# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:41:37 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N~4~-(5-chloro-1,3-benzodioxol-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(Nc3c(Cl)ccc4OCOc34)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
 7X5  7X5  N~4~-(5-chloro-1,3-benzodioxol-4-yl)-N~2~-[3-(methylsulfonyl)phenyl]pyrimidine-2,4-diamine  ligand  43  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7X5
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
 7X5  N1    N   NH1   0  -0.773  13.6035   7.5619  11.6623
 7X5  C7    C   CR6   0   0.606  13.1075   6.3419  12.0260
 7X5  N2    N   N     0  -0.485  14.0051   5.5357  12.5947
 7X5  C8    C   CR16  0  -0.028  13.5523   4.3351  12.9355
 7X5  C9    C   CR16  0  -0.426  12.2545   3.9157  12.7421
 7X5  C10   C   CR6   0   0.550  11.3989   4.8533  12.1503
 7X5  N3    N   NH1   0  -0.731  10.0911   4.6133  11.8850
 7X5  C11   C   CR6   0   0.280   9.4026   3.4428  12.2059
 7X5  C12   C   CR56  0   0.293   9.2224   3.0364  13.5100
 7X5  O3    O   O     0  -0.468   9.6517   3.6490  14.6300
 7X5  C13   C   CH2   0   0.067   9.3773   2.7476  15.7002
 7X5  O4    O   O     0  -0.481   8.4988   1.7559  15.1856
 7X5  C14   C   CR56  0   0.317   8.5243   1.8863  13.8394
 7X5  C15   C   CR16  0  -0.352   7.9387   1.0945  12.8847
 7X5  C16   C   CR16  0  -0.250   8.0888   1.4911  11.5513
 7X5  C17   C   CR6   0  -0.125   8.8071   2.6255  11.2266
 7X5  CL1   CL  CL    0  -0.105   8.9934   3.0752   9.5675
 7X5  N4    N   N     0  -0.528  11.8359   6.0603  11.7947
 7X5  C1    C   CH3   0  -0.789   9.1880   9.0318   8.3581
 7X5  O1    O   OS    0  -0.668   9.0896  11.3895   9.5289
 7X5  O2    O   OS    0  -0.668   8.7256   9.3341  10.9306
 7X5  C2    C   CR6   0  -0.183  11.1714   9.8896  10.1302
 7X5  C3    C   CR16  0  -0.268  11.9989  10.9112   9.6988
 7X5  C4    C   CR16  0  -0.234  13.3596  10.7820   9.9485
 7X5  C5    C   CR16  0  -0.331  13.8576   9.6668  10.5932
 7X5  C6    C   CR6   0   0.387  13.0102   8.6335  11.0179
 7X5  C18   C   CR16  0  -0.293  11.6398   8.7610  10.7882
 7X5  H1    H   HNH1  0   0.411  14.5907   7.6570  11.8481
 7X5  H8    H   HCR6  0   0.273  14.2725   3.6619  13.3871
 7X5  H9    H   HCR6  0   0.278  11.9437   2.9201  13.0181
 7X5  H3    H   HNH1  0   0.399   9.6145   5.3133  11.3356
 7X5  H131  H   HCH2  0   0.243  10.3088   2.2834  16.0383
 7X5  H132  H   HCH2  0   0.254   8.8942   3.2841  16.5156
 7X5  H15   H   HCR6  0   0.288   7.3816   0.2038  13.1386
 7X5  H16   H   HCR6  0   0.287   7.6464   0.8939  10.7666
 7X5  H1C1  H   HCH3  0   0.297   9.7581   9.4705   7.5427
 7X5  H1C2  H   HCH3  0   0.291   9.5126   8.0097   8.5386
 7X5  H1C3  H   HCH3  0   0.312   8.1240   9.0498   8.1236
 7X5  HA    H   HCR6  0   0.281  11.6106  11.7821   9.1904
 7X5  H18   H   HCR6  0   0.304  10.9641   7.9892  11.1198
 7X5  H4    H   HCR6  0   0.274  14.0407  11.5611   9.6338
