# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 06:00:11 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-{3-[(4-{[3-(trifluoromethyl)phenyl]amino}pyrimidin-2-yl)amino]phenyl}cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(Nc2ccnc(Nc3cccc(NC(=O)C4CC4)c3)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
 CC3  CC3  N-{3-[(4-{[3-(trifluoromethyl)phenyl]amino}pyrimidin-2-yl)amino]phenyl}cyclopropanecarboxamide  ligand  48  30  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CC3
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
 CC3  O27   O  O     0  -0.474   2.8776  -3.9839   7.2581
 CC3  C26   C  C     0   0.589   3.9978  -4.1400   7.7117
 CC3  C28   C  CH1   0  -0.426   4.8179  -5.3430   7.4114
 CC3  C30   C  CH2   0  -0.459   4.6660  -5.9720   6.0528
 CC3  C29   C  CH2   0  -0.469   4.0944  -6.6547   7.2399
 CC3  N25   N  NH1   0  -0.765   4.6082  -3.2535   8.5441
 CC3  C21   C  CR6   0   0.393   4.0966  -2.0587   9.0649
 CC3  C20   C  CR16  0  -0.378   3.1346  -1.3079   8.3952
 CC3  C22   C  CR16  0  -0.364   4.6077  -1.6211  10.2862
 CC3  C23   C  CR16  0  -0.238   4.1413  -0.4376  10.8336
 CC3  C24   C  CR16  0  -0.364   3.1810   0.3169  10.1832
 CC3  C19   C  CR6   0   0.379   2.6781  -0.1131   8.9522
 CC3  N18   N  NH1   0  -0.770   1.6965   0.6789   8.3613
 CC3  C16   C  CR6   0   0.596   1.2681   0.7488   7.0699
 CC3  N15   N  N     0  -0.489   0.2455   1.5805   6.8682
 CC3  C14   C  CR16  0  -0.023  -0.1855   1.6580   5.6125
 CC3  C13   C  CR16  0  -0.455   0.3605   0.9479   4.5695
 CC3  N17   N  N     0  -0.519   1.8841   0.0229   6.1457
 CC3  C12   C  CR6   0   0.576   1.4419   0.1142   4.9000
 CC3  N11   N  NH1   0  -0.780   2.0433  -0.6202   3.9279
 CC3  C1    C  CR6   0   0.387   3.1478  -1.4696   4.0114
 CC3  C6    C  CR16  0  -0.325   4.2089  -1.2630   4.8941
 CC3  C5    C  CR6   0  -0.181   5.2963  -2.1231   4.8704
 CC3  C7    C  CT    0   1.055   6.4729  -1.8678   5.7604
 CC3  F10   F  F     0  -0.311   6.9597  -2.9978   6.2910
 CC3  F9    F  F     0  -0.317   7.4868  -1.3076   5.0777
 CC3  F8    F  F     0  -0.301   6.1945  -1.0449   6.7744
 CC3  C4    C  CR16  0  -0.284   5.3581  -3.1845   3.9751
 CC3  C3    C  CR16  0  -0.233   4.3067  -3.3780   3.0950
 CC3  C2    C  CR16  0  -0.335   3.2101  -2.5332   3.1118
 CC3  H28   H  HCH1  0   0.277   5.8027  -5.3905   7.8607
 CC3  H301  H  HCH2  0   0.259   5.5635  -6.3725   5.6007
 CC3  H302  H  HCH2  0   0.262   3.9867  -5.4886   5.3634
 CC3  H291  H  HCH2  0   0.257   3.0194  -6.6449   7.3638
 CC3  H292  H  HCH2  0   0.262   4.5883  -7.5370   7.6242
 CC3  HN25  H  HNH1  0   0.407   5.4963  -3.5381   8.9266
 CC3  H20   H  HCR6  0   0.306   2.7593  -1.6289   7.4415
 CC3  H22   H  HCR6  0   0.263   5.3569  -2.2059  10.8053
 CC3  H23   H  HCR6  0   0.259   4.5324  -0.0984  11.7838
 CC3  H24   H  HCR6  0   0.264   2.8270   1.2415  10.6230
 CC3  HN18  H  HNH1  0   0.404   1.2518   1.3513   8.9672
 CC3  H14   H  HCR6  0   0.271  -1.0183   2.3291   5.4329
 CC3  H13   H  HCR6  0   0.277  -0.0168   1.0348   3.5609
 CC3  HN11  H  HNH1  0   0.416   1.5719  -0.6176   3.0365
 CC3  H6    H  HCR6  0   0.287   4.1750  -0.4377   5.5866
 CC3  H4    H  HCR6  0   0.268   6.2054  -3.8564   3.9587
