# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 27 23:16:10 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-[2-fluoro-6-(trifluoromethyl)anilino]-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2CCN(C)Cc2cc1Nc3ncc(C(N)=O)c(Nc4c(F)cccc4C(F)(F)F)n3
#
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
 YK1  YK1  4-[2-fluoro-6-(trifluoromethyl)anilino]-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyrimidine-5-carboxamide  ligand  57  35  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YK1
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
 YK1  C2   C  CR6   0   0.608  14.3491  -36.7505  35.7978
 YK1  C4   C  CR6   0   0.546  13.9539  -35.5725  33.8925
 YK1  C5   C  CR6   0  -0.276  15.2590  -35.8705  33.4192
 YK1  C6   C  CR16  0   0.012  16.0182  -36.6432  34.2932
 YK1  C7   C  C     0   0.487  15.7365  -35.3954  32.1052
 YK1  N10  N  NH1   0  -0.788  13.0942  -34.8137  33.1890
 YK1  C11  C  CR6   0   0.303  11.7519  -34.6435  33.5667
 YK1  C12  C  CR6   0  -0.354  11.2539  -33.4270  34.0395
 YK1  C15  C  CR16  0  -0.312   9.5223  -35.5855  33.7445
 YK1  C16  C  CR6   0   0.428  10.8622  -35.7002  33.4370
 YK1  C18  C  CT    0   1.043  12.1975  -32.2750  34.2285
 YK1  N22  N  NH1   0  -0.586  13.9510  -37.2187  37.0007
 YK1  C23  C  CR6   0   0.256  12.7888  -36.9840  37.7351
 YK1  C24  C  CR16  0  -0.358  11.7417  -36.1619  37.3498
 YK1  C27  C  CR16  0  -0.345  11.6014  -37.4348  39.7964
 YK1  C30  C  CH3   0  -0.389  13.7948  -39.0259  40.5796
 YK1  C31  C  CH2   0  -0.479   9.3594  -36.3956  40.2868
 YK1  C32  C  CH2   0  -0.258   8.1884  -35.8088  39.5173
 YK1  C34  C  CH2   0  -0.251   9.5203  -35.0738  37.6829
 YK1  N1   N  N     0  -0.483  15.6056  -37.0871  35.4611
 YK1  N3   N  N     0  -0.513  13.5232  -36.0281  35.0622
 YK1  O8   O  O     0  -0.492  15.0596  -34.6227  31.4215
 YK1  N9   N  NH2   0  -0.845  16.9355  -35.8172  31.6755
 YK1  C13  C  CR16  0  -0.210   9.9055  -33.2861  34.3408
 YK1  C14  C  CR16  0  -0.237   9.0468  -34.3650  34.1929
 YK1  F17  F  F     0  -0.307  11.3311  -36.8648  32.9866
 YK1  F19  F  F     0  -0.333  12.7622  -31.8974  33.0738
 YK1  F20  F  F     0  -0.384  11.5869  -31.1998  34.7311
 YK1  F21  F  F     0  -0.308  13.1902  -32.5792  35.0722
 YK1  C25  C  CR6   0   0.119  10.6308  -35.9653  38.1706
 YK1  C26  C  CR6   0  -0.066  10.5520  -36.6029  39.3970
 YK1  C28  C  CR6   0   0.311  12.7047  -37.6322  38.9888
 YK1  N33  N  NT    0  -0.447   8.6323  -34.6639  38.7474
 YK1  H1   H  HCR6  0   0.291  17.0380  -36.9174  34.0442
 YK1  H2   H  HNH1  0   0.413  13.4523  -34.4272  32.3181
 YK1  H3   H  HCR6  0   0.287   8.8628  -36.4359  33.6287
 YK1  H4   H  HNH1  0   0.392  14.6523  -37.7759  37.4664
 YK1  H5   H  HCR6  0   0.279  11.7837  -35.6572  36.3970
 YK1  H6   H  HCR6  0   0.282  11.5322  -37.9321  40.7561
 YK1  H7   H  HCH3  0   0.266  14.7328  -39.5726  40.6326
