# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 07:10:07 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[3-({4-[(5-chloro-1,3-benzodioxol-4-yl)amino]pyrimidin-2-yl}amino)phenyl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Nc1cccc(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
 7X6  7X6  N-[3-({4-[(5-chloro-1,3-benzodioxol-4-yl)amino]pyrimidin-2-yl}amino)phenyl]methanesulfonamide  ligand  45  29  .  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_7X6
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
 7X6  N2    N   NH1   0  -0.770  13.6037   7.6227  11.8773
 7X6  C7    C   CR6   0   0.603  13.0635   6.3996  12.1578
 7X6  N3    N   N     0  -0.485  13.9459   5.4735  12.5383
 7X6  C8    C   CR16  0  -0.031  13.4358   4.2698  12.7699
 7X6  C9    C   CR16  0  -0.425  12.0989   3.9543  12.6472
 7X6  C10   C   CR6   0   0.550  11.2636   5.0152  12.2764
 7X6  N4    N   NH1   0  -0.737   9.9189   4.9143  12.1220
 7X6  C11   C   CR6   0   0.289   9.1672   3.7518  12.2864
 7X6  C12   C   CR56  0   0.285   9.0911   3.0882  13.4915
 7X6  O3    O   O     0  -0.468   9.6823   3.4207  14.6562
 7X6  C13   C   CH2   0   0.065   9.4747   2.3112  15.5265
 7X6  O4    O   O     0  -0.481   8.4483   1.5209  14.9411
 7X6  C14   C   CR56  0   0.318   8.3381   1.9372  13.6586
 7X6  C15   C   CR16  0  -0.353   7.5849   1.4077  12.6419
 7X6  C16   C   CR16  0  -0.249   7.6211   2.0741  11.4124
 7X6  C17   C   CR6   0  -0.126   8.3974   3.2039  11.2425
 7X6  CL1   CL  CL    0  -0.106   8.4427   3.9837   9.6982
 7X6  N5    N   N     0  -0.529  11.7582   6.2267  12.0386
 7X6  C1    C   CH3   0  -0.799   9.4417   7.8067   8.6778
 7X6  S1    S   S     0   1.341   8.7441   8.9030   9.8880
 7X6  O1    O   OS    0  -0.652   8.6351   8.1729  11.1429
 7X6  O2    O   OS    0  -0.657   7.5544   9.5293   9.3381
 7X6  C2    C   CR6   0   0.393  11.1988   9.9915  10.3492
 7X6  C3    C   CR16  0  -0.353  12.0698  10.9879   9.9185
 7X6  C4    C   CR16  0  -0.238  13.4239  10.8535  10.1869
 7X6  C5    C   CR16  0  -0.366  13.9215   9.7396  10.8380
 7X6  C6    C   CR6   0   0.377  13.0454   8.7321  11.2563
 7X6  C18   C   CR16  0  -0.415  11.6755   8.8825  11.0391
 7X6  H2    H   HNH1  0   0.407  14.6060   7.6481  11.9907
 7X6  H8    H   HCR6  0   0.272  14.1411   3.5013  13.0672
 7X6  H9    H   HCR6  0   0.276  11.7467   2.9500  12.8236
 7X6  H4    H   HNH1  0   0.393   9.4588   5.7365  11.7553
 7X6  H131  H   HCH2  0   0.242  10.3971   1.7267  15.6051
 7X6  H132  H   HCH2  0   0.255   9.1566   2.6677  16.5047
 7X6  H15   H   HCR6  0   0.288   6.9836   0.5193  12.7728
 7X6  H16   H   HCR6  0   0.288   7.0435   1.6905  10.5835
 7X6  H1C1  H   HCH3  0   0.304   8.7404   6.9837   8.5504
 7X6  H1C2  H   HCH3  0   0.305   9.5648   8.3451   7.7414
 7X6  H1C3  H   HCH3  0   0.296  10.3989   7.4216   9.0232
 7X6  H1    H   HNC1  0   0.428   9.5907  10.9419   9.4975
 7X6  H3    H   HCR6  0   0.269  11.6990  11.8527   9.3832
 7X6  H18   H   HCR6  0   0.323  11.0082   8.1277  11.4145
