# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:12:29 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [4-[[4-(ethylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-fluoranyl-5-methoxy-phenyl]-morpholin-4-yl-methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNc1nc(Nc2cc(F)c(cc2OC)C(=O)N3CCOCC3)ncc1C(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
 A0T  A0T  '[4-[[4-(ethylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-2-fluoranyl-5-methoxy-phenyl]-morpholin-4-yl-methanone'  ligand  52  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A0T
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
 A0T  C01  C  CH3   0  -0.706   6.7194   3.0498  -0.8700
 A0T  C02  C  CH2   0  -0.263   5.3531   2.5313  -0.4641
 A0T  N03  N  NH1   0  -0.667   5.4284   1.1062  -0.1921
 A0T  C04  C  CR6   0   0.588   4.3572   0.3425   0.0384
 A0T  C05  C  CR6   0  -0.443   4.4323  -1.0599   0.2948
 A0T  C06  C  CR16  0   0.004   3.2321  -1.7006   0.4949
 A0T  N07  N  N     0  -0.502   2.0497  -1.0973   0.4634
 A0T  C08  C  CR6   0   0.627   2.0842   0.2077   0.2203
 A0T  N09  N  N     0  -0.528   3.1727   0.9419   0.0108
 A0T  N10  N  NH1   0  -0.759   0.9262   0.9201   0.1718
 A0T  C11  C  CR6   0   0.299  -0.3923   0.5344   0.3388
 A0T  C12  C  CR16  0  -0.493  -0.8256  -0.7673   0.5571
 A0T  C13  C  CR6   0   0.569  -2.1771  -1.0167   0.7101
 A0T  C14  C  CR6   0  -0.311  -3.1331  -0.0317   0.6362
 A0T  C15  C  CR16  0  -0.359  -2.6986   1.2773   0.4109
 A0T  C16  C  CR6   0   0.328  -1.3570   1.5688   0.2678
 A0T  O17  O  O2    0  -0.484  -0.8619   2.8040   0.0554
 A0T  C18  C  CH3   0  -0.436  -1.7627   3.8906  -0.0410
 A0T  C19  C  C     0   0.524  -4.5751  -0.3228   0.9072
 A0T  O20  O  O     0  -0.481  -4.9170  -0.7251   2.0104
 A0T  N21  N  NT    0  -0.453  -5.4410  -0.0661  -0.0918
 A0T  C22  C  CH2   0  -0.331  -6.8761  -0.1887   0.1058
 A0T  C23  C  CH2   0  -0.183  -7.4391  -1.2454  -0.8285
 A0T  O24  O  O2    0  -0.481  -7.1134  -0.9663  -2.1726
 A0T  C25  C  CH2   0  -0.175  -5.7183  -0.8989  -2.3576
 A0T  C26  C  CH2   0  -0.328  -5.0821   0.1694  -1.4811
 A0T  C28  C  CT    0   1.074   5.7167  -1.8002   0.3249
 A0T  F27  F  F     0  -0.309  -2.5636  -2.2879   0.9101
 A0T  F29  F  F     0  -0.320   6.3861  -1.7081  -0.8393
 A0T  F30  F  F     0  -0.322   6.5574  -1.3298   1.2660
 A0T  F31  F  F     0  -0.298   5.5502  -3.1010   0.5719
 A0T  H1   H  HCH3  0   0.237   7.4530   2.9090  -0.0750
 A0T  H2   H  HCH3  0   0.237   7.0822   2.5465  -1.7665
 A0T  H3   H  HCH3  0   0.250   6.6617   4.1158  -1.0835
 A0T  H4   H  HCH2  0   0.238   4.9902   3.0667   0.4170
 A0T  H5   H  HCH2  0   0.243   4.6305   2.7076  -1.2617
 A0T  H6   H  HNH1  0   0.402   6.3518   0.7200  -0.0985
 A0T  H7   H  HCR6  0   0.283   3.2035  -2.7657   0.6909
 A0T  H8   H  HNH1  0   0.414   1.0714   1.9033  -0.0038
 A0T  H9   H  HCR6  0   0.312  -0.1166  -1.5778   0.6067
 A0T  H10  H  HCR6  0   0.300  -3.4395   2.0640   0.3593
 A0T  H11  H  HCH3  0   0.233  -2.4659   3.7595  -0.8672
 A0T  H12  H  HCH3  0   0.234  -2.3238   4.0318   0.8860
 A0T  H13  H  HCH3  0   0.267  -1.1598   4.7753  -0.2264
 A0T  H14  H  HCH2  0   0.272  -7.0901  -0.4469   1.1395
 A0T  H15  H  HCH2  0   0.254  -7.3391   0.7800  -0.1071
