# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:57:55 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-[(4-{[3-(trifluoromethyl)phenyl]amino}pyrimidin-2-yl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(Nc2nccc(Nc3cccc(c3)C(F)(F)F)n2)cc1
#
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
 NHJ  NHJ  4-[(4-{[3-(trifluoromethyl)phenyl]amino}pyrimidin-2-yl)amino]benzamide  ligand  41  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NHJ
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
 NHJ  N01   N  NH1   0  -0.771  -2.0909   0.0364   0.1367
 NHJ  N02   N  N     0  -0.535   0.0193  -0.7618   0.0988
 NHJ  N03   N  N     0  -0.492  -1.8011  -2.2446  -0.2487
 NHJ  N05   N  NH2   0  -0.822  -8.1838   2.0609   0.4404
 NHJ  C06   C  CR16  0  -0.302  -4.3768  -0.8583  -0.1438
 NHJ  C07   C  CR16  0  -0.259  -5.7335  -0.5866  -0.1787
 NHJ  C08   C  CR6   0  -0.061  -6.2369   0.6953   0.0219
 NHJ  C09   C  CR16  0  -0.271  -5.3208   1.7251   0.2423
 NHJ  C10   C  CR16  0  -0.344  -3.9653   1.4739   0.2716
 NHJ  C11   C  CR6   0   0.373  -3.4650   0.1778   0.0836
 NHJ  C12   C  CR6   0   0.627  -1.2804  -1.0531  -0.0144
 NHJ  C13   C  CR6   0   0.581   0.8792  -1.7546  -0.0381
 NHJ  C14   C  CR16  0  -0.465   0.4369  -3.0699  -0.2914
 NHJ  C15   C  CR16  0   0.007  -0.9178  -3.2390  -0.3833
 NHJ  C16   C  CR6   0   0.397   2.9386  -0.3623   0.2849
 NHJ  C17   C  CR16  0  -0.303   2.3842   0.8793   0.6113
 NHJ  C18   C  CR16  0  -0.230   3.2152   1.9665   0.8274
 NHJ  C19   C  CR16  0  -0.310   4.5945   1.8628   0.7303
 NHJ  C20   C  CR6   0  -0.172   5.1421   0.6291   0.4069
 NHJ  C21   C  CR16  0  -0.394   4.3274  -0.4703   0.1850
 NHJ  C22   C  CT    0   1.051   6.6225   0.4412   0.2866
 NHJ  O24   O  O     0  -0.488  -8.4508   0.0402  -0.5083
 NHJ  F25   F  F     0  -0.315   7.0779  -0.4716   1.1576
 NHJ  F26   F  F     0  -0.314   6.9712   0.0070  -0.9335
 NHJ  F27   F  F     0  -0.301   7.3050   1.5670   0.5090
 NHJ  HN01  H  HNH1  0   0.413  -1.5765   0.8866   0.3126
 NHJ  HN04  H  HNH1  0   0.422   2.7844  -2.3459  -0.0929
 NHJ  HN05  H  HNH2  0   0.412  -7.6135   2.7198   0.9395
 NHJ  HN0A  H  HNH2  0   0.403  -9.1759   2.2323   0.4359
 NHJ  H06   H  HCR6  0   0.289  -4.0286  -1.8665  -0.2946
 NHJ  H07   H  HCR6  0   0.260  -6.4169  -1.4054  -0.3606
 NHJ  H09   H  HCR6  0   0.256  -5.6433   2.7499   0.3767
 NHJ  H10   H  HCR6  0   0.274  -3.2784   2.2956   0.4364
 NHJ  H14   H  HCR6  0   0.284   1.1232  -3.8966  -0.4069
 NHJ  H15   H  HCR6  0   0.273  -1.3315  -4.2220  -0.5769
 NHJ  H17   H  HCR6  0   0.298   1.3171   0.9961   0.6950
 NHJ  H18   H  HCR6  0   0.269   2.7709   2.9196   1.0812
 NHJ  H19   H  HCR6  0   0.270   5.2136   2.7306   0.9070
 NHJ  H21   H  HCR6  0   0.287   4.7618  -1.4298  -0.0734
 NHJ  C23   C  C     0   0.489  -7.7124   0.8981  -0.0385
