# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 16:57:43 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 3-(4-{[4-(dimethylamino)piperidin-1-yl]methyl}phenyl)-5-methylisoquinolin-1(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C1CCN(CC1)Cc2ccc(cc2)C3=Cc4c(C)cccc4C(=O)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
 3DN  3DN  3-(4-{[4-(dimethylamino)piperidin-1-yl]methyl}phenyl)-5-methylisoquinolin-1(2H)-one  ligand  57  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3DN
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
 3DN  N1   N  NT    0  -0.414   3.7864  -0.6893   0.8093
 3DN  C1   C  CR66  0   0.235  -4.7983  -0.4702  -0.4516
 3DN  C2   C  CR66  0  -0.154  -5.3500   0.7371   0.0158
 3DN  C3   C  CR6   0   0.512  -4.5246   1.6885   0.7587
 3DN  C4   C  CR6   0   0.395  -2.6672   0.1231   0.5196
 3DN  C5   C  CR16  0  -0.502  -3.4242  -0.7590  -0.1731
 3DN  C6   C  CR16  0  -0.291  -0.7335   0.3355   2.0829
 3DN  C7   C  CR16  0  -0.266   0.9064  -1.0341   0.3234
 3DN  C8   C  CH2   0  -0.316   2.8632  -0.8706   1.9091
 3DN  C9   C  CH2   0  -0.454   4.7868   0.8689  -0.8052
 3DN  C10  C  CH2   0  -0.280   5.0988  -1.2130   1.1468
 3DN  C11  C  CH3   0  -0.532   6.8564  -0.1479  -2.8031
 3DN  C12  C  CH3   0  -0.522   7.5633   1.8695  -1.7517
 3DN  C13  C  CR16  0  -0.301  -6.6908   1.0513  -0.2281
 3DN  N2   N  NR16  0  -0.742  -3.2264   1.2992   0.9517
 3DN  C14  C  CR6   0   0.061  -5.6176  -1.3708  -1.1736
 3DN  C15  C  CH3   0  -0.752  -5.0658  -2.6671  -1.6874
 3DN  C16  C  CR16  0  -0.296  -6.9365  -1.0299  -1.3983
 3DN  C17  C  CR16  0  -0.249  -7.4795   0.1719  -0.9318
 3DN  C18  C  CR6   0   0.050  -1.2592  -0.1123   0.8719
 3DN  C19  C  CR16  0  -0.289  -0.4166  -0.7991  -0.0051
 3DN  C20  C  CR6   0   0.077   1.4332  -0.5869   1.5341
 3DN  C21  C  CR16  0  -0.297   0.5954   0.1008   2.4033
 3DN  C22  C  CH2   0  -0.442   6.0581  -1.1137  -0.0287
 3DN  C23  C  CH1   0  -0.067   6.1873   0.3330  -0.4924
 3DN  N3   N  NT    0  -0.411   7.1831   0.4894  -1.5454
 3DN  C24  C  CH2   0  -0.273   3.8688   0.7017   0.3962
 3DN  H2   H  HCR6  0   0.270  -2.9882  -1.6971  -0.4826
 3DN  H4   H  HCR6  0   0.262  -1.3559   0.8559   2.8007
 3DN  H5   H  HCR6  0   0.252   1.5481  -1.5524  -0.3778
 3DN  H6   H  HCH2  0   0.255   2.9335  -1.9130   2.2379
 3DN  H7   H  HCH2  0   0.212   3.1370  -0.2588   2.7859
 3DN  H8   H  HCH2  0   0.234   4.8218   1.9265  -1.0774
 3DN  H9   H  HCH2  0   0.220   4.3612   0.3312  -1.6579
 3DN  H10  H  HCH2  0   0.187   5.5298  -0.6816   2.0142
 3DN  H11  H  HCH2  0   0.237   4.9896  -2.2586   1.4447
 3DN  H12  H  HCH3  0   0.232   7.7182  -0.0892  -3.4701