 A0T  H16  H  HCH2  0   0.212  -7.0592  -2.2336  -0.5344
 A0T  H17  H  HCH2  0   0.246  -8.5271  -1.2655  -0.7526
 A0T  H18  H  HCH2  0   0.208  -5.2520  -1.8694  -2.1360
 A0T  H19  H  HCH2  0   0.248  -5.5350  -0.6681  -3.4078
 A0T  H20  H  HCH2  0   0.253  -5.4302   1.1624  -1.7819
 A0T  H21  H  HCH2  0   0.279  -4.0030   0.1418  -1.6124

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
 A0T  C01  C02  single    1.517  0.020  1.517
 A0T  F29  C28  single    1.346  0.020  1.346
 A0T  C02  N03  single    1.453  0.020  1.453
 A0T  N03  C04  single    1.336  0.020  1.336
 A0T  F27  C13  single    1.344  0.020  1.344
 A0T  C28  F31  single    1.334  0.020  1.334
 A0T  C28  F30  single    1.347  0.020  1.347
 A0T  C28  C05  single    1.483  0.020  1.483
 A0T  C04  C05  aromatic  1.428  0.020  1.428
 A0T  C04  N09  aromatic  1.328  0.020  1.328
 A0T  C05  C06  aromatic  1.375  0.020  1.375
 A0T  N09  C08  aromatic  1.330  0.020  1.330
 A0T  C13  C12  aromatic  1.383  0.020  1.383
 A0T  C13  C14  aromatic  1.375  0.020  1.375
 A0T  C12  C11  aromatic  1.389  0.020  1.389
 A0T  C06  N07  aromatic  1.328  0.020  1.328
 A0T  O20  C19  double    1.223  0.020  1.223
 A0T  C08  N07  aromatic  1.328  0.020  1.328
 A0T  C08  N10  single    1.360  0.020  1.360
 A0T  C19  C14  single    1.496  0.020  1.496
 A0T  C19  N21  single    1.347  0.020  1.347
 A0T  C14  C15  aromatic  1.397  0.020  1.397
 A0T  C11  N10  single    1.384  0.020  1.384
 A0T  C11  C16  aromatic  1.416  0.020  1.416
 A0T  N21  C26  single    1.454  0.020  1.454
 A0T  N21  C22  single    1.454  0.020  1.454
 A0T  C26  C25  single    1.521  0.020  1.521
 A0T  C22  C23  single    1.519  0.020  1.519
 A0T  C15  C16  aromatic  1.380  0.020  1.380
 A0T  C16  O17  single    1.348  0.020  1.348
 A0T  C25  O24  single    1.409  0.020  1.409
 A0T  C23  O24  single    1.411  0.020  1.411
 A0T  O17  C18  single    1.415  0.020  1.415
 A0T  C01  H1   single    0.970  0.020  1.090
 A0T  C01  H2   single    0.970  0.020  1.090
 A0T  C01  H3   single    0.970  0.020  1.090
 A0T  C02  H4   single    0.970  0.020  1.090
 A0T  C02  H5   single    0.970  0.020  1.090
 A0T  N03  H6   single    0.860  0.020  1.020
 A0T  C06  H7   single    0.930  0.020  1.080
 A0T  N10  H8   single    0.860  0.020  1.020
 A0T  C12  H9   single    0.930  0.020  1.080
 A0T  C15  H10  single    0.930  0.020  1.080
 A0T  C18  H11  single    0.970  0.020  1.090
 A0T  C18  H12  single    0.970  0.020  1.090
 A0T  C18  H13  single    0.970  0.020  1.090
 A0T  C22  H14  single    0.970  0.020  1.090
 A0T  C22  H15  single    0.970  0.020  1.090
 A0T  C23  H16  single    0.970  0.020  1.090
 A0T  C23  H17  single    0.970  0.020  1.090
 A0T  C25  H18  single    0.970  0.020  1.090
 A0T  C25  H19  single    0.970  0.020  1.090
 A0T  C26  H20  single    0.970  0.020  1.090
 A0T  C26  H21  single    0.970  0.020  1.090

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
 A0T  H3   C01  H2   107.96  3.000
 A0T  H3   C01  H1   107.75  3.000
 A0T  H2   C01  H1   108.41  3.000
 A0T  H3   C01  C02  109.84  3.000
 A0T  H2   C01  C02  111.22  3.000
 A0T  H1   C01  C02  111.52  3.000
 A0T  H5   C02  H4   106.88  3.000
 A0T  H5   C02  N03  109.26  3.000
