# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:07:37 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 6-ethyl-5-[(2S)-1-(3-methoxypropyl)-2-phenyl-1,2,3,4-tetrahydroquinolin-7-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1c2ccc3CC[C@H](N(CCCOC)c3c2)c4ccccc4
#
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
 LIY  LIY  6-ethyl-5-[(2S)-1-(3-methoxypropyl)-2-phenyl-1,2,3,4-tetrahydroquinolin-7-yl]pyrimidine-2,4-diamine  ligand  62  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LIY
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
 LIY  N1    N  N     0  -0.510  -1.2037  -1.5268   1.7981
 LIY  N3    N  NH2   0  -0.826   0.2771   0.0983   2.4129
 LIY  C4    C  CR6   0  -0.156  -0.1228  -0.2625   0.0691
 LIY  C6    C  CH2   0  -0.502  -0.7200  -0.7875  -2.3278
 LIY  C7    C  CR16  0  -0.329   2.2045   0.5839  -0.2649
 LIY  C8    C  CR16  0  -0.306   3.0618   1.6050  -0.6502
 LIY  C10   C  CR6   0   0.393   1.2095   3.0690  -1.1518
 LIY  C13   C  CH2   0  -0.494   3.5672   3.8950  -1.5382
 LIY  C15   C  CH1   0  -0.192   1.5879   5.2933  -2.1345
 LIY  C17   C  CH2   0  -0.466  -1.4405   4.8870  -0.4796
 LIY  C20   C  CH3   0  -0.661  -1.9048  -0.0005  -2.8838
 LIY  C21   C  CR6   0   0.149   1.7549   5.1968  -3.6411
 LIY  C22   C  CR16  0  -0.304   2.2260   6.3062  -4.3415
 LIY  C24   C  CR16  0  -0.271   2.1292   5.0894  -6.4141
 LIY  C26   C  CR16  0  -0.302   1.4662   4.0360  -4.3504
 LIY  C1    C  CR6   0   0.474  -0.3478  -0.5790   1.4295
 LIY  C3    C  CR6   0   0.275  -0.8437  -1.0080  -0.8476
 LIY  N2    N  N     0  -0.506  -1.7084  -1.9592  -0.4806
 LIY  C2    C  CR6   0   0.517  -1.8486  -2.1673   0.8248
 LIY  N4    N  NH2   0  -0.825  -2.7567  -3.1004   1.2069
 LIY  C12   C  CR6   0   0.019   0.8313   0.8013  -0.3198
 LIY  C11   C  CR16  0  -0.384   0.3516   2.0373  -0.7373
 LIY  C9    C  CR6   0   0.035   2.6005   2.8313  -1.1025
 LIY  C14   C  CH2   0  -0.453   2.9353   5.2678  -1.4165
 LIY  C23   C  CR16  0  -0.242   2.4139   6.2563  -5.7146
 LIY  C25   C  CR16  0  -0.238   1.6541   3.9818  -5.7270
 LIY  N5    N  NT    0  -0.519   0.7122   4.2742  -1.5958
 LIY  C16   C  CH2   0  -0.359  -0.7106   4.4859  -1.7598
 LIY  C18   C  CH2   0  -0.121  -0.9627   6.2152   0.0736
 LIY  O1    O  O2    0  -0.487  -1.7206   6.5346   1.2142
 LIY  C19   C  CH3   0  -0.397  -1.3438   7.7595   1.7873
 LIY  HN31  H  HNH2  0   0.390   0.2285  -0.2682   3.3483
 LIY  HN32  H  HNH2  0   0.401   1.0713   0.6753   2.1962
 LIY  H61   H  HCH2  0   0.242   0.2106  -0.2710  -2.5637
 LIY  H62   H  HCH2  0   0.243  -0.6788  -1.7642  -2.8148
 LIY  H7    H  HCR6  0   0.239   2.5976  -0.3706   0.0621
 LIY  H8    H  HCR6  0   0.241   4.1333   1.4422  -0.6090
 LIY  H131  H  HCH2  0   0.254   4.4768   3.8421  -0.9365
 LIY  H132  H  HCH2  0   0.246   3.8764   3.7226  -2.5745
 LIY  H15   H  HCH1  0   0.265   1.1304   6.2643  -1.9201
 LIY  H171  H  HCH2  0   0.236  -2.5076   4.9518  -0.7092
 LIY  H172  H  HCH2  0   0.236  -1.3243   4.1125   0.2824
 LIY  H201  H  HCH3  0   0.228  -2.8477  -0.4966  -2.6535
 LIY  H202  H  HCH3  0   0.234  -1.8291   0.0937  -3.9671
