# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 20:27:48 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-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(Nc4ccccc4)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
 YK7  YK7  4-anilino-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyrimidine-5-carboxamide  ligand  54  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YK7
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
 YK7  C2   C  CR6   0   0.594  15.3803   2.2026  -39.3465
 YK7  C4   C  CR6   0   0.569  14.4711   1.5105  -37.3760
 YK7  C5   C  CR6   0  -0.283  15.1060   2.5960  -36.7012
 YK7  C6   C  CR16  0  -0.035  15.8982   3.3941  -37.5162
 YK7  C7   C  C     0   0.532  14.9676   2.8225  -35.2494
 YK7  N10  N  NH1   0  -0.783  13.7165   0.6269  -36.6934
 YK7  C11  C  CR6   0   0.355  13.0221  -0.4951  -37.1575
 YK7  C12  C  CR16  0  -0.287  12.4931  -0.6212  -38.4436
 YK7  C15  C  CR16  0  -0.243  12.0985  -2.6599  -36.5943
 YK7  C16  C  CR16  0  -0.347  12.8101  -1.5263  -36.2376
 YK7  C18  C  CR6   0   0.242  14.8890   1.0674  -41.4689
 YK7  C19  C  CR6   0   0.348  14.1994   1.4649  -42.6270
 YK7  C21  C  CR6   0   0.075  13.6041  -0.8453  -43.0514
 YK7  C23  C  CR16  0  -0.296  14.9448  -0.2765  -41.1474
 YK7  C24  C  CH2   0  -0.307  14.3386  -2.6787  -41.4785
 YK7  C27  C  CH2   0  -0.299  12.6810  -3.1625  -43.1191
 YK7  C31  C  CH3   0  -0.435  13.5681   3.2401  -44.0688
 YK7  N1   N  N     0  -0.479  16.0570   3.2311  -38.8149
 YK7  N3   N  N     0  -0.504  14.6146   1.3510  -38.6831
 YK7  O8   O  O     0  -0.505  14.5123   1.9548  -34.4999
 YK7  N9   N  NH2   0  -0.817  15.3717   4.0086  -34.7645
 YK7  C13  C  CR16  0  -0.249  11.7873  -1.7655  -38.7901
 YK7  C14  C  CR16  0  -0.276  11.5866  -2.7922  -37.8786
 YK7  N17  N  NH1   0  -0.740  15.5178   2.0454  -40.6818
 YK7  C20  C  CR16  0  -0.441  13.5737   0.5036  -43.4073
 YK7  C22  C  CR6   0   0.015  14.3008  -1.2399  -41.9169
 YK7  N25  N  NT    0  -0.415  13.9325  -3.5909  -42.5252
 YK7  C28  C  CH2   0  -0.495  12.8920  -1.8702  -43.8892
 YK7  C29  C  CH3   0  -0.518  13.8642  -4.9437  -42.0237
 YK7  O30  O  O2    0  -0.467  14.1993   2.7861  -42.8890
 YK7  H1   H  HCR6  0   0.264  16.4636   4.2163  -37.0897
 YK7  H2   H  HNH1  0   0.429  13.7718   0.7489  -35.6848
 YK7  H3   H  HCR6  0   0.272  12.6316   0.1591  -39.1736
 YK7  H4   H  HCR6  0   0.255  11.9514  -3.4454  -35.8643
 YK7  H5   H  HCR6  0   0.264  13.2113  -1.4380  -35.2347
 YK7  H6   H  HCR6  0   0.250  15.4947  -0.5833  -40.2672
 YK7  H7   H  HCH2  0   0.213  13.6977  -2.7849  -40.5838
 YK7  H8   H  HCH2  0   0.246  15.3514  -2.9377  -41.1551
 YK7  H9   H  HCH2  0   0.199  11.8940  -3.0230  -42.3566
