# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:15:00 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-methyl-N-{2-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]phenyl}methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(c1ccccc1CNc2nc(Nc3ccc4NC(=O)Cc4c3)ncc2C(F)(F)F)[S](C)(=O)=O
#
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
 3JZ  3JZ  N-methyl-N-{2-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]phenyl}methanesulfonamide  ligand  56  35  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3JZ
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
 3JZ  C35   C  CH3   0  -0.543  -3.6521  -2.4409  -1.9695
 3JZ  C34   C  CH3   0  -0.798  -5.4039   0.0685  -3.1338
 3JZ  N2    N  N     0  -0.497   2.0640   1.2305   0.2950
 3JZ  C7    C  CR16  0  -0.008   1.1481   2.1838   0.1946
 3JZ  C6    C  CR6   0  -0.436  -0.2064   1.9841   0.3451
 3JZ  C13   C  CR6   0   0.049  -3.7242  -1.2780   1.1952
 3JZ  C20   C  CR6   0   0.287  -4.5294  -1.3324   0.0562
 3JZ  C21   C  CR56  0   0.396   6.5827  -1.4682   0.4164
 3JZ  C8    C  CT    0   1.072  -1.1623   3.1032   0.1661
 3JZ  C18   C  CR16  0  -0.232  -5.6955  -1.6013   2.5573
 3JZ  C16   C  CR16  0  -0.359   4.4475  -2.2423   1.0991
 3JZ  C19   C  CR16  0  -0.269  -6.4834  -1.6693   1.4176
 3JZ  O33   O  OS    0  -0.656  -2.8276   0.3717  -2.8405
 3JZ  S31   S  S     0   1.336  -4.0210   0.2187  -2.0252
 3JZ  O32   O  OS    0  -0.657  -4.3482   1.2240  -1.0242
 3JZ  N30   N  N     0  -0.685  -3.9050  -1.2174  -1.2178
 3JZ  C17   C  CR16  0  -0.316  -4.3255  -1.4107   2.4421
 3JZ  C1    C  CR16  0  -0.250  -5.8976  -1.5403   0.1667
 3JZ  N10   N  NH1   0  -0.672  -1.8781   0.2669   0.8041
 3JZ  C5    C  CR6   0   0.583  -0.6073   0.6434   0.6262
 3JZ  F29   F  F     0  -0.304  -0.5498   4.2911   0.1244
 3JZ  F28   F  F     0  -0.310  -1.8728   2.9983  -0.9682
 3JZ  F27   F  F     0  -0.324  -2.0657   3.1726   1.1636
 3JZ  N4    N  N     0  -0.535   0.3118  -0.3078   0.7319
 3JZ  C3    C  CR6   0   0.615   1.5927   0.0149   0.5606
 3JZ  N9    N  NH1   0  -0.762   2.4482  -1.0276   0.6841
 3JZ  C11   C  CR6   0   0.358   3.8403  -1.0955   0.5796
 3JZ  C14   C  CR16  0  -0.375   4.6331  -0.1203  -0.0404
 3JZ  C22   C  CR56  0   0.016   5.9950  -0.3208  -0.1076
 3JZ  C23   C  CH2   0  -0.621   7.0776   0.5252  -0.6992
 3JZ  C15   C  CR16  0  -0.295   5.8194  -2.4457   1.0226
 3JZ  N25   N  NR15  0  -0.740   7.9578  -1.4171   0.2098
 3JZ  C24   C  CR5   0   0.513   8.3408  -0.2813  -0.4352
 3JZ  O26   O  O     0  -0.462   9.4786   0.0151  -0.7379
 3JZ  H35   H  HCH3  0   0.250  -4.5715  -2.9021  -2.3362
 3JZ  H35A  H  HCH3  0   0.265  -2.9934  -2.2362  -2.8104
 3JZ  H35B  H  HCH3  0   0.270  -3.1431  -3.1494  -1.3184
 3JZ  H34   H  HCH3  0   0.292  -5.2479  -0.7707  -3.8081
 3JZ  H34A  H  HCH3  0   0.289  -6.3180  -0.0712  -2.5622
 3JZ  H34B  H  HCH3  0   0.311  -5.4671   0.9911  -3.7091
