# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 08:43:26 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: ~{N}-[2-[[2-[(5-methoxypyridin-3-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl]amino]phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccccc1Nc2nc(Nc3cncc(OC)c3)ncc2C(F)(F)F
#
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
 6TT  6TT  ~{N}-[2-[[2-[(5-methoxypyridin-3-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl]amino]phenyl]propanamide  ligand  50  31  .  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_6TT
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
 6TT  C1   C  CH3   0  -0.438   8.1448   0.9530  -0.7664
 6TT  C3   C  CR6   0   0.346   6.0233  -0.0799  -0.5493
 6TT  C6   C  CR16  0  -0.168   4.4823  -2.3075  -0.4769
 6TT  C7   C  CR6   0   0.298   3.8553  -1.0623  -0.3051
 6TT  C11  C  CR16  0   0.011   1.0379   2.0872   0.2032
 6TT  C12  C  CR6   0  -0.453  -0.2929   1.7844   0.3961
 6TT  C13  C  CR6   0   0.586  -0.6148   0.3990   0.4057
 6TT  C15  C  CR6   0   0.309  -2.3182  -1.3712   0.6379
 6TT  C16  C  CR16  0  -0.282  -1.6593  -2.3482   1.3795
 6TT  C19  C  CR16  0  -0.274  -4.0189  -2.9814   0.0553
 6TT  C22  C  C     0   0.542  -5.4396  -0.3155  -0.6361
 6TT  C24  C  CH2   0  -0.584  -5.8964   0.7325  -1.6265
 6TT  C25  C  CH3   0  -0.658  -7.2715   1.2966  -1.3199
 6TT  C27  C  CT    0   1.080  -1.3048   2.8526   0.5941
 6TT  C31  C  CR16  0  -0.326   4.6523   0.0718  -0.3433
 6TT  O23  O  O     0  -0.465  -6.1535  -0.7760   0.2333
 6TT  C20  C  CR6   0   0.275  -3.5024  -1.6940  -0.0346
 6TT  C18  C  CR16  0  -0.269  -3.3603  -3.9485   0.7958
 6TT  C17  C  CR16  0  -0.260  -2.1791  -3.6295   1.4534
 6TT  N14  N  NH1   0  -0.776  -1.8820  -0.0376   0.5859
 6TT  N26  N  N     0  -0.511   0.3327  -0.5025   0.2321
 6TT  C9   C  CR6   0   0.635   1.5842  -0.0842   0.0606
 6TT  N8   N  NH1   0  -0.768   2.4837  -1.0871  -0.1040
 6TT  N5   N  N     0  -0.371   5.7754  -2.4382  -0.6698
 6TT  C4   C  CR16  0  -0.213   6.5503  -1.3581  -0.7094
 6TT  O2   O  O2    0  -0.467   6.7450   1.0511  -0.5753
 6TT  N10  N  N     0  -0.492   1.9899   1.1805   0.0366
 6TT  F28  F  F     0  -0.324  -2.2921   2.7921  -0.3229
 6TT  F29  F  F     0  -0.316  -1.9123   2.7647   1.7900
 6TT  F30  F  F     0  -0.295  -0.7788   4.0744   0.5146
 6TT  H33  H  HCH3  0   0.262   8.5299   1.9691  -0.7460
 6TT  H34  H  HCH3  0   0.232   8.6238   0.3774   0.0296
 6TT  H32  H  HCH3  0   0.232   8.3932   0.5003  -1.7295
 6TT  H36  H  HCR6  0   0.269   3.8905  -3.2182  -0.4506
 6TT  H38  H  HCR6  0   0.287   1.3693   3.1184   0.1813
 6TT  H40  H  HCR6  0   0.272  -0.7509  -2.1042   1.9092
 6TT  H43  H  HCR6  0   0.269  -4.9281  -3.2297  -0.4748
 6TT  H45  H  HCH2  0   0.260  -5.1539   1.5349  -1.6602
 6TT  H49  H  HCH2  0   0.277  -5.8834   0.2807  -2.6232
 6TT  H47  H  HCH3  0   0.231  -8.0370   0.5225  -1.3379
 6TT  H46  H  HCH3  0   0.230  -7.2998   1.7764  -0.3421
 6TT  H1   H  HCH3  0   0.236  -7.5393   2.0459  -2.0638
 6TT  H48  H  HCR6  0   0.304   4.2332   1.0575  -0.2147
 6TT  H44  H  HNH1  0   0.410  -3.6133  -0.2742  -1.5477
 6TT  H42  H  HCR6  0   0.262  -3.7645  -4.9501   0.8538