 LIY  H203  H  HCH3  0   0.223  -1.9421   1.0052  -2.4639
 LIY  H22   H  HCR6  0   0.249   2.4445   7.2241  -3.8068
 LIY  H24   H  HCR6  0   0.254   2.2707   5.0472  -7.4863
 LIY  H26   H  HCR6  0   0.247   1.0839   3.1625  -3.8378
 LIY  HN41  H  HNH2  0   0.386  -2.6966  -3.4522   2.1471
 LIY  HN42  H  HNH2  0   0.386  -3.0571  -3.7616   0.5113
 LIY  H11   H  HCR6  0   0.245  -0.7199   2.1794  -0.7403
 LIY  H141  H  HCH2  0   0.245   2.7754   5.5177  -0.3640
 LIY  H142  H  HCH2  0   0.251   3.5862   6.0359  -1.8348
 LIY  H23   H  HCR6  0   0.254   2.7769   7.1306  -6.2395
 LIY  H25   H  HCR6  0   0.254   1.4225   3.0697  -6.2622
 LIY  H161  H  HCH2  0   0.251  -1.1834   3.5967  -2.1874
 LIY  H162  H  HCH2  0   0.263  -0.8467   5.2672  -2.5111
 LIY  H181  H  HCH2  0   0.197   0.1061   6.1610   0.3290
 LIY  H182  H  HCH2  0   0.192  -1.0670   7.0007  -0.6914
 LIY  H191  H  HCH3  0   0.202  -0.2990   7.7550   2.1213
 LIY  H192  H  HCH3  0   0.233  -1.9799   7.9388   2.6537
 LIY  H193  H  HCH3  0   0.203  -1.4678   8.5966   1.0892

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
 LIY  N1   C1    aromatic  1.329  0.020  1.329
 LIY  N1   C2    aromatic  1.332  0.020  1.332
 LIY  N3   C1    single    1.348  0.020  1.348
 LIY  N3   HN31  single    0.890  0.020  1.040
 LIY  N3   HN32  single    0.890  0.020  1.040
 LIY  C4   C12   single    1.481  0.020  1.481
 LIY  C4   C1    aromatic  1.415  0.020  1.415
 LIY  C4   C3    aromatic  1.384  0.020  1.384
 LIY  C6   C3    single    1.502  0.020  1.502
 LIY  C6   C20   single    1.527  0.020  1.527
 LIY  C6   H61   single    0.970  0.020  1.090
 LIY  C6   H62   single    0.970  0.020  1.090
 LIY  C7   C8    aromatic  1.388  0.020  1.388
 LIY  C7   C12   aromatic  1.391  0.020  1.391
 LIY  C7   H7    single    0.930  0.020  1.080
 LIY  C8   C9    aromatic  1.386  0.020  1.386
 LIY  C8   H8    single    0.930  0.020  1.080
 LIY  C10  C9    aromatic  1.412  0.020  1.412
 LIY  C10  N5    single    1.377  0.020  1.377
 LIY  C10  C11   aromatic  1.404  0.020  1.404
 LIY  C13  C14   single    1.516  0.020  1.516
 LIY  C13  C9    single    1.502  0.020  1.502
 LIY  C13  H131  single    0.970  0.020  1.090
 LIY  C13  H132  single    0.970  0.020  1.090
 LIY  C15  C21   single    1.519  0.020  1.519
 LIY  C15  C14   single    1.527  0.020  1.527
 LIY  C15  N5    single    1.448  0.020  1.448
 LIY  C15  H15   single    0.970  0.020  1.090
 LIY  C17  C16   single    1.527  0.020  1.527
 LIY  C17  C18   single    1.516  0.020  1.516
 LIY  C17  H171  single    0.970  0.020  1.090
 LIY  C17  H172  single    0.970  0.020  1.090
 LIY  C20  H201  single    0.970  0.020  1.090
 LIY  C20  H202  single    0.970  0.020  1.090
 LIY  C20  H203  single    0.970  0.020  1.090
 LIY  C21  C26   aromatic  1.391  0.020  1.391
 LIY  C21  C22   aromatic  1.394  0.020  1.394
 LIY  C22  C23   aromatic  1.387  0.020  1.387
 LIY  C22  H22   single    0.930  0.020  1.080
 LIY  C24  C25   aromatic  1.387  0.020  1.387
 LIY  C24  C23   aromatic  1.390  0.020  1.390
 LIY  C24  H24   single    0.930  0.020  1.080
 LIY  C26  C25   aromatic  1.390  0.020  1.390
