# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:11:34 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (E)-N-(4-benzylpiperazin-1-yl)-1-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)methanimine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nn(c2ccccc2)c(C)c1\C=N\N3CCN(CC3)Cc4ccccc4
#
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
 SNT  SNT  (E)-N-(4-benzylpiperazin-1-yl)-1-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)methanimine  ligand  55  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SNT
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
 SNT  C4   C  CR6   0   0.326  -5.6134   0.4206   0.3879
 SNT  C3   C  CR16  0  -0.283  -5.8177   1.5556   1.1638
 SNT  C2   C  CR16  0  -0.254  -7.0931   2.0922   1.2731
 SNT  C1   C  CR16  0  -0.255  -8.1660   1.4886   0.6327
 SNT  N1   N  NR5   0  -0.452  -4.3238  -0.1338   0.2550
 SNT  N2   N  N     0  -0.206   0.0144  -1.2756  -0.4370
 SNT  N3   N  NT    0  -0.293   1.3264  -1.1206  -0.7077
 SNT  N4   N  NT    0  -0.421   4.1362  -0.9127  -0.3675
 SNT  N5   N  N     0  -0.301  -4.1761  -1.4654   0.3396
 SNT  C5   C  CR5   0   0.415  -3.1536   0.4999  -0.0042
 SNT  C6   C  CR5   0  -0.213  -2.1922  -0.4925  -0.0739
 SNT  C7   C  C1    0  -0.201  -0.7792  -0.2819  -0.3167
 SNT  C8   C  CH2   0  -0.270   2.0992  -2.2220  -0.1619
 SNT  C9   C  CH2   0  -0.298   3.5226  -2.1884  -0.6755
 SNT  C10  C  CH2   0  -0.319   5.5399  -0.8821  -0.7186
 SNT  C11  C  CR6   0   0.084   6.2598   0.3036  -0.1288
 SNT  C12  C  CR16  0  -0.314   7.2099   0.9963  -0.8724
 SNT  C13  C  CR16  0  -0.241   7.9097   2.0623  -0.3194
 SNT  C14  C  CR16  0  -0.271   7.6596   2.4546   0.9879
 SNT  C15  C  CR16  0  -0.253  -7.9576   0.3419  -0.1239
 SNT  C16  C  CR16  0  -0.283  -6.6851  -0.1918  -0.2543
 SNT  C17  C  CR5   0   0.281  -2.8983  -1.7040   0.1486
 SNT  C18  C  CH3   0  -0.725  -2.3697  -3.0937   0.1908
 SNT  C19  C  CH2   0  -0.281   3.3901   0.1491  -1.0094
 SNT  C20  C  CH2   0  -0.318   1.9490   0.1769  -0.5358
 SNT  C21  C  CR16  0  -0.241   6.7067   1.7727   1.7364
 SNT  C22  C  CR16  0  -0.284   6.0139   0.7060   1.1827
 SNT  C23  C  CH3   0  -0.752  -3.0199   1.9669  -0.2078
 SNT  H1   H  HCR6  0   0.274  -4.9953   2.0129   1.6972
 SNT  H2   H  HCR6  0   0.265  -7.2455   2.9781   1.8751
 SNT  H3   H  HCR6  0   0.262  -9.1598   1.9058   0.7259
 SNT  H5   H  H     0   0.225  -0.4576   0.7561  -0.3924
 SNT  H6   H  HCH2  0   0.209   2.1070  -2.1900   0.9363
 SNT  H7   H  HCH2  0   0.247   1.6220  -3.1556  -0.4607
 SNT  H8   H  HCH2  0   0.199   3.5304  -2.3947  -1.7594
 SNT  H9   H  HCH2  0   0.245   4.0861  -2.9881  -0.1902
 SNT  H10  H  HCH2  0   0.255   5.9985  -1.7989  -0.3343
 SNT  H11  H  HCH2  0   0.214   5.6960  -0.8972  -1.8103
