# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:12:38 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-[2-[(3,4-dichlorophenyl)carbonylamino]ethyl]-~{N}-oxidanyl-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1cc(CCNC(=O)c2ccc(Cl)c(Cl)c2)on1
#
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
 JNN  JNN  5-[2-[(3,4-dichlorophenyl)carbonylamino]ethyl]-~{N}-oxidanyl-1,2-oxazole-3-carboxamide  ligand  33  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JNN
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
 JNN  O1   O   O     0  -0.449  -7.2403   1.1850   1.0777
 JNN  C1   C   C     0   0.507  -6.8890   0.3760   0.2408
 JNN  N1   N   NH1   0  -0.375  -7.6981  -0.4917  -0.3841
 JNN  O2   O   OH1   0  -0.533  -9.0441  -0.3769  -0.2369
 JNN  C2   C   CR5   0   0.132  -5.4564   0.2584  -0.1476
 JNN  C3   C   CR15  0  -0.497  -4.3797   0.9798   0.4144
 JNN  C4   C   CR5   0   0.458  -3.3047   0.5238  -0.2725
 JNN  C5   C   CH2   0  -0.550  -1.8527   0.8088  -0.1906
 JNN  C6   C   CH2   0  -0.289  -1.0801  -0.3409   0.4719
 JNN  N2   N   NH1   0  -0.647   0.3308  -0.0563   0.5647
 JNN  C7   C   C     0   0.537   1.1885  -0.3073  -0.4366
 JNN  O3   O   O     0  -0.479   0.8572  -0.8468  -1.4821
 JNN  C8   C   CR6   0  -0.029   2.6084   0.1015  -0.1994
 JNN  C9   C   CR16  0  -0.290   2.9586   1.1955   0.5856
 JNN  C10  C   CR16  0  -0.201   4.2881   1.5484   0.7413
 JNN  C11  C   CR6   0  -0.003   5.2808   0.8061   0.1209
 JNN  CL1  CL  CL    0  -0.084   6.9275   1.2514   0.3286
 JNN  C12  C   CR6   0   0.018   4.9354  -0.2872  -0.6685
 JNN  CL2  CL  CL    0  -0.088   6.1520  -1.2220  -1.4480
 JNN  C13  C   CR16  0  -0.232   3.6050  -0.6278  -0.8370
 JNN  O4   O   O     0  -0.323  -3.7147  -0.3905  -1.1644
 JNN  N3   N   N     0  -0.163  -5.0516  -0.5508  -1.0841
 JNN  H1   H   HNH1  0   0.423  -7.3917  -1.0521  -1.1682
 JNN  H2   H   HOH1  0   0.483  -9.2987  -1.0360   0.4227
 JNN  H3   H   HCR5  0   0.291  -4.4019   1.7144   1.2003
 JNN  H4   H   HCH2  0   0.284  -1.4530   0.9956  -1.1899
 JNN  H5   H   HCH2  0   0.281  -1.7196   1.7215   0.3902
 JNN  H6   H   HCH2  0   0.275  -1.4535  -0.5029   1.4820
 JNN  H7   H   HCH2  0   0.261  -1.2267  -1.2674  -0.0828
 JNN  H8   H   HNH1  0   0.416   0.6721   0.3210   1.4331
 JNN  H9   H   HCR6  0   0.278   2.2054   1.8071   1.0647
 JNN  H10  H   HCR6  0   0.297   4.5552   2.4084   1.3395
 JNN  H11  H   HCR6  0   0.291   3.3471  -1.4738  -1.4594

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
 JNN  CL1  C11  single    1.718  0.020  1.718
 JNN  C10  C11  aromatic  1.386  0.020  1.386
 JNN  C10  C9   aromatic  1.384  0.020  1.384
 JNN  C11  C12  aromatic  1.392  0.020  1.392
 JNN  C9   C8   aromatic  1.391  0.020  1.391
 JNN  C12  CL2  single    1.721  0.020  1.721
 JNN  C12  C13  aromatic  1.384  0.020  1.384
 JNN  C8   C13  aromatic  1.390  0.020  1.390
 JNN  C8   C7   single    1.497  0.020  1.497
