# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 16:40:17 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 7-chloro-6-fluoro-3-{2-oxo-3-[(2S)-piperidin-2-yl]propyl}quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc2C(=O)N(CC(=O)C[C@@H]3CCCCN3)C=Nc2cc1Cl
#
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
 9G3  9G3  7-chloro-6-fluoro-3-{2-oxo-3-[(2S)-piperidin-2-yl]propyl}quinazolin-4(3H)-one  ligand  40  23  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9G3
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
 9G3  C1   C   CR6   0   0.626   4.0868  -1.0231   0.7022
 9G3  C2   C   CR6   0  -0.216   4.6963  -0.1823  -0.2345
 9G3  C3   C   CR16  0  -0.266   3.9990   0.8725  -0.7735
 9G3  C4   C   CR66  0   0.242   2.6744   1.1031  -0.3802
 9G3  C5   C   CR66  0  -0.076   2.0813   0.2514   0.5597
 9G3  C6   C   CR16  0  -0.450   2.7945  -0.8199   1.1015
 9G3  C8   C   CR16  0   0.158   0.7906   2.3470  -0.5530
 9G3  C10  C   CR6   0   0.607   0.7007   0.4843   0.9623
 9G3  C15  C   C     0   0.406  -2.1907   0.8799  -0.0047
 9G3  C16  C   CH2   0  -0.573  -3.6103   0.9204   0.4800
 9G3  C17  C   CH1   0  -0.061  -4.6029   0.0685  -0.2986
 9G3  C20  C   CH2   0  -0.292  -5.2740  -2.2099  -0.7766
 9G3  C21  C   CH2   0  -0.428  -6.7159  -1.9306  -0.3834
 9G3  C22  C   CH2   0  -0.445  -7.0453  -0.4590  -0.6037
 9G3  C23  C   CH2   0  -0.415  -6.0300   0.4268   0.1082
 9G3  N7   N   N     0  -0.462   1.9967   2.1605  -0.9364
 9G3  N9   N   NR6   0  -0.513   0.1258   1.5942   0.3679
 9G3  O11  O   O     0  -0.446   0.0745  -0.2016   1.7469
 9G3  F12  F   F     0  -0.289   4.7910  -2.0360   1.2045
 9G3  CL1  CL  CL    0  -0.067   6.3204  -0.4931  -0.6961
 9G3  O18  O   O     0  -0.387  -1.7887   0.1545  -0.8810
 9G3  N19  N   NH1   0  -0.606  -4.3710  -1.3449  -0.0332
 9G3  H1   H   HCR6  0   0.302   4.4608   1.5273  -1.4998
 9G3  H2   H   HCR6  0   0.299   2.3383  -1.4810   1.8266
 9G3  H3   H   HCR6  0   0.300   0.2235   3.1721  -0.9674
 9G3  H4   H   HCH2  0   0.325  -1.5081   2.8728   0.3148
 9G3  H5   H   HCH2  0   0.312  -1.4196   1.8782   1.7505
 9G3  H6   H   HCH2  0   0.281  -3.6105   0.6244   1.5358
 9G3  H7   H   HCH2  0   0.281  -3.9279   1.9693   0.4784
 9G3  H8   H   HCH1  0   0.198  -4.4968   0.3040  -1.3723
 9G3  H9   H   HCH2  0   0.230  -5.0152  -3.2479  -0.5576
 9G3  H10  H   HCH2  0   0.185  -5.1732  -2.0818  -1.8674
 9G3  H11  H   HCH2  0   0.227  -7.3866  -2.5684  -0.9632
 9G3  H12  H   HCH2  0   0.213  -6.8589  -2.1885   0.6704
 9G3  H13  H   HCH2  0   0.211  -7.0271  -0.2404  -1.6770
 9G3  H14  H   HCH2  0   0.232  -8.0555  -0.2315  -0.2567
 9G3  H15  H   HCH2  0   0.212  -6.1309   0.3076   1.1926
 9G3  H16  H   HCH2  0   0.229  -6.2156   1.4800  -0.1169
 9G3  H17  H   HNH1  0   0.349  -3.4216  -1.5776  -0.2934
 9G3  C14  C   CH2   0  -0.435  -1.2584   1.8716   0.6723

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
 9G3  C8   N7   double    1.279  0.020  1.279
 9G3  C8   N9   single    1.363  0.020  1.363
 9G3  N7   C4   single    1.374  0.020  1.374
 9G3  C14  N9   single    1.444  0.020  1.444
 9G3  C14  C15  single    1.520  0.020  1.520
 9G3  N9   C10  single    1.384  0.020  1.384
 9G3  C4   C3   aromatic  1.401  0.020  1.401
