  CONST_23  C17   C15  N4   N5      0.00   0.0  0
 X9F  CONST_24  C5    C4   C3   C2      0.00   0.0  0
 X9F  CONST_25  C5    C6   C18  C2      0.00   0.0  0
 X9F  CONST_26  C6    C18  C2   C3      0.00   0.0  0
 X9F  CONST_27  C6    C5   C4   C3      0.00   0.0  0
 X9F  CONST_28  C18   C2   C3   C4      0.00   0.0  0
 X9F  CONST_29  C18   C6   C5   C4      0.00   0.0  0
 X9F  CONST_30  N3    C10  N6   C7    180.00   0.0  0
 X9F  CONST_31  N1    C7   N2   C8    180.00   0.0  0
 X9F  CONST_32  N3    C10  C9   C8    180.00   0.0  0
 X9F  CONST_33  N1    C7   N6   C10   180.00   0.0  0
 X9F  CONST_34  C13   C12  C11  N3    180.00   0.0  0
 X9F  CONST_35  C15   C17  C11  N3    180.00   0.0  0
 X9F  CONST_36  C16   C17  C11  N3      0.00   0.0  0
 X9F  CONST_37  C4    C3   C2   S1    180.00   0.0  0
 X9F  CONST_38  C6    C18  C2   S1    180.00   0.0  0
 X9F  CONST_39  N1    C6   C18  C2    180.00   0.0  0
 X9F  CONST_40  N1    C6   C5   C4    180.00   0.0  0
 X9F  CONST_41  H8    C8   N2   C7    180.00   0.0  0
 X9F  CONST_42  H9    C9   C8   N2    180.00   0.0  0
 X9F  CONST_43  H13   C13  C12  C11   180.00   0.0  0
 X9F  CONST_44  H16   C16  C17  C11     0.00   0.0  0
 X9F  CONST_45  H14   C14  C13  C12   180.00   0.0  0
 X9F  CONST_46  H12   C12  C13  C14   180.00   0.0  0
 X9F  CONST_47  H4    N4   C15  C14     0.00   0.0  0
 X9F  CONST_48  HB    C4   C3   C2    180.00   0.0  0
 X9F  CONST_49  H18   C18  C2   C3    180.00   0.0  0
 X9F  CONST_50  H5    C5   C4   C3    180.00   0.0  0
 X9F  CONST_51  HA    C3   C4   C5    180.00   0.0  0
 X9F  Var_01    C5    C6   N1   C7      1.56  30.0  3
 X9F  Var_02    C6    N1   C7   N2      2.90  30.0  2
 X9F  Var_03    C11   N3   C10  C9   -177.04  30.0  2
 X9F  Var_04    C12   C11  N3   C10    -3.96  30.0  2
 X9F  Var_05    C3    C2   S1   C1     90.37  30.0  2
 X9F  Var_06    H11C  C1   S1   C2    -59.13  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
 X9F  plan-1  C7   0.020
 X9F  plan-1  N2   0.020
 X9F  plan-1  C8   0.020
 X9F  plan-1  C9   0.020
 X9F  plan-1  C10  0.020
 X9F  plan-1  N3   0.020
 X9F  plan-1  N6   0.020
 X9F  plan-1  N1   0.020
 X9F  plan-1  H8   0.020
 X9F  plan-1  H9   0.020
 X9F  plan-2  C2   0.020
 X9F  plan-2  C3   0.020
 X9F  plan-2  C4   0.020
 X9F  plan-2  C5   0.020
 X9F  plan-2  C6   0.020
 X9F  plan-2  N1   0.020
 X9F  plan-2  C18  0.020
 X9F  plan-2  HA   0.020
 X9F  plan-2  H18  0.020
 X9F  plan-2  HB   0.020
 X9F  plan-2  H5   0.020
 X9F  plan-2  S1   0.020
 X9F  plan-3  N3   0.020
 X9F  plan-3  C11  0.020
 X9F  plan-3  C12  0.020
 X9F  plan-3  C13  0.020
 X9F  plan-3  C14  0.020
 X9F  plan-3  C15  0.020
 X9F  plan-3  N4   0.020
 X9F  plan-3  N5   0.020
 X9F  plan-3  C16  0.020
 X9F  plan-3  C17  0.020
 X9F  plan-3  H12  0.020
 X9F  plan-3  H13  0.020
 X9F  plan-3  H14  0.020
 X9F  plan-3  H4   0.020
 X9F  plan-3  H16  0.020