 3DN  H13  H  HCH3  0   0.234   6.6305  -1.2044  -2.6612
 3DN  H14  H  HCH3  0   0.194   6.0059   0.3081  -3.3315
 3DN  H15  H  HCH3  0   0.228   7.8621   2.3239  -0.8054
 3DN  H16  H  HCH3  0   0.230   8.4197   1.9199  -2.4270
 3DN  H17  H  HCH3  0   0.192   6.7691   2.4953  -2.1862
 3DN  H18  H  HCR6  0   0.261  -7.0982   1.9833   0.1394
 3DN  H19  H  HCH3  0   0.249  -4.2466  -2.5062  -2.3907
 3DN  H20  H  HCH3  0   0.249  -4.6756  -3.2891  -0.8797
 3DN  H21  H  HCH3  0   0.258  -5.8356  -3.2387  -2.2026
 3DN  H22  H  HCR6  0   0.257  -7.5676  -1.7134  -1.9536
 3DN  H23  H  HCR6  0   0.260  -8.5180   0.4037  -1.1267
 3DN  H24  H  HCR6  0   0.258  -0.7936  -1.1352  -0.9627
 3DN  H25  H  HCR6  0   0.256   0.9812   0.4607   3.3495
 3DN  H26  H  HCH2  0   0.233   7.0354  -1.5033   0.2656
 3DN  H27  H  HCH2  0   0.220   5.6838  -1.7462  -0.8387
 3DN  H28  H  HCH1  0   0.214   6.5708   0.9051   0.3633
 3DN  H30  H  HCH2  0   0.240   2.8683   1.0564   0.1411
 3DN  H31  H  HCH2  0   0.189   4.2274   1.3388   1.2254
 3DN  H1   H  HNR6  0   0.418  -2.6342   1.9732   1.4186
 3DN  O1   O  O     0  -0.478  -4.9224   2.7662   1.1823

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
 3DN  C12  N3   single    1.446  0.020  1.446
 3DN  C15  C14  single    1.500  0.020  1.500
 3DN  N3   C23  single    1.458  0.020  1.458
 3DN  N3   C11  single    1.447  0.020  1.447
 3DN  C23  C22  single    1.525  0.020  1.525
 3DN  C23  C9   single    1.532  0.020  1.532
 3DN  C10  C22  single    1.521  0.020  1.521
 3DN  C10  N1   single    1.453  0.020  1.453
 3DN  C7   C19  aromatic  1.383  0.020  1.383
 3DN  C7   C20  aromatic  1.394  0.020  1.394
 3DN  C14  C16  aromatic  1.381  0.020  1.381
 3DN  C14  C1   aromatic  1.415  0.020  1.415
 3DN  C19  C18  aromatic  1.397  0.020  1.397
 3DN  C16  C17  aromatic  1.399  0.020  1.399
 3DN  C24  C9   single    1.521  0.020  1.521
 3DN  C24  N1   single    1.453  0.020  1.453
 3DN  C5   C1   single    1.432  0.020  1.432
 3DN  C5   C4   double    1.353  0.020  1.353
 3DN  C8   N1   single    1.447  0.020  1.447
 3DN  C8   C20  single    1.505  0.020  1.505
 3DN  C1   C2   aromatic  1.407  0.020  1.407
 3DN  C20  C21  aromatic  1.389  0.020  1.389
 3DN  C18  C4   single    1.470  0.020  1.470
 3DN  C18  C6   aromatic  1.394  0.020  1.394
 3DN  C17  C13  aromatic  1.375  0.020  1.375
 3DN  C4   N2   single    1.372  0.020  1.372
 3DN  C2   C13  aromatic  1.399  0.020  1.399
 3DN  C2   C3   single    1.462  0.020  1.462
 3DN  C21  C6   aromatic  1.387  0.020  1.387
 3DN  N2   C3   single    1.369  0.020  1.369
 3DN  C3   O1   double    1.224  0.020  1.224
 3DN  C5   H2   single    0.930  0.020  1.080
 3DN  C6   H4   single    0.930  0.020  1.080