 JNN  O1   C1   double    1.216  0.020  1.216
 JNN  C7   O3   double    1.222  0.020  1.222
 JNN  C7   N2   single    1.342  0.020  1.342
 JNN  N3   O4   aromatic  1.349  0.020  1.349
 JNN  N3   C2   aromatic  1.302  0.020  1.302
 JNN  O4   C4   aromatic  1.341  0.020  1.341
 JNN  C1   C2   single    1.489  0.020  1.489
 JNN  C1   N1   single    1.341  0.020  1.341
 JNN  C2   C3   aromatic  1.413  0.020  1.413
 JNN  N2   C6   single    1.442  0.020  1.442
 JNN  C4   C3   aromatic  1.355  0.020  1.355
 JNN  C4   C5   single    1.482  0.020  1.482
 JNN  N1   O2   single    1.359  0.020  1.359
 JNN  C5   C6   single    1.535  0.020  1.535
 JNN  N1   H1   single    0.860  0.020  1.020
 JNN  O2   H2   single    0.850  0.020  0.980
 JNN  C3   H3   single    0.930  0.020  1.080
 JNN  C5   H4   single    0.970  0.020  1.090
 JNN  C5   H5   single    0.970  0.020  1.090
 JNN  C6   H6   single    0.970  0.020  1.090
 JNN  C6   H7   single    0.970  0.020  1.090
 JNN  N2   H8   single    0.860  0.020  1.020
 JNN  C9   H9   single    0.930  0.020  1.080
 JNN  C10  H10  single    0.930  0.020  1.080
 JNN  C13  H11  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
 JNN  C2   C1   N1   114.07  3.000
 JNN  N1   C1   O1   125.24  3.000
 JNN  C2   C1   O1   120.67  3.000
 JNN  H1   N1   O2   115.52  3.000
 JNN  H1   N1   C1   122.49  3.000
 JNN  O2   N1   C1   119.51  3.000
 JNN  H2   O2   N1   106.10  3.000
 JNN  N3   C2   C3   111.50  3.000
 JNN  C3   C2   C1   126.10  3.000
 JNN  N3   C2   C1   122.39  3.000
 JNN  H3   C3   C4   128.06  3.000
 JNN  H3   C3   C2   128.58  3.000
 JNN  C4   C3   C2   103.37  3.000
 JNN  O4   C4   C5   117.86  3.000
 JNN  C5   C4   C3   133.21  3.000
 JNN  O4   C4   C3   108.91  3.000
 JNN  H5   C5   H4   107.43  3.000
 JNN  H5   C5   C6   109.61  3.000
 JNN  H4   C5   C6   109.79  3.000
 JNN  H5   C5   C4   108.07  3.000
 JNN  H4   C5   C4   109.93  3.000
 JNN  C6   C5   C4   111.89  3.000
 JNN  H7   C6   H6   107.42  3.000
 JNN  H7   C6   N2   109.40  3.000
 JNN  H6   C6   N2   107.76  3.000
 JNN  H7   C6   C5   110.45  3.000
 JNN  H6   C6   C5   109.81  3.000
 JNN  N2   C6   C5   111.85  3.000
 JNN  H8   N2   C7   119.81  3.000
 JNN  H8   N2   C6   117.47  3.000
 JNN  C7   N2   C6   122.70  3.000
 JNN  C8   C7   O3   120.88  3.000
 JNN  O3   C7   N2   123.20  3.000
 JNN  C8   C7   N2   115.91  3.000
 JNN  C13  C8   C9   119.41  3.000
 JNN  C13  C8   C7   117.67  3.000
 JNN  C9   C8   C7   122.89  3.000
 JNN  H9   C9   C10  118.33  3.000
 JNN  H9   C9   C8   121.27  3.000
 JNN  C10  C9   C8   120.37  3.000
 JNN  H10  C10  C11  119.79  3.000
 JNN  H10  C10  C9   120.15  3.000
 JNN  C11  C10  C9   120.06  3.000
 JNN  C12  C11  CL1  120.65  3.000
 JNN  C12  C11  C10  119.78  3.000
 JNN  CL1  C11  C10  119.56  3.000
 JNN  C13  C12  CL2  119.40  3.000
 JNN  C13  C12  C11  120.06  3.000
 JNN  CL2  C12  C11  120.54  3.000
 JNN  H11  C13  C12  119.46  3.000
 JNN  H11  C13  C8   120.23  3.000