 YK1  H8   H  HCH3  0   0.260  13.7703  -38.2866  41.3843
 YK1  H9   H  HCH3  0   0.194  12.9692  -39.7283  40.7198
 YK1  H10  H  HCH2  0   0.228   9.0640  -37.3404  40.7495
 YK1  H11  H  HCH2  0   0.264   9.6259  -35.7209  41.1064
 YK1  H12  H  HCH2  0   0.187   7.4154  -35.4876  40.2181
 YK1  H13  H  HCH2  0   0.237   7.7338  -36.5815  38.8727
 YK1  H14  H  HCH2  0   0.276   9.9455  -34.1812  37.2129
 YK1  H15  H  HCH2  0   0.175   8.9684  -35.5981  36.8800
 YK1  H16  H  HCH3  0   0.250   6.8984  -33.5403  39.0448
 YK1  H17  H  HCH3  0   0.187   7.9095  -33.0102  37.7009
 YK1  H18  H  HCH3  0   0.233   6.8956  -34.4487  37.5230
 YK1  H19  H  HNH2  0   0.410  17.2555  -35.5163  30.7694
 YK1  H20  H  HNH2  0   0.385  17.4792  -36.5300  32.1281
 YK1  H21  H  HCR6  0   0.282   9.5137  -32.3473  34.7046
 YK1  H22  H  HCR6  0   0.250   7.9989  -34.2545  34.4346
 YK1  O29  O  O2    0  -0.578  13.7578  -38.4161  39.3058
 YK1  C35  C  CH3   0  -0.540   7.5312  -33.8882  38.2274

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
 YK1  O8   C7   double    1.234  0.020  1.234
 YK1  N9   C7   single    1.342  0.020  1.342
 YK1  F19  C18  single    1.340  0.020  1.340
 YK1  C7   C5   single    1.477  0.020  1.477
 YK1  C18  F20  single    1.335  0.020  1.335
 YK1  C18  C12  single    1.501  0.020  1.501
 YK1  C18  F21  single    1.338  0.020  1.338
 YK1  N10  C11  single    1.405  0.020  1.405
 YK1  N10  C4   single    1.345  0.020  1.345
 YK1  C12  C11  aromatic  1.397  0.020  1.397
 YK1  C12  C13  aromatic  1.389  0.020  1.389
 YK1  C5   C4   aromatic  1.420  0.020  1.420
 YK1  C5   C6   aromatic  1.392  0.020  1.392
 YK1  C11  C16  aromatic  1.387  0.020  1.387
 YK1  C13  C14  aromatic  1.387  0.020  1.387
 YK1  C16  F17  single    1.334  0.020  1.334
 YK1  C16  C15  aromatic  1.379  0.020  1.379
 YK1  C4   N3   aromatic  1.327  0.020  1.327
 YK1  C14  C15  aromatic  1.385  0.020  1.385
 YK1  C6   N1   aromatic  1.316  0.020  1.316
 YK1  N3   C2   aromatic  1.321  0.020  1.321
 YK1  N1   C2   aromatic  1.344  0.020  1.344
 YK1  C2   N22  single    1.351  0.020  1.351
 YK1  N22  C23  single    1.395  0.020  1.395
 YK1  C24  C23  aromatic  1.386  0.020  1.386
 YK1  C24  C25  aromatic  1.395  0.020  1.395
 YK1  C34  C25  single    1.505  0.020  1.505
 YK1  C34  N33  single    1.446  0.020  1.446
 YK1  C23  C28  aromatic  1.414  0.020  1.414
 YK1  C25  C26  aromatic  1.385  0.020  1.385
 YK1  C35  N33  single    1.444  0.020  1.444
 YK1  N33  C32  single    1.449  0.020  1.449
 YK1  C28  O29  single    1.351  0.020  1.351
 YK1  C28  C27  aromatic  1.381  0.020  1.381
 YK1  C26  C27  aromatic  1.397  0.020  1.397
 YK1  C26  C31  single    1.502  0.020  1.502
 YK1  O29  C30  single    1.413  0.020  1.413
 YK1  C32  C31  single    1.519  0.020  1.519
 YK1  C6   H1   single    0.930  0.020  1.080