 LIY  C26  H26   single    0.930  0.020  1.080
 LIY  C3   N2    aromatic  1.337  0.020  1.337
 LIY  N2   C2    aromatic  1.329  0.020  1.329
 LIY  C2   N4    single    1.357  0.020  1.357
 LIY  N4   HN41  single    0.890  0.020  1.040
 LIY  N4   HN42  single    0.890  0.020  1.040
 LIY  C12  C11   aromatic  1.390  0.020  1.390
 LIY  C11  H11   single    0.930  0.020  1.080
 LIY  C14  H141  single    0.970  0.020  1.090
 LIY  C14  H142  single    0.970  0.020  1.090
 LIY  C23  H23   single    0.930  0.020  1.080
 LIY  C25  H25   single    0.930  0.020  1.080
 LIY  N5   C16   single    1.448  0.020  1.448
 LIY  C16  H161  single    0.970  0.020  1.090
 LIY  C16  H162  single    0.970  0.020  1.090
 LIY  C18  O1    single    1.406  0.020  1.406
 LIY  C18  H181  single    0.970  0.020  1.090
 LIY  C18  H182  single    0.970  0.020  1.090
 LIY  O1   C19   single    1.404  0.020  1.404
 LIY  C19  H191  single    0.970  0.020  1.090
 LIY  C19  H192  single    0.970  0.020  1.090
 LIY  C19  H193  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
 LIY  C2    N1   C1    116.88  3.000
 LIY  HN32  N3   HN31  116.60  3.000
 LIY  HN32  N3   C1    119.83  3.000
 LIY  HN31  N3   C1    118.24  3.000
 LIY  C12   C4   C3    123.27  3.000
 LIY  C3    C4   C1    115.69  3.000
 LIY  C12   C4   C1    121.04  3.000
 LIY  H62   C6   H61   107.15  3.000
 LIY  H62   C6   C3    108.14  3.000
 LIY  H61   C6   C3    110.69  3.000
 LIY  H62   C6   C20   109.13  3.000
 LIY  H61   C6   C20   109.84  3.000
 LIY  C3    C6   C20   111.76  3.000
 LIY  H7    C7   C12   120.52  3.000
 LIY  H7    C7   C8    120.54  3.000
 LIY  C12   C7   C8    118.93  3.000
 LIY  H8    C8   C9    118.30  3.000
 LIY  H8    C8   C7    119.29  3.000
 LIY  C9    C8   C7    122.41  3.000
 LIY  N5    C10  C9    120.95  3.000
 LIY  N5    C10  C11   121.16  3.000
 LIY  C9    C10  C11   117.89  3.000
 LIY  H132  C13  H131  106.19  3.000
 LIY  H132  C13  C14   109.64  3.000
 LIY  H131  C13  C14   110.30  3.000
 LIY  H132  C13  C9    110.16  3.000
 LIY  H131  C13  C9    110.00  3.000
 LIY  C14   C13  C9    110.47  3.000
 LIY  H15   C15  N5    107.39  3.000
 LIY  H15   C15  C14   106.95  3.000
 LIY  N5    C15  C14   110.31  3.000
 LIY  H15   C15  C21   107.25  3.000
 LIY  N5    C15  C21   113.01  3.000
 LIY  C14   C15  C21   111.61  3.000
 LIY  H172  C17  H171  106.98  3.000
 LIY  H172  C17  C18   109.46  3.000
 LIY  H171  C17  C18   109.41  3.000
 LIY  H172  C17  C16   110.34  3.000
 LIY  H171  C17  C16   107.81  3.000
 LIY  C18   C17  C16   112.67  3.000
 LIY  H203  C20  H202  107.78  3.000
 LIY  H203  C20  H201  107.99  3.000
 LIY  H202  C20  H201  108.02  3.000
 LIY  H203  C20  C6    111.19  3.000
 LIY  H202  C20  C6    110.64  3.000
 LIY  H201  C20  C6    111.08  3.000
 LIY  C26   C21  C22   118.57  3.000
 LIY  C22   C21  C15   119.01  3.000
 LIY  C26   C21  C15   122.42  3.000
 LIY  H22   C22  C23   119.43  3.000
 LIY  H22   C22  C21   119.60  3.000
 LIY  C23   C22  C21   120.97  3.000
 LIY  H24   C24  C25   120.29  3.000
 LIY  H24   C24  C23   120.29  3.000
 LIY  C25   C24  C23   119.42  3.000