 SNT  H12  H  HCR6  0   0.248   7.4037   0.7023  -1.8977
 SNT  H13  H  HCR6  0   0.253   8.6446   2.5890  -0.9147
 SNT  H14  H  HCR6  0   0.253   8.1985   3.2876   1.4208
 SNT  H15  H  HCR6  0   0.264  -8.7884  -0.1357  -0.6263
 SNT  H16  H  HCR6  0   0.270  -6.5215  -1.0768  -0.8540
 SNT  H17  H  HCH3  0   0.243  -1.9258  -3.3775  -0.7632
 SNT  H18  H  HCH3  0   0.243  -1.5845  -3.1967   0.9394
 SNT  H19  H  HCH3  0   0.239  -3.1693  -3.7953   0.4241
 SNT  H20  H  HCH2  0   0.250   3.8403   1.1137  -0.7691
 SNT  H21  H  HCH2  0   0.203   3.4122   0.0455  -2.1080
 SNT  H22  H  HCH2  0   0.251   1.4215   0.9223  -1.1339
 SNT  H23  H  HCH2  0   0.219   1.9003   0.5015   0.5151
 SNT  H24  H  HCR6  0   0.252   6.5033   2.0738   2.7563
 SNT  H25  H  HCR6  0   0.244   5.2659   0.1851   1.7672
 SNT  H26  H  HCH3  0   0.265  -2.8646   2.4989   0.7319
 SNT  H27  H  HCH3  0   0.266  -2.1636   2.1805  -0.8449
 SNT  H28  H  HCH3  0   0.267  -3.9001   2.3927  -0.6882

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
 SNT  C2   C1   aromatic  1.388  0.020  1.388
 SNT  C2   C3   aromatic  1.388  0.020  1.388
 SNT  C1   C15  aromatic  1.390  0.020  1.390
 SNT  C3   C4   aromatic  1.390  0.020  1.390
 SNT  C15  C16  aromatic  1.386  0.020  1.386
 SNT  C4   C16  aromatic  1.391  0.020  1.391
 SNT  C4   N1   single    1.410  0.020  1.410
 SNT  N1   N5   aromatic  1.342  0.020  1.342
 SNT  N1   C5   aromatic  1.356  0.020  1.356
 SNT  N5   C17  aromatic  1.314  0.020  1.314
 SNT  C5   C23  single    1.487  0.020  1.487
 SNT  C5   C6   aromatic  1.384  0.020  1.384
 SNT  C17  C18  single    1.487  0.020  1.487
 SNT  C17  C6   aromatic  1.420  0.020  1.420
 SNT  C6   C7   single    1.449  0.020  1.449
 SNT  C7   N2   double    1.277  0.020  1.277
 SNT  N2   N3   single    1.348  0.020  1.348
 SNT  N3   C20  single    1.449  0.020  1.449
 SNT  N3   C8   single    1.452  0.020  1.452
 SNT  C20  C19  single    1.517  0.020  1.517
 SNT  C8   C9   single    1.514  0.020  1.514
 SNT  C19  N4   single    1.448  0.020  1.448
 SNT  C9   N4   single    1.449  0.020  1.449
 SNT  N4   C10  single    1.447  0.020  1.447
 SNT  C10  C11  single    1.507  0.020  1.507
 SNT  C11  C22  aromatic  1.394  0.020  1.394
 SNT  C11  C12  aromatic  1.391  0.020  1.391
 SNT  C22  C21  aromatic  1.387  0.020  1.387
 SNT  C12  C13  aromatic  1.390  0.020  1.390
 SNT  C21  C14  aromatic  1.390  0.020  1.390
 SNT  C13  C14  aromatic  1.388  0.020  1.388
 SNT  C3   H1   single    0.930  0.020  1.080
 SNT  C2   H2   single    0.930  0.020  1.080
 SNT  C1   H3   single    0.930  0.020  1.080
 SNT  C7   H5   single    0.930  0.020  1.080
 SNT  C8   H6   single    0.970  0.020  1.090
 SNT  C8   H7   single    0.970  0.020  1.090
 SNT  C9   H8   single    0.970  0.020  1.090