 YK7  H10  H  HCH2  0   0.239  12.3267  -3.9400  -43.7987
 YK7  H11  H  HCH3  0   0.260  13.7049   4.3183  -44.0966
 YK7  H12  H  HCH3  0   0.229  14.0164   2.8040  -44.9653
 YK7  H13  H  HCH3  0   0.228  12.4971   3.0214  -44.0688
 YK7  H14  H  HNH2  0   0.405  15.2552   4.1902  -33.7807
 YK7  H15  H  HNH2  0   0.411  15.5638   4.8061  -35.3449
 YK7  H16  H  HCR6  0   0.258  11.3889  -1.8477  -39.7939
 YK7  H17  H  HCR6  0   0.251  11.0361  -3.6794  -38.1626
 YK7  H18  H  HNH1  0   0.400  16.0197   2.7839  -41.1512
 YK7  H19  H  HCR6  0   0.272  13.0291   0.7885  -44.2992
 YK7  H21  H  HCH2  0   0.245  13.4760  -2.0804  -44.7904
 YK7  H22  H  HCH2  0   0.243  11.9304  -1.4780  -44.2279
 YK7  H23  H  HCH3  0   0.232  14.8316  -5.2390  -41.6139
 YK7  H24  H  HCH3  0   0.191  13.1122  -5.0749  -41.2297
 YK7  H25  H  HCH3  0   0.235  13.6199  -5.6323  -42.8335

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
 YK7  C31  O30  single    1.413  0.020  1.413
 YK7  C28  C27  single    1.519  0.020  1.519
 YK7  C28  C21  single    1.503  0.020  1.503
 YK7  C20  C21  aromatic  1.395  0.020  1.395
 YK7  C20  C19  aromatic  1.387  0.020  1.387
 YK7  C27  N25  single    1.450  0.020  1.450
 YK7  C21  C22  aromatic  1.389  0.020  1.389
 YK7  O30  C19  single    1.347  0.020  1.347
 YK7  C19  C18  aromatic  1.405  0.020  1.405
 YK7  N25  C29  single    1.444  0.020  1.444
 YK7  N25  C24  single    1.447  0.020  1.447
 YK7  C22  C24  single    1.505  0.020  1.505
 YK7  C22  C23  aromatic  1.391  0.020  1.391
 YK7  C18  C23  aromatic  1.383  0.020  1.383
 YK7  C18  N17  single    1.404  0.020  1.404
 YK7  N17  C2   single    1.351  0.020  1.351
 YK7  C2   N1   aromatic  1.341  0.020  1.341
 YK7  C2   N3   aromatic  1.324  0.020  1.324
 YK7  N1   C6   aromatic  1.319  0.020  1.319
 YK7  N3   C4   aromatic  1.325  0.020  1.325
 YK7  C13  C12  aromatic  1.388  0.020  1.388
 YK7  C13  C14  aromatic  1.388  0.020  1.388
 YK7  C12  C11  aromatic  1.396  0.020  1.396
 YK7  C6   C5   aromatic  1.389  0.020  1.389
 YK7  C14  C15  aromatic  1.389  0.020  1.389
 YK7  C4   C5   aromatic  1.427  0.020  1.427
 YK7  C4   N10  single    1.348  0.020  1.348
 YK7  C11  N10  single    1.399  0.020  1.399
 YK7  C11  C16  aromatic  1.398  0.020  1.398
 YK7  C5   C7   single    1.476  0.020  1.476
 YK7  C15  C16  aromatic  1.385  0.020  1.385
 YK7  C7   N9   single    1.344  0.020  1.344
 YK7  C7   O8   double    1.234  0.020  1.234
 YK7  C6   H1   single    0.930  0.020  1.080
 YK7  N10  H2   single    0.860  0.020  1.020
 YK7  C12  H3   single    0.930  0.020  1.080
 YK7  C15  H4   single    0.930  0.020  1.080
 YK7  C16  H5   single    0.930  0.020  1.080
 YK7  C23  H6   single    0.930  0.020  1.080