 6TT  H41  H  HCR6  0   0.263  -1.6619  -4.3787   2.0377
 6TT  H39  H  HNH1  0   0.403  -2.6282   0.6379   0.5637
 6TT  H37  H  HNH1  0   0.414   2.0675  -2.0066  -0.0715
 6TT  H35  H  HCR6  0   0.275   7.6072  -1.5288  -0.8713
 6TT  N21  N  NH1   0  -0.759  -4.1432  -0.7002  -0.8009

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
 6TT  O2   C1   single    1.416  0.020  1.416
 6TT  O2   C3   single    1.342  0.020  1.342
 6TT  C4   C3   aromatic  1.392  0.020  1.392
 6TT  C4   N5   aromatic  1.330  0.020  1.330
 6TT  C3   C31  aromatic  1.395  0.020  1.395
 6TT  N5   C6   aromatic  1.314  0.020  1.314
 6TT  C31  C7   aromatic  1.387  0.020  1.387
 6TT  C6   C7   aromatic  1.405  0.020  1.405
 6TT  C7   N8   single    1.387  0.020  1.387
 6TT  N8   C9   single    1.357  0.020  1.357
 6TT  N21  C20  single    1.409  0.020  1.409
 6TT  N21  C22  single    1.362  0.020  1.362
 6TT  C19  C18  aromatic  1.385  0.020  1.385
 6TT  C19  C20  aromatic  1.390  0.020  1.390
 6TT  C24  C25  single    1.518  0.020  1.518
 6TT  C24  C22  single    1.513  0.020  1.513
 6TT  C18  C17  aromatic  1.389  0.020  1.389
 6TT  C20  C15  aromatic  1.400  0.020  1.400
 6TT  C9   N26  aromatic  1.331  0.020  1.331
 6TT  C9   N10  aromatic  1.328  0.020  1.328
 6TT  N26  C13  aromatic  1.319  0.020  1.319
 6TT  C22  O23  double    1.216  0.020  1.216
 6TT  N10  C11  aromatic  1.325  0.020  1.325
 6TT  C17  C16  aromatic  1.385  0.020  1.385
 6TT  C15  C16  aromatic  1.392  0.020  1.392
 6TT  C15  N14  single    1.404  0.020  1.404
 6TT  C13  N14  single    1.352  0.020  1.352
 6TT  C13  C12  aromatic  1.422  0.020  1.422
 6TT  C11  C12  aromatic  1.378  0.020  1.378
 6TT  C12  C27  single    1.485  0.020  1.485
 6TT  F29  C27  single    1.344  0.020  1.344
 6TT  C27  F30  single    1.333  0.020  1.333
 6TT  C27  F28  single    1.349  0.020  1.349
 6TT  C1   H33  single    0.970  0.020  1.090
 6TT  C1   H34  single    0.970  0.020  1.090
 6TT  C1   H32  single    0.970  0.020  1.090
 6TT  C6   H36  single    0.930  0.020  1.080
 6TT  C11  H38  single    0.930  0.020  1.080
 6TT  C16  H40  single    0.930  0.020  1.080
 6TT  C19  H43  single    0.930  0.020  1.080
 6TT  C24  H45  single    0.970  0.020  1.090
 6TT  C24  H49  single    0.970  0.020  1.090
 6TT  C25  H47  single    0.970  0.020  1.090
 6TT  C25  H46  single    0.970  0.020  1.090
 6TT  C25  H1   single    0.970  0.020  1.090
 6TT  C31  H48  single    0.930  0.020  1.080
 6TT  N21  H44  single    0.860  0.020  1.020
 6TT  C18  H42  single    0.930  0.020  1.080
 6TT  C17  H41  single    0.930  0.020  1.080
 6TT  N14  H39  single    0.860  0.020  1.020
 6TT  N8   H37  single    0.860  0.020  1.020
 6TT  C4   H35  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
 6TT  H32  C1   H34  108.91  3.000
 6TT  H32  C1   H33  108.86  3.000
 6TT  H34  C1   H33  108.88  3.000
 6TT  H32  C1   O2   111.85  3.000
 6TT  H34  C1   O2   111.80  3.000
 6TT  H33  C1   O2   106.43  3.000
 6TT  O2   C3   C4   124.62  3.000
 6TT  C4   C3   C31  119.28  3.000
 6TT  O2   C3   C31  116.10  3.000
 6TT  H36  C6   N5   117.14  3.000
 6TT  H36  C6   C7   119.80  3.000
 6TT  N5   C6   C7   123.06  3.000