 3JZ  H7    H  HCR6  0   0.279   1.5324   3.1732  -0.0235
 3JZ  H18   H  HCR6  0   0.265  -6.1449  -1.7025   3.5363
 3JZ  H16   H  HCR6  0   0.271   3.8345  -2.9978   1.5761
 3JZ  H19   H  HCR6  0   0.267  -7.5513  -1.8211   1.4988
 3JZ  H17   H  HCR6  0   0.261  -3.7104  -1.3688   3.3327
 3JZ  H1    H  HCR6  0   0.268  -6.5105  -1.6001  -0.7243
 3JZ  H12   H  HCH2  0   0.262  -1.7680  -1.4320   2.0194
 3JZ  H12A  H  HCH2  0   0.258  -1.8362  -1.7572   0.2983
 3JZ  HN10  H  HNH1  0   0.404  -2.6264   0.9350   0.7358
 3JZ  HN9   H  HNH1  0   0.408   1.9926  -1.8880   0.9483
 3JZ  H14   H  HCR6  0   0.280   4.1896   0.7709  -0.4545
 3JZ  H23   H  HCH2  0   0.303   6.9595   0.6895  -1.7731
 3JZ  H23A  H  HCH2  0   0.302   7.1608   1.5110  -0.2353
 3JZ  H15   H  HCR6  0   0.270   6.2617  -3.3436   1.4327
 3JZ  HN25  H  HNR5  0   0.410   8.6073  -2.1305   0.5048
 3JZ  C12   C  CH2   0  -0.301  -2.2337  -1.1128   1.0848

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
 3JZ  C35  N30   single    1.458  0.020  1.458
 3JZ  C34  S31   single    1.779  0.020  1.779
 3JZ  N2   C7    aromatic  1.326  0.020  1.326
 3JZ  N2   C3    aromatic  1.331  0.020  1.331
 3JZ  C7   C6    aromatic  1.377  0.020  1.377
 3JZ  C6   C8    single    1.483  0.020  1.483
 3JZ  C6   C5    aromatic  1.427  0.020  1.427
 3JZ  C13  C20   aromatic  1.396  0.020  1.396
 3JZ  C13  C17   aromatic  1.391  0.020  1.391
 3JZ  C13  C12   single    1.504  0.020  1.504
 3JZ  C20  N30   single    1.423  0.020  1.423
 3JZ  C20  C1    aromatic  1.388  0.020  1.388
 3JZ  C21  C22   aromatic  1.392  0.020  1.392
 3JZ  C21  C15   aromatic  1.380  0.020  1.380
 3JZ  C21  N25   single    1.392  0.020  1.392
 3JZ  C8   F29   single    1.337  0.020  1.337
 3JZ  C8   F28   single    1.343  0.020  1.343
 3JZ  C8   F27   single    1.348  0.020  1.348
 3JZ  C18  C19   aromatic  1.387  0.020  1.387
 3JZ  C18  C17   aromatic  1.388  0.020  1.388
 3JZ  C16  C11   aromatic  1.398  0.020  1.398
 3JZ  C16  C15   aromatic  1.389  0.020  1.389
 3JZ  C19  C1    aromatic  1.387  0.020  1.387
 3JZ  O33  S31   double    1.453  0.020  1.453
 3JZ  S31  O32   double    1.456  0.020  1.456
 3JZ  S31  N30   single    1.652  0.020  1.652
 3JZ  C12  N10   single    1.452  0.020  1.452
 3JZ  N10  C5    single    1.337  0.020  1.337
 3JZ  C5   N4    aromatic  1.327  0.020  1.327
 3JZ  N4   C3    aromatic  1.332  0.020  1.332
 3JZ  C3   N9    single    1.354  0.020  1.354
 3JZ  N9   C11   single    1.398  0.020  1.398
 3JZ  C11  C14   aromatic  1.401  0.020  1.401
 3JZ  C14  C22   aromatic  1.378  0.020  1.378
 3JZ  C22  C23   single    1.496  0.020  1.496
 3JZ  C23  C24   single    1.522  0.020  1.522
 3JZ  N25  C24   single    1.361  0.020  1.361
 3JZ  C24  O26   double    1.214  0.020  1.214
 3JZ  C35  H35   single    0.970  0.020  1.090
 3JZ  C35  H35A  single    0.970  0.020  1.090
 3JZ  C35  H35B  single    0.970  0.020  1.090