 7X5  H5    H   HCR6  0   0.283  14.9234   9.5884  10.7727
 7X5  S1    S   S     0   1.213   9.4230   9.9993   9.8314

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
 7X5  N1   C7    single    1.366  0.020  1.366
 7X5  N1   C6    single    1.384  0.020  1.384
 7X5  C7   N2    aromatic  1.334  0.020  1.334
 7X5  C7   N4    aromatic  1.323  0.020  1.323
 7X5  N2   C8    aromatic  1.328  0.020  1.328
 7X5  C8   C9    aromatic  1.377  0.020  1.377
 7X5  C9   C10   aromatic  1.401  0.020  1.401
 7X5  C10  N3    single    1.356  0.020  1.356
 7X5  C10  N4    aromatic  1.332  0.020  1.332
 7X5  N3   C11   single    1.395  0.020  1.395
 7X5  C11  C12   aromatic  1.378  0.020  1.378
 7X5  C11  C17   aromatic  1.408  0.020  1.408
 7X5  C12  O3    single    1.347  0.020  1.347
 7X5  C12  C14   aromatic  1.385  0.020  1.385
 7X5  O3   C13   single    1.426  0.020  1.426
 7X5  C13  O4    single    1.421  0.020  1.421
 7X5  O4   C14   single    1.353  0.020  1.353
 7X5  C14  C15   aromatic  1.372  0.020  1.372
 7X5  C15  C16   aromatic  1.399  0.020  1.399
 7X5  C16  C17   aromatic  1.381  0.020  1.381
 7X5  C17  CL1   single    1.729  0.020  1.729
 7X5  C1   S1    single    1.778  0.020  1.778
 7X5  S1   O1    double    1.461  0.020  1.461
 7X5  S1   O2    double    1.462  0.020  1.462
 7X5  S1   C2    single    1.777  0.020  1.777
 7X5  C2   C3    aromatic  1.384  0.020  1.384
 7X5  C2   C18   aromatic  1.388  0.020  1.388
 7X5  C3   C4    aromatic  1.389  0.020  1.389
 7X5  C4   C5    aromatic  1.381  0.020  1.381
 7X5  C5   C6    aromatic  1.402  0.020  1.402
 7X5  C6   C18   aromatic  1.395  0.020  1.395
 7X5  N1   H1    single    0.860  0.020  1.020
 7X5  C8   H8    single    0.930  0.020  1.080
 7X5  C9   H9    single    0.930  0.020  1.080
 7X5  N3   H3    single    0.860  0.020  1.020
 7X5  C13  H131  single    0.970  0.020  1.090
 7X5  C13  H132  single    0.970  0.020  1.090
 7X5  C15  H15   single    0.930  0.020  1.080
 7X5  C16  H16   single    0.930  0.020  1.080
 7X5  C1   H1C1  single    0.970  0.020  1.090
 7X5  C1   H1C2  single    0.970  0.020  1.090
 7X5  C1   H1C3  single    0.970  0.020  1.090
 7X5  C3   HA    single    0.930  0.020  1.080
 7X5  C18  H18   single    0.930  0.020  1.080
 7X5  C4   H4    single    0.930  0.020  1.080
 7X5  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
 7X5  H1    N1   C6    115.61  3.000
 7X5  H1    N1   C7    112.97  3.000
 7X5  C6    N1   C7    131.28  3.000
 7X5  N4    C7   N2    126.36  3.000
 7X5  N4    C7   N1    119.50  3.000
 7X5  N2    C7   N1    114.14  3.000
 7X5  C8    N2   C7    115.25  3.000
 7X5  H8    C8   C9    119.68  3.000
 7X5  H8    C8   N2    116.22  3.000
 7X5  C9    C8   N2    124.10  3.000
 7X5  H9    C9   C10   123.36  3.000
 7X5  H9    C9   C8    121.10  3.000
 7X5  C10   C9   C8    115.53  3.000
 7X5  N4    C10  N3    115.13  3.000
 7X5  N4    C10  C9    121.27  3.000