 7X6  HA    H   HCR6  0   0.263  14.1073  11.6274   9.8629
 7X6  H5    H   HCR6  0   0.268  14.9860   9.6428  11.0143
 7X6  N1    N   NC1   0  -0.858   9.8272  10.1461  10.0790

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
 7X6  N2   C7    single    1.366  0.020  1.366
 7X6  N2   C6    single    1.389  0.020  1.389
 7X6  C7   N3    aromatic  1.335  0.020  1.335
 7X6  C7   N5    aromatic  1.322  0.020  1.322
 7X6  N3   C8    aromatic  1.328  0.020  1.328
 7X6  C8   C9    aromatic  1.379  0.020  1.379
 7X6  C9   C10   aromatic  1.400  0.020  1.400
 7X6  C10  N4    single    1.357  0.020  1.357
 7X6  C10  N5    aromatic  1.330  0.020  1.330
 7X6  N4   C11   single    1.394  0.020  1.394
 7X6  C11  C12   aromatic  1.378  0.020  1.378
 7X6  C11  C17   aromatic  1.408  0.020  1.408
 7X6  C12  O3    single    1.348  0.020  1.348
 7X6  C12  C14   aromatic  1.386  0.020  1.386
 7X6  O3   C13   single    1.425  0.020  1.425
 7X6  C13  O4    single    1.421  0.020  1.421
 7X6  O4   C14   single    1.353  0.020  1.353
 7X6  C14  C15   aromatic  1.372  0.020  1.372
 7X6  C15  C16   aromatic  1.399  0.020  1.399
 7X6  C16  C17   aromatic  1.381  0.020  1.381
 7X6  C17  CL1   single    1.731  0.020  1.731
 7X6  C1   S1    single    1.776  0.020  1.776
 7X6  S1   O1    double    1.456  0.020  1.456
 7X6  S1   O2    double    1.453  0.020  1.453
 7X6  S1   N1    single    1.660  0.020  1.660
 7X6  N1   C2    single    1.407  0.020  1.407
 7X6  C2   C3    aromatic  1.392  0.020  1.392
 7X6  C2   C18   aromatic  1.390  0.020  1.390
 7X6  C3   C4    aromatic  1.387  0.020  1.387
 7X6  C4   C5    aromatic  1.383  0.020  1.383
 7X6  C5   C6    aromatic  1.399  0.020  1.399
 7X6  C6   C18   aromatic  1.395  0.020  1.395
 7X6  N2   H2    single    0.860  0.020  1.020
 7X6  C8   H8    single    0.930  0.020  1.080
 7X6  C9   H9    single    0.930  0.020  1.080
 7X6  N4   H4    single    0.860  0.020  1.020
 7X6  C13  H131  single    0.970  0.020  1.090
 7X6  C13  H132  single    0.970  0.020  1.090
 7X6  C15  H15   single    0.930  0.020  1.080
 7X6  C16  H16   single    0.930  0.020  1.080
 7X6  C1   H1C1  single    0.970  0.020  1.090
 7X6  C1   H1C2  single    0.970  0.020  1.090
 7X6  C1   H1C3  single    0.970  0.020  1.090
 7X6  N1   H1    single    0.890  0.020  1.040
 7X6  C3   H3    single    0.930  0.020  1.080
 7X6  C18  H18   single    0.930  0.020  1.080
 7X6  C4   HA    single    0.930  0.020  1.080
 7X6  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
 7X6  H2    N2   C6    115.44  3.000
 7X6  H2    N2   C7    113.10  3.000
 7X6  C6    N2   C7    130.40  3.000
 7X6  N5    C7   N3    126.00  3.000
 7X6  N5    C7   N2    119.27  3.000
 7X6  N3    C7   N2    114.73  3.000
 7X6  C8    N3   C7    115.14  3.000
 7X6  H8    C8   C9    119.52  3.000
 7X6  H8    C8   N3    116.13  3.000
 7X6  C9    C8   N3    124.36  3.000
 7X6  H9    C9   C10   123.64  3.000
 7X6  H9    C9   C8    120.99  3.000
 7X6  C10   C9   C8    115.37  3.000
 7X6  N5    C10  N4    114.57  3.000
 7X6  N5    C10  C9    121.04  3.000