 JNN  C12  C13  C8   120.30  3.000
 JNN  N3   O4   C4   110.14  3.000
 JNN  O4   N3   C2   106.08  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
 JNN  CONST_01  C4   O4   N3   C2      0.00   0.0  0
 JNN  CONST_02  O4   C4   C3   C2      0.00   0.0  0
 JNN  CONST_03  O4   N3   C2   C3      0.00   0.0  0
 JNN  CONST_04  N3   O4   C4   C3      0.00   0.0  0
 JNN  CONST_05  N3   C2   C3   C4      0.00   0.0  0
 JNN  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 JNN  CONST_07  C11  C12  C13  C8      0.00   0.0  0
 JNN  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 JNN  CONST_09  C12  C13  C8   C9      0.00   0.0  0
 JNN  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 JNN  CONST_11  C13  C8   C9   C10     0.00   0.0  0
 JNN  CONST_12  O4   N3   C2   C1    180.00   0.0  0
 JNN  CONST_13  C4   C3   C2   C1    180.00   0.0  0
 JNN  CONST_14  C5   C4   C3   C2    180.00   0.0  0
 JNN  CONST_15  N3   O4   C4   C5    180.00   0.0  0
 JNN  CONST_16  C10  C9   C8   C7    180.00   0.0  0
 JNN  CONST_17  C12  C13  C8   C7    180.00   0.0  0
 JNN  CONST_18  CL2  C12  C13  C8    180.00   0.0  0
 JNN  CONST_19  CL1  C11  C10  C9    180.00   0.0  0
 JNN  CONST_20  CL2  C12  C11  C10   180.00   0.0  0
 JNN  CONST_21  C13  C12  C11  CL1   180.00   0.0  0
 JNN  CONST_22  H10  C10  C9   C8    180.00   0.0  0
 JNN  CONST_23  H11  C13  C8   C9    180.00   0.0  0
 JNN  CONST_24  H9   C9   C10  C11   180.00   0.0  0
 JNN  CONST_25  H3   C3   C4   O4    180.00   0.0  0
 JNN  CONST_26  C2   C1   N1   O2    180.00   0.0  0
 JNN  CONST_27  C8   C7   N2   C6    180.00   0.0  0
 JNN  CONST_28  H1   N1   C1   C2      0.00   0.0  0
 JNN  CONST_29  H8   N2   C7   C8      0.00   0.0  0
 JNN  CONST_30  O2   N1   C1   O1      0.00   0.0  0
 JNN  CONST_31  O3   C7   N2   C6      0.00   0.0  0
 JNN  Var_01    N3   C2   C1   O1   -176.67  30.0  2
 JNN  Var_02    C6   C5   C4   C3    105.19  30.0  2
 JNN  Var_03    C9   C8   C7   N2    -31.43  30.0  2
 JNN  Var_04    N2   C6   C5   C4   -179.35  30.0  3
 JNN  Var_05    C7   N2   C6   C5    -85.49  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
 JNN  plan-1  C1   0.020
 JNN  plan-1  C2   0.020
 JNN  plan-1  C3   0.020
 JNN  plan-1  C4   0.020
 JNN  plan-1  C5   0.020
 JNN  plan-1  O4   0.020
 JNN  plan-1  N3   0.020
 JNN  plan-1  H3   0.020
 JNN  plan-2  C7   0.020
 JNN  plan-2  C8   0.020
 JNN  plan-2  C9   0.020
 JNN  plan-2  C10  0.020
 JNN  plan-2  C11  0.020
 JNN  plan-2  CL1  0.020
 JNN  plan-2  C12  0.020
 JNN  plan-2  CL2  0.020
 JNN  plan-2  C13  0.020
 JNN  plan-2  H9   0.020
 JNN  plan-2  H10  0.020
 JNN  plan-2  H11  0.020
 JNN  plan-3  O1   0.020
 JNN  plan-3  C1   0.020
 JNN  plan-3  N1   0.020
 JNN  plan-3  O2   0.020
 JNN  plan-3  C2   0.020
 JNN  plan-3  H1   0.020
 JNN  plan-4  C6   0.020
 JNN  plan-4  N2   0.020
 JNN  plan-4  C7   0.020
 JNN  plan-4  O3   0.020
 JNN  plan-4  C8   0.020
 JNN  plan-4  H8   0.020