 SNT  C9   H9   single    0.970  0.020  1.090
 SNT  C10  H10  single    0.970  0.020  1.090
 SNT  C10  H11  single    0.970  0.020  1.090
 SNT  C12  H12  single    0.930  0.020  1.080
 SNT  C13  H13  single    0.930  0.020  1.080
 SNT  C14  H14  single    0.930  0.020  1.080
 SNT  C15  H15  single    0.930  0.020  1.080
 SNT  C16  H16  single    0.930  0.020  1.080
 SNT  C18  H17  single    0.970  0.020  1.090
 SNT  C18  H18  single    0.970  0.020  1.090
 SNT  C18  H19  single    0.970  0.020  1.090
 SNT  C19  H20  single    0.970  0.020  1.090
 SNT  C19  H21  single    0.970  0.020  1.090
 SNT  C20  H22  single    0.970  0.020  1.090
 SNT  C20  H23  single    0.970  0.020  1.090
 SNT  C21  H24  single    0.930  0.020  1.080
 SNT  C22  H25  single    0.930  0.020  1.080
 SNT  C23  H26  single    0.970  0.020  1.090
 SNT  C23  H27  single    0.970  0.020  1.090
 SNT  C23  H28  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
 SNT  C16  C4   N1   119.20  3.000
 SNT  N1   C4   C3   120.54  3.000
 SNT  C16  C4   C3   120.26  3.000
 SNT  H1   C3   C2   119.76  3.000
 SNT  H1   C3   C4   120.58  3.000
 SNT  C2   C3   C4   119.65  3.000
 SNT  H2   C2   C1   120.27  3.000
 SNT  H2   C2   C3   119.33  3.000
 SNT  C1   C2   C3   120.40  3.000
 SNT  H3   C1   C15  120.19  3.000
 SNT  H3   C1   C2   120.18  3.000
 SNT  C15  C1   C2   119.62  3.000
 SNT  C5   N1   N5   112.38  3.000
 SNT  C5   N1   C4   128.58  3.000
 SNT  N5   N1   C4   118.99  3.000
 SNT  C7   N2   N3   122.27  3.000
 SNT  C20  N3   C8   113.94  3.000
 SNT  C8   N3   N2   110.81  3.000
 SNT  C20  N3   N2   119.80  3.000
 SNT  C19  N4   C10  112.13  3.000
 SNT  C10  N4   C9   112.20  3.000
 SNT  C19  N4   C9   109.47  3.000
 SNT  C17  N5   N1   106.14  3.000
 SNT  C23  C5   C6   129.66  3.000
 SNT  C6   C5   N1   105.91  3.000
 SNT  C23  C5   N1   124.39  3.000
 SNT  C17  C6   C7   129.44  3.000
 SNT  C7   C6   C5   125.58  3.000
 SNT  C17  C6   C5   104.99  3.000
 SNT  H5   C7   C6   115.98  3.000
 SNT  H5   C7   N2   123.46  3.000
 SNT  C6   C7   N2   120.56  3.000
 SNT  H7   C8   H6   107.57  3.000
 SNT  H7   C8   C9   109.73  3.000
 SNT  H6   C8   C9   109.38  3.000
 SNT  H7   C8   N3   108.28  3.000
 SNT  H6   C8   N3   110.94  3.000
 SNT  C9   C8   N3   110.87  3.000
 SNT  H9   C9   H8   107.22  3.000
 SNT  H9   C9   C8   108.56  3.000
 SNT  H8   C9   C8   109.62  3.000
 SNT  H9   C9   N4   109.38  3.000
 SNT  H8   C9   N4   111.75  3.000
 SNT  C8   C9   N4   110.22  3.000
 SNT  H11  C10  H10  106.07  3.000
 SNT  H11  C10  C11  109.30  3.000
 SNT  H10  C10  C11  108.74  3.000
 SNT  H11  C10  N4   112.15  3.000
 SNT  H10  C10  N4   107.66  3.000
 SNT  C11  C10  N4   112.64  3.000
 SNT  C22  C11  C12  118.66  3.000
 SNT  C12  C11  C10  120.58  3.000