 YK1  N10  H2   single    0.860  0.020  1.020
 YK1  C15  H3   single    0.930  0.020  1.080
 YK1  N22  H4   single    0.860  0.020  1.020
 YK1  C24  H5   single    0.930  0.020  1.080
 YK1  C27  H6   single    0.930  0.020  1.080
 YK1  C30  H7   single    0.970  0.020  1.090
 YK1  C30  H8   single    0.970  0.020  1.090
 YK1  C30  H9   single    0.970  0.020  1.090
 YK1  C31  H10  single    0.970  0.020  1.090
 YK1  C31  H11  single    0.970  0.020  1.090
 YK1  C32  H12  single    0.970  0.020  1.090
 YK1  C32  H13  single    0.970  0.020  1.090
 YK1  C34  H14  single    0.970  0.020  1.090
 YK1  C34  H15  single    0.970  0.020  1.090
 YK1  C35  H16  single    0.970  0.020  1.090
 YK1  C35  H17  single    0.970  0.020  1.090
 YK1  C35  H18  single    0.970  0.020  1.090
 YK1  N9   H19  single    0.860  0.020  1.020
 YK1  N9   H20  single    0.860  0.020  1.020
 YK1  C13  H21  single    0.930  0.020  1.080
 YK1  C14  H22  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
 YK1  N3   C2   N1   125.60  3.000
 YK1  N1   C2   N22  114.32  3.000
 YK1  N3   C2   N22  120.07  3.000
 YK1  N3   C4   N10  116.56  3.000
 YK1  N3   C4   C5   121.34  3.000
 YK1  N10  C4   C5   122.10  3.000
 YK1  C7   C5   C6   124.13  3.000
 YK1  C6   C5   C4   114.11  3.000
 YK1  C7   C5   C4   121.76  3.000
 YK1  H1   C6   N1   114.41  3.000
 YK1  H1   C6   C5   120.59  3.000
 YK1  N1   C6   C5   125.00  3.000
 YK1  N9   C7   O8   120.64  3.000
 YK1  N9   C7   C5   118.22  3.000
 YK1  O8   C7   C5   121.14  3.000
 YK1  H2   N10  C11  121.34  3.000
 YK1  H2   N10  C4   115.90  3.000
 YK1  C11  N10  C4   122.58  3.000
 YK1  C16  C11  C12  117.80  3.000
 YK1  C16  C11  N10  119.69  3.000
 YK1  C12  C11  N10  122.49  3.000
 YK1  C13  C12  C18  120.34  3.000
 YK1  C13  C12  C11  120.52  3.000
 YK1  C18  C12  C11  119.14  3.000
 YK1  H3   C15  C14  121.20  3.000
 YK1  H3   C15  C16  120.18  3.000
 YK1  C14  C15  C16  118.62  3.000
 YK1  F17  C16  C15  119.29  3.000
 YK1  C15  C16  C11  122.59  3.000
 YK1  F17  C16  C11  118.11  3.000
 YK1  F21  C18  F20  106.57  3.000
 YK1  F21  C18  F19  107.15  3.000
 YK1  F20  C18  F19  106.88  3.000
 YK1  F21  C18  C12  111.80  3.000
 YK1  F20  C18  C12  112.21  3.000
 YK1  F19  C18  C12  111.89  3.000
 YK1  H4   N22  C23  115.40  3.000
 YK1  H4   N22  C2   113.41  3.000
 YK1  C23  N22  C2   131.01  3.000
 YK1  C28  C23  C24  118.26  3.000
 YK1  C28  C23  N22  116.06  3.000
 YK1  C24  C23  N22  125.66  3.000
 YK1  H5   C24  C25  118.99  3.000
 YK1  H5   C24  C23  119.57  3.000
 YK1  C25  C24  C23  121.44  3.000
 YK1  H6   C27  C28  120.23  3.000
 YK1  H6   C27  C26  118.59  3.000
 YK1  C28  C27  C26  121.18  3.000
 YK1  H9   C30  H8   108.86  3.000
 YK1  H9   C30  H7   108.80  3.000
 YK1  H8   C30  H7   108.88  3.000
 YK1  H9   C30  O29  111.91  3.000
 YK1  H8   C30  O29  111.80  3.000
 YK1  H7   C30  O29  106.48  3.000