 3DN  C7   H5   single    0.930  0.020  1.080
 3DN  C8   H6   single    0.970  0.020  1.090
 3DN  C8   H7   single    0.970  0.020  1.090
 3DN  C9   H8   single    0.970  0.020  1.090
 3DN  C9   H9   single    0.970  0.020  1.090
 3DN  C10  H10  single    0.970  0.020  1.090
 3DN  C10  H11  single    0.970  0.020  1.090
 3DN  C11  H12  single    0.970  0.020  1.090
 3DN  C11  H13  single    0.970  0.020  1.090
 3DN  C11  H14  single    0.970  0.020  1.090
 3DN  C12  H15  single    0.970  0.020  1.090
 3DN  C12  H16  single    0.970  0.020  1.090
 3DN  C12  H17  single    0.970  0.020  1.090
 3DN  C13  H18  single    0.930  0.020  1.080
 3DN  C15  H19  single    0.970  0.020  1.090
 3DN  C15  H20  single    0.970  0.020  1.090
 3DN  C15  H21  single    0.970  0.020  1.090
 3DN  C16  H22  single    0.930  0.020  1.080
 3DN  C17  H23  single    0.930  0.020  1.080
 3DN  C19  H24  single    0.930  0.020  1.080
 3DN  C21  H25  single    0.930  0.020  1.080
 3DN  C22  H26  single    0.970  0.020  1.090
 3DN  C22  H27  single    0.970  0.020  1.090
 3DN  C23  H28  single    0.970  0.020  1.090
 3DN  C24  H30  single    0.970  0.020  1.090
 3DN  C24  H31  single    0.970  0.020  1.090
 3DN  N2   H1   single    0.860  0.020  1.020

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
 3DN  C24  N1   C10  111.09  3.000
 3DN  C24  N1   C8   111.84  3.000
 3DN  C10  N1   C8   110.77  3.000
 3DN  C14  C1   C5   121.77  3.000
 3DN  C5   C1   C2   118.99  3.000
 3DN  C14  C1   C2   119.23  3.000
 3DN  C13  C2   C3   118.92  3.000
 3DN  C3   C2   C1   120.37  3.000
 3DN  C13  C2   C1   120.70  3.000
 3DN  N2   C3   O1   120.64  3.000
 3DN  O1   C3   C2   124.41  3.000
 3DN  N2   C3   C2   114.95  3.000
 3DN  C18  C4   N2   116.88  3.000
 3DN  N2   C4   C5   119.47  3.000
 3DN  C18  C4   C5   123.64  3.000
 3DN  H2   C5   C4   119.15  3.000
 3DN  H2   C5   C1   120.47  3.000
 3DN  C4   C5   C1   120.34  3.000
 3DN  H4   C6   C21  118.60  3.000
 3DN  H4   C6   C18  120.88  3.000
 3DN  C21  C6   C18  120.50  3.000
 3DN  H5   C7   C20  119.48  3.000
 3DN  H5   C7   C19  119.63  3.000
 3DN  C20  C7   C19  120.88  3.000
 3DN  H7   C8   H6   105.86  3.000
 3DN  H7   C8   C20  109.22  3.000
 3DN  H6   C8   C20  108.37  3.000
 3DN  H7   C8   N1   112.08  3.000
 3DN  H6   C8   N1   107.84  3.000
 3DN  C20  C8   N1   113.14  3.000
 3DN  H9   C9   H8   107.10  3.000
 3DN  H9   C9   C24  109.06  3.000
 3DN  H8   C9   C24  108.81  3.000
 3DN  H9   C9   C23  110.05  3.000
 3DN  H8   C9   C23  111.11  3.000
 3DN  C24  C9   C23  110.61  3.000
 3DN  H11  C10  H10  106.57  3.000
 3DN  H11  C10  C22  109.65  3.000
 3DN  H10  C10  C22  109.23  3.000
 3DN  H11  C10  N1   108.55  3.000