 9G3  C4   C5   aromatic  1.400  0.020  1.400
 9G3  C3   C2   aromatic  1.375  0.020  1.375
 9G3  C16  C15  single    1.501  0.020  1.501
 9G3  C16  C17  single    1.522  0.020  1.522
 9G3  C15  O18  double    1.207  0.020  1.207
 9G3  C23  C17  single    1.527  0.020  1.527
 9G3  C23  C22  single    1.524  0.020  1.524
 9G3  C10  C5   single    1.457  0.020  1.457
 9G3  C10  O11  double    1.216  0.020  1.216
 9G3  C5   C6   aromatic  1.396  0.020  1.396
 9G3  C17  N19  single    1.457  0.020  1.457
 9G3  C2   CL1  single    1.717  0.020  1.717
 9G3  C2   C1   aromatic  1.398  0.020  1.398
 9G3  C22  C21  single    1.524  0.020  1.524
 9G3  C6   C1   aromatic  1.368  0.020  1.368
 9G3  C1   F12  single    1.332  0.020  1.332
 9G3  N19  C20  single    1.455  0.020  1.455
 9G3  C21  C20  single    1.520  0.020  1.520
 9G3  C3   H1   single    0.930  0.020  1.080
 9G3  C6   H2   single    0.930  0.020  1.080
 9G3  C8   H3   single    0.930  0.020  1.080
 9G3  C14  H4   single    0.970  0.020  1.090
 9G3  C14  H5   single    0.970  0.020  1.090
 9G3  C16  H6   single    0.970  0.020  1.090
 9G3  C16  H7   single    0.970  0.020  1.090
 9G3  C17  H8   single    0.970  0.020  1.090
 9G3  C20  H9   single    0.970  0.020  1.090
 9G3  C20  H10  single    0.970  0.020  1.090
 9G3  C21  H11  single    0.970  0.020  1.090
 9G3  C21  H12  single    0.970  0.020  1.090
 9G3  C22  H13  single    0.970  0.020  1.090
 9G3  C22  H14  single    0.970  0.020  1.090
 9G3  C23  H15  single    0.970  0.020  1.090
 9G3  C23  H16  single    0.970  0.020  1.090
 9G3  N19  H17  single    0.890  0.020  1.040

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
 9G3  F12  C1   C6   120.16  3.000
 9G3  F12  C1   C2   118.64  3.000
 9G3  C6   C1   C2   121.20  3.000
 9G3  CL1  C2   C3   120.89  3.000
 9G3  CL1  C2   C1   118.92  3.000
 9G3  C3   C2   C1   120.19  3.000
 9G3  H1   C3   C4   119.52  3.000
 9G3  H1   C3   C2   120.76  3.000
 9G3  C4   C3   C2   119.73  3.000
 9G3  N7   C4   C5   122.08  3.000
 9G3  C5   C4   C3   119.27  3.000
 9G3  N7   C4   C3   118.66  3.000
 9G3  C10  C5   C6   119.97  3.000
 9G3  C6   C5   C4   120.71  3.000
 9G3  C10  C5   C4   119.32  3.000
 9G3  H2   C6   C5   120.88  3.000
 9G3  H2   C6   C1   120.22  3.000
 9G3  C5   C6   C1   118.90  3.000
 9G3  H3   C8   N9   115.08  3.000
 9G3  H3   C8   N7   119.33  3.000
 9G3  N9   C8   N7   125.59  3.000
 9G3  O11  C10  N9   121.04  3.000
 9G3  O11  C10  C5   125.18  3.000
 9G3  N9   C10  C5   113.78  3.000
 9G3  O18  C15  C16  124.47  3.000
 9G3  O18  C15  C14  120.75  3.000
 9G3  C16  C15  C14  114.75  3.000
 9G3  H7   C16  H6   105.05  3.000
 9G3  H7   C16  C17  110.24  3.000
 9G3  H6   C16  C17  109.95  3.000
 9G3  H7   C16  C15  107.43  3.000
 9G3  H6   C16  C15  107.69  3.000
 9G3  C17  C16  C15  115.89  3.000
 9G3  H8   C17  N19  111.64  3.000
 9G3  H8   C17  C23  107.39  3.000
 9G3  N19  C17  C23  109.15  3.000
 9G3  H8   C17  C16  108.38  3.000
 9G3  N19  C17  C16  110.24  3.000
 9G3  C23  C17  C16  109.99  3.000
 9G3  H10  C20  H9   106.68  3.000
 9G3  H10  C20  N19  112.31  3.000
 9G3  H9   C20  N19  108.39  3.000
 9G3  H10  C20  C21  108.73  3.000
 9G3  H9   C20  C21  110.34  3.000
 9G3  N19  C20  C21  110.32  3.000