 YK1  H11  C31  H10  106.37  3.000
 YK1  H11  C31  C26  109.59  3.000
 YK1  H10  C31  C26  110.25  3.000
 YK1  H11  C31  C32  109.20  3.000
 YK1  H10  C31  C32  109.88  3.000
 YK1  C26  C31  C32  111.42  3.000
 YK1  H13  C32  H12  106.81  3.000
 YK1  H13  C32  N33  111.64  3.000
 YK1  H12  C32  N33  108.99  3.000
 YK1  H13  C32  C31  110.05  3.000
 YK1  H12  C32  C31  109.53  3.000
 YK1  N33  C32  C31  109.76  3.000
 YK1  H15  C34  H14  105.58  3.000
 YK1  H15  C34  N33  111.24  3.000
 YK1  H14  C34  N33  108.87  3.000
 YK1  H15  C34  C25  108.82  3.000
 YK1  H14  C34  C25  109.60  3.000
 YK1  N33  C34  C25  112.49  3.000
 YK1  C6   N1   C2   115.54  3.000
 YK1  C4   N3   C2   118.40  3.000
 YK1  H20  N9   H19  116.46  3.000
 YK1  H20  N9   C7   124.24  3.000
 YK1  H19  N9   C7   118.57  3.000
 YK1  H21  C13  C14  119.17  3.000
 YK1  H21  C13  C12  120.89  3.000
 YK1  C14  C13  C12  119.94  3.000
 YK1  H22  C14  C13  119.79  3.000
 YK1  H22  C14  C15  119.70  3.000
 YK1  C13  C14  C15  120.51  3.000
 YK1  C26  C25  C34  121.18  3.000
 YK1  C26  C25  C24  120.10  3.000
 YK1  C34  C25  C24  118.71  3.000
 YK1  C25  C26  C31  120.42  3.000
 YK1  C31  C26  C27  120.60  3.000
 YK1  C25  C26  C27  118.99  3.000
 YK1  O29  C28  C27  124.64  3.000
 YK1  C27  C28  C23  120.03  3.000
 YK1  O29  C28  C23  115.33  3.000
 YK1  C35  N33  C34  110.83  3.000
 YK1  C35  N33  C32  112.47  3.000
 YK1  C34  N33  C32  110.81  3.000
 YK1  C28  O29  C30  118.86  3.000
 YK1  H18  C35  H17  107.50  3.000
 YK1  H18  C35  H16  107.86  3.000
 YK1  H17  C35  H16  107.82  3.000
 YK1  H18  C35  N33  113.38  3.000
 YK1  H17  C35  N33  109.97  3.000
 YK1  H16  C35  N33  110.12  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
 YK1  CONST_01  C5   C4   N3   C2      0.00   0.0  0
 YK1  CONST_02  C5   C6   N1   C2      0.00   0.0  0
 YK1  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 YK1  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 YK1  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 YK1  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 YK1  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 YK1  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 YK1  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 YK1  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 YK1  CONST_11  C13  C12  C11  C16     0.00   0.0  0
 YK1  CONST_12  C13  C14  C15  C16     0.00   0.0  0
 YK1  CONST_13  C26  C25  C24  C23     0.00   0.0  0
 YK1  CONST_14  C26  C27  C28  C23     0.00   0.0  0
 YK1  CONST_15  C27  C28  C23  C24     0.00   0.0  0
 YK1  CONST_16  C27  C26  C25  C24     0.00   0.0  0
 YK1  CONST_17  C28  C23  C24  C25     0.00   0.0  0
 YK1  CONST_18  C28  C27  C26  C25     0.00   0.0  0
 YK1  CONST_19  N10  C4   N3   C2    180.00   0.0  0
 YK1  CONST_20  N22  C2   N3   C4    180.00   0.0  0
 YK1  CONST_21  N10  C4   C5   C6    180.00   0.0  0
