# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 23:47:33 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-[2-(4-pyridin-2-ylpiperazin-1-yl)ethylsulfanyl]-3~{H}-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=Nc2ccccc12)SCCN3CCN(CC3)c4ccccn4
#
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
 O3H  O3H  2-[2-(4-pyridin-2-ylpiperazin-1-yl)ethylsulfanyl]-3~{H}-quinazolin-4-one  ligand  47  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O3H
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
 O3H  C2   C  CR16  0  -0.275  18.7033  -13.8021  -13.0884
 O3H  C3   C  CR16  0  -0.263  18.9091  -12.4410  -13.1453
 O3H  C4   C  CR16  0  -0.236  18.0537  -11.6413  -13.9115
 O3H  C5   C  CR16  0  -0.316  17.0056  -12.1980  -14.6118
 O3H  C6   C  CR66  0   0.266  16.7830  -13.5810  -14.5648
 O3H  C7   C  CR6   0   0.332  15.5457  -15.3729  -15.2226
 O3H  C10  C  CH2   0  -0.288  11.0179  -17.1293  -18.4726
 O3H  C11  C  CH2   0  -0.287  13.0355  -16.2803  -19.3674
 O3H  C12  C  CH2   0  -0.297  13.3311  -17.6035  -20.0485
 O3H  C14  C  CR16  0  -0.415  13.1328  -19.5443  -22.1558
 O3H  C16  C  CR16  0  -0.063  10.8460  -20.9879  -22.2600
 O3H  C18  C  CH2   0  -0.279  12.0885  -15.2649  -17.3890
 O3H  C19  C  CH2   0  -0.581  13.3986  -14.7495  -16.8188
 O3H  C1   C  CR66  0  -0.117  17.6443  -14.3786  -13.7947
 O3H  C13  C  CR16  0  -0.149  12.9883  -20.5091  -23.1309
 O3H  C15  C  CR6   0   0.537  12.0721  -19.3261  -21.2528
 O3H  C17  C  CR16  0  -0.366  11.8181  -21.2573  -23.2050
 O3H  C8   C  CR6   0   0.547  17.4136  -15.8173  -13.7438
 O3H  C9   C  CH2   0  -0.295  11.2665  -18.4784  -19.1143
 O3H  N1   N  N     0  -0.458  15.7312  -14.1052  -15.2787
 O3H  N2   N  NR16  0  -0.702  16.3321  -16.2226  -14.4969
 O3H  N3   N  NT    0  -0.425  12.2724  -16.4787  -18.1536
 O3H  N4   N  NT    0  -0.506  12.1126  -18.3483  -20.2887
 O3H  N5   N  N     0  -0.474  10.9615  -20.0633  -21.3165
 O3H  O1   O  O     0  -0.449  18.0767  -16.6205  -13.1147
 O3H  S1   S  S2    0   0.065  14.2646  -16.1768  -16.1007
 O3H  H21  H  HCR6  0   0.269  19.3574  -14.4318  -12.5001
 O3H  H31  H  HCR6  0   0.266  19.7291  -11.9907  -12.6026
 O3H  H4   H  HCR6  0   0.269  18.2183  -10.5725  -13.9565
 O3H  H5   H  HCR6  0   0.265  16.3435  -11.5829  -15.2071
 O3H  H10  H  HCH2  0   0.202  10.3985  -16.5113  -19.1444
 O3H  H93  H  HCH2  0   0.245  10.4481  -17.2835  -17.5539
 O3H  H94  H  HCH2  0   0.252  13.9929  -15.8096  -19.1384
 O3H  H11  H  HCH2  0   0.208  12.5049  -15.6174  -20.0720
 O3H  H95  H  HCH2  0   0.224  14.0353  -18.1831  -19.4359
 O3H  H12  H  HCH2  0   0.256  13.8234  -17.3742  -20.9917
 O3H  H16  H  HCR6  0   0.254   9.9174  -21.5498  -22.2585
 O3H  H18  H  HCH2  0   0.233  11.6280  -14.4531  -17.9750
 O3H  H96  H  HCH2  0   0.254  11.4060  -15.4871  -16.5659
 O3H  H19  H  HCH2  0   0.288  14.0352  -14.2873  -17.5717