 NHJ  N04   N  NH1   0  -0.784   2.2152  -1.5272   0.0581

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
 NHJ  C11  N01   single    1.382  0.020  1.382
 NHJ  N01  C12   single    1.366  0.020  1.366
 NHJ  N01  HN01  single    0.860  0.020  1.020
 NHJ  N02  C13   aromatic  1.321  0.020  1.321
 NHJ  N02  C12   aromatic  1.337  0.020  1.337
 NHJ  C12  N03   aromatic  1.321  0.020  1.321
 NHJ  N03  C15   aromatic  1.337  0.020  1.337
 NHJ  C16  N04   single    1.390  0.020  1.390
 NHJ  N04  C13   single    1.359  0.020  1.359
 NHJ  N04  HN04  single    0.860  0.020  1.020
 NHJ  N05  C23   single    1.343  0.020  1.343
 NHJ  N05  HN05  single    0.860  0.020  1.020
 NHJ  N05  HN0A  single    0.860  0.020  1.020
 NHJ  C07  C06   aromatic  1.384  0.020  1.384
 NHJ  C06  C11   aromatic  1.399  0.020  1.399
 NHJ  C06  H06   single    0.930  0.020  1.080
 NHJ  C08  C07   aromatic  1.392  0.020  1.392
 NHJ  C07  H07   single    0.930  0.020  1.080
 NHJ  C23  C08   single    1.491  0.020  1.491
 NHJ  C08  C09   aromatic  1.396  0.020  1.396
 NHJ  C09  C10   aromatic  1.379  0.020  1.379
 NHJ  C09  H09   single    0.930  0.020  1.080
 NHJ  C10  C11   aromatic  1.402  0.020  1.402
 NHJ  C10  H10   single    0.930  0.020  1.080
 NHJ  C13  C14   aromatic  1.411  0.020  1.411
 NHJ  C14  C15   aromatic  1.368  0.020  1.368
 NHJ  C14  H14   single    0.930  0.020  1.080
 NHJ  C15  H15   single    0.930  0.020  1.080
 NHJ  C17  C16   aromatic  1.398  0.020  1.398
 NHJ  C16  C21   aromatic  1.397  0.020  1.397
 NHJ  C18  C17   aromatic  1.385  0.020  1.385
 NHJ  C17  H17   single    0.930  0.020  1.080
 NHJ  C18  C19   aromatic  1.387  0.020  1.387
 NHJ  C18  H18   single    0.930  0.020  1.080
 NHJ  C19  C20   aromatic  1.388  0.020  1.388
 NHJ  C19  H19   single    0.930  0.020  1.080
 NHJ  C20  C22   single    1.497  0.020  1.497
 NHJ  C20  C21   aromatic  1.386  0.020  1.386
 NHJ  C21  H21   single    0.930  0.020  1.080
 NHJ  F26  C22   single    1.341  0.020  1.341
 NHJ  C22  F27   single    1.335  0.020  1.335
 NHJ  C22  F25   single    1.341  0.020  1.341
 NHJ  O24  C23   double    1.226  0.020  1.226

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
 NHJ  HN01  N01  C12   112.87  3.000
 NHJ  HN01  N01  C11   115.29  3.000
 NHJ  C12   N01  C11   131.83  3.000
 NHJ  C13   N02  C12   117.42  3.000
 NHJ  C15   N03  C12   115.36  3.000
 NHJ  HN0A  N05  HN05  116.75  3.000
 NHJ  HN0A  N05  C23   119.45  3.000
 NHJ  HN05  N05  C23   123.09  3.000
 NHJ  H06   C06  C11   120.35  3.000
 NHJ  H06   C06  C07   119.81  3.000
 NHJ  C11   C06  C07   119.84  3.000
 NHJ  H07   C07  C08   119.52  3.000
 NHJ  H07   C07  C06   118.35  3.000
 NHJ  C08   C07  C06   122.13  3.000
 NHJ  C23   C08  C09   123.76  3.000
 NHJ  C09   C08  C07   117.70  3.000
 NHJ  C23   C08  C07   118.52  3.000
