# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:05:50 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-[(5-chloranyl-8-oxidanyl-quinolin-7-yl)methyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(CN2CCCC2=O)cc(Cl)c3cccnc13
#
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
 EC3  EC3  1-[(5-chloranyl-8-oxidanyl-quinolin-7-yl)methyl]pyrrolidin-2-one  ligand  32  19  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EC3
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
 EC3  C1   C   CH2   0  -0.578  10.9538  -3.0569   1.3047
 EC3  C10  C   CR6   0  -0.155   8.0963  -8.0613  -1.4373
 EC3  C11  C   CR66  0   0.174   8.9246  -8.1686  -2.5774
 EC3  C12  C   CR66  0   0.117  10.2764  -7.7539  -2.4695
 EC3  C13  C   CR6   0   0.276  10.7749  -7.2345  -1.2333
 EC3  C14  C   CR16  0  -0.182   8.4995  -8.6679  -3.8279
 EC3  C15  C   CR16  0  -0.317   9.3889  -8.7362  -4.8612
 EC3  C16  C   CR16  0  -0.081  10.7102  -8.3006  -4.6455
 EC3  C2   C   CH2   0  -0.479   9.7458  -3.2090   2.2268
 EC3  C3   C   CH2   0  -0.263   9.2049  -4.6008   1.8916
 EC3  C5   C   CR5   0   0.585  11.3614  -4.4767   1.0091
 EC3  C8   C   CR6   0   0.003   9.9386  -7.1827  -0.1339
 EC3  C9   C   CR16  0  -0.260   8.5952  -7.5919  -0.2584
 EC3  N17  N   N     0  -0.408  11.1366  -7.8284  -3.5059
 EC3  N4   N   NR5   0  -0.431  10.3890  -5.2964   1.4163
 EC3  O6   O   O     0  -0.536  12.4011  -4.8408   0.4544
 EC3  CL1  CL  CL    0  -0.133   6.4345  -8.5507  -1.5268
 EC3  H1   H   HCH2  0   0.284  11.7775  -2.4897   1.7363
 EC3  H2   H   HCH2  0   0.281  10.6909  -2.5790   0.3564
 EC3  H3   H   HCR6  0   0.271   7.4776  -8.9946  -3.9640
 EC3  H4   H   HCR6  0   0.278   9.0942  -9.1151  -5.8297
 EC3  H5   H   HCR6  0   0.268  11.4299  -8.3477  -5.4557
 EC3  H6   H   HCH2  0   0.257  10.0646  -3.1797   3.2688
 EC3  H7   H   HCH2  0   0.262   8.9962  -2.4342   2.0837
 EC3  H8   H   HCH2  0   0.249   8.4392  -4.5675   1.1108
 EC3  H9   H   HCH2  0   0.259   8.7844  -5.1136   2.7565
 EC3  H10  H   HCH2  0   0.292   9.8217  -7.1858   1.9965
 EC3  H11  H   HCH2  0   0.288  11.4533  -7.0708   1.3939
 EC3  H12  H   HCR6  0   0.281   7.9555  -7.5452   0.6142
 EC3  H13  H   HOH1  0   0.486  12.2440  -6.1975  -0.5137
 EC3  C7   C   CH2   0  -0.457  10.4316  -6.7289   1.2174
 EC3  O19  O   OH1   0  -0.634  12.0519  -6.8588  -1.2250

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
 EC3  C15  C16  aromatic  1.408  0.020  1.408
 EC3  C15  C14  aromatic  1.365  0.020  1.365
 EC3  C16  N17  aromatic  1.305  0.020  1.305
 EC3  C14  C11  aromatic  1.412  0.020  1.412
 EC3  N17  C12  aromatic  1.349  0.020  1.349
 EC3  C11  C12  aromatic  1.418  0.020  1.418
 EC3  C11  C10  aromatic  1.413  0.020  1.413
 EC3  C12  C13  aromatic  1.430  0.020  1.430
 EC3  CL1  C10  single    1.735  0.020  1.735
 EC3  C10  C9   aromatic  1.363  0.020  1.363
 EC3  C13  O19  single    1.331  0.020  1.331
 EC3  C13  C8   aromatic  1.382  0.020  1.382