 7X5  N3    C10  C9    123.60  3.000
 7X5  H3    N3   C11   118.29  3.000
 7X5  H3    N3   C10   116.05  3.000
 7X5  C11   N3   C10   125.41  3.000
 7X5  C17   C11  C12   115.59  3.000
 7X5  C17   C11  N3    122.40  3.000
 7X5  C12   C11  N3    121.98  3.000
 7X5  C14   C12  O3    109.91  3.000
 7X5  C14   C12  C11   122.41  3.000
 7X5  O3    C12  C11   127.68  3.000
 7X5  C13   O3   C12   105.98  3.000
 7X5  H132  C13  H131  110.81  3.000
 7X5  H132  C13  O4    109.92  3.000
 7X5  H131  C13  O4    110.01  3.000
 7X5  H132  C13  O3    109.62  3.000
 7X5  H131  C13  O3    109.64  3.000
 7X5  O4    C13  O3    106.75  3.000
 7X5  C14   O4   C13   106.35  3.000
 7X5  C15   C14  O4    128.98  3.000
 7X5  C15   C14  C12   121.93  3.000
 7X5  O4    C14  C12   109.04  3.000
 7X5  H15   C15  C16   120.85  3.000
 7X5  H15   C15  C14   122.16  3.000
 7X5  C16   C15  C14   117.00  3.000
 7X5  H16   C16  C17   119.73  3.000
 7X5  H16   C16  C15   119.43  3.000
 7X5  C17   C16  C15   120.83  3.000
 7X5  CL1   C17  C16   119.68  3.000
 7X5  CL1   C17  C11   118.09  3.000
 7X5  C16   C17  C11   122.22  3.000
 7X5  C10   N4   C7    117.49  3.000
 7X5  H1C3  C1   H1C2  110.04  3.000
 7X5  H1C3  C1   H1C1  110.12  3.000
 7X5  H1C2  C1   H1C1  110.31  3.000
 7X5  H1C3  C1   S1    107.36  3.000
 7X5  H1C2  C1   S1    109.53  3.000
 7X5  H1C1  C1   S1    109.42  3.000
 7X5  C18   C2   C3    123.12  3.000
 7X5  C18   C2   S1    117.51  3.000
 7X5  C3    C2   S1    119.37  3.000
 7X5  HA    C3   C4    120.75  3.000
 7X5  HA    C3   C2    121.79  3.000
 7X5  C4    C3   C2    117.45  3.000
 7X5  H4    C4   C5    119.37  3.000
 7X5  H4    C4   C3    119.83  3.000
 7X5  C5    C4   C3    120.80  3.000
 7X5  H5    C5   C6    119.40  3.000
 7X5  H5    C5   C4    119.36  3.000
 7X5  C6    C5   C4    121.23  3.000
 7X5  C18   C6   C5    118.45  3.000
 7X5  C18   C6   N1    124.64  3.000
 7X5  C5    C6   N1    116.90  3.000
 7X5  H18   C18  C6    119.97  3.000
 7X5  H18   C18  C2    121.10  3.000
 7X5  C6    C18  C2    118.93  3.000
 7X5  C2    S1   O2    108.35  3.000
 7X5  C2    S1   O1    108.54  3.000
 7X5  O2    S1   O1    118.67  3.000
 7X5  C2    S1   C1    103.64  3.000
 7X5  O2    S1   C1    108.20  3.000
 7X5  O1    S1   C1    108.41  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
 7X5  CONST_01  C9    C8   N2   C7      0.00   0.0  0
 7X5  CONST_02  C9    C10  N4   C7      0.00   0.0  0
 7X5  CONST_03  C10   N4   C7   N2      0.00   0.0  0
 7X5  CONST_04  C10   C9   C8   N2      0.00   0.0  0
 7X5  CONST_05  N4    C7   N2   C8      0.00   0.0  0
 7X5  CONST_06  N4    C10  C9   C8      0.00   0.0  0
 7X5  CONST_07  C15   C14  C12  C11     0.00   0.0  0
 7X5  CONST_08  C15   C16  C17  C11     0.00   0.0  0
 7X5  CONST_09  C16   C17  C11  C12     0.00   0.0  0
 7X5  CONST_10  C16   C15  C14  C12     0.00   0.0  0
 7X5  CONST_11  C17   C11  C12  C14     0.00   0.0  0