 3JZ  C34  H34   single    0.970  0.020  1.090
 3JZ  C34  H34A  single    0.970  0.020  1.090
 3JZ  C34  H34B  single    0.970  0.020  1.090
 3JZ  C7   H7    single    0.930  0.020  1.080
 3JZ  C18  H18   single    0.930  0.020  1.080
 3JZ  C16  H16   single    0.930  0.020  1.080
 3JZ  C19  H19   single    0.930  0.020  1.080
 3JZ  C17  H17   single    0.930  0.020  1.080
 3JZ  C1   H1    single    0.930  0.020  1.080
 3JZ  C12  H12   single    0.970  0.020  1.090
 3JZ  C12  H12A  single    0.970  0.020  1.090
 3JZ  N10  HN10  single    0.860  0.020  1.020
 3JZ  N9   HN9   single    0.860  0.020  1.020
 3JZ  C14  H14   single    0.930  0.020  1.080
 3JZ  C23  H23   single    0.970  0.020  1.090
 3JZ  C23  H23A  single    0.970  0.020  1.090
 3JZ  C15  H15   single    0.930  0.020  1.080
 3JZ  N25  HN25  single    0.860  0.020  1.020

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
 3JZ  H35B  C35  H35A  107.56  3.000
 3JZ  H35B  C35  H35   108.64  3.000
 3JZ  H35A  C35  H35   109.26  3.000
 3JZ  H35B  C35  N30   108.59  3.000
 3JZ  H35A  C35  N30   110.22  3.000
 3JZ  H35   C35  N30   112.43  3.000
 3JZ  H34B  C34  H34A  109.74  3.000
 3JZ  H34B  C34  H34   109.54  3.000
 3JZ  H34A  C34  H34   110.32  3.000
 3JZ  H34B  C34  S31   107.63  3.000
 3JZ  H34A  C34  S31   109.69  3.000
 3JZ  H34   C34  S31   109.87  3.000
 3JZ  C3    N2   C7    115.29  3.000
 3JZ  H7    C7   C6    120.21  3.000
 3JZ  H7    C7   N2    115.26  3.000
 3JZ  C6    C7   N2    124.53  3.000
 3JZ  C5    C6   C8    123.49  3.000
 3JZ  C5    C6   C7    115.71  3.000
 3JZ  C8    C6   C7    120.76  3.000
 3JZ  C12   C13  C17   120.33  3.000
 3JZ  C12   C13  C20   121.08  3.000
 3JZ  C17   C13  C20   118.58  3.000
 3JZ  C1    C20  N30   121.04  3.000
 3JZ  C1    C20  C13   120.63  3.000
 3JZ  N30   C20  C13   118.30  3.000
 3JZ  N25   C21  C15   129.61  3.000
 3JZ  N25   C21  C22   109.34  3.000
 3JZ  C15   C21  C22   121.05  3.000
 3JZ  F27   C8   F28   105.94  3.000
 3JZ  F27   C8   F29   106.53  3.000
 3JZ  F28   C8   F29   106.59  3.000
 3JZ  F27   C8   C6    112.44  3.000
 3JZ  F28   C8   C6    112.59  3.000
 3JZ  F29   C8   C6    112.27  3.000
 3JZ  H18   C18  C17   119.86  3.000
 3JZ  H18   C18  C19   120.19  3.000
 3JZ  C17   C18  C19   119.95  3.000
 3JZ  H16   C16  C15   118.74  3.000
 3JZ  H16   C16  C11   119.34  3.000
 3JZ  C15   C16  C11   121.92  3.000
 3JZ  H19   C19  C1    119.84  3.000
 3JZ  H19   C19  C18   120.39  3.000
 3JZ  C1    C19  C18   119.76  3.000
 3JZ  N30   S31  O32   106.27  3.000
 3JZ  N30   S31  O33   107.95  3.000
 3JZ  O32   S31  O33   119.84  3.000
 3JZ  N30   S31  C34   106.61  3.000
 3JZ  O32   S31  C34   108.18  3.000
 3JZ  O33   S31  C34   107.32  3.000
 3JZ  S31   N30  C20   118.49  3.000
 3JZ  S31   N30  C35   119.32  3.000
 3JZ  C20   N30  C35   118.02  3.000
 3JZ  H17   C17  C18   119.84  3.000
 3JZ  H17   C17  C13   119.20  3.000
 3JZ  C18   C17  C13   120.95  3.000
