# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 01:20:27 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 3-[3-[(2~{R})-3-oxidanylidenepiperidin-2-yl]propyl]quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCCN[C@@H]1CCCN2C=Nc3ccccc3C2=O
#
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
 87F  87F  3-[3-[(2~{R})-3-oxidanylidenepiperidin-2-yl]propyl]quinazolin-4-one  ligand  40  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_87F
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
 87F  C1   C  CR16  0  -0.311   5.2356   0.3227  -1.1767
 87F  C2   C  CR16  0  -0.238   6.0033  -0.7273  -0.7236
 87F  C3   C  CR16  0  -0.258   5.5153  -1.5967   0.2593
 87F  C7   C  CR16  0   0.147   2.0374   1.7402  -0.6167
 87F  C6   C  CR66  0   0.245   3.9522   0.5305  -0.6538
 87F  O2   O  O     0  -0.399  -5.0017   1.5856   0.8475
 87F  C4   C  CR16  0  -0.275   4.2561  -1.4047   0.7826
 87F  C5   C  CR66  0  -0.098   3.4669  -0.3410   0.3324
 87F  C8   C  CR6   0   0.587   2.1313  -0.1311   0.8801
 87F  N1   N  N     0  -0.464   3.2029   1.5839  -1.1227
 87F  N2   N  NR6   0  -0.518   1.4706   0.9635   0.3482
 87F  C9   C  CH2   0  -0.310   0.1112   1.2683   0.7898
 87F  C10  C  CH2   0  -0.449  -0.9391   0.4609   0.0408
 87F  C11  C  CH2   0  -0.433  -2.3404   0.8334   0.5138
 87F  C12  C  CH1   0  -0.190  -3.4412   0.1633  -0.2944
 87F  N3   N  NH1   0  -0.613  -3.4189  -1.2861  -0.1291
 87F  C16  C  CH2   0  -0.299  -4.3952  -1.9684  -0.9614
 87F  C13  C  C     0   0.433  -4.8304   0.6558   0.0932
 87F  C14  C  CH2   0  -0.562  -5.9694  -0.0666  -0.5766
 87F  C15  C  CH2   0  -0.436  -5.7937  -1.5842  -0.5155
 87F  H1   H  HCR6  0   0.267   5.6079   0.9984  -1.9359
 87F  H2   H  HCR6  0   0.270   6.9942  -0.8815  -1.1303
 87F  H3   H  HCR6  0   0.267   6.1290  -2.4160   0.6087
 87F  H4   H  HCR6  0   0.292   1.4188   2.5611  -0.9622
 87F  H5   H  HCR6  0   0.266   3.8712  -2.0713   1.5428
 87F  H6   H  HCH2  0   0.272   0.0470   1.0913   1.8622
 87F  H7   H  HCH2  0   0.270  -0.0483   2.3354   0.6329
 87F  H8   H  HCH2  0   0.239  -0.8440   0.6532  -1.0322
 87F  H9   H  HCH2  0   0.241  -0.7454  -0.6024   0.1967
 87F  H10  H  HCH2  0   0.234  -2.4560   0.5750   1.5701
 87F  H11  H  HCH2  0   0.239  -2.4611   1.9164   0.4390
 87F  H12  H  HCH1  0   0.234  -3.3164   0.4506  -1.3577
 87F  H13  H  HNH1  0   0.364  -2.4958  -1.6299  -0.3601
 87F  H15  H  HCH2  0   0.198  -4.2765  -1.7287  -2.0306
 87F  H16  H  HCH2  0   0.244  -4.2487  -3.0443  -0.8559
 87F  H17  H  HCH2  0   0.264  -6.9182   0.2544  -0.1459
 87F  H18  H  HCH2  0   0.264  -5.9633   0.2487  -1.6272
 87F  H19  H  HCH2  0   0.244  -6.5401  -2.0671  -1.1474
 87F  H20  H  HCH2  0   0.233  -5.9575  -1.9342   0.5064
 87F  O1   O  O     0  -0.460   1.6126  -0.8315   1.7312

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
 87F  C2   C3   aromatic  1.400  0.020  1.400
 87F  C2   C1   aromatic  1.377  0.020  1.377
 87F  C3   C4   aromatic  1.377  0.020  1.377
 87F  C1   C6   aromatic  1.401  0.020  1.401
 87F  C4   C5   aromatic  1.399  0.020  1.399
 87F  C6   C5   aromatic  1.403  0.020  1.403
 87F  C6   N1   single    1.375  0.020  1.375
