# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 01:03:11 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2,6-dichloro-N-(2-oxo-2,5-dihydropyridin-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(Cl)c1C(=O)NC2=CC(=O)N=CC2
#
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
 0X2  0X2  2,6-dichloro-N-(2-oxo-2,5-dihydropyridin-4-yl)benzamide  ligand  26  18  .  2022-07-22  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_0X2
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
 0X2  C4   C   CR6   0   0.090   1.7632  -0.0249   0.1657
 0X2  C5   C   CR6   0  -0.082   2.4583   1.1475  -0.1015
 0X2  C6   C   CR16  0  -0.190   3.7508   1.1246  -0.5974
 0X2  C11  C   CR6   0   0.470  -4.2100   0.0134  -0.9922
 0X2  C7   C   C     0   0.479   0.3833   0.0177   0.7579
 0X2  C8   C   CR6   0   0.492  -1.9648   0.0329  -0.0222
 0X2  C9   C   C     0  -0.611  -2.5658   0.1403   1.3312
 0X2  C10  C   CR16  0   0.005  -4.0494   0.1890   1.2984
 0X2  C12  C   CR16  0  -0.524  -2.7620  -0.0260  -1.1051
 0X2  N1   N   NH1   0  -0.689  -0.5950  -0.0013  -0.1888
 0X2  N2   N   N     0  -0.411  -4.8053   0.1349   0.2791
 0X2  C3   C   CR6   0  -0.080   2.3989  -1.2356  -0.0761
 0X2  O1   O   O     0  -0.397   0.2074   0.0649   1.9527
 0X2  CL2  CL  CL    0  -0.096   1.5446  -2.7038   0.2429
 0X2  C2   C   CR16  0  -0.190   3.6905  -1.2875  -0.5719
 0X2  CL1  CL  CL    0  -0.096   1.6781   2.6627   0.1838
 0X2  C1   C   CR16  0  -0.272   4.3585  -0.1000  -0.8289
 0X2  H1   H   HCR6  0   0.294   4.2742   2.0482  -0.8003
 0X2  H2   H   H     0   0.325  -2.2729  -0.6963   1.9733
 0X2  H3   H   H     0   0.323  -2.2125   1.0305   1.8607
 0X2  H4   H   HCR6  0   0.287  -4.5275   0.2804   2.2708
 0X2  H5   H   HCR6  0   0.285  -2.3464  -0.1067  -2.1027
 0X2  H6   H   HNH1  0   0.438  -0.2807  -0.0535  -1.1490
 0X2  H7   H   HCR6  0   0.294   4.1675  -2.2397  -0.7561
 0X2  H8   H   HCR6  0   0.288   5.3677  -0.1296  -1.2161
 0X2  O2   O   O     0  -0.436  -4.9350  -0.0532  -1.9651

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
 0X2  C10  N2   double    1.270  0.020  1.270
 0X2  C10  C9   single    1.485  0.020  1.485
 0X2  CL1  C5   single    1.728  0.020  1.728
 0X2  N2   C11  single    1.409  0.020  1.409
 0X2  C9   C8   single    1.485  0.020  1.485
 0X2  C11  O2   double    1.215  0.020  1.215
 0X2  C11  C12  single    1.453  0.020  1.453
 0X2  C8   C12  double    1.346  0.020  1.346
 0X2  C8   N1   single    1.380  0.020  1.380
 0X2  C5   C6   aromatic  1.385  0.020  1.385
 0X2  C5   C4   aromatic  1.389  0.020  1.389
 0X2  N1   C7   single    1.362  0.020  1.362
 0X2  C6   C1   aromatic  1.386  0.020  1.386
 0X2  C7   O1   double    1.209  0.020  1.209
 0X2  C7   C4   single    1.502  0.020  1.502
 0X2  C4   C3   aromatic  1.389  0.020  1.389
 0X2  C1   C2   aromatic  1.387  0.020  1.387
 0X2  C3   C2   aromatic  1.385  0.020  1.385
 0X2  C3   CL2  single    1.728  0.020  1.728
 0X2  C6   H1   single    0.930  0.020  1.080
 0X2  C9   H2   single    0.970  0.020  1.090
 0X2  C9   H3   single    0.970  0.020  1.090
 0X2  C10  H4   single    0.930  0.020  1.080
 0X2  C12  H5   single    0.930  0.020  1.080
 0X2  N1   H6   single    0.860  0.020  1.020
 0X2  C2   H7   single    0.930  0.020  1.080
 0X2  C1   H8   single    0.930  0.020  1.080

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
 0X2  C3   C4   C7   120.92  3.000
 0X2  C3   C4   C5   118.25  3.000
