# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 06:32:39 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)c(C(=O)N[C@H]2CC(=O)NC2=O)c(Cl)c1
#
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
 JPB  JPB  ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide  ligand  26  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JPB
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
 JPB  C4   C   CR15  0  -0.233  -2.7224   0.4346   0.2428
 JPB  C5   C   C     0   0.496  -0.3899   0.2757   0.9413
 JPB  C6   C   CR6   0   0.095   1.0126   0.1290   0.4199
 JPB  C11  C   CR6   0  -0.094   1.5609  -1.1234   0.1772
 JPB  C7   C   CR6   0  -0.094   1.8241   1.2395   0.2286
 JPB  C8   C   CR16  0  -0.146   3.1368   1.1247  -0.1952
 JPB  C9   C   CR6   0  -0.063   3.6419  -0.1449  -0.4235
 JPB  C10  C   CR16  0  -0.146   2.8699  -1.2810  -0.2451
 JPB  N1   N   NR15  0  -0.678  -4.6136  -0.7413  -0.4399
 JPB  N2   N   NH1   0  -0.599  -1.3185   0.3394  -0.0241
 JPB  C3   C   CH2   0  -0.604  -3.5060   1.2844  -0.7523
 JPB  O1   O   O     0  -0.397  -3.0028  -1.9591   0.6551
 JPB  C1   C   CR5   0   0.578  -3.4158  -0.9259   0.2003
 JPB  C2   C   CR5   0   0.552  -4.7816   0.5118  -0.9851
 JPB  O2   O   O     0  -0.417  -5.7714   0.8848  -1.5604
 JPB  O3   O   O     0  -0.438  -0.6127   0.3469   2.1333
 JPB  CL1  CL  CL    0  -0.084   1.1743   2.8114   0.5154
 JPB  CL2  CL  CL    0  -0.090   5.2753  -0.3145  -0.9465
 JPB  CL3  CL  CL    0  -0.079   0.5807  -2.5250   0.3998
 JPB  H1   H   HCR5  0   0.337  -2.8580   0.8226   1.2553
 JPB  H2   H   HCR6  0   0.312   3.7483   2.0035  -0.3422
 JPB  H3   H   HCR6  0   0.312   3.2756  -2.2653  -0.4305
 JPB  H4   H   HNR5  0   0.429  -5.3047  -1.4750  -0.5369
 JPB  H5   H   HNH1  0   0.423  -1.0260   0.2218  -0.9827
 JPB  H6   H   HCH2  0   0.316  -3.7158   2.2916  -0.3980
 JPB  H7   H   HCH2  0   0.313  -2.9853   1.3716  -1.7099

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
 JPB  CL1  C7   single    1.725  0.020  1.725
 JPB  C8   C7   aromatic  1.384  0.020  1.384
 JPB  C8   C9   aromatic  1.385  0.020  1.385
 JPB  CL2  C9   single    1.723  0.020  1.723
 JPB  C7   C6   aromatic  1.389  0.020  1.389
 JPB  C9   C10  aromatic  1.385  0.020  1.385
 JPB  O1   C1   double    1.202  0.020  1.202
 JPB  N1   C1   single    1.371  0.020  1.371
 JPB  N1   C2   single    1.377  0.020  1.377
 JPB  C1   C4   single    1.528  0.020  1.528
 JPB  C6   C5   single    1.504  0.020  1.504
 JPB  C6   C11  aromatic  1.389  0.020  1.389
 JPB  O2   C2   double    1.204  0.020  1.204
 JPB  C2   C3   single    1.509  0.020  1.509
 JPB  N2   C5   single    1.341  0.020  1.341
 JPB  N2   C4   single    1.432  0.020  1.432
 JPB  C10  C11  aromatic  1.384  0.020  1.384
 JPB  C5   O3   double    1.215  0.020  1.215
 JPB  C4   C3   single    1.525  0.020  1.525
 JPB  C11  CL3  single    1.725  0.020  1.725
 JPB  C4   H1   single    0.970  0.020  1.090
 JPB  C8   H2   single    0.930  0.020  1.080
 JPB  C10  H3   single    0.930  0.020  1.080
 JPB  N1   H4   single    0.860  0.020  1.020
 JPB  N2   H5   single    0.860  0.020  1.020
 JPB  C3   H6   single    0.970  0.020  1.090
 JPB  C3   H7   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
 JPB  H1   C4   C1   106.60  3.000
 JPB  H1   C4   C3   110.05  3.000
 JPB  C1   C4   C3   104.17  3.000
 JPB  H1   C4   N2   108.54  3.000
 JPB  C3   C4   N2   114.77  3.000
 JPB  C1   C4   N2   112.37  3.000
 JPB  O3   C5   N2   125.21  3.000
 JPB  O3   C5   C6   121.14  3.000