 87F  C5   C8   single    1.459  0.020  1.459
 87F  N1   C7   double    1.280  0.020  1.280
 87F  C8   O1   double    1.218  0.020  1.218
 87F  C8   N2   single    1.385  0.020  1.385
 87F  C7   N2   single    1.362  0.020  1.362
 87F  N2   C9   single    1.462  0.020  1.462
 87F  C9   C10  single    1.522  0.020  1.522
 87F  C10  C11  single    1.525  0.020  1.525
 87F  C11  C12  single    1.521  0.020  1.521
 87F  N3   C12  single    1.459  0.020  1.459
 87F  N3   C16  single    1.453  0.020  1.453
 87F  C12  C13  single    1.524  0.020  1.524
 87F  C16  C15  single    1.517  0.020  1.517
 87F  C13  O2   double    1.209  0.020  1.209
 87F  C13  C14  single    1.506  0.020  1.506
 87F  C14  C15  single    1.529  0.020  1.529
 87F  C1   H1   single    0.930  0.020  1.080
 87F  C2   H2   single    0.930  0.020  1.080
 87F  C3   H3   single    0.930  0.020  1.080
 87F  C7   H4   single    0.930  0.020  1.080
 87F  C4   H5   single    0.930  0.020  1.080
 87F  C9   H6   single    0.970  0.020  1.090
 87F  C9   H7   single    0.970  0.020  1.090
 87F  C10  H8   single    0.970  0.020  1.090
 87F  C10  H9   single    0.970  0.020  1.090
 87F  C11  H10  single    0.970  0.020  1.090
 87F  C11  H11  single    0.970  0.020  1.090
 87F  C12  H12  single    0.970  0.020  1.090
 87F  N3   H13  single    0.890  0.020  1.040
 87F  C16  H15  single    0.970  0.020  1.090
 87F  C16  H16  single    0.970  0.020  1.090
 87F  C14  H17  single    0.970  0.020  1.090
 87F  C14  H18  single    0.970  0.020  1.090
 87F  C15  H19  single    0.970  0.020  1.090
 87F  C15  H20  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
 87F  H1   C1   C6   118.96  3.000
 87F  H1   C1   C2   120.99  3.000
 87F  C6   C1   C2   120.05  3.000
 87F  H2   C2   C3   119.64  3.000
 87F  H2   C2   C1   119.69  3.000
 87F  C3   C2   C1   120.67  3.000
 87F  H3   C3   C4   120.11  3.000
 87F  H3   C3   C2   119.96  3.000
 87F  C4   C3   C2   119.93  3.000
 87F  H4   C7   N2   114.83  3.000
 87F  H4   C7   N1   119.07  3.000
 87F  N2   C7   N1   126.10  3.000
 87F  N1   C6   C5   121.81  3.000
 87F  N1   C6   C1   119.04  3.000
 87F  C5   C6   C1   119.15  3.000
 87F  H5   C4   C5   119.60  3.000
 87F  H5   C4   C3   120.43  3.000
 87F  C5   C4   C3   119.97  3.000
 87F  C8   C5   C4   120.34  3.000
 87F  C8   C5   C6   119.43  3.000
 87F  C4   C5   C6   120.23  3.000
 87F  N2   C8   O1   121.31  3.000
 87F  N2   C8   C5   113.98  3.000
 87F  O1   C8   C5   124.71  3.000
 87F  C6   N1   C7   117.06  3.000
 87F  C9   N2   C8   119.52  3.000
 87F  C9   N2   C7   118.82  3.000
 87F  C8   N2   C7   121.62  3.000
 87F  H7   C9   H6   106.99  3.000
 87F  H7   C9   C10  110.33  3.000
 87F  H6   C9   C10  110.97  3.000
 87F  H7   C9   N2   107.26  3.000
 87F  H6   C9   N2   108.57  3.000
 87F  C10  C9   N2   112.49  3.000
 87F  H9   C10  H8   107.20  3.000
 87F  H9   C10  C11  110.88  3.000
 87F  H8   C10  C11  109.95  3.000
 87F  H9   C10  C9   108.90  3.000
 87F  H8   C10  C9   109.23  3.000
 87F  C11  C10  C9   110.60  3.000
 87F  H11  C11  H10  106.78  3.000
 87F  H11  C11  C12  108.69  3.000
 87F  H10  C11  C12  109.42  3.000
 87F  H11  C11  C10  108.81  3.000