 9G3  H12  C21  H11  107.05  3.000
 9G3  H12  C21  C22  109.79  3.000
 9G3  H11  C21  C22  110.76  3.000
 9G3  H12  C21  C20  109.25  3.000
 9G3  H11  C21  C20  109.74  3.000
 9G3  C22  C21  C20  110.18  3.000
 9G3  H14  C22  H13  106.57  3.000
 9G3  H14  C22  C23  110.29  3.000
 9G3  H13  C22  C23  109.31  3.000
 9G3  H14  C22  C21  110.80  3.000
 9G3  H13  C22  C21  109.31  3.000
 9G3  C23  C22  C21  110.47  3.000
 9G3  H16  C23  H15  107.05  3.000
 9G3  H16  C23  C22  110.54  3.000
 9G3  H15  C23  C22  109.74  3.000
 9G3  H16  C23  C17  109.27  3.000
 9G3  H15  C23  C17  108.92  3.000
 9G3  C22  C23  C17  111.21  3.000
 9G3  C8   N7   C4   117.14  3.000
 9G3  C14  N9   C10  117.49  3.000
 9G3  C10  N9   C8   122.05  3.000
 9G3  C14  N9   C8   120.26  3.000
 9G3  H17  N19  C20  108.33  3.000
 9G3  H17  N19  C17  109.02  3.000
 9G3  C20  N19  C17  112.64  3.000
 9G3  H5   C14  H4   106.53  3.000
 9G3  H5   C14  N9   110.58  3.000
 9G3  H4   C14  N9   109.05  3.000
 9G3  H5   C14  C15  110.71  3.000
 9G3  H4   C14  C15  108.18  3.000
 9G3  N9   C14  C15  111.63  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
 9G3  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 9G3  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 9G3  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 9G3  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 9G3  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 9G3  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 9G3  CONST_07  N9   C8   N7   C4     0.00   0.0  0
 9G3  CONST_08  C8   N9   C10  C5     0.00   0.0  0
 9G3  CONST_09  N7   C8   N9   C10    0.00   0.0  0
 9G3  CONST_10  F12  C1   C2   C3   180.00   0.0  0
 9G3  CONST_11  CL1  C2   C3   C4   180.00   0.0  0
 9G3  CONST_12  F12  C1   C6   C5   180.00   0.0  0
 9G3  CONST_13  CL1  C2   C1   C6   180.00   0.0  0
 9G3  CONST_14  C14  N9   C10  C5   180.00   0.0  0
 9G3  CONST_15  O11  C10  N9   C8   180.00   0.0  0
 9G3  CONST_16  N7   C8   N9   C14  180.00   0.0  0
 9G3  CONST_17  H1   C3   C2   C1   180.00   0.0  0
 9G3  CONST_18  H2   C6   C1   C2   180.00   0.0  0
 9G3  CONST_19  H3   C8   N7   C4   180.00   0.0  0
 9G3  CONST_20  O11  C10  N9   C14    0.00   0.0  0
 9G3  Var_01    C21  C22  C23  C17   53.72  30.0  1
 9G3  Var_02    C21  C20  N19  C17  -61.28  30.0  1
 9G3  Var_03    C23  C22  C21  C20  -53.35  30.0  1
 9G3  Var_04    N19  C20  C21  C22   56.49  30.0  1
 9G3  Var_05    C15  C14  N9   C8   102.44  30.0  2
 9G3  Var_06    C17  C16  C15  C14  172.47  30.0  2
 9G3  Var_07    N9   C14  C15  C16  167.98  30.0  1

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
 9G3  chir_01  C17  C16  C23  N19  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
 9G3  plan-1  C1   0.020
 9G3  plan-1  C2   0.020
 9G3  plan-1  C3   0.020
 9G3  plan-1  C4   0.020
 9G3  plan-1  C5   0.020
 9G3  plan-1  C6   0.020
 9G3  plan-1  C8   0.020
 9G3  plan-1  C10  0.020
 9G3  plan-1  N7   0.020
 9G3  plan-1  N9   0.020
 9G3  plan-1  O11  0.020
 9G3  plan-1  F12  0.020
 9G3  plan-1  CL1  0.020
 9G3  plan-1  H1   0.020
 9G3  plan-1  H2   0.020
 9G3  plan-1  H3   0.020
 9G3  plan-1  C14  0.020
 9G3  plan-2  C15  0.020
 9G3  plan-2  C16  0.020
 9G3  plan-2  O18  0.020
 9G3  plan-2  C14  0.020