 3JZ  H1    C1   C19   119.85  3.000
 3JZ  H1    C1   C20   120.03  3.000
 3JZ  C19   C1   C20   120.12  3.000
 3JZ  HN10  N10  C5    120.74  3.000
 3JZ  HN10  N10  C12   117.53  3.000
 3JZ  C5    N10  C12   121.73  3.000
 3JZ  N4    C5   N10   116.47  3.000
 3JZ  N4    C5   C6    119.64  3.000
 3JZ  N10   C5   C6    123.88  3.000
 3JZ  C3    N4   C5    118.83  3.000
 3JZ  N9    C3   N4    114.16  3.000
 3JZ  N9    C3   N2    119.85  3.000
 3JZ  N4    C3   N2    125.99  3.000
 3JZ  HN9   N9   C11   115.34  3.000
 3JZ  HN9   N9   C3    113.28  3.000
 3JZ  C11   N9   C3    131.28  3.000
 3JZ  C14   C11  N9    124.24  3.000
 3JZ  C14   C11  C16   119.32  3.000
 3JZ  N9    C11  C16   116.41  3.000
 3JZ  H14   C14  C22   120.53  3.000
 3JZ  H14   C14  C11   120.83  3.000
 3JZ  C22   C14  C11   118.64  3.000
 3JZ  C23   C22  C14   130.71  3.000
 3JZ  C23   C22  C21   108.04  3.000
 3JZ  C14   C22  C21   121.25  3.000
 3JZ  H23A  C23  H23   106.84  3.000
 3JZ  H23A  C23  C24   109.96  3.000
 3JZ  H23   C23  C24   109.87  3.000
 3JZ  H23A  C23  C22   113.41  3.000
 3JZ  H23   C23  C22   113.29  3.000
 3JZ  C24   C23  C22   103.44  3.000
 3JZ  H15   C15  C16   120.30  3.000
 3JZ  H15   C15  C21   121.89  3.000
 3JZ  C16   C15  C21   117.81  3.000
 3JZ  HN25  N25  C24   123.20  3.000
 3JZ  HN25  N25  C21   124.53  3.000
 3JZ  C24   N25  C21   112.27  3.000
 3JZ  O26   C24  N25   125.84  3.000
 3JZ  O26   C24  C23   127.25  3.000
 3JZ  N25   C24  C23   106.91  3.000
 3JZ  H12A  C12  H12   106.78  3.000
 3JZ  H12A  C12  N10   109.42  3.000
 3JZ  H12   C12  N10   109.80  3.000
 3JZ  H12A  C12  C13   110.42  3.000
 3JZ  H12   C12  C13   109.14  3.000
 3JZ  N10   C12  C13   111.18  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
 3JZ  CONST_01  C5    C6   C7   N2      0.00   0.0  0
 3JZ  CONST_02  C5    N4   C3   N2      0.00   0.0  0
 3JZ  CONST_03  N4    C3   N2   C7      0.00   0.0  0
 3JZ  CONST_04  N4    C5   C6   C7      0.00   0.0  0
 3JZ  CONST_05  C3    N2   C7   C6      0.00   0.0  0
 3JZ  CONST_06  C3    N4   C5   C6      0.00   0.0  0
 3JZ  CONST_07  C19   C1   C20  C13     0.00   0.0  0
 3JZ  CONST_08  C19   C18  C17  C13     0.00   0.0  0
 3JZ  CONST_09  C18   C17  C13  C20     0.00   0.0  0
 3JZ  CONST_10  C18   C19  C1   C20     0.00   0.0  0
 3JZ  CONST_11  C11   C14  C22  C21     0.00   0.0  0
 3JZ  CONST_12  C11   C16  C15  C21     0.00   0.0  0
 3JZ  CONST_13  C22   C14  C11  C16     0.00   0.0  0
 3JZ  CONST_14  C22   C21  C15  C16     0.00   0.0  0
 3JZ  CONST_15  C1    C20  C13  C17     0.00   0.0  0
 3JZ  CONST_16  C1    C19  C18  C17     0.00   0.0  0
 3JZ  CONST_17  C15   C16  C11  C14     0.00   0.0  0
 3JZ  CONST_18  C15   C21  C22  C14     0.00   0.0  0
 3JZ  CONST_19  C23   C24  N25  C21     0.00   0.0  0
 3JZ  CONST_20  C8    C6   C7   N2    180.00   0.0  0
 3JZ  CONST_21  N9    C3   N2   C7    180.00   0.0  0