 O3H  H97  H  HCH2  0   0.305  13.2118  -14.0126  -16.0400
 O3H  H13  H  HCR6  0   0.266  13.7982  -20.6842  -23.8277
 O3H  H17  H  HCR6  0   0.258  11.6733  -22.0230  -23.9535
 O3H  H92  H  HCH2  0   0.263  10.3182  -18.9213  -19.4030
 O3H  H91  H  HCH2  0   0.219  11.7366  -19.1456  -18.3789
 O3H  H22  H  HNR6  0   0.430  16.1200  -17.2132  -14.4874
 O3H  H14  H  HCR6  0   0.268  14.0565  -18.9886  -22.0996

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
 O3H  C17  C13  aromatic  1.391  0.020  1.391
 O3H  C17  C16  aromatic  1.382  0.020  1.382
 O3H  C13  C14  aromatic  1.379  0.020  1.379
 O3H  C16  N5   aromatic  1.326  0.020  1.326
 O3H  C14  C15  aromatic  1.410  0.020  1.410
 O3H  N5   C15  aromatic  1.334  0.020  1.334
 O3H  C15  N4   single    1.374  0.020  1.374
 O3H  N4   C12  single    1.448  0.020  1.448
 O3H  N4   C9   single    1.453  0.020  1.453
 O3H  C12  C11  single    1.517  0.020  1.517
 O3H  C9   C10  single    1.514  0.020  1.514
 O3H  C11  N3   single    1.447  0.020  1.447
 O3H  C10  N3   single    1.449  0.020  1.449
 O3H  N3   C18  single    1.446  0.020  1.446
 O3H  C18  C19  single    1.519  0.020  1.519
 O3H  C19  S1   single    1.817  0.020  1.817
 O3H  C5   C4   aromatic  1.378  0.020  1.378
 O3H  C5   C6   aromatic  1.402  0.020  1.402
 O3H  S1   C7   single    1.749  0.020  1.749
 O3H  N1   C6   single    1.375  0.020  1.375
 O3H  N1   C7   double    1.282  0.020  1.282
 O3H  C4   C3   aromatic  1.399  0.020  1.399
 O3H  C6   C1   aromatic  1.404  0.020  1.404
 O3H  C7   N2   single    1.366  0.020  1.366
 O3H  C3   C2   aromatic  1.378  0.020  1.378
 O3H  C1   C2   aromatic  1.397  0.020  1.397
 O3H  C1   C8   single    1.458  0.020  1.458
 O3H  N2   C8   single    1.379  0.020  1.379
 O3H  C8   O1   double    1.217  0.020  1.217
 O3H  C2   H21  single    0.930  0.020  1.080
 O3H  C3   H31  single    0.930  0.020  1.080
 O3H  C4   H4   single    0.930  0.020  1.080
 O3H  C5   H5   single    0.930  0.020  1.080
 O3H  C10  H10  single    0.970  0.020  1.090
 O3H  C10  H93  single    0.970  0.020  1.090
 O3H  C11  H94  single    0.970  0.020  1.090
 O3H  C11  H11  single    0.970  0.020  1.090
 O3H  C12  H95  single    0.970  0.020  1.090
 O3H  C12  H12  single    0.970  0.020  1.090
 O3H  C14  H14  single    0.930  0.020  1.080
 O3H  C16  H16  single    0.930  0.020  1.080
 O3H  C18  H18  single    0.970  0.020  1.090
 O3H  C18  H96  single    0.970  0.020  1.090
 O3H  C19  H19  single    0.970  0.020  1.090
 O3H  C19  H97  single    0.970  0.020  1.090
 O3H  C13  H13  single    0.930  0.020  1.080
 O3H  C17  H17  single    0.930  0.020  1.080
 O3H  C9   H92  single    0.970  0.020  1.090
 O3H  C9   H91  single    0.970  0.020  1.090
 O3H  N2   H22  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
 O3H  H21  C2   C1   119.53  3.000
 O3H  H21  C2   C3   120.47  3.000
 O3H  C1   C2   C3   120.00  3.000
 O3H  H31  C3   C4   120.02  3.000