 3DN  H10  C10  N1   111.19  3.000
 3DN  C22  C10  N1   111.52  3.000
 3DN  H14  C11  H13  107.71  3.000
 3DN  H14  C11  H12  107.13  3.000
 3DN  H13  C11  H12  107.18  3.000
 3DN  H14  C11  N3   114.16  3.000
 3DN  H13  C11  N3   111.14  3.000
 3DN  H12  C11  N3   109.22  3.000
 3DN  H17  C12  H16  107.20  3.000
 3DN  H17  C12  H15  107.65  3.000
 3DN  H16  C12  H15  107.59  3.000
 3DN  H17  C12  N3   114.15  3.000
 3DN  H16  C12  N3   109.78  3.000
 3DN  H15  C12  N3   110.22  3.000
 3DN  H18  C13  C17  120.60  3.000
 3DN  H18  C13  C2   119.70  3.000
 3DN  C17  C13  C2   119.70  3.000
 3DN  H1   N2   C4   118.55  3.000
 3DN  H1   N2   C3   115.52  3.000
 3DN  C4   N2   C3   125.87  3.000
 3DN  C16  C14  C15  120.61  3.000
 3DN  C16  C14  C1   118.61  3.000
 3DN  C15  C14  C1   120.78  3.000
 3DN  H21  C15  H20  107.69  3.000
 3DN  H21  C15  H19  107.65  3.000
 3DN  H20  C15  H19  107.00  3.000
 3DN  H21  C15  C14  110.85  3.000
 3DN  H20  C15  C14  111.75  3.000
 3DN  H19  C15  C14  111.68  3.000
 3DN  H22  C16  C17  119.13  3.000
 3DN  H22  C16  C14  118.96  3.000
 3DN  C17  C16  C14  121.92  3.000
 3DN  H23  C17  C16  119.78  3.000
 3DN  H23  C17  C13  120.39  3.000
 3DN  C16  C17  C13  119.83  3.000
 3DN  C19  C18  C6   118.42  3.000
 3DN  C6   C18  C4   121.18  3.000
 3DN  C19  C18  C4   120.40  3.000
 3DN  H24  C19  C18  119.86  3.000
 3DN  H24  C19  C7   119.37  3.000
 3DN  C18  C19  C7   120.76  3.000
 3DN  C21  C20  C8   120.68  3.000
 3DN  C21  C20  C7   118.31  3.000
 3DN  C8   C20  C7   120.99  3.000
 3DN  H25  C21  C20  119.74  3.000
 3DN  H25  C21  C6   119.13  3.000
 3DN  C20  C21  C6   121.13  3.000
 3DN  H27  C22  H26  107.43  3.000
 3DN  H27  C22  C23  110.64  3.000
 3DN  H26  C22  C23  110.15  3.000
 3DN  H27  C22  C10  108.59  3.000
 3DN  H26  C22  C10  109.44  3.000
 3DN  C23  C22  C10  110.52  3.000
 3DN  H28  C23  N3   105.57  3.000
 3DN  H28  C23  C22  106.67  3.000
 3DN  N3   C23  C22  112.29  3.000
 3DN  H28  C23  C9   107.22  3.000
 3DN  C22  C23  C9   108.46  3.000
 3DN  N3   C23  C9   116.07  3.000
 3DN  C23  N3   C12  112.65  3.000
 3DN  C23  N3   C11  115.23  3.000
 3DN  C12  N3   C11  110.83  3.000
 3DN  H31  C24  H30  106.58  3.000
 3DN  H31  C24  C9   109.47  3.000
 3DN  H30  C24  C9   109.44  3.000
 3DN  H31  C24  N1   110.90  3.000
 3DN  H30  C24  N1   108.99  3.000
 3DN  C9   C24  N1   111.34  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
 3DN  CONST_01  C17  C16  C14  C1      0.00   0.0  0
 3DN  CONST_02  C17  C13  C2   C1      0.00   0.0  0
 3DN  CONST_03  C16  C14  C1   C2      0.00   0.0  0
 3DN  CONST_04  C16  C17  C13  C2      0.00   0.0  0
 3DN  CONST_05  C7   C19  C18  C6      0.00   0.0  0