 3JZ  CONST_22  N10   C5   C6   C7    180.00   0.0  0
 3JZ  CONST_23  N4    C5   C6   C8    180.00   0.0  0
 3JZ  CONST_24  C12   C13  C17  C18   180.00   0.0  0
 3JZ  CONST_25  N30   C20  C1   C19   180.00   0.0  0
 3JZ  CONST_26  C17   C13  C20  N30   180.00   0.0  0
 3JZ  CONST_27  C12   C13  C20  C1    180.00   0.0  0
 3JZ  CONST_28  C3    N4   C5   N10   180.00   0.0  0
 3JZ  CONST_29  N9    C3   N4   C5    180.00   0.0  0
 3JZ  CONST_30  C15   C16  C11  N9    180.00   0.0  0
 3JZ  CONST_31  C22   C14  C11  N9    180.00   0.0  0
 3JZ  CONST_32  O26   C24  N25  C21   180.00   0.0  0
 3JZ  CONST_33  H1    C1   C20  C13   180.00   0.0  0
 3JZ  CONST_34  H18   C18  C17  C13   180.00   0.0  0
 3JZ  CONST_35  H17   C17  C13  C20   180.00   0.0  0
 3JZ  CONST_36  H19   C19  C1   C20   180.00   0.0  0
 3JZ  CONST_37  H14   C14  C22  C21   180.00   0.0  0
 3JZ  CONST_38  H16   C16  C15  C21   180.00   0.0  0
 3JZ  CONST_39  H7    C7   C6   C5    180.00   0.0  0
 3JZ  CONST_40  H15   C15  C16  C11   180.00   0.0  0
 3JZ  CONST_41  HN25  N25  C24  C23   180.00   0.0  0
 3JZ  CONST_44  C12   N10  C5   C6    180.00   0.0  0
 3JZ  CONST_47  N4    C5   N10  C12     0.00   0.0  0
 3JZ  CONST_48  HN10  N10  C5   C6      0.00   0.0  0
 3JZ  Var_01    C11   N9   C3   N2     -0.10  30.0  2
 3JZ  Var_02    C3    N9   C11  C16   163.84  30.0  3
 3JZ  Var_03    H23   C23  C22  C21   118.54  30.0  1
 3JZ  Var_04    F29   C8   C6   C7    -12.47  30.0  2
 3JZ  Var_05    C5    N10  C12  C13  -178.07  30.0  3
 3JZ  Var_06    N10   C12  C13  C20    78.01  30.0  2
 3JZ  Var_07    C20   N30  S31  C34   -95.01  30.0  3
 3JZ  Var_08    H35   C35  N30  C20    69.77  30.0  3
 3JZ  Var_09    H34   C34  S31  O33    57.27  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
 3JZ  plan-1  N2    0.020
 3JZ  plan-1  C7    0.020
 3JZ  plan-1  C6    0.020
 3JZ  plan-1  C8    0.020
 3JZ  plan-1  N10   0.020
 3JZ  plan-1  C5    0.020
 3JZ  plan-1  N4    0.020
 3JZ  plan-1  C3    0.020
 3JZ  plan-1  N9    0.020
 3JZ  plan-1  H7    0.020
 3JZ  plan-2  C13   0.020
 3JZ  plan-2  C20   0.020
 3JZ  plan-2  C18   0.020
 3JZ  plan-2  C19   0.020
 3JZ  plan-2  N30   0.020
 3JZ  plan-2  C17   0.020
 3JZ  plan-2  C1    0.020
 3JZ  plan-2  H18   0.020
 3JZ  plan-2  H19   0.020
 3JZ  plan-2  H17   0.020
 3JZ  plan-2  H1    0.020
 3JZ  plan-2  C12   0.020
 3JZ  plan-3  C35   0.020
 3JZ  plan-3  C20   0.020
 3JZ  plan-3  S31   0.020
 3JZ  plan-3  N30   0.020
 3JZ  plan-4  N10   0.020
 3JZ  plan-4  C5    0.020
 3JZ  plan-4  HN10  0.020
 3JZ  plan-4  C12   0.020
 3JZ  plan-5  C21   0.020
 3JZ  plan-5  C16   0.020
 3JZ  plan-5  N9    0.020
 3JZ  plan-5  C11   0.020
 3JZ  plan-5  C14   0.020
 3JZ  plan-5  C22   0.020
 3JZ  plan-5  C23   0.020
 3JZ  plan-5  C15   0.020
 3JZ  plan-5  N25   0.020
 3JZ  plan-5  C24   0.020
 3JZ  plan-5  O26   0.020
 3JZ  plan-5  H16   0.020
 3JZ  plan-5  H14   0.020
 3JZ  plan-5  H15   0.020
 3JZ  plan-5  HN25  0.020