 O3H  H31  C3   C2   120.26  3.000
 O3H  C4   C3   C2   119.73  3.000
 O3H  H4   C4   C5   119.57  3.000
 O3H  H4   C4   C3   119.61  3.000
 O3H  C5   C4   C3   120.82  3.000
 O3H  H5   C5   C6   118.82  3.000
 O3H  H5   C5   C4   121.02  3.000
 O3H  C6   C5   C4   120.16  3.000
 O3H  N1   C6   C1   122.51  3.000
 O3H  C1   C6   C5   118.78  3.000
 O3H  N1   C6   C5   118.70  3.000
 O3H  S1   C7   N2   113.73  3.000
 O3H  N2   C7   N1   123.69  3.000
 O3H  S1   C7   N1   122.58  3.000
 O3H  H93  C10  H10  107.37  3.000
 O3H  H93  C10  N3   109.26  3.000
 O3H  H10  C10  N3   111.64  3.000
 O3H  H93  C10  C9   108.44  3.000
 O3H  H10  C10  C9   109.47  3.000
 O3H  N3   C10  C9   110.56  3.000
 O3H  H11  C11  H94  107.26  3.000
 O3H  H11  C11  N3   111.37  3.000
 O3H  H94  C11  N3   110.23  3.000
 O3H  H11  C11  C12  109.33  3.000
 O3H  H94  C11  C12  107.43  3.000
 O3H  N3   C11  C12  111.08  3.000
 O3H  H12  C12  H95  107.73  3.000
 O3H  H12  C12  N4   110.19  3.000
 O3H  H95  C12  N4   111.12  3.000
 O3H  H12  C12  C11  107.07  3.000
 O3H  H95  C12  C11  109.55  3.000
 O3H  N4   C12  C11  111.04  3.000
 O3H  H14  C14  C15  122.06  3.000
 O3H  H14  C14  C13  119.11  3.000
 O3H  C15  C14  C13  118.83  3.000
 O3H  H16  C16  N5   115.75  3.000
 O3H  H16  C16  C17  120.12  3.000
 O3H  N5   C16  C17  124.13  3.000
 O3H  H96  C18  H18  106.83  3.000
 O3H  H96  C18  N3   107.89  3.000
 O3H  H18  C18  N3   112.98  3.000
 O3H  H96  C18  C19  108.97  3.000
 O3H  H18  C18  C19  108.06  3.000
 O3H  N3   C18  C19  111.93  3.000
 O3H  H97  C19  H19  107.92  3.000
 O3H  H97  C19  S1   109.32  3.000
 O3H  H19  C19  S1   109.15  3.000
 O3H  H97  C19  C18  110.51  3.000
 O3H  H19  C19  C18  112.87  3.000
 O3H  S1   C19  C18  107.03  3.000
 O3H  C8   C1   C6   118.86  3.000
 O3H  C8   C1   C2   120.62  3.000
 O3H  C6   C1   C2   120.52  3.000
 O3H  H13  C13  C17  120.53  3.000
 O3H  H13  C13  C14  119.33  3.000
 O3H  C17  C13  C14  120.14  3.000
 O3H  N5   C15  N4   116.82  3.000
 O3H  N4   C15  C14  122.51  3.000
 O3H  N5   C15  C14  120.66  3.000
 O3H  H17  C17  C13  122.06  3.000
 O3H  H17  C17  C16  121.16  3.000
 O3H  C13  C17  C16  116.77  3.000
 O3H  O1   C8   N2   121.05  3.000
 O3H  O1   C8   C1   125.68  3.000
 O3H  N2   C8   C1   113.27  3.000
 O3H  H91  C9   H92  107.69  3.000
 O3H  H91  C9   N4   110.25  3.000
 O3H  H92  C9   N4   109.28  3.000
 O3H  H91  C9   C10  109.12  3.000
 O3H  H92  C9   C10  109.43  3.000
 O3H  N4   C9   C10  110.99  3.000
 O3H  C7   N1   C6   117.70  3.000
 O3H  H22  N2   C8   116.52  3.000
 O3H  H22  N2   C7   119.51  3.000
 O3H  C8   N2   C7   123.97  3.000
 O3H  C18  N3   C11  113.29  3.000
 O3H  C18  N3   C10  112.53  3.000
 O3H  C11  N3   C10  109.48  3.000
 O3H  C9   N4   C15  119.09  3.000
 O3H  C9   N4   C12  113.69  3.000
 O3H  C15  N4   C12  120.49  3.000
 O3H  C15  N5   C16  119.45  3.000