 JPB  N2   C5   C6   113.64  3.000
 JPB  C7   C6   C11  117.81  3.000
 JPB  C11  C6   C5   121.13  3.000
 JPB  C7   C6   C5   120.99  3.000
 JPB  CL3  C11  C10  118.96  3.000
 JPB  CL3  C11  C6   119.08  3.000
 JPB  C10  C11  C6   121.96  3.000
 JPB  CL1  C7   C8   118.93  3.000
 JPB  C8   C7   C6   122.01  3.000
 JPB  CL1  C7   C6   119.06  3.000
 JPB  H2   C8   C9   121.09  3.000
 JPB  H2   C8   C7   120.72  3.000
 JPB  C9   C8   C7   118.18  3.000
 JPB  CL2  C9   C10  119.12  3.000
 JPB  C10  C9   C8   121.82  3.000
 JPB  CL2  C9   C8   119.06  3.000
 JPB  H3   C10  C9   121.05  3.000
 JPB  H3   C10  C11  120.73  3.000
 JPB  C9   C10  C11  118.22  3.000
 JPB  H4   N1   C2   122.56  3.000
 JPB  H4   N1   C1   122.93  3.000
 JPB  C2   N1   C1   114.47  3.000
 JPB  H5   N2   C5   118.53  3.000
 JPB  H5   N2   C4   117.96  3.000
 JPB  C5   N2   C4   123.22  3.000
 JPB  H7   C3   H6   107.65  3.000
 JPB  H7   C3   C2   107.95  3.000
 JPB  H6   C3   C2   111.17  3.000
 JPB  H7   C3   C4   111.78  3.000
 JPB  H6   C3   C4   113.73  3.000
 JPB  C2   C3   C4   104.46  3.000
 JPB  O1   C1   N1   126.35  3.000
 JPB  N1   C1   C4   106.84  3.000
 JPB  O1   C1   C4   126.80  3.000
 JPB  O2   C2   C3   127.58  3.000
 JPB  C3   C2   N1   107.56  3.000
 JPB  O2   C2   N1   124.85  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
 JPB  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 JPB  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 JPB  CONST_03  C8   C7   C6   C11    0.00   0.0  0
 JPB  CONST_04  C8   C9   C10  C11    0.00   0.0  0
 JPB  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 JPB  CONST_06  C10  C11  C6   C7     0.00   0.0  0
 JPB  CONST_07  C2   N1   C1   C4     0.00   0.0  0
 JPB  CONST_08  C8   C7   C6   C5   180.00   0.0  0
 JPB  CONST_09  C10  C11  C6   C5   180.00   0.0  0
 JPB  CONST_10  CL1  C7   C6   C11  180.00   0.0  0
 JPB  CONST_11  CL2  C9   C10  C11  180.00   0.0  0
 JPB  CONST_12  CL2  C9   C8   C7   180.00   0.0  0
 JPB  CONST_13  CL3  C11  C6   C7   180.00   0.0  0
 JPB  CONST_14  CL1  C7   C8   C9   180.00   0.0  0
 JPB  CONST_15  CL3  C11  C10  C9   180.00   0.0  0
 JPB  CONST_16  C2   N1   C1   O1   180.00   0.0  0
 JPB  CONST_17  H2   C8   C7   C6   180.00   0.0  0
 JPB  CONST_18  H3   C10  C11  C6   180.00   0.0  0
 JPB  CONST_19  H4   N1   C1   C4   180.00   0.0  0
 JPB  CONST_20  C6   C5   N2   C4   180.00   0.0  0
 JPB  CONST_21  O3   C5   N2   C4     0.00   0.0  0
 JPB  CONST_22  H5   N2   C5   C6     0.00   0.0  0
 JPB  Var_01    N1   C2   C3   C4   -11.89  30.0  1
 JPB  Var_02    C1   N1   C2   C3     3.04  30.0  1
 JPB  Var_03    N2   C5   C6   C11  -88.77  30.0  2

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
 JPB  chir_01  C4  C1  N2  C3  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
 JPB  plan-1  C5   0.020
 JPB  plan-1  C6   0.020
 JPB  plan-1  C11  0.020
 JPB  plan-1  C7   0.020
 JPB  plan-1  C8   0.020
 JPB  plan-1  C9   0.020
 JPB  plan-1  C10  0.020
 JPB  plan-1  CL1  0.020
 JPB  plan-1  CL2  0.020
 JPB  plan-1  CL3  0.020
 JPB  plan-1  H2   0.020
 JPB  plan-1  H3   0.020
 JPB  plan-2  C4   0.020
 JPB  plan-2  C5   0.020
 JPB  plan-2  C6   0.020
 JPB  plan-2  N2   0.020
 JPB  plan-2  O3   0.020
 JPB  plan-2  H5   0.020
 JPB  plan-3  N1   0.020
 JPB  plan-3  C3   0.020
 JPB  plan-3  C2   0.020
 JPB  plan-3  O2   0.020
 JPB  plan-4  C4   0.020
 JPB  plan-4  N1   0.020
 JPB  plan-4  O1   0.020
 JPB  plan-4  C1   0.020
 JPB  plan-4  C2   0.020
 JPB  plan-4  H4   0.020