 0X2  C7   C4   C5   120.77  3.000
 0X2  CL1  C5   C6   119.68  3.000
 0X2  C6   C5   C4   121.47  3.000
 0X2  CL1  C5   C4   118.85  3.000
 0X2  H1   C6   C1   120.74  3.000
 0X2  H1   C6   C5   120.34  3.000
 0X2  C1   C6   C5   118.92  3.000
 0X2  O2   C11  N2   118.36  3.000
 0X2  O2   C11  C12  122.06  3.000
 0X2  N2   C11  C12  119.58  3.000
 0X2  O1   C7   N1   125.68  3.000
 0X2  O1   C7   C4   121.64  3.000
 0X2  N1   C7   C4   112.68  3.000
 0X2  N1   C8   C12  119.31  3.000
 0X2  N1   C8   C9   120.90  3.000
 0X2  C12  C8   C9   119.79  3.000
 0X2  H3   C9   H2   104.57  3.000
 0X2  H3   C9   C10  107.85  3.000
 0X2  H2   C9   C10  107.79  3.000
 0X2  H3   C9   C8   111.67  3.000
 0X2  H2   C9   C8   111.78  3.000
 0X2  C10  C9   C8   112.75  3.000
 0X2  H4   C10  N2   117.35  3.000
 0X2  H4   C10  C9   114.98  3.000
 0X2  N2   C10  C9   127.67  3.000
 0X2  H5   C12  C8   121.11  3.000
 0X2  H5   C12  C11  117.11  3.000
 0X2  C8   C12  C11  121.77  3.000
 0X2  H6   N1   C8   115.10  3.000
 0X2  H6   N1   C7   115.94  3.000
 0X2  C8   N1   C7   128.96  3.000
 0X2  C10  N2   C11  118.44  3.000
 0X2  C2   C3   CL2  119.70  3.000
 0X2  CL2  C3   C4   118.83  3.000
 0X2  C2   C3   C4   121.47  3.000
 0X2  H7   C2   C1   120.69  3.000
 0X2  H7   C2   C3   120.38  3.000
 0X2  C1   C2   C3   118.93  3.000
 0X2  H8   C1   C2   119.51  3.000
 0X2  H8   C1   C6   119.54  3.000
 0X2  C2   C1   C6   120.95  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
 0X2  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 0X2  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 0X2  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 0X2  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 0X2  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 0X2  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 0X2  CONST_07  CL2  C3   C4   C5   180.00   0.0  0
 0X2  CONST_08  C7   C4   C5   C6   180.00   0.0  0
 0X2  CONST_09  C2   C3   C4   C7   180.00   0.0  0
 0X2  CONST_10  CL1  C5   C4   C3   180.00   0.0  0
 0X2  CONST_11  C1   C2   C3   CL2  180.00   0.0  0
 0X2  CONST_12  C1   C6   C5   CL1  180.00   0.0  0
 0X2  CONST_13  H1   C6   C5   C4   180.00   0.0  0
 0X2  CONST_14  H7   C2   C3   C4   180.00   0.0  0
 0X2  CONST_15  H8   C1   C6   C5   180.00   0.0  0
 0X2  CONST_16  C8   N1   C7   C4   180.00   0.0  0
 0X2  CONST_17  O1   C7   N1   C8     0.00   0.0  0
 0X2  CONST_18  H6   N1   C7   C4     0.00   0.0  0
 0X2  Var_01    C9   C10  N2   C11    0.04  30.0  1
 0X2  Var_02    C9   C8   C12  C11    0.04  30.0  1
 0X2  Var_03    N2   C10  C9   C8     0.83  30.0  1
 0X2  Var_04    N2   C11  C12  C8     0.89  30.0  1
 0X2  Var_05    C12  C11  N2   C10   -0.92  30.0  1
 0X2  Var_06    C12  C8   C9   C10   -0.82  30.0  1
 0X2  Var_07    N1   C7   C4   C5    92.92  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
 0X2  plan-1  C4   0.020
 0X2  plan-1  C5   0.020
 0X2  plan-1  C6   0.020
 0X2  plan-1  C7   0.020
 0X2  plan-1  C3   0.020
 0X2  plan-1  CL2  0.020
 0X2  plan-1  C2   0.020
 0X2  plan-1  CL1  0.020
 0X2  plan-1  C1   0.020
 0X2  plan-1  H1   0.020
 0X2  plan-1  H7   0.020
 0X2  plan-1  H8   0.020
 0X2  plan-2  C4   0.020
 0X2  plan-2  C7   0.020
 0X2  plan-2  C8   0.020
 0X2  plan-2  N1   0.020
 0X2  plan-2  O1   0.020
 0X2  plan-2  H6   0.020
 0X2  plan-3  C11  0.020
 0X2  plan-3  C12  0.020
 0X2  plan-3  N2   0.020
 0X2  plan-3  O2   0.020