 SNT  C22  C11  C10  120.73  3.000
 SNT  H12  C12  C13  119.62  3.000
 SNT  H12  C12  C11  119.51  3.000
 SNT  C13  C12  C11  120.87  3.000
 SNT  H13  C13  C14  120.20  3.000
 SNT  H13  C13  C12  119.74  3.000
 SNT  C14  C13  C12  120.06  3.000
 SNT  H14  C14  C21  120.22  3.000
 SNT  H14  C14  C13  120.30  3.000
 SNT  C21  C14  C13  119.48  3.000
 SNT  H15  C15  C16  119.43  3.000
 SNT  H15  C15  C1   120.13  3.000
 SNT  C16  C15  C1   120.44  3.000
 SNT  H16  C16  C15  120.40  3.000
 SNT  H16  C16  C4   119.98  3.000
 SNT  C15  C16  C4   119.62  3.000
 SNT  C18  C17  C6   128.68  3.000
 SNT  C6   C17  N5   110.58  3.000
 SNT  C18  C17  N5   120.74  3.000
 SNT  H19  C18  H18  108.73  3.000
 SNT  H19  C18  H17  108.59  3.000
 SNT  H18  C18  H17  106.45  3.000
 SNT  H19  C18  C17  110.31  3.000
 SNT  H18  C18  C17  111.33  3.000
 SNT  H17  C18  C17  111.30  3.000
 SNT  H21  C19  H20  107.09  3.000
 SNT  H21  C19  C20  109.36  3.000
 SNT  H20  C19  C20  107.88  3.000
 SNT  H21  C19  N4   111.23  3.000
 SNT  H20  C19  N4   109.76  3.000
 SNT  C20  C19  N4   111.38  3.000
 SNT  H23  C20  H22  107.48  3.000
 SNT  H23  C20  C19  110.20  3.000
 SNT  H22  C20  C19  107.49  3.000
 SNT  H23  C20  N3   110.98  3.000
 SNT  H22  C20  N3   109.80  3.000
 SNT  C19  C20  N3   110.77  3.000
 SNT  H24  C21  C22  119.73  3.000
 SNT  H24  C21  C14  119.97  3.000
 SNT  C22  C21  C14  120.30  3.000
 SNT  H25  C22  C21  119.97  3.000
 SNT  H25  C22  C11  119.40  3.000
 SNT  C21  C22  C11  120.63  3.000
 SNT  H28  C23  H27  107.51  3.000
 SNT  H28  C23  H26  107.72  3.000
 SNT  H27  C23  H26  107.25  3.000
 SNT  H28  C23  C5   111.92  3.000
 SNT  H27  C23  C5   110.14  3.000
 SNT  H26  C23  C5   112.08  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
 SNT  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 SNT  CONST_02  C1   C15  C16  C4      0.00   0.0  0
 SNT  CONST_03  C17  N5   N1   C4    180.00   0.0  0
 SNT  CONST_04  C6   C5   N1   C4    180.00   0.0  0
 SNT  CONST_05  C15  C1   C2   C3      0.00   0.0  0
 SNT  CONST_06  C15  C16  C4   C3      0.00   0.0  0
 SNT  CONST_09  C16  C15  C1   C2      0.00   0.0  0
 SNT  CONST_10  C16  C4   C3   C2      0.00   0.0  0
 SNT  CONST_11  N1   C4   C3   C2    180.00   0.0  0
 SNT  CONST_12  C15  C16  C4   N1    180.00   0.0  0
 SNT  CONST_13  C6   C17  N5   N1      0.00   0.0  0
 SNT  CONST_14  C17  C6   C5   N1      0.00   0.0  0
 SNT  CONST_16  C6   C5   N1   N5      0.00   0.0  0
 SNT  CONST_17  C5   C6   C17  N5      0.00   0.0  0
 SNT  CONST_19  C17  N5   N1   C5      0.00   0.0  0
 SNT  CONST_20  C14  C21  C22  C11     0.00   0.0  0
 SNT  CONST_21  C14  C13  C12  C11     0.00   0.0  0
 SNT  CONST_22  C21  C22  C11  C12     0.00   0.0  0
 SNT  CONST_23  C21  C14  C13  C12     0.00   0.0  0