 NHJ  H09   C09  C10   117.56  3.000
 NHJ  H09   C09  C08   121.49  3.000
 NHJ  C10   C09  C08   120.94  3.000
 NHJ  H10   C10  C11   119.69  3.000
 NHJ  H10   C10  C09   119.22  3.000
 NHJ  C11   C10  C09   121.09  3.000
 NHJ  C10   C11  C06   118.30  3.000
 NHJ  C10   C11  N01   116.37  3.000
 NHJ  C06   C11  N01   125.34  3.000
 NHJ  N03   C12  N02   126.49  3.000
 NHJ  N03   C12  N01   120.33  3.000
 NHJ  N02   C12  N01   113.18  3.000
 NHJ  C14   C13  N04   118.50  3.000
 NHJ  C14   C13  N02   121.03  3.000
 NHJ  N04   C13  N02   120.47  3.000
 NHJ  H14   C14  C15   121.81  3.000
 NHJ  H14   C14  C13   122.24  3.000
 NHJ  C15   C14  C13   115.96  3.000
 NHJ  H15   C15  C14   120.13  3.000
 NHJ  H15   C15  N03   116.13  3.000
 NHJ  C14   C15  N03   123.74  3.000
 NHJ  C21   C16  C17   118.67  3.000
 NHJ  C21   C16  N04   116.17  3.000
 NHJ  C17   C16  N04   125.16  3.000
 NHJ  H17   C17  C18   119.82  3.000
 NHJ  H17   C17  C16   120.49  3.000
 NHJ  C18   C17  C16   119.69  3.000
 NHJ  H18   C18  C19   119.40  3.000
 NHJ  H18   C18  C17   118.79  3.000
 NHJ  C19   C18  C17   121.81  3.000
 NHJ  H19   C19  C20   121.72  3.000
 NHJ  H19   C19  C18   119.90  3.000
 NHJ  C20   C19  C18   118.38  3.000
 NHJ  C22   C20  C21   117.95  3.000
 NHJ  C21   C20  C19   120.69  3.000
 NHJ  C22   C20  C19   121.36  3.000
 NHJ  H21   C21  C20   120.29  3.000
 NHJ  H21   C21  C16   118.94  3.000
 NHJ  C20   C21  C16   120.77  3.000
 NHJ  F27   C22  F26   106.96  3.000
 NHJ  F27   C22  F25   106.98  3.000
 NHJ  F26   C22  F25   106.39  3.000
 NHJ  F25   C22  C20   111.65  3.000
 NHJ  F27   C22  C20   112.72  3.000
 NHJ  F26   C22  C20   111.77  3.000
 NHJ  O24   C23  C08   121.11  3.000
 NHJ  O24   C23  N05   122.10  3.000
 NHJ  C08   C23  N05   116.79  3.000
 NHJ  HN04  N04  C16   114.27  3.000
 NHJ  HN04  N04  C13   114.11  3.000
 NHJ  C16   N04  C13   131.58  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
 NHJ  CONST_01  C15   C14  C13  N02     0.00   0.0  0
 NHJ  CONST_02  C15   N03  C12  N02     0.00   0.0  0
 NHJ  CONST_03  C13   N02  C12  N03     0.00   0.0  0
 NHJ  CONST_04  C13   C14  C15  N03     0.00   0.0  0
 NHJ  CONST_05  C09   C08  C07  C06     0.00   0.0  0
 NHJ  CONST_06  C09   C10  C11  C06     0.00   0.0  0
 NHJ  CONST_07  C10   C11  C06  C07     0.00   0.0  0
 NHJ  CONST_08  C10   C09  C08  C07     0.00   0.0  0
 NHJ  CONST_09  C11   C06  C07  C08     0.00   0.0  0
 NHJ  CONST_10  C11   C10  C09  C08     0.00   0.0  0
 NHJ  CONST_11  C14   C13  N02  C12     0.00   0.0  0
 NHJ  CONST_12  C14   C15  N03  C12     0.00   0.0  0
 NHJ  CONST_13  C19   C18  C17  C16     0.00   0.0  0
 NHJ  CONST_14  C19   C20  C21  C16     0.00   0.0  0
 NHJ  CONST_15  C20   C21  C16  C17     0.00   0.0  0
 NHJ  CONST_16  C20   C19  C18  C17     0.00   0.0  0