 YK7  C24  H7   single    0.970  0.020  1.090
 YK7  C24  H8   single    0.970  0.020  1.090
 YK7  C27  H9   single    0.970  0.020  1.090
 YK7  C27  H10  single    0.970  0.020  1.090
 YK7  C31  H11  single    0.970  0.020  1.090
 YK7  C31  H12  single    0.970  0.020  1.090
 YK7  C31  H13  single    0.970  0.020  1.090
 YK7  N9   H14  single    0.860  0.020  1.020
 YK7  N9   H15  single    0.860  0.020  1.020
 YK7  C13  H16  single    0.930  0.020  1.080
 YK7  C14  H17  single    0.930  0.020  1.080
 YK7  N17  H18  single    0.860  0.020  1.020
 YK7  C20  H19  single    0.930  0.020  1.080
 YK7  C28  H21  single    0.970  0.020  1.090
 YK7  C28  H22  single    0.970  0.020  1.090
 YK7  C29  H23  single    0.970  0.020  1.090
 YK7  C29  H24  single    0.970  0.020  1.090
 YK7  C29  H25  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
 YK7  N17  C2   N3   118.64  3.000
 YK7  N3   C2   N1   125.93  3.000
 YK7  N17  C2   N1   115.44  3.000
 YK7  N3   C4   N10  118.79  3.000
 YK7  N10  C4   C5   120.55  3.000
 YK7  N3   C4   C5   120.66  3.000
 YK7  C7   C5   C6   122.86  3.000
 YK7  C7   C5   C4   122.69  3.000
 YK7  C6   C5   C4   114.42  3.000
 YK7  H1   C6   N1   114.71  3.000
 YK7  H1   C6   C5   120.13  3.000
 YK7  N1   C6   C5   125.15  3.000
 YK7  N9   C7   O8   120.84  3.000
 YK7  O8   C7   C5   121.63  3.000
 YK7  N9   C7   C5   117.53  3.000
 YK7  H2   N10  C11  116.88  3.000
 YK7  H2   N10  C4   113.15  3.000
 YK7  C11  N10  C4   129.48  3.000
 YK7  C16  C11  C12  118.82  3.000
 YK7  C16  C11  N10  116.65  3.000
 YK7  C12  C11  N10  124.48  3.000
 YK7  H3   C12  C13  119.55  3.000
 YK7  H3   C12  C11  120.66  3.000
 YK7  C13  C12  C11  119.79  3.000
 YK7  H4   C15  C14  120.29  3.000
 YK7  H4   C15  C16  119.34  3.000
 YK7  C14  C15  C16  120.37  3.000
 YK7  H5   C16  C15  119.68  3.000
 YK7  H5   C16  C11  119.52  3.000
 YK7  C15  C16  C11  120.80  3.000
 YK7  N17  C18  C23  121.90  3.000
 YK7  N17  C18  C19  118.99  3.000
 YK7  C23  C18  C19  119.10  3.000
 YK7  O30  C19  C20  124.77  3.000
 YK7  O30  C19  C18  115.97  3.000
 YK7  C20  C19  C18  119.26  3.000
 YK7  C28  C21  C22  119.95  3.000
 YK7  C22  C21  C20  119.61  3.000
 YK7  C28  C21  C20  120.44  3.000
 YK7  H6   C23  C22  119.26  3.000
 YK7  H6   C23  C18  119.01  3.000
 YK7  C22  C23  C18  121.72  3.000
 YK7  H8   C24  H7   105.94  3.000
 YK7  H8   C24  N25  108.93  3.000
 YK7  H7   C24  N25  111.24  3.000
 YK7  H8   C24  C22  109.62  3.000
 YK7  H7   C24  C22  108.24  3.000
 YK7  N25  C24  C22  112.65  3.000
 YK7  H10  C27  H9   106.76  3.000
 YK7  H10  C27  C28  109.60  3.000
 YK7  H9   C27  C28  109.96  3.000
 YK7  H10  C27  N25  108.95  3.000
 YK7  H9   C27  N25  111.68  3.000
 YK7  C28  C27  N25  109.82  3.000