 SNT  CONST_24  C22  C11  C12  C13     0.00   0.0  0
 SNT  CONST_25  C22  C21  C14  C13     0.00   0.0  0
 SNT  CONST_26  C23  C5   N1   C4      0.00   0.0  0
 SNT  CONST_27  C18  C17  N5   N1    180.00   0.0  0
 SNT  CONST_28  C7   C6   C5   N1    180.00   0.0  0
 SNT  CONST_29  C23  C5   N1   N5    180.00   0.0  0
 SNT  CONST_30  C7   C6   C17  N5    180.00   0.0  0
 SNT  CONST_31  C18  C17  C6   C5    180.00   0.0  0
 SNT  CONST_32  C21  C22  C11  C10   180.00   0.0  0
 SNT  CONST_33  C13  C12  C11  C10   180.00   0.0  0
 SNT  CONST_34  C23  C5   C6   C17   180.00   0.0  0
 SNT  CONST_35  H2   C2   C3   C4    180.00   0.0  0
 SNT  CONST_36  H15  C15  C16  C4    180.00   0.0  0
 SNT  CONST_37  H3   C1   C2   C3    180.00   0.0  0
 SNT  CONST_38  H16  C16  C4   C3    180.00   0.0  0
 SNT  CONST_39  H1   C3   C2   C1    180.00   0.0  0
 SNT  CONST_40  H24  C21  C22  C11   180.00   0.0  0
 SNT  CONST_41  H13  C13  C12  C11   180.00   0.0  0
 SNT  CONST_42  H25  C22  C11  C12   180.00   0.0  0
 SNT  CONST_43  H14  C14  C13  C12   180.00   0.0  0
 SNT  CONST_44  H12  C12  C13  C14   180.00   0.0  0
 SNT  Var_01    N4   C19  C20  N3    -53.99  30.0  1
 SNT  Var_02    N4   C9   C8   N3     56.36  30.0  1
 SNT  Var_03    C19  C20  N3   C8     50.28  30.0  1
 SNT  Var_04    C19  N4   C9   C8    -60.69  30.0  1
 SNT  Var_05    C20  N3   C8   C9    -51.79  30.0  1
 SNT  Var_06    C20  C19  N4   C9     59.82  30.0  1
 SNT  Var_07    C22  C11  C10  N4     41.95  30.0  2
 SNT  Var_08    C11  C10  N4   C9   -167.03  30.0  3
 SNT  Var_09    C6   C7   N2   N3    177.73   0.0  2
 SNT  Var_10    C5   C6   C7   N2   -176.03  30.0  3
 SNT  Var_11    H26  C23  C5   N1     88.03  30.0  2
 SNT  Var_12    H17  C18  C17  N5    118.74  30.0  2

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
 SNT  plan-1  C4   0.020
 SNT  plan-1  N1   0.020
 SNT  plan-1  N5   0.020
 SNT  plan-1  C5   0.020
 SNT  plan-1  C6   0.020
 SNT  plan-1  C7   0.020
 SNT  plan-1  C17  0.020
 SNT  plan-1  C18  0.020
 SNT  plan-1  C23  0.020
 SNT  plan-2  C4   0.020
 SNT  plan-2  C3   0.020
 SNT  plan-2  C2   0.020
 SNT  plan-2  C1   0.020
 SNT  plan-2  N1   0.020
 SNT  plan-2  C15  0.020
 SNT  plan-2  C16  0.020
 SNT  plan-2  H1   0.020
 SNT  plan-2  H2   0.020
 SNT  plan-2  H3   0.020
 SNT  plan-2  H15  0.020
 SNT  plan-2  H16  0.020
 SNT  plan-3  N2   0.020
 SNT  plan-3  N3   0.020
 SNT  plan-3  C6   0.020
 SNT  plan-3  C7   0.020
 SNT  plan-3  H5   0.020
 SNT  plan-4  C10  0.020
 SNT  plan-4  C11  0.020
 SNT  plan-4  C12  0.020
 SNT  plan-4  C13  0.020
 SNT  plan-4  C14  0.020
 SNT  plan-4  C21  0.020
 SNT  plan-4  C22  0.020
 SNT  plan-4  H12  0.020
 SNT  plan-4  H13  0.020
 SNT  plan-4  H14  0.020
 SNT  plan-4  H24  0.020
 SNT  plan-4  H25  0.020