 YK1  CONST_22  N22  C2   N1   C6    180.00   0.0  0
 YK1  CONST_23  N3   C4   C5   C7    180.00   0.0  0
 YK1  CONST_24  N1   C6   C5   C7    180.00   0.0  0
 YK1  CONST_25  C13  C12  C11  N10   180.00   0.0  0
 YK1  CONST_26  C15  C16  C11  N10   180.00   0.0  0
 YK1  CONST_27  F17  C16  C11  C12   180.00   0.0  0
 YK1  CONST_28  C18  C12  C11  C16   180.00   0.0  0
 YK1  CONST_29  C14  C13  C12  C18   180.00   0.0  0
 YK1  CONST_30  C25  C24  C23  N22   180.00   0.0  0
 YK1  CONST_31  C27  C28  C23  N22   180.00   0.0  0
 YK1  CONST_32  O29  C28  C23  C24   180.00   0.0  0
 YK1  CONST_33  C26  C27  C28  O29   180.00   0.0  0
 YK1  CONST_34  F17  C16  C15  C14   180.00   0.0  0
 YK1  CONST_35  H1   C6   N1   C2    180.00   0.0  0
 YK1  CONST_36  H21  C13  C12  C11   180.00   0.0  0
 YK1  CONST_37  H3   C15  C16  C11   180.00   0.0  0
 YK1  CONST_38  H22  C14  C13  C12   180.00   0.0  0
 YK1  CONST_39  H6   C27  C28  C23   180.00   0.0  0
 YK1  CONST_40  H5   C24  C25  C34     0.00   0.0  0
 YK1  CONST_41  H19  N9   C7   C5    180.00   0.0  0
 YK1  CONST_42  H20  N9   C7   C5      0.00   0.0  0
 YK1  Var_01    N33  C34  C25  C24  -163.89  30.0  1
 YK1  Var_02    C32  C31  C26  C27  -163.35  30.0  1
 YK1  Var_03    C34  N33  C32  C31    67.95  30.0  1
 YK1  Var_04    C25  C34  N33  C32   -50.45  30.0  1
 YK1  Var_05    N33  C32  C31  C26   -49.22  30.0  1
 YK1  Var_06    C24  C23  N22  C2     -0.28  30.0  2
 YK1  Var_07    C12  C11  N10  C4    110.84  30.0  2
 YK1  Var_08    C11  N10  C4   C5    172.18  30.0  2
 YK1  Var_09    N3   C2   N22  C23    -6.62  30.0  1
 YK1  Var_10    O8   C7   C5   C4      6.47  30.0  2
 YK1  Var_11    F19  C18  C12  C11    62.20  30.0  3
 YK1  Var_12    H16  C35  N33  C32    58.36  30.0  3
 YK1  Var_13    H7   C30  O29  C28  -178.00  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
 YK1  plan-1  C2   0.020
 YK1  plan-1  C4   0.020
 YK1  plan-1  C5   0.020
 YK1  plan-1  C6   0.020
 YK1  plan-1  C7   0.020
 YK1  plan-1  N10  0.020
 YK1  plan-1  N22  0.020
 YK1  plan-1  N1   0.020
 YK1  plan-1  N3   0.020
 YK1  plan-1  H1   0.020
 YK1  plan-2  N10  0.020
 YK1  plan-2  C11  0.020
 YK1  plan-2  C12  0.020
 YK1  plan-2  C15  0.020
 YK1  plan-2  C16  0.020
 YK1  plan-2  C18  0.020
 YK1  plan-2  C13  0.020
 YK1  plan-2  C14  0.020
 YK1  plan-2  F17  0.020
 YK1  plan-2  H3   0.020
 YK1  plan-2  H21  0.020
 YK1  plan-2  H22  0.020
 YK1  plan-3  N22  0.020
 YK1  plan-3  C23  0.020
 YK1  plan-3  C24  0.020
 YK1  plan-3  C27  0.020
 YK1  plan-3  C31  0.020
 YK1  plan-3  C34  0.020
 YK1  plan-3  C25  0.020
 YK1  plan-3  C26  0.020
 YK1  plan-3  C28  0.020
 YK1  plan-3  H5   0.020
 YK1  plan-3  H6   0.020
 YK1  plan-3  O29  0.020
 YK1  plan-4  C5   0.020
 YK1  plan-4  C7   0.020
 YK1  plan-4  O8   0.020
 YK1  plan-4  N9   0.020
 YK1  plan-4  H19  0.020
 YK1  plan-4  H20  0.020