 6TT  N8   C7   C31  125.96  3.000
 6TT  N8   C7   C6   116.33  3.000
 6TT  C31  C7   C6   117.71  3.000
 6TT  H38  C11  N10  115.40  3.000
 6TT  H38  C11  C12  120.48  3.000
 6TT  N10  C11  C12  124.12  3.000
 6TT  C27  C12  C13  123.07  3.000
 6TT  C27  C12  C11  121.24  3.000
 6TT  C13  C12  C11  115.68  3.000
 6TT  N26  C13  N14  118.02  3.000
 6TT  N14  C13  C12  121.83  3.000
 6TT  N26  C13  C12  120.15  3.000
 6TT  N14  C15  C20  117.65  3.000
 6TT  N14  C15  C16  122.63  3.000
 6TT  C20  C15  C16  119.63  3.000
 6TT  H40  C16  C17  119.93  3.000
 6TT  H40  C16  C15  120.06  3.000
 6TT  C17  C16  C15  120.01  3.000
 6TT  H43  C19  C18  120.11  3.000
 6TT  H43  C19  C20  119.56  3.000
 6TT  C18  C19  C20  120.31  3.000
 6TT  N21  C22  O23  122.58  3.000
 6TT  O23  C22  C24  123.60  3.000
 6TT  N21  C22  C24  113.82  3.000
 6TT  H49  C24  H45  105.47  3.000
 6TT  H49  C24  C25  110.38  3.000
 6TT  H45  C24  C25  110.41  3.000
 6TT  H49  C24  C22  107.86  3.000
 6TT  H45  C24  C22  108.87  3.000
 6TT  C25  C24  C22  113.51  3.000
 6TT  H1   C25  H46  107.67  3.000
 6TT  H1   C25  H47  107.75  3.000
 6TT  H46  C25  H47  108.04  3.000
 6TT  H1   C25  C24  109.91  3.000
 6TT  H46  C25  C24  111.63  3.000
 6TT  H47  C25  C24  111.68  3.000
 6TT  F30  C27  F29  106.94  3.000
 6TT  F30  C27  F28  106.83  3.000
 6TT  F29  C27  F28  105.74  3.000
 6TT  F28  C27  C12  112.08  3.000
 6TT  F30  C27  C12  112.50  3.000
 6TT  F29  C27  C12  112.31  3.000
 6TT  H48  C31  C7   121.38  3.000
 6TT  H48  C31  C3   119.93  3.000
 6TT  C7   C31  C3   118.69  3.000
 6TT  N21  C20  C19  121.29  3.000
 6TT  C19  C20  C15  119.80  3.000
 6TT  N21  C20  C15  118.91  3.000
 6TT  H42  C18  C17  120.33  3.000
 6TT  H42  C18  C19  119.85  3.000
 6TT  C17  C18  C19  119.81  3.000
 6TT  H41  C17  C18  120.21  3.000
 6TT  H41  C17  C16  119.35  3.000
 6TT  C18  C17  C16  120.43  3.000
 6TT  H39  N14  C15  114.07  3.000
 6TT  H39  N14  C13  118.35  3.000
 6TT  C15  N14  C13  127.06  3.000
 6TT  C9   N26  C13  118.52  3.000
 6TT  N10  C9   N8   119.93  3.000
 6TT  N10  C9   N26  126.08  3.000
 6TT  N8   C9   N26  113.99  3.000
 6TT  H37  N8   C9   113.32  3.000
 6TT  H37  N8   C7   115.38  3.000
 6TT  C9   N8   C7   131.30  3.000
 6TT  C4   N5   C6   119.80  3.000
 6TT  H35  C4   N5   116.43  3.000
 6TT  H35  C4   C3   122.11  3.000
 6TT  N5   C4   C3   121.45  3.000
 6TT  C3   O2   C1   118.41  3.000
 6TT  C9   N10  C11  115.45  3.000
 6TT  H44  N21  C20  117.46  3.000
 6TT  H44  N21  C22  118.01  3.000
 6TT  C20  N21  C22  124.48  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
 6TT  CONST_01  C6   N5   C4   C3      0.00   0.0  0
 6TT  CONST_02  C6   C7   C31  C3      0.00   0.0  0
 6TT  CONST_03  C4   C3   C31  C7      0.00   0.0  0
 6TT  CONST_04  C4   N5   C6   C7      0.00   0.0  0
 6TT  CONST_05  N26  C9   N10  C11     0.00   0.0  0
 6TT  CONST_06  N26  C13  C12  C11     0.00   0.0  0
 6TT  CONST_07  C9   N26  C13  C12     0.00   0.0  0
 6TT  CONST_08  C9   N10  C11  C12     0.00   0.0  0
 6TT  CONST_09  N10  C9   N26  C13     0.00   0.0  0
 6TT  CONST_10  N10  C11  C12  C13     0.00   0.0  0
 6TT  CONST_11  C18  C19  C20  C15     0.00   0.0  0