 NHJ  CONST_17  C21   C16  C17  C18     0.00   0.0  0
 NHJ  CONST_18  C21   C20  C19  C18     0.00   0.0  0
 NHJ  CONST_19  C07   C06  C11  N01   180.00   0.0  0
 NHJ  CONST_20  C09   C10  C11  N01   180.00   0.0  0
 NHJ  CONST_21  C13   N02  C12  N01   180.00   0.0  0
 NHJ  CONST_22  C15   N03  C12  N01   180.00   0.0  0
 NHJ  CONST_23  C18   C17  C16  N04   180.00   0.0  0
 NHJ  CONST_24  C20   C21  C16  N04   180.00   0.0  0
 NHJ  CONST_25  C12   N02  C13  N04   180.00   0.0  0
 NHJ  CONST_26  C15   C14  C13  N04   180.00   0.0  0
 NHJ  CONST_27  C23   C08  C07  C06   180.00   0.0  0
 NHJ  CONST_28  C23   C08  C09  C10   180.00   0.0  0
 NHJ  CONST_29  C22   C20  C21  C16   180.00   0.0  0
 NHJ  CONST_30  C22   C20  C19  C18   180.00   0.0  0
 NHJ  CONST_31  H14   C14  C13  N02   180.00   0.0  0
 NHJ  CONST_32  H10   C10  C11  C06   180.00   0.0  0
 NHJ  CONST_33  H09   C09  C08  C07   180.00   0.0  0
 NHJ  CONST_34  H06   C06  C07  C08   180.00   0.0  0
 NHJ  CONST_35  H07   C07  C08  C09   180.00   0.0  0
 NHJ  CONST_36  H15   C15  N03  C12   180.00   0.0  0
 NHJ  CONST_37  H18   C18  C17  C16   180.00   0.0  0
 NHJ  CONST_38  H21   C21  C16  C17   180.00   0.0  0
 NHJ  CONST_39  H19   C19  C18  C17   180.00   0.0  0
 NHJ  CONST_40  H17   C17  C18  C19   180.00   0.0  0
 NHJ  CONST_41  HN05  N05  C23  C08     0.00   0.0  0
 NHJ  CONST_42  HN0A  N05  C23  C08   180.00   0.0  0
 NHJ  Var_01    C16   N04  C13  N02    -0.39  30.0  2
 NHJ  Var_02    C11   N01  C12  N02   179.35  30.0  1
 NHJ  Var_03    C12   N01  C11  C06     0.63  30.0  2
 NHJ  Var_04    C17   C16  N04  C13     7.05  30.0  2
 NHJ  Var_05    C07   C08  C23  N05   165.88  30.0  2
 NHJ  Var_06    F26   C22  C20  C19  -121.08  30.0  2

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
 NHJ  plan-1  N01   0.020
 NHJ  plan-1  N02   0.020
 NHJ  plan-1  N03   0.020
 NHJ  plan-1  C12   0.020
 NHJ  plan-1  C13   0.020
 NHJ  plan-1  C14   0.020
 NHJ  plan-1  C15   0.020
 NHJ  plan-1  H14   0.020
 NHJ  plan-1  H15   0.020
 NHJ  plan-1  N04   0.020
 NHJ  plan-2  N01   0.020
 NHJ  plan-2  C06   0.020
 NHJ  plan-2  C07   0.020
 NHJ  plan-2  C08   0.020
 NHJ  plan-2  C09   0.020
 NHJ  plan-2  C10   0.020
 NHJ  plan-2  C11   0.020
 NHJ  plan-2  H06   0.020
 NHJ  plan-2  H07   0.020
 NHJ  plan-2  H09   0.020
 NHJ  plan-2  H10   0.020
 NHJ  plan-2  C23   0.020
 NHJ  plan-3  C16   0.020
 NHJ  plan-3  C17   0.020
 NHJ  plan-3  C18   0.020
 NHJ  plan-3  C19   0.020
 NHJ  plan-3  C20   0.020
 NHJ  plan-3  C21   0.020
 NHJ  plan-3  C22   0.020
 NHJ  plan-3  H17   0.020
 NHJ  plan-3  H18   0.020
 NHJ  plan-3  H19   0.020
 NHJ  plan-3  H21   0.020
 NHJ  plan-3  N04   0.020
 NHJ  plan-4  N05   0.020
 NHJ  plan-4  C08   0.020
 NHJ  plan-4  O24   0.020
 NHJ  plan-4  HN05  0.020
 NHJ  plan-4  HN0A  0.020
 NHJ  plan-4  C23   0.020