 O3H  C19  S1   C7   100.74  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
 O3H  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 O3H  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 O3H  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 O3H  CONST_04  C6   C1   C2   C3      0.00   0.0  0
 O3H  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 O3H  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 O3H  CONST_07  C16  C17  C13  C14     0.00   0.0  0
 O3H  CONST_08  C16  N5   C15  C14     0.00   0.0  0
 O3H  CONST_09  N5   C16  C17  C13     0.00   0.0  0
 O3H  CONST_10  N5   C15  C14  C13     0.00   0.0  0
 O3H  CONST_11  C17  C13  C14  C15     0.00   0.0  0
 O3H  CONST_12  C17  C16  N5   C15     0.00   0.0  0
 O3H  CONST_13  N4   C15  N5   C16   180.00   0.0  0
 O3H  CONST_14  N4   C15  C14  C13   180.00   0.0  0
 O3H  CONST_15  N2   C7   N1   C6      0.00   0.0  0
 O3H  CONST_16  C1   C8   N2   C7      0.00   0.0  0
 O3H  CONST_17  N1   C7   N2   C8      0.00   0.0  0
 O3H  CONST_18  S1   C7   N1   C6    180.00   0.0  0
 O3H  CONST_19  O1   C8   N2   C7    180.00   0.0  0
 O3H  CONST_20  S1   C7   N2   C8    180.00   0.0  0
 O3H  CONST_21  H4   C4   C3   C2    180.00   0.0  0
 O3H  CONST_22  H5   C5   C4   C3    180.00   0.0  0
 O3H  CONST_23  H21  C2   C3   C4    180.00   0.0  0
 O3H  CONST_24  H31  C3   C4   C5    180.00   0.0  0
 O3H  CONST_25  H17  C17  C13  C14   180.00   0.0  0
 O3H  CONST_26  H13  C13  C17  C16   180.00   0.0  0
 O3H  CONST_27  H16  C16  C17  C13   180.00   0.0  0
 O3H  CONST_28  H14  C14  C13  C17   180.00   0.0  0
 O3H  CONST_29  H22  N2   C8   C1    180.00   0.0  0
 O3H  Var_01    C15  N4   C9   C10  -157.25  30.0  1
 O3H  Var_02    C12  C11  N3   C10   -59.86  30.0  1
 O3H  Var_03    C9   C10  N3   C11    60.34  30.0  1
 O3H  Var_04    C14  C15  N4   C12    -7.95  30.0  3
 O3H  Var_05    N4   C12  C11  N3     54.63  30.0  1
 O3H  Var_06    N4   C9   C10  N3    -55.74  30.0  1
 O3H  Var_07    C19  C18  N3   C10   168.23  30.0  3
 O3H  Var_08    N1   C7   S1   C19    -4.74  30.0  3
 O3H  Var_09    C18  C19  S1   C7   -168.86  30.0  2
 O3H  Var_10    S1   C19  C18  N3    -45.63  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
 O3H  plan-1  C14  0.020
 O3H  plan-1  C16  0.020
 O3H  plan-1  C13  0.020
 O3H  plan-1  C15  0.020
 O3H  plan-1  C17  0.020
 O3H  plan-1  N4   0.020
 O3H  plan-1  N5   0.020
 O3H  plan-1  H16  0.020
 O3H  plan-1  H13  0.020
 O3H  plan-1  H17  0.020
 O3H  plan-1  H14  0.020
 O3H  plan-2  C2   0.020
 O3H  plan-2  C3   0.020
 O3H  plan-2  C4   0.020
 O3H  plan-2  C5   0.020
 O3H  plan-2  C6   0.020
 O3H  plan-2  C7   0.020
 O3H  plan-2  C1   0.020
 O3H  plan-2  C8   0.020
 O3H  plan-2  N1   0.020
 O3H  plan-2  N2   0.020
 O3H  plan-2  O1   0.020
 O3H  plan-2  S1   0.020
 O3H  plan-2  H21  0.020
 O3H  plan-2  H31  0.020
 O3H  plan-2  H4   0.020
 O3H  plan-2  H5   0.020
 O3H  plan-2  H22  0.020