 87F  H10  C11  C10  109.82  3.000
 87F  C12  C11  C10  113.11  3.000
 87F  H12  C12  C13  105.24  3.000
 87F  H12  C12  N3   111.37  3.000
 87F  C13  C12  N3   107.83  3.000
 87F  H12  C12  C11  108.30  3.000
 87F  C13  C12  C11  112.47  3.000
 87F  N3   C12  C11  111.49  3.000
 87F  H13  N3   C16  108.83  3.000
 87F  H13  N3   C12  109.00  3.000
 87F  C16  N3   C12  113.04  3.000
 87F  H16  C16  H15  107.09  3.000
 87F  H16  C16  C15  110.19  3.000
 87F  H15  C16  C15  109.23  3.000
 87F  H16  C16  N3   108.51  3.000
 87F  H15  C16  N3   112.41  3.000
 87F  C15  C16  N3   109.39  3.000
 87F  C14  C13  C12  114.92  3.000
 87F  C14  C13  O2   122.62  3.000
 87F  C12  C13  O2   122.42  3.000
 87F  H18  C14  H17  107.38  3.000
 87F  H18  C14  C15  108.84  3.000
 87F  H17  C14  C15  112.11  3.000
 87F  H18  C14  C13  106.49  3.000
 87F  H17  C14  C13  109.95  3.000
 87F  C15  C14  C13  111.80  3.000
 87F  H20  C15  H19  107.30  3.000
 87F  H20  C15  C14  109.77  3.000
 87F  H19  C15  C14  109.73  3.000
 87F  H20  C15  C16  109.39  3.000
 87F  H19  C15  C16  110.38  3.000
 87F  C14  C15  C16  110.22  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
 87F  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 87F  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 87F  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 87F  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 87F  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 87F  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 87F  CONST_07  C5   C8   N2   C7      0.00   0.0  0
 87F  CONST_08  N2   C7   N1   C6      0.00   0.0  0
 87F  CONST_09  N1   C7   N2   C8      0.00   0.0  0
 87F  CONST_10  O1   C8   N2   C7    180.00   0.0  0
 87F  CONST_11  C9   N2   C8   C5    180.00   0.0  0
 87F  CONST_12  C9   N2   C7   N1    180.00   0.0  0
 87F  CONST_13  H3   C3   C2   C1    180.00   0.0  0
 87F  CONST_14  H5   C4   C3   C2    180.00   0.0  0
 87F  CONST_15  H1   C1   C2   C3    180.00   0.0  0
 87F  CONST_16  H2   C2   C1   C6    180.00   0.0  0
 87F  CONST_17  H4   C7   N1   C6    180.00   0.0  0
 87F  CONST_18  C9   N2   C8   O1      0.00   0.0  0
 87F  Var_01    C15  C16  N3   C12   -65.33  30.0  1
 87F  Var_02    C15  C14  C13  C12    47.23  30.0  1
 87F  Var_03    C14  C15  C16  N3     57.11  30.0  1
 87F  Var_04    C13  C14  C15  C16   -48.86  30.0  1
 87F  Var_05    C10  C9   N2   C7     94.01  30.0  3
 87F  Var_06    C11  C10  C9   N2   -178.81  30.0  3
 87F  Var_07    C12  C11  C10  C9    174.19  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
 87F  chir_01  C12  C11  N3  C13  negativ

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
 87F  plan-1  C1   0.020
 87F  plan-1  C2   0.020
 87F  plan-1  C3   0.020
 87F  plan-1  C7   0.020
 87F  plan-1  C6   0.020
 87F  plan-1  C4   0.020
 87F  plan-1  C5   0.020
 87F  plan-1  C8   0.020
 87F  plan-1  N1   0.020
 87F  plan-1  N2   0.020
 87F  plan-1  C9   0.020
 87F  plan-1  H1   0.020
 87F  plan-1  H2   0.020
 87F  plan-1  H3   0.020
 87F  plan-1  H4   0.020
 87F  plan-1  H5   0.020
 87F  plan-1  O1   0.020
 87F  plan-2  O2   0.020
 87F  plan-2  C12  0.020
 87F  plan-2  C13  0.020
 87F  plan-2  C14  0.020