 A0T  H4   C02  N03  110.29  3.000
 A0T  H5   C02  C01  110.24  3.000
 A0T  H4   C02  C01  110.33  3.000
 A0T  N03  C02  C01  109.80  3.000
 A0T  H6   N03  C04  120.07  3.000
 A0T  H6   N03  C02  116.22  3.000
 A0T  C04  N03  C02  123.48  3.000
 A0T  N09  C04  C05  119.61  3.000
 A0T  N09  C04  N03  116.99  3.000
 A0T  C05  C04  N03  123.40  3.000
 A0T  C28  C05  C06  121.36  3.000
 A0T  C06  C05  C04  115.97  3.000
 A0T  C28  C05  C04  122.66  3.000
 A0T  H7   C06  N07  115.31  3.000
 A0T  H7   C06  C05  120.49  3.000
 A0T  N07  C06  C05  124.20  3.000
 A0T  C08  N07  C06  115.32  3.000
 A0T  N10  C08  N09  113.71  3.000
 A0T  N10  C08  N07  119.94  3.000
 A0T  N09  C08  N07  126.36  3.000
 A0T  C08  N09  C04  118.54  3.000
 A0T  H8   N10  C11  115.44  3.000
 A0T  H8   N10  C08  113.19  3.000
 A0T  C11  N10  C08  131.36  3.000
 A0T  C16  C11  C12  118.67  3.000
 A0T  C16  C11  N10  116.07  3.000
 A0T  C12  C11  N10  125.26  3.000
 A0T  H9   C12  C13  120.14  3.000
 A0T  H9   C12  C11  120.43  3.000
 A0T  C13  C12  C11  119.42  3.000
 A0T  F27  C13  C14  119.07  3.000
 A0T  C14  C13  C12  122.99  3.000
 A0T  F27  C13  C12  117.92  3.000
 A0T  C19  C14  C15  120.74  3.000
 A0T  C15  C14  C13  117.62  3.000
 A0T  C19  C14  C13  121.42  3.000
 A0T  H10  C15  C16  120.47  3.000
 A0T  H10  C15  C14  118.42  3.000
 A0T  C16  C15  C14  121.11  3.000
 A0T  O17  C16  C15  124.54  3.000
 A0T  O17  C16  C11  115.29  3.000
 A0T  C15  C16  C11  120.18  3.000
 A0T  C18  O17  C16  118.74  3.000
 A0T  H13  C18  H12  108.93  3.000
 A0T  H13  C18  H11  109.01  3.000
 A0T  H12  C18  H11  109.05  3.000
 A0T  H13  C18  O17  106.48  3.000
 A0T  H12  C18  O17  111.61  3.000
 A0T  H11  C18  O17  111.66  3.000
 A0T  N21  C19  O20  123.51  3.000
 A0T  N21  C19  C14  116.64  3.000
 A0T  O20  C19  C14  119.79  3.000
 A0T  C26  N21  C22  112.78  3.000
 A0T  C22  N21  C19  121.18  3.000
 A0T  C26  N21  C19  125.52  3.000
 A0T  H15  C22  H14  108.19  3.000
 A0T  H15  C22  C23  109.83  3.000
 A0T  H14  C22  C23  110.29  3.000
 A0T  H15  C22  N21  108.45  3.000
 A0T  H14  C22  N21  110.10  3.000
 A0T  C23  C22  N21  109.93  3.000
 A0T  H17  C23  H16  108.04  3.000
 A0T  H17  C23  O24  107.47  3.000
 A0T  H16  C23  O24  110.68  3.000
 A0T  H17  C23  C22  109.86  3.000
 A0T  H16  C23  C22  109.44  3.000
 A0T  O24  C23  C22  111.27  3.000
 A0T  C25  O24  C23  111.30  3.000
 A0T  H19  C25  H18  108.04  3.000
 A0T  H19  C25  C26  109.63  3.000
 A0T  H18  C25  C26  109.05  3.000
 A0T  H19  C25  O24  107.63  3.000
 A0T  H18  C25  O24  110.57  3.000
 A0T  C26  C25  O24  111.84  3.000
 A0T  H21  C26  H20  107.79  3.000
 A0T  H21  C26  C25  109.12  3.000
 A0T  H20  C26  C25  110.23  3.000
 A0T  H21  C26  N21  110.86  3.000
 A0T  H20  C26  N21  109.33  3.000
 A0T  C25  C26  N21  109.48  3.000
 A0T  F31  C28  F30  106.80  3.000
 A0T  F30  C28  F29  105.67  3.000
 A0T  F31  C28  F29  106.79  3.000
 A0T  F30  C28  C05  112.36  3.000
 A0T  F31  C28  C05  112.48  3.000
 A0T  F29  C28  C05  112.27  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
 A0T  CONST_01  N07  C06  C05  C04     0.00   0.0  0
 A0T  CONST_02  N07  C08  N09  C04     0.00   0.0  0
 A0T  CONST_03  C08  N09  C04  C05     0.00   0.0  0
 A0T  CONST_04  C08  N07  C06  C05     0.00   0.0  0