 3DN  CONST_06  C7   C20  C21  C6      0.00   0.0  0
 3DN  CONST_07  C14  C16  C17  C13     0.00   0.0  0
 3DN  CONST_08  C14  C1   C2   C13     0.00   0.0  0
 3DN  CONST_09  C20  C7   C19  C18     0.00   0.0  0
 3DN  CONST_10  C20  C21  C6   C18     0.00   0.0  0
 3DN  CONST_11  C21  C20  C7   C19     0.00   0.0  0
 3DN  CONST_12  C21  C6   C18  C19     0.00   0.0  0
 3DN  CONST_13  C7   C19  C18  C4    180.00   0.0  0
 3DN  CONST_14  C21  C6   C18  C4    180.00   0.0  0
 3DN  CONST_15  C4   N2   C3   C2      0.00   0.0  0
 3DN  CONST_16  C15  C14  C1   C2    180.00   0.0  0
 3DN  CONST_17  C15  C14  C1   C5      0.00   0.0  0
 3DN  CONST_18  C8   C20  C21  C6    180.00   0.0  0
 3DN  CONST_19  C19  C7   C20  C8    180.00   0.0  0
 3DN  CONST_20  C17  C16  C14  C15   180.00   0.0  0
 3DN  CONST_21  O1   C3   N2   C4    180.00   0.0  0
 3DN  CONST_22  H22  C16  C14  C1    180.00   0.0  0
 3DN  CONST_23  H18  C13  C2   C1    180.00   0.0  0
 3DN  CONST_24  H23  C17  C13  C2    180.00   0.0  0
 3DN  CONST_25  H24  C19  C18  C4      0.00   0.0  0
 3DN  CONST_26  H4   C6   C18  C4      0.00   0.0  0
 3DN  CONST_27  H25  C21  C20  C7    180.00   0.0  0
 3DN  CONST_28  H5   C7   C19  C18   180.00   0.0  0
 3DN  CONST_29  H1   N2   C3   C2    180.00   0.0  0
 3DN  Var_01    C23  C22  C10  N1     57.76  30.0  1
 3DN  Var_02    C23  C9   C24  N1    -57.44  30.0  1
 3DN  Var_03    C19  C18  C4   C5     35.47  30.0  2
 3DN  Var_04    C10  N1   C24  C9     58.58  30.0  1
 3DN  Var_05    C24  N1   C10  C22   -58.77  30.0  1
 3DN  Var_06    C7   C20  C8   N1     42.51  30.0  2
 3DN  Var_07    C20  C8   N1   C10  -169.22  30.0  1
 3DN  Var_08    H19  C15  C14  C1    -60.87  30.0  2
 3DN  Var_09    H15  C12  N3   C23    52.46  30.0  3
 3DN  Var_10    H12  C11  N3   C23  -172.26  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
 3DN  chir_01  C23  N3  C22  C9  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
 3DN  plan-1  C4   0.020
 3DN  plan-1  C6   0.020
 3DN  plan-1  C7   0.020
 3DN  plan-1  C8   0.020
 3DN  plan-1  C18  0.020
 3DN  plan-1  C19  0.020
 3DN  plan-1  C20  0.020
 3DN  plan-1  C21  0.020
 3DN  plan-1  H4   0.020
 3DN  plan-1  H5   0.020
 3DN  plan-1  H24  0.020
 3DN  plan-1  H25  0.020
 3DN  plan-2  C1   0.020
 3DN  plan-2  C2   0.020
 3DN  plan-2  C3   0.020
 3DN  plan-2  C4   0.020
 3DN  plan-2  C5   0.020
 3DN  plan-2  C13  0.020
 3DN  plan-2  N2   0.020
 3DN  plan-2  C14  0.020
 3DN  plan-2  C15  0.020
 3DN  plan-2  C16  0.020
 3DN  plan-2  C17  0.020
 3DN  plan-2  C18  0.020
 3DN  plan-2  H2   0.020
 3DN  plan-2  H18  0.020
 3DN  plan-2  H22  0.020
 3DN  plan-2  H23  0.020
 3DN  plan-2  H1   0.020
 3DN  plan-2  O1   0.020