 7X6  N4    C10  C9    124.39  3.000
 7X6  H4    N4   C11   118.39  3.000
 7X6  H4    N4   C10   115.57  3.000
 7X6  C11   N4   C10   125.64  3.000
 7X6  C17   C11  C12   115.52  3.000
 7X6  C17   C11  N4    122.13  3.000
 7X6  C12   C11  N4    122.31  3.000
 7X6  C14   C12  O3    109.82  3.000
 7X6  C14   C12  C11   122.38  3.000
 7X6  O3    C12  C11   127.79  3.000
 7X6  C13   O3   C12   105.77  3.000
 7X6  H132  C13  H131  110.88  3.000
 7X6  H132  C13  O4    109.95  3.000
 7X6  H131  C13  O4    109.94  3.000
 7X6  H132  C13  O3    109.65  3.000
 7X6  H131  C13  O3    109.67  3.000
 7X6  O4    C13  O3    106.65  3.000
 7X6  C14   O4   C13   106.15  3.000
 7X6  C15   C14  O4    128.95  3.000
 7X6  C15   C14  C12   121.99  3.000
 7X6  O4    C14  C12   109.00  3.000
 7X6  H15   C15  C16   120.83  3.000
 7X6  H15   C15  C14   122.21  3.000
 7X6  C16   C15  C14   116.96  3.000
 7X6  H16   C16  C17   119.76  3.000
 7X6  H16   C16  C15   119.42  3.000
 7X6  C17   C16  C15   120.81  3.000
 7X6  CL1   C17  C16   119.54  3.000
 7X6  CL1   C17  C11   118.16  3.000
 7X6  C16   C17  C11   122.30  3.000
 7X6  C10   N5   C7    118.05  3.000
 7X6  H1C3  C1   H1C2  110.44  3.000
 7X6  H1C3  C1   H1C1  109.65  3.000
 7X6  H1C2  C1   H1C1  110.28  3.000
 7X6  H1C3  C1   S1    110.35  3.000
 7X6  H1C2  C1   S1    109.01  3.000
 7X6  H1C1  C1   S1    107.05  3.000
 7X6  N1    S1   O2    104.78  3.000
 7X6  N1    S1   O1    108.98  3.000
 7X6  O2    S1   O1    118.77  3.000
 7X6  N1    S1   C1    106.52  3.000
 7X6  O2    S1   C1    109.27  3.000
 7X6  O1    S1   C1    107.90  3.000
 7X6  C18   C2   C3    120.67  3.000
 7X6  C18   C2   N1    121.15  3.000
 7X6  C3    C2   N1    118.18  3.000
 7X6  H3    C3   C4    120.49  3.000
 7X6  H3    C3   C2    120.70  3.000
 7X6  C4    C3   C2    118.80  3.000
 7X6  HA    C4   C5    119.33  3.000
 7X6  HA    C4   C3    119.30  3.000
 7X6  C5    C4   C3    121.36  3.000
 7X6  H5    C5   C6    120.15  3.000
 7X6  H5    C5   C4    120.14  3.000
 7X6  C6    C5   C4    119.70  3.000
 7X6  C18   C6   C5    119.39  3.000
 7X6  C18   C6   N2    123.40  3.000
 7X6  C5    C6   N2    117.21  3.000
 7X6  H18   C18  C6    118.65  3.000
 7X6  H18   C18  C2    121.37  3.000
 7X6  C6    C18  C2    119.99  3.000
 7X6  H1    N1   C2    115.09  3.000
 7X6  H1    N1   S1    111.71  3.000
 7X6  C2    N1   S1    125.18  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
 7X6  CONST_01  C9    C8   N3   C7      0.00   0.0  0
 7X6  CONST_02  C9    C10  N5   C7      0.00   0.0  0
 7X6  CONST_03  C10   N5   C7   N3      0.00   0.0  0
 7X6  CONST_04  C10   C9   C8   N3      0.00   0.0  0
 7X6  CONST_05  N5    C7   N3   C8      0.00   0.0  0
 7X6  CONST_06  N5    C10  C9   C8      0.00   0.0  0
 7X6  CONST_07  C15   C14  C12  C11     0.00   0.0  0
 7X6  CONST_08  C15   C16  C17  C11     0.00   0.0  0
 7X6  CONST_09  C16   C17  C11  C12     0.00   0.0  0
 7X6  CONST_10  C16   C15  C14  C12     0.00   0.0  0
 7X6  CONST_11  C17   C11  C12  C14     0.00   0.0  0