 6TT  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 6TT  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 6TT  CONST_14  C19  C20  C15  C16     0.00   0.0  0
 6TT  CONST_15  N5   C4   C3   C31     0.00   0.0  0
 6TT  CONST_16  N5   C6   C7   C31     0.00   0.0  0
 6TT  CONST_17  C17  C18  C19  C20     0.00   0.0  0
 6TT  CONST_18  C17  C16  C15  C20     0.00   0.0  0
 6TT  CONST_19  N8   C7   C31  C3    180.00   0.0  0
 6TT  CONST_20  O2   C3   C31  C7    180.00   0.0  0
 6TT  CONST_21  N8   C9   N10  C11   180.00   0.0  0
 6TT  CONST_22  N14  C13  C12  C11   180.00   0.0  0
 6TT  CONST_23  N8   C9   N26  C13   180.00   0.0  0
 6TT  CONST_24  N21  C20  C15  C16   180.00   0.0  0
 6TT  CONST_25  N14  C15  C20  C19   180.00   0.0  0
 6TT  CONST_26  N26  C13  C12  C27   180.00   0.0  0
 6TT  CONST_27  N10  C11  C12  C27   180.00   0.0  0
 6TT  CONST_28  C18  C19  C20  N21   180.00   0.0  0
 6TT  CONST_29  N14  C15  C16  C17   180.00   0.0  0
 6TT  CONST_30  C9   N26  C13  N14   180.00   0.0  0
 6TT  CONST_31  N5   C6   C7   N8    180.00   0.0  0
 6TT  CONST_32  O2   C3   C4   N5    180.00   0.0  0
 6TT  CONST_33  H35  C4   N5   C6    180.00   0.0  0
 6TT  CONST_34  H48  C31  C7   C6    180.00   0.0  0
 6TT  CONST_35  H38  C11  C12  C13   180.00   0.0  0
 6TT  CONST_36  H43  C19  C20  C15   180.00   0.0  0
 6TT  CONST_37  H41  C17  C16  C15   180.00   0.0  0
 6TT  CONST_38  H42  C18  C17  C16   180.00   0.0  0
 6TT  CONST_39  H36  C6   C7   C31   180.00   0.0  0
 6TT  CONST_40  H40  C16  C15  C20   180.00   0.0  0
 6TT  CONST_44  C20  N21  C22  C24   180.00   0.0  0
 6TT  CONST_45  C20  N21  C22  O23     0.00   0.0  0
 6TT  Var_01    C9   N8   C7   C6   -178.22  30.0  2
 6TT  Var_02    N26  C9   N8   C7   -179.97  30.0  2
 6TT  Var_03    C15  N14  C13  C12  -178.81  30.0  2
 6TT  Var_04    C20  C15  N14  C13  -137.79  30.0  2
 6TT  Var_05    C4   C3   O2   C1     -0.59  30.0  2
 6TT  Var_06    F29  C27  C12  C11  -118.57  30.0  2
 6TT  Var_07    H33  C1   O2   C3   -179.51  30.0  3
 6TT  Var_08    N21  C22  C24  C25  -171.93  30.0  3
 6TT  Var_09    H47  C25  C24  C22   -60.72  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
 6TT  plan-1  C15  0.020
 6TT  plan-1  C16  0.020
 6TT  plan-1  C19  0.020
 6TT  plan-1  C20  0.020
 6TT  plan-1  C18  0.020
 6TT  plan-1  C17  0.020
 6TT  plan-1  N14  0.020
 6TT  plan-1  H40  0.020
 6TT  plan-1  H43  0.020
 6TT  plan-1  H42  0.020
 6TT  plan-1  H41  0.020
 6TT  plan-1  N21  0.020
 6TT  plan-2  C11  0.020
 6TT  plan-2  C12  0.020
 6TT  plan-2  C13  0.020
 6TT  plan-2  C27  0.020
 6TT  plan-2  N14  0.020
 6TT  plan-2  N26  0.020
 6TT  plan-2  C9   0.020
 6TT  plan-2  N8   0.020
 6TT  plan-2  N10  0.020
 6TT  plan-2  H38  0.020
 6TT  plan-3  C3   0.020
 6TT  plan-3  C6   0.020
 6TT  plan-3  C7   0.020
 6TT  plan-3  C31  0.020
 6TT  plan-3  N8   0.020
 6TT  plan-3  N5   0.020
 6TT  plan-3  C4   0.020
 6TT  plan-3  O2   0.020
 6TT  plan-3  H36  0.020
 6TT  plan-3  H48  0.020
 6TT  plan-3  H35  0.020
 6TT  plan-4  C22  0.020
 6TT  plan-4  C24  0.020
 6TT  plan-4  O23  0.020
 6TT  plan-4  C20  0.020
 6TT  plan-4  H44  0.020
 6TT  plan-4  N21  0.020