 CC3  H3    H  HCR6  0   0.269   4.3365  -4.1994   2.3921
 CC3  H2    H  HCR6  0   0.276   2.3928  -2.7009   2.4205

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
 CC3  O27  C26   double    1.219  0.020  1.219
 CC3  C26  N25   single    1.361  0.020  1.361
 CC3  C26  C28   single    1.487  0.020  1.487
 CC3  C28  C30   single    1.505  0.020  1.505
 CC3  C28  C29   single    1.508  0.020  1.508
 CC3  C28  H28   single    0.970  0.020  1.090
 CC3  C30  C29   single    1.484  0.020  1.484
 CC3  C30  H301  single    0.970  0.020  1.090
 CC3  C30  H302  single    0.970  0.020  1.090
 CC3  C29  H291  single    0.970  0.020  1.090
 CC3  C29  H292  single    0.970  0.020  1.090
 CC3  N25  C21   single    1.400  0.020  1.400
 CC3  N25  HN25  single    0.860  0.020  1.020
 CC3  C21  C20   aromatic  1.392  0.020  1.392
 CC3  C21  C22   aromatic  1.394  0.020  1.394
 CC3  C20  C19   aromatic  1.395  0.020  1.395
 CC3  C20  H20   single    0.930  0.020  1.080
 CC3  C22  C23   aromatic  1.385  0.020  1.385
 CC3  C22  H22   single    0.930  0.020  1.080
 CC3  C23  C24   aromatic  1.384  0.020  1.384
 CC3  C23  H23   single    0.930  0.020  1.080
 CC3  C24  C19   aromatic  1.398  0.020  1.398
 CC3  C24  H24   single    0.930  0.020  1.080
 CC3  C19  N18   single    1.393  0.020  1.393
 CC3  N18  C16   single    1.362  0.020  1.362
 CC3  N18  HN18  single    0.860  0.020  1.020
 CC3  C16  N15   aromatic  1.334  0.020  1.334
 CC3  C16  N17   aromatic  1.327  0.020  1.327
 CC3  N15  C14   aromatic  1.330  0.020  1.330
 CC3  C14  C13   aromatic  1.375  0.020  1.375
 CC3  C14  H14   single    0.930  0.020  1.080
 CC3  C13  C12   aromatic  1.405  0.020  1.405
 CC3  C13  H13   single    0.930  0.020  1.080
 CC3  N17  C12   aromatic  1.325  0.020  1.325
 CC3  C12  N11   single    1.359  0.020  1.359
 CC3  N11  C1    single    1.396  0.020  1.396
 CC3  N11  HN11  single    0.860  0.020  1.020
 CC3  C1   C6    aromatic  1.396  0.020  1.396
 CC3  C1   C2    aromatic  1.394  0.020  1.394
 CC3  C6   C5    aromatic  1.387  0.020  1.387
 CC3  C6   H6    single    0.930  0.020  1.080
 CC3  C5   C7    single    1.497  0.020  1.497
 CC3  C5   C4    aromatic  1.390  0.020  1.390
 CC3  C7   F10   single    1.340  0.020  1.340
 CC3  C7   F9    single    1.345  0.020  1.345
 CC3  C7   F8    single    1.335  0.020  1.335
 CC3  C4   C3    aromatic  1.385  0.020  1.385
 CC3  C4   H4    single    0.930  0.020  1.080
 CC3  C3   C2    aromatic  1.384  0.020  1.384
 CC3  C3   H3    single    0.930  0.020  1.080
 CC3  C2   H2    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
 CC3  N25   C26  C28   113.79  3.000
 CC3  C28   C26  O27   122.38  3.000
 CC3  N25   C26  O27   123.82  3.000
 CC3  H28   C28  C29   116.43  3.000
 CC3  H28   C28  C30   116.60  3.000
 CC3  C29   C28  C30    59.02  3.000
 CC3  H28   C28  C26   116.94  3.000
 CC3  C29   C28  C26   117.53  3.000
 CC3  C30   C28  C26   117.71  3.000
 CC3  H302  C30  H301  114.84  3.000
 CC3  H302  C30  C29   118.26  3.000
 CC3  H301  C30  C29   118.92  3.000
 CC3  H302  C30  C28   116.87  3.000
 CC3  H301  C30  C28   116.63  3.000
 CC3  C29   C30  C28    60.59  3.000
 CC3  H292  C29  H291  114.86  3.000
 CC3  H292  C29  C30   118.92  3.000