 YK7  H13  C31  H12  108.79  3.000
 YK7  H13  C31  H11  108.76  3.000
 YK7  H12  C31  H11  108.85  3.000
 YK7  H13  C31  O30  111.93  3.000
 YK7  H12  C31  O30  111.93  3.000
 YK7  H11  C31  O30  106.49  3.000
 YK7  C6   N1   C2   115.12  3.000
 YK7  C4   N3   C2   118.67  3.000
 YK7  H15  N9   H14  116.31  3.000
 YK7  H15  N9   C7   123.34  3.000
 YK7  H14  N9   C7   118.48  3.000
 YK7  H16  C13  C14  119.96  3.000
 YK7  H16  C13  C12  118.74  3.000
 YK7  C14  C13  C12  121.30  3.000
 YK7  H17  C14  C13  120.52  3.000
 YK7  H17  C14  C15  120.56  3.000
 YK7  C13  C14  C15  118.92  3.000
 YK7  H18  N17  C18  118.15  3.000
 YK7  H18  N17  C2   115.16  3.000
 YK7  C18  N17  C2   126.11  3.000
 YK7  H19  C20  C21  118.37  3.000
 YK7  H19  C20  C19  120.51  3.000
 YK7  C21  C20  C19  121.10  3.000
 YK7  C24  C22  C23  119.30  3.000
 YK7  C23  C22  C21  119.17  3.000
 YK7  C24  C22  C21  121.50  3.000
 YK7  C29  N25  C27  112.22  3.000
 YK7  C29  N25  C24  110.65  3.000
 YK7  C27  N25  C24  110.63  3.000
 YK7  H22  C28  H21  106.47  3.000
 YK7  H22  C28  C27  109.90  3.000
 YK7  H21  C28  C27  109.16  3.000
 YK7  H22  C28  C21  110.19  3.000
 YK7  H21  C28  C21  109.71  3.000
 YK7  C27  C28  C21  111.30  3.000
 YK7  H25  C29  H24  107.88  3.000
 YK7  H25  C29  H23  107.85  3.000
 YK7  H24  C29  H23  107.59  3.000
 YK7  H25  C29  N25  110.13  3.000
 YK7  H24  C29  N25  113.21  3.000
 YK7  H23  C29  N25  110.00  3.000
 YK7  C31  O30  C19  118.53  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
 YK7  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 YK7  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 YK7  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 YK7  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 YK7  CONST_05  N3   C2   N1   C6      0.00   0.0  0
 YK7  CONST_06  N3   C4   C5   C6      0.00   0.0  0
 YK7  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 YK7  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 YK7  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 YK7  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 YK7  CONST_11  C13  C12  C11  C16     0.00   0.0  0
 YK7  CONST_12  C13  C14  C15  C16     0.00   0.0  0
 YK7  CONST_13  C21  C20  C19  C18     0.00   0.0  0
 YK7  CONST_14  C21  C22  C23  C18     0.00   0.0  0
 YK7  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 YK7  CONST_16  C22  C23  C18  C19     0.00   0.0  0
 YK7  CONST_17  C20  C21  C22  C23     0.00   0.0  0
 YK7  CONST_18  C20  C19  C18  C23     0.00   0.0  0
 YK7  CONST_19  N10  C4   N3   C2    180.00   0.0  0
 YK7  CONST_20  N17  C2   N3   C4    180.00   0.0  0
 YK7  CONST_21  N17  C2   N1   C6    180.00   0.0  0