 LIY  H26   C26  C25   119.02  3.000
 LIY  H26   C26  C21   120.35  3.000
 LIY  C25   C26  C21   120.63  3.000
 LIY  C4    C1   N3    121.03  3.000
 LIY  C4    C1   N1    121.91  3.000
 LIY  N3    C1   N1    117.04  3.000
 LIY  N2    C3   C6    115.37  3.000
 LIY  N2    C3   C4    122.57  3.000
 LIY  C6    C3   C4    122.06  3.000
 LIY  C2    N2   C3    116.69  3.000
 LIY  N4    C2   N2    117.05  3.000
 LIY  N4    C2   N1    116.68  3.000
 LIY  N2    C2   N1    126.25  3.000
 LIY  HN42  N4   HN41  115.75  3.000
 LIY  HN42  N4   C2    117.21  3.000
 LIY  HN41  N4   C2    117.64  3.000
 LIY  C11   C12  C7    119.43  3.000
 LIY  C11   C12  C4    119.69  3.000
 LIY  C7    C12  C4    120.88  3.000
 LIY  H11   C11  C12   117.38  3.000
 LIY  H11   C11  C10   120.54  3.000
 LIY  C12   C11  C10   122.08  3.000
 LIY  C13   C9   C10   120.31  3.000
 LIY  C13   C9   C8    120.46  3.000
 LIY  C10   C9   C8    119.22  3.000
 LIY  H142  C14  H141  107.19  3.000
 LIY  H142  C14  C15   109.55  3.000
 LIY  H141  C14  C15   108.65  3.000
 LIY  H142  C14  C13   110.99  3.000
 LIY  H141  C14  C13   110.18  3.000
 LIY  C15   C14  C13   110.19  3.000
 LIY  H23   C23  C24   120.18  3.000
 LIY  H23   C23  C22   119.77  3.000
 LIY  C24   C23  C22   120.04  3.000
 LIY  H25   C25  C26   119.56  3.000
 LIY  H25   C25  C24   120.07  3.000
 LIY  C26   C25  C24   120.37  3.000
 LIY  C16   N5   C15   116.70  3.000
 LIY  C16   N5   C10   121.29  3.000
 LIY  C15   N5   C10   121.17  3.000
 LIY  H162  C16  H161  104.99  3.000
 LIY  H162  C16  N5    107.75  3.000
 LIY  H161  C16  N5    110.50  3.000
 LIY  H162  C16  C17   109.21  3.000
 LIY  H161  C16  C17   109.55  3.000
 LIY  N5    C16  C17   114.40  3.000
 LIY  H182  C18  H181  106.76  3.000
 LIY  H182  C18  O1    110.51  3.000
 LIY  H181  C18  O1    110.27  3.000
 LIY  H182  C18  C17   109.97  3.000
 LIY  H181  C18  C17   110.35  3.000
 LIY  O1    C18  C17   108.97  3.000
 LIY  C19   O1   C18   112.62  3.000
 LIY  H193  C19  H192  108.33  3.000
 LIY  H193  C19  H191  107.73  3.000
 LIY  H192  C19  H191  108.34  3.000
 LIY  H193  C19  O1    112.06  3.000
 LIY  H192  C19  O1    108.14  3.000
 LIY  H191  C19  O1    112.11  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
 LIY  CONST_01  C12   C4   C1   N1    180.00   0.0  0
 LIY  CONST_02  C3    C4   C1   N1      0.00   0.0  0
 LIY  CONST_03  C3    N2   C2   N1      0.00   0.0  0
 LIY  CONST_04  C8    C7   C12  C4    180.00   0.0  0
 LIY  CONST_05  C10   C11  C12  C4    180.00   0.0  0
 LIY  CONST_06  C2    N1   C1   C4      0.00   0.0  0
 LIY  CONST_07  C2    N2   C3   C4      0.00   0.0  0
 LIY  CONST_08  C10   C9   C8   C7      0.00   0.0  0
 LIY  CONST_11  C10   C11  C12  C7      0.00   0.0  0
 LIY  CONST_12  C11   C12  C7   C8      0.00   0.0  0
 LIY  CONST_13  C11   C10  C9   C8      0.00   0.0  0
 LIY  CONST_14  C24   C25  C26  C21     0.00   0.0  0
 LIY  CONST_15  C24   C23  C22  C21     0.00   0.0  0
 LIY  CONST_16  C25   C26  C21  C22     0.00   0.0  0
 LIY  CONST_17  C25   C24  C23  C22     0.00   0.0  0
 LIY  CONST_18  C23   C22  C21  C26     0.00   0.0  0