 CC3  H291  C29  C30   118.04  3.000
 CC3  H292  C29  C28   116.75  3.000
 CC3  H291  C29  C28   117.11  3.000
 CC3  C30   C29  C28    60.39  3.000
 CC3  HN25  N25  C21   114.94  3.000
 CC3  HN25  N25  C26   116.33  3.000
 CC3  C21   N25  C26   128.29  3.000
 CC3  C22   C21  C20   120.36  3.000
 CC3  C22   C21  N25   117.36  3.000
 CC3  C20   C21  N25   122.26  3.000
 CC3  H20   C20  C19   119.75  3.000
 CC3  H20   C20  C21   120.50  3.000
 CC3  C19   C20  C21   119.73  3.000
 CC3  H22   C22  C23   120.33  3.000
 CC3  H22   C22  C21   120.26  3.000
 CC3  C23   C22  C21   119.40  3.000
 CC3  H23   C23  C24   119.52  3.000
 CC3  H23   C23  C22   119.55  3.000
 CC3  C24   C23  C22   120.93  3.000
 CC3  H24   C24  C19   120.17  3.000
 CC3  H24   C24  C23   120.09  3.000
 CC3  C19   C24  C23   119.73  3.000
 CC3  N18   C19  C24   116.89  3.000
 CC3  N18   C19  C20   123.25  3.000
 CC3  C24   C19  C20   119.83  3.000
 CC3  HN18  N18  C16   113.36  3.000
 CC3  HN18  N18  C19   115.79  3.000
 CC3  C16   N18  C19   130.76  3.000
 CC3  N17   C16  N15   126.29  3.000
 CC3  N17   C16  N18   119.09  3.000
 CC3  N15   C16  N18   114.62  3.000
 CC3  C14   N15  C16   115.32  3.000
 CC3  H14   C14  C13   119.93  3.000
 CC3  H14   C14  N15   116.19  3.000
 CC3  C13   C14  N15   123.88  3.000
 CC3  H13   C13  C12   122.42  3.000
 CC3  H13   C13  C14   121.87  3.000
 CC3  C12   C13  C14   115.71  3.000
 CC3  C12   N17  C16   117.53  3.000
 CC3  N11   C12  N17   119.20  3.000
 CC3  N11   C12  C13   119.55  3.000
 CC3  N17   C12  C13   121.26  3.000
 CC3  HN11  N11  C1    115.11  3.000
 CC3  HN11  N11  C12   115.10  3.000
 CC3  C1    N11  C12   129.52  3.000
 CC3  C2    C1   C6    119.14  3.000
 CC3  C2    C1   N11   117.45  3.000
 CC3  C6    C1   N11   123.32  3.000
 CC3  H6    C6   C5    120.70  3.000
 CC3  H6    C6   C1    119.72  3.000
 CC3  C5    C6   C1    119.58  3.000
 CC3  C4    C5   C7    118.56  3.000
 CC3  C4    C5   C6    121.30  3.000
 CC3  C7    C5   C6    120.03  3.000
 CC3  F8    C7   F9    106.62  3.000
 CC3  F8    C7   F10   107.14  3.000
 CC3  F9    C7   F10   106.17  3.000
 CC3  F8    C7   C5    113.12  3.000
 CC3  F9    C7   C5    111.21  3.000
 CC3  F10   C7   C5    112.16  3.000
 CC3  H4    C4   C3    119.89  3.000
 CC3  H4    C4   C5    121.26  3.000
 CC3  C3    C4   C5    118.84  3.000
 CC3  H3    C3   C2    119.55  3.000
 CC3  H3    C3   C4    119.89  3.000
 CC3  C2    C3   C4    120.56  3.000
 CC3  H2    C2   C3    119.69  3.000
 CC3  H2    C2   C1    119.73  3.000
 CC3  C3    C2   C1    120.58  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
 CC3  CONST_01  C24   C19  C20  C21     0.00   0.0  0
 CC3  CONST_02  C24   C23  C22  C21     0.00   0.0  0
 CC3  CONST_03  C23   C22  C21  C20     0.00   0.0  0
 CC3  CONST_04  C23   C24  C19  C20     0.00   0.0  0
 CC3  CONST_05  C19   C20  C21  C22     0.00   0.0  0
 CC3  CONST_06  C19   C24  C23  C22     0.00   0.0  0
 CC3  CONST_07  C13   C14  N15  C16     0.00   0.0  0
 CC3  CONST_08  C13   C12  N17  C16     0.00   0.0  0
 CC3  CONST_09  C12   N17  C16  N15     0.00   0.0  0
 CC3  CONST_10  C12   C13  C14  N15     0.00   0.0  0
 CC3  CONST_11  N17   C16  N15  C14     0.00   0.0  0
 CC3  CONST_12  N17   C12  C13  C14     0.00   0.0  0