 EC3  C9   C8   aromatic  1.410  0.020  1.410
 EC3  C8   C7   single    1.508  0.020  1.508
 EC3  O6   C5   double    1.233  0.020  1.233
 EC3  C7   N4   single    1.447  0.020  1.447
 EC3  C5   N4   single    1.335  0.020  1.335
 EC3  C5   C1   single    1.506  0.020  1.506
 EC3  N4   C3   single    1.453  0.020  1.453
 EC3  C1   C2   single    1.527  0.020  1.527
 EC3  C3   C2   single    1.530  0.020  1.530
 EC3  C1   H1   single    0.970  0.020  1.090
 EC3  C1   H2   single    0.970  0.020  1.090
 EC3  C14  H3   single    0.930  0.020  1.080
 EC3  C15  H4   single    0.930  0.020  1.080
 EC3  C16  H5   single    0.930  0.020  1.080
 EC3  C2   H6   single    0.970  0.020  1.090
 EC3  C2   H7   single    0.970  0.020  1.090
 EC3  C3   H8   single    0.970  0.020  1.090
 EC3  C3   H9   single    0.970  0.020  1.090
 EC3  C7   H10  single    0.970  0.020  1.090
 EC3  C7   H11  single    0.970  0.020  1.090
 EC3  C9   H12  single    0.930  0.020  1.080
 EC3  O19  H13  single    0.850  0.020  0.980

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
 EC3  H2   C1   H1   107.32  3.000
 EC3  H2   C1   C5   107.86  3.000
 EC3  H1   C1   C5   111.34  3.000
 EC3  H2   C1   C2   112.14  3.000
 EC3  H1   C1   C2   114.26  3.000
 EC3  C5   C1   C2   103.80  3.000
 EC3  CL1  C10  C9   119.49  3.000
 EC3  C9   C10  C11  120.61  3.000
 EC3  CL1  C10  C11  119.89  3.000
 EC3  C14  C11  C12  117.25  3.000
 EC3  C12  C11  C10  118.37  3.000
 EC3  C14  C11  C10  124.39  3.000
 EC3  N17  C12  C13  117.50  3.000
 EC3  C13  C12  C11  120.27  3.000
 EC3  N17  C12  C11  122.23  3.000
 EC3  O19  C13  C8   124.39  3.000
 EC3  C8   C13  C12  119.35  3.000
 EC3  O19  C13  C12  116.24  3.000
 EC3  H3   C14  C15  120.35  3.000
 EC3  H3   C14  C11  120.19  3.000
 EC3  C15  C14  C11  119.47  3.000
 EC3  H4   C15  C16  120.10  3.000
 EC3  H4   C15  C14  121.21  3.000
 EC3  C16  C15  C14  118.69  3.000
 EC3  H5   C16  N17  116.81  3.000
 EC3  H5   C16  C15  119.66  3.000
 EC3  N17  C16  C15  123.53  3.000
 EC3  H7   C2   H6   107.95  3.000
 EC3  H7   C2   C3   112.06  3.000
 EC3  H6   C2   C3   109.71  3.000
 EC3  H7   C2   C1   113.25  3.000
 EC3  H6   C2   C1   110.07  3.000
 EC3  C3   C2   C1   103.76  3.000
 EC3  H9   C3   H8   108.09  3.000
 EC3  H9   C3   N4   110.41  3.000
 EC3  H8   C3   N4   110.57  3.000
 EC3  H9   C3   C2   112.98  3.000
 EC3  H8   C3   C2   112.09  3.000
 EC3  N4   C3   C2   102.65  3.000
 EC3  O6   C5   N4   124.74  3.000
 EC3  N4   C5   C1   108.76  3.000
 EC3  O6   C5   C1   126.48  3.000
 EC3  C9   C8   C7   118.55  3.000
 EC3  C7   C8   C13  121.74  3.000
 EC3  C9   C8   C13  119.69  3.000
 EC3  H12  C9   C8   118.63  3.000
 EC3  H12  C9   C10  119.70  3.000
 EC3  C8   C9   C10  121.66  3.000
 EC3  C16  N17  C12  118.85  3.000
 EC3  C7   N4   C5   122.98  3.000
 EC3  C5   N4   C3   113.53  3.000
 EC3  C7   N4   C3   122.88  3.000
 EC3  H11  C7   H10  106.08  3.000
 EC3  H11  C7   N4   108.39  3.000