 LIY  CONST_19  C23   C24  C25  C26     0.00   0.0  0
 LIY  CONST_20  N2    C2   N1   C1      0.00   0.0  0
 LIY  CONST_22  N2    C3   C4   C1      0.00   0.0  0
 LIY  CONST_24  C12   C4   C3   N2    180.00   0.0  0
 LIY  CONST_25  C9    C8   C7   C12     0.00   0.0  0
 LIY  CONST_26  C9    C10  C11  C12     0.00   0.0  0
 LIY  CONST_27  C25   C26  C21  C15   180.00   0.0  0
 LIY  CONST_28  C23   C22  C21  C15   180.00   0.0  0
 LIY  CONST_29  C2    N1   C1   N3    180.00   0.0  0
 LIY  CONST_30  C12   C4   C1   N3      0.00   0.0  0
 LIY  CONST_31  C3    C4   C1   N3    180.00   0.0  0
 LIY  CONST_32  C12   C4   C3   C6      0.00   0.0  0
 LIY  CONST_33  C1    C4   C3   C6    180.00   0.0  0
 LIY  CONST_34  C2    N2   C3   C6    180.00   0.0  0
 LIY  CONST_35  N4    C2   N1   C1    180.00   0.0  0
 LIY  CONST_36  N4    C2   N2   C3    180.00   0.0  0
 LIY  CONST_37  H7    C7   C12  C4      0.00   0.0  0
 LIY  CONST_38  H11   C11  C12  C4      0.00   0.0  0
 LIY  CONST_39  H8    C8   C9   C10   180.00   0.0  0
 LIY  CONST_40  H26   C26  C21  C15     0.00   0.0  0
 LIY  CONST_41  H22   C22  C21  C15     0.00   0.0  0
 LIY  CONST_42  H25   C25  C26  C21   180.00   0.0  0
 LIY  CONST_43  H23   C23  C22  C21   180.00   0.0  0
 LIY  CONST_44  H24   C24  C23  C22   180.00   0.0  0
 LIY  CONST_45  HN31  N3   C1   N1      0.00   0.0  0
 LIY  CONST_46  HN32  N3   C1   N1    180.00   0.0  0
 LIY  Var_01    C14   C13  C9   C8   -155.76  30.0  1
 LIY  Var_02    C9    C13  C14  C15   -52.07  30.0  1
 LIY  Var_03    C9    C10  N5   C15     5.40  30.0  1
 LIY  Var_04    C20   C6   C3   C4   -102.54  30.0  2
 LIY  Var_05    C17   C16  N5   C10    83.93  30.0  3
 LIY  Var_06    C18   C17  C16  N5     62.96  30.0  1
 LIY  Var_07    H201  C20  C6   C3    -56.40  30.0  3
 LIY  Var_08    O1    C18  C17  C16   177.57  30.0  3
 LIY  Var_09    H191  C19  O1   C18   -61.19  30.0  3

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
 LIY  chir_01  C15  C21  C14  N5  positiv

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
 LIY  plan-1  N1    0.020
 LIY  plan-1  N3    0.020
 LIY  plan-1  C4    0.020
 LIY  plan-1  C6    0.020
 LIY  plan-1  C1    0.020
 LIY  plan-1  C3    0.020
 LIY  plan-1  N2    0.020
 LIY  plan-1  C2    0.020
 LIY  plan-1  N4    0.020
 LIY  plan-1  C12   0.020
 LIY  plan-2  C15   0.020
 LIY  plan-2  C21   0.020
 LIY  plan-2  C22   0.020
 LIY  plan-2  C24   0.020
 LIY  plan-2  C26   0.020
 LIY  plan-2  C23   0.020
 LIY  plan-2  C25   0.020
 LIY  plan-2  H22   0.020
 LIY  plan-2  H24   0.020
 LIY  plan-2  H26   0.020
 LIY  plan-2  H23   0.020
 LIY  plan-2  H25   0.020
 LIY  plan-3  C4    0.020
 LIY  plan-3  C7    0.020
 LIY  plan-3  C8    0.020
 LIY  plan-3  C10   0.020
 LIY  plan-3  C13   0.020
 LIY  plan-3  C12   0.020
 LIY  plan-3  C11   0.020
 LIY  plan-3  C9    0.020
 LIY  plan-3  N5    0.020
 LIY  plan-3  H7    0.020
 LIY  plan-3  H8    0.020
 LIY  plan-3  H11   0.020
 LIY  plan-4  N3    0.020
 LIY  plan-4  C1    0.020
 LIY  plan-4  HN31  0.020
 LIY  plan-4  HN32  0.020
 LIY  plan-5  C2    0.020
 LIY  plan-5  N4    0.020
 LIY  plan-5  HN41  0.020
 LIY  plan-5  HN42  0.020