 CC3  CONST_13  C4    C5   C6   C1      0.00   0.0  0
 CC3  CONST_14  C4    C3   C2   C1      0.00   0.0  0
 CC3  CONST_15  C3    C2   C1   C6      0.00   0.0  0
 CC3  CONST_16  C3    C4   C5   C6      0.00   0.0  0
 CC3  CONST_17  C2    C1   C6   C5      0.00   0.0  0
 CC3  CONST_18  C2    C3   C4   C5      0.00   0.0  0
 CC3  CONST_19  C19   C20  C21  N25   180.00   0.0  0
 CC3  CONST_20  C23   C22  C21  N25   180.00   0.0  0
 CC3  CONST_21  N18   C19  C20  C21   180.00   0.0  0
 CC3  CONST_22  N18   C19  C24  C23   180.00   0.0  0
 CC3  CONST_23  C14   N15  C16  N18   180.00   0.0  0
 CC3  CONST_24  C12   N17  C16  N18   180.00   0.0  0
 CC3  CONST_25  N11   C12  N17  C16   180.00   0.0  0
 CC3  CONST_26  N11   C12  C13  C14   180.00   0.0  0
 CC3  CONST_27  C5    C6   C1   N11   180.00   0.0  0
 CC3  CONST_28  C3    C2   C1   N11   180.00   0.0  0
 CC3  CONST_29  C7    C5   C6   C1    180.00   0.0  0
 CC3  CONST_30  C3    C4   C5   C7    180.00   0.0  0
 CC3  CONST_31  H23   C23  C22  C21   180.00   0.0  0
 CC3  CONST_32  H22   C22  C21  C20   180.00   0.0  0
 CC3  CONST_33  H24   C24  C19  C20   180.00   0.0  0
 CC3  CONST_34  H20   C20  C21  C22   180.00   0.0  0
 CC3  CONST_35  H14   C14  N15  C16   180.00   0.0  0
 CC3  CONST_36  H13   C13  C14  N15   180.00   0.0  0
 CC3  CONST_37  H3    C3   C2   C1    180.00   0.0  0
 CC3  CONST_38  H2    C2   C1   C6    180.00   0.0  0
 CC3  CONST_39  H4    C4   C5   C6    180.00   0.0  0
 CC3  CONST_40  H6    C6   C5   C4    180.00   0.0  0
 CC3  CONST_41  C21   N25  C26  C28   180.00   0.0  0
 CC3  CONST_45  C21   N25  C26  O27     0.00   0.0  0
 CC3  Var_01    C29   C30  C28  C26  -107.08  30.0  1
 CC3  Var_02    C16   N18  C19  C20   -21.46  30.0  2
 CC3  Var_03    N15   C16  N18  C19   176.54  30.0  2
 CC3  Var_04    C1    N11  C12  C13   177.54  30.0  2
 CC3  Var_05    C6    C1   N11  C12   -32.18  30.0  2
 CC3  Var_06    H291  C29  C30  C28   106.93  30.0  1
 CC3  Var_07    C30   C28  C26  O27    33.38  30.0  3
 CC3  Var_08    F10   C7   C5   C6    139.80  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CC3  chir_01  C28  C26  C30  C29  both

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
 CC3  plan-1  N25   0.020
 CC3  plan-1  C21   0.020
 CC3  plan-1  C20   0.020
 CC3  plan-1  C22   0.020
 CC3  plan-1  C23   0.020
 CC3  plan-1  C24   0.020
 CC3  plan-1  C19   0.020
 CC3  plan-1  N18   0.020
 CC3  plan-1  H20   0.020
 CC3  plan-1  H22   0.020
 CC3  plan-1  H23   0.020
 CC3  plan-1  H24   0.020
 CC3  plan-2  N18   0.020
 CC3  plan-2  C16   0.020
 CC3  plan-2  N15   0.020
 CC3  plan-2  C14   0.020
 CC3  plan-2  C13   0.020
 CC3  plan-2  N17   0.020
 CC3  plan-2  C12   0.020
 CC3  plan-2  N11   0.020
 CC3  plan-2  H14   0.020
 CC3  plan-2  H13   0.020
 CC3  plan-3  N11   0.020
 CC3  plan-3  C1    0.020
 CC3  plan-3  C6    0.020
 CC3  plan-3  C5    0.020
 CC3  plan-3  C7    0.020
 CC3  plan-3  C4    0.020
 CC3  plan-3  C3    0.020
 CC3  plan-3  C2    0.020
 CC3  plan-3  H6    0.020
 CC3  plan-3  H4    0.020
 CC3  plan-3  H3    0.020
 CC3  plan-3  H2    0.020
 CC3  plan-4  O27   0.020
 CC3  plan-4  C26   0.020
 CC3  plan-4  C28   0.020
 CC3  plan-4  N25   0.020
 CC3  plan-4  C21   0.020
 CC3  plan-4  HN25  0.020