 EC3  H10  C7   N4   107.48  3.000
 EC3  H11  C7   C8   110.89  3.000
 EC3  H10  C7   C8   109.35  3.000
 EC3  N4   C7   C8   114.29  3.000
 EC3  H13  O19  C13  112.28  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
 EC3  CONST_01  C15  C14  C11  C10  180.00   0.0  0
 EC3  CONST_02  N17  C12  C11  C10  180.00   0.0  0
 EC3  CONST_03  C13  C12  C11  C10    0.00   0.0  0
 EC3  CONST_04  C13  C8   C9   C10    0.00   0.0  0
 EC3  CONST_05  C16  C15  C14  C11    0.00   0.0  0
 EC3  CONST_06  C16  N17  C12  C11    0.00   0.0  0
 EC3  CONST_07  C8   C13  C12  C11    0.00   0.0  0
 EC3  CONST_08  C8   C9   C10  C11    0.00   0.0  0
 EC3  CONST_09  C15  C16  N17  C12    0.00   0.0  0
 EC3  CONST_10  C15  C14  C11  C12    0.00   0.0  0
 EC3  CONST_11  C9   C10  C11  C12    0.00   0.0  0
 EC3  CONST_12  C9   C8   C13  C12    0.00   0.0  0
 EC3  CONST_13  C16  N17  C12  C13  180.00   0.0  0
 EC3  CONST_14  C14  C11  C12  C13  180.00   0.0  0
 EC3  CONST_15  N17  C16  C15  C14    0.00   0.0  0
 EC3  CONST_16  N17  C12  C11  C14    0.00   0.0  0
 EC3  CONST_17  C9   C10  C11  C14  180.00   0.0  0
 EC3  CONST_18  N17  C12  C13  C8   180.00   0.0  0
 EC3  CONST_19  C3   N4   C5   C1     0.00   0.0  0
 EC3  CONST_20  C7   C8   C9   C10  180.00   0.0  0
 EC3  CONST_21  O19  C13  C12  C11  180.00   0.0  0
 EC3  CONST_22  CL1  C10  C11  C12  180.00   0.0  0
 EC3  CONST_23  C7   C8   C13  C12  180.00   0.0  0
 EC3  CONST_24  CL1  C10  C11  C14    0.00   0.0  0
 EC3  CONST_25  CL1  C10  C9   C8   180.00   0.0  0
 EC3  CONST_26  O19  C13  C8   C9   180.00   0.0  0
 EC3  CONST_27  O19  C13  C12  N17    0.00   0.0  0
 EC3  CONST_28  C7   N4   C5   C1   180.00   0.0  0
 EC3  CONST_29  O6   C5   N4   C3   180.00   0.0  0
 EC3  CONST_30  H3   C14  C11  C10    0.00   0.0  0
 EC3  CONST_31  H4   C15  C14  C11  180.00   0.0  0
 EC3  CONST_32  H12  C9   C10  C11  180.00   0.0  0
 EC3  CONST_33  H5   C16  N17  C12  180.00   0.0  0
 EC3  CONST_34  O6   C5   N4   C7     0.00   0.0  0
 EC3  Var_01    N4   C3   C2   C1    26.74  30.0  1
 EC3  Var_02    N4   C5   C1   C2    12.44  30.0  1
 EC3  Var_03    C5   N4   C3   C2   -20.80  30.0  1
 EC3  Var_04    C5   C1   C2   C3   -24.07  30.0  1
 EC3  Var_05    N4   C7   C8   C13   86.14  30.0  2
 EC3  Var_06    C8   C7   N4   C3    86.06  30.0  1

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
 EC3  plan-1  C10  0.020
 EC3  plan-1  C11  0.020
 EC3  plan-1  C12  0.020
 EC3  plan-1  C13  0.020
 EC3  plan-1  C14  0.020
 EC3  plan-1  C15  0.020
 EC3  plan-1  C16  0.020
 EC3  plan-1  C8   0.020
 EC3  plan-1  C9   0.020
 EC3  plan-1  N17  0.020
 EC3  plan-1  CL1  0.020
 EC3  plan-1  H3   0.020
 EC3  plan-1  H4   0.020
 EC3  plan-1  H5   0.020
 EC3  plan-1  H12  0.020
 EC3  plan-1  C7   0.020
 EC3  plan-1  O19  0.020
 EC3  plan-2  C1   0.020
 EC3  plan-2  C3   0.020
 EC3  plan-2  C5   0.020
 EC3  plan-2  N4   0.020
 EC3  plan-2  O6   0.020
 EC3  plan-2  C7   0.020