 A0T  CONST_05  N09  C04  C05  C06     0.00   0.0  0
 A0T  CONST_06  N09  C08  N07  C06     0.00   0.0  0
 A0T  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 A0T  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 A0T  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 A0T  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 A0T  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 A0T  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 A0T  CONST_13  C06  C05  C04  N03   180.00   0.0  0
 A0T  CONST_14  C08  N09  C04  N03   180.00   0.0  0
 A0T  CONST_15  N10  C08  N09  C04   180.00   0.0  0
 A0T  CONST_16  N10  C08  N07  C06   180.00   0.0  0
 A0T  CONST_17  C28  C05  C06  N07   180.00   0.0  0
 A0T  CONST_18  C28  C05  C04  N09   180.00   0.0  0
 A0T  CONST_19  C13  C12  C11  N10   180.00   0.0  0
 A0T  CONST_20  C15  C16  C11  N10   180.00   0.0  0
 A0T  CONST_21  F27  C13  C12  C11   180.00   0.0  0
 A0T  CONST_22  C19  C14  C13  C12   180.00   0.0  0
 A0T  CONST_23  O17  C16  C11  C12   180.00   0.0  0
 A0T  CONST_24  O17  C16  C15  C14   180.00   0.0  0
 A0T  CONST_25  F27  C13  C14  C15   180.00   0.0  0
 A0T  CONST_26  C19  C14  C15  C16   180.00   0.0  0
 A0T  CONST_27  C26  N21  C19  C14     0.00   0.0  0
 A0T  CONST_28  C22  N21  C19  C14   180.00   0.0  0
 A0T  CONST_29  H7   C06  C05  C04   180.00   0.0  0
 A0T  CONST_30  H10  C15  C16  C11   180.00   0.0  0
 A0T  CONST_31  H9   C12  C13  C14   180.00   0.0  0
 A0T  CONST_32  C26  N21  C19  O20   180.00   0.0  0
 A0T  CONST_33  C22  N21  C19  O20     0.00   0.0  0
 A0T  CONST_34  C05  C04  N03  C02   180.00   0.0  0
 A0T  CONST_35  N09  C04  N03  C02     0.00   0.0  0
 A0T  CONST_36  H6   N03  C04  C05     0.00   0.0  0
 A0T  Var_01    O24  C25  C26  N21    55.02  30.0  1
 A0T  Var_02    O24  C23  C22  N21   -55.37  30.0  1
 A0T  Var_03    C25  C26  N21  C22   -53.03  30.0  1
 A0T  Var_04    C26  N21  C22  C23    53.50  30.0  1
 A0T  Var_05    C26  C25  O24  C23   -58.76  30.0  1
 A0T  Var_06    C11  N10  C08  N07     0.08  30.0  2
 A0T  Var_07    C12  C11  N10  C08    -2.72  30.0  3
 A0T  Var_08    N21  C19  C14  C13  -120.73  30.0  2
 A0T  Var_09    F29  C28  C05  C04   -59.02  30.0  3
 A0T  Var_10    C04  N03  C02  C01  -172.09  30.0  3
 A0T  Var_11    H11  C18  O17  C16   -60.22  30.0  3
 A0T  Var_12    H1   C01  C02  N03   -61.17  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
 A0T  plan-1  N03  0.020
 A0T  plan-1  C04  0.020
 A0T  plan-1  C05  0.020
 A0T  plan-1  C06  0.020
 A0T  plan-1  N07  0.020
 A0T  plan-1  C08  0.020
 A0T  plan-1  N09  0.020
 A0T  plan-1  N10  0.020
 A0T  plan-1  C28  0.020
 A0T  plan-1  H7   0.020
 A0T  plan-2  N10  0.020
 A0T  plan-2  C11  0.020
 A0T  plan-2  C12  0.020
 A0T  plan-2  C13  0.020
 A0T  plan-2  C14  0.020
 A0T  plan-2  C15  0.020
 A0T  plan-2  C16  0.020
 A0T  plan-2  O17  0.020
 A0T  plan-2  C19  0.020
 A0T  plan-2  F27  0.020
 A0T  plan-2  H9   0.020
 A0T  plan-2  H10  0.020
 A0T  plan-3  C14  0.020
 A0T  plan-3  C19  0.020
 A0T  plan-3  O20  0.020
 A0T  plan-3  N21  0.020
 A0T  plan-3  C22  0.020
 A0T  plan-3  C26  0.020
 A0T  plan-4  C02  0.020
 A0T  plan-4  N03  0.020
 A0T  plan-4  C04  0.020
 A0T  plan-4  H6   0.020