 YK7  CONST_22  N10  C4   C5   C6    180.00   0.0  0
 YK7  CONST_23  N1   C6   C5   C7    180.00   0.0  0
 YK7  CONST_24  N3   C4   C5   C7    180.00   0.0  0
 YK7  CONST_25  C13  C12  C11  N10   180.00   0.0  0
 YK7  CONST_26  C15  C16  C11  N10   180.00   0.0  0
 YK7  CONST_27  O30  C19  C20  C21   180.00   0.0  0
 YK7  CONST_28  O30  C19  C18  C23   180.00   0.0  0
 YK7  CONST_29  C20  C19  C18  N17   180.00   0.0  0
 YK7  CONST_30  C22  C23  C18  N17   180.00   0.0  0
 YK7  CONST_31  H1   C6   N1   C2    180.00   0.0  0
 YK7  CONST_32  H16  C13  C12  C11   180.00   0.0  0
 YK7  CONST_33  H4   C15  C16  C11   180.00   0.0  0
 YK7  CONST_34  H17  C14  C13  C12   180.00   0.0  0
 YK7  CONST_35  H5   C16  C11  C12   180.00   0.0  0
 YK7  CONST_36  H3   C12  C11  C16   180.00   0.0  0
 YK7  CONST_37  H19  C20  C19  C18   180.00   0.0  0
 YK7  CONST_38  H6   C23  C18  C19   180.00   0.0  0
 YK7  CONST_39  H14  N9   C7   C5    180.00   0.0  0
 YK7  CONST_40  H15  N9   C7   C5      0.00   0.0  0
 YK7  Var_01    N25  C27  C28  C21   -50.38  30.0  1
 YK7  Var_02    N25  C24  C22  C21    16.62  30.0  1
 YK7  Var_03    C28  C27  N25  C24    68.12  30.0  1
 YK7  Var_04    C20  C21  C28  C27  -162.15  30.0  1
 YK7  Var_05    C22  C24  N25  C27   -49.64  30.0  1
 YK7  Var_06    C19  C18  N17  C2    129.10  30.0  2
 YK7  Var_07    C12  C11  N10  C4    -29.24  30.0  2
 YK7  Var_08    C11  N10  C4   C5   -179.70  30.0  2
 YK7  Var_09    N1   C2   N17  C18  -178.43  30.0  2
 YK7  Var_10    N9   C7   C5   C4   -166.69  30.0  2
 YK7  Var_11    C20  C19  O30  C31    -2.74  30.0  2
 YK7  Var_12    H23  C29  N25  C24   -57.65  30.0  3
 YK7  Var_13    H11  C31  O30  C19  -178.62  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
 YK7  plan-1  C2   0.020
 YK7  plan-1  C4   0.020
 YK7  plan-1  C5   0.020
 YK7  plan-1  C6   0.020
 YK7  plan-1  C7   0.020
 YK7  plan-1  N10  0.020
 YK7  plan-1  N1   0.020
 YK7  plan-1  N3   0.020
 YK7  plan-1  N17  0.020
 YK7  plan-1  H1   0.020
 YK7  plan-2  N10  0.020
 YK7  plan-2  C11  0.020
 YK7  plan-2  C12  0.020
 YK7  plan-2  C15  0.020
 YK7  plan-2  C16  0.020
 YK7  plan-2  C13  0.020
 YK7  plan-2  C14  0.020
 YK7  plan-2  H3   0.020
 YK7  plan-2  H4   0.020
 YK7  plan-2  H5   0.020
 YK7  plan-2  H16  0.020
 YK7  plan-2  H17  0.020
 YK7  plan-3  C18  0.020
 YK7  plan-3  C19  0.020
 YK7  plan-3  C21  0.020
 YK7  plan-3  C23  0.020
 YK7  plan-3  C24  0.020
 YK7  plan-3  N17  0.020
 YK7  plan-3  C20  0.020
 YK7  plan-3  C22  0.020
 YK7  plan-3  C28  0.020
 YK7  plan-3  O30  0.020
 YK7  plan-3  H6   0.020
 YK7  plan-3  H19  0.020
 YK7  plan-4  C5   0.020
 YK7  plan-4  C7   0.020
 YK7  plan-4  O8   0.020
 YK7  plan-4  N9   0.020
 YK7  plan-4  H14  0.020
 YK7  plan-4  H15  0.020