 7X6  CONST_12  C17   C16  C15  C14     0.00   0.0  0
 7X6  CONST_13  C5    C4   C3   C2      0.00   0.0  0
 7X6  CONST_14  C5    C6   C18  C2      0.00   0.0  0
 7X6  CONST_15  C6    C18  C2   C3      0.00   0.0  0
 7X6  CONST_16  C6    C5   C4   C3      0.00   0.0  0
 7X6  CONST_17  C18   C2   C3   C4      0.00   0.0  0
 7X6  CONST_18  C18   C6   C5   C4      0.00   0.0  0
 7X6  CONST_19  C8    N3   C7   N2    180.00   0.0  0
 7X6  CONST_20  C10   N5   C7   N2    180.00   0.0  0
 7X6  CONST_21  C4    C5   C6   N2    180.00   0.0  0
 7X6  CONST_22  C2    C18  C6   N2    180.00   0.0  0
 7X6  CONST_23  N4    C10  N5   C7    180.00   0.0  0
 7X6  CONST_24  N4    C10  C9   C8    180.00   0.0  0
 7X6  CONST_25  O3    C12  C11  N4      0.00   0.0  0
 7X6  CONST_26  C14   C12  C11  N4    180.00   0.0  0
 7X6  CONST_27  C16   C17  C11  N4    180.00   0.0  0
 7X6  CONST_28  CL1   C17  C11  C12   180.00   0.0  0
 7X6  CONST_29  CL1   C17  C16  C15   180.00   0.0  0
 7X6  CONST_30  C4    C3   C2   N1    180.00   0.0  0
 7X6  CONST_31  C6    C18  C2   N1    180.00   0.0  0
 7X6  CONST_32  H8    C8   N3   C7    180.00   0.0  0
 7X6  CONST_33  H9    C9   C8   N3    180.00   0.0  0
 7X6  CONST_34  H16   C16  C17  C11   180.00   0.0  0
 7X6  CONST_35  H15   C15  C14  C12   180.00   0.0  0
 7X6  CONST_36  HA    C4   C3   C2    180.00   0.0  0
 7X6  CONST_37  H18   C18  C2   C3    180.00   0.0  0
 7X6  CONST_38  H5    C5   C4   C3    180.00   0.0  0
 7X6  CONST_39  H3    C3   C4   C5    180.00   0.0  0
 7X6  CONST_42  H1    N1   C2   C3      0.00   0.0  0
 7X6  Var_01    O4    C13  O3   C12   -15.72  30.0  1
 7X6  Var_02    C14   C12  O3   C13    10.00  30.0  1
 7X6  Var_03    C15   C14  O4   C13   173.04  30.0  1
 7X6  Var_04    C5    C6   N2   C7   -166.05  30.0  2
 7X6  Var_05    C6    N2   C7   N3    168.02  30.0  1
 7X6  Var_06    C11   N4   C10  C9     -0.98  30.0  2
 7X6  Var_07    C12   C11  N4   C10    62.19  30.0  2
 7X6  Var_08    C2    N1   S1   C1    -51.86  30.0  3
 7X6  Var_09    H1C1  C1   S1   O1     62.75  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
 7X6  plan-1  N2   0.020
 7X6  plan-1  C7   0.020
 7X6  plan-1  N3   0.020
 7X6  plan-1  C8   0.020
 7X6  plan-1  C9   0.020
 7X6  plan-1  C10  0.020
 7X6  plan-1  N4   0.020
 7X6  plan-1  N5   0.020
 7X6  plan-1  H8   0.020
 7X6  plan-1  H9   0.020
 7X6  plan-2  N2   0.020
 7X6  plan-2  C2   0.020
 7X6  plan-2  C3   0.020
 7X6  plan-2  C4   0.020
 7X6  plan-2  C5   0.020
 7X6  plan-2  C6   0.020
 7X6  plan-2  C18  0.020
 7X6  plan-2  H3   0.020
 7X6  plan-2  H18  0.020
 7X6  plan-2  HA   0.020
 7X6  plan-2  H5   0.020
 7X6  plan-2  N1   0.020
 7X6  plan-3  N4   0.020
 7X6  plan-3  C11  0.020
 7X6  plan-3  C12  0.020
 7X6  plan-3  O3   0.020
 7X6  plan-3  O4   0.020
 7X6  plan-3  C14  0.020
 7X6  plan-3  C15  0.020
 7X6  plan-3  C16  0.020
 7X6  plan-3  C17  0.020
 7X6  plan-3  CL1  0.020
 7X6  plan-3  H15  0.020
 7X6  plan-3  H16  0.020
 7X6  plan-4  S1   0.020
 7X6  plan-4  C2   0.020
 7X6  plan-4  H1   0.020
 7X6  plan-4  N1   0.020