 7X5  CONST_12  C17   C16  C15  C14     0.00   0.0  0
 7X5  CONST_13  C5    C4   C3   C2      0.00   0.0  0
 7X5  CONST_14  C5    C6   C18  C2      0.00   0.0  0
 7X5  CONST_15  C6    C18  C2   C3      0.00   0.0  0
 7X5  CONST_16  C6    C5   C4   C3      0.00   0.0  0
 7X5  CONST_17  C18   C2   C3   C4      0.00   0.0  0
 7X5  CONST_18  C18   C6   C5   C4      0.00   0.0  0
 7X5  CONST_19  C8    N2   C7   N1    180.00   0.0  0
 7X5  CONST_20  C10   N4   C7   N1    180.00   0.0  0
 7X5  CONST_21  C4    C5   C6   N1    180.00   0.0  0
 7X5  CONST_22  C2    C18  C6   N1    180.00   0.0  0
 7X5  CONST_23  N3    C10  N4   C7    180.00   0.0  0
 7X5  CONST_24  N3    C10  C9   C8    180.00   0.0  0
 7X5  CONST_25  O3    C12  C11  N3      0.00   0.0  0
 7X5  CONST_26  C14   C12  C11  N3    180.00   0.0  0
 7X5  CONST_27  C16   C17  C11  N3    180.00   0.0  0
 7X5  CONST_28  CL1   C17  C11  C12   180.00   0.0  0
 7X5  CONST_29  CL1   C17  C16  C15   180.00   0.0  0
 7X5  CONST_30  C4    C3   C2   S1    180.00   0.0  0
 7X5  CONST_31  C6    C18  C2   S1    180.00   0.0  0
 7X5  CONST_32  H8    C8   N2   C7    180.00   0.0  0
 7X5  CONST_33  H9    C9   C8   N2    180.00   0.0  0
 7X5  CONST_34  H16   C16  C17  C11   180.00   0.0  0
 7X5  CONST_35  H15   C15  C14  C12   180.00   0.0  0
 7X5  CONST_36  H4    C4   C3   C2    180.00   0.0  0
 7X5  CONST_37  H18   C18  C2   C3    180.00   0.0  0
 7X5  CONST_38  H5    C5   C4   C3    180.00   0.0  0
 7X5  CONST_39  HA    C3   C4   C5    180.00   0.0  0
 7X5  Var_01    O4    C13  O3   C12   -13.58  30.0  1
 7X5  Var_02    C14   C12  O3   C13     8.44  30.0  1
 7X5  Var_03    C15   C14  O4   C13   173.84  30.0  1
 7X5  Var_04    C5    C6   N1   C7   -169.76  30.0  2
 7X5  Var_05    C6    N1   C7   N2    177.56  30.0  1
 7X5  Var_06    C11   N3   C10  C9      2.81  30.0  2
 7X5  Var_07    C12   C11  N3   C10    63.02  30.0  2
 7X5  Var_08    C3    C2   S1   C1     97.24  30.0  2
 7X5  Var_09    H1C1  C1   S1   C2    -61.07  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
 7X5  plan-1  N1   0.020
 7X5  plan-1  C7   0.020
 7X5  plan-1  N2   0.020
 7X5  plan-1  C8   0.020
 7X5  plan-1  C9   0.020
 7X5  plan-1  C10  0.020
 7X5  plan-1  N3   0.020
 7X5  plan-1  N4   0.020
 7X5  plan-1  H8   0.020
 7X5  plan-1  H9   0.020
 7X5  plan-2  N1   0.020
 7X5  plan-2  C2   0.020
 7X5  plan-2  C3   0.020
 7X5  plan-2  C4   0.020
 7X5  plan-2  C5   0.020
 7X5  plan-2  C6   0.020
 7X5  plan-2  C18  0.020
 7X5  plan-2  HA   0.020
 7X5  plan-2  H18  0.020
 7X5  plan-2  H4   0.020
 7X5  plan-2  H5   0.020
 7X5  plan-2  S1   0.020
 7X5  plan-3  N3   0.020
 7X5  plan-3  C11  0.020
 7X5  plan-3  C12  0.020
 7X5  plan-3  O3   0.020
 7X5  plan-3  O4   0.020
 7X5  plan-3  C14  0.020
 7X5  plan-3  C15  0.020
 7X5  plan-3  C16  0.020
 7X5  plan-3  C17  0.020
 7X5  plan-3  CL1  0.020
 7X5  plan-3  H15  0.020
 7X5  plan-3  H16  0.020

