# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 10:51:29 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: (3~{R},4~{S})-1-[[6-chloranyl-5-(trifluoromethyl)pyridin-2-yl]amino]-3,4-dimethyl-pyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@@H](C)C(=O)N(Nc2ccc(c(Cl)n2)C(F)(F)F)C1=O
#
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
 EQF  EQF  (3~{R},4~{S})-1-[[6-chloranyl-5-(trifluoromethyl)pyridin-2-yl]amino]-3,4-dimethyl-pyrrolidine-2,5-dione  ligand  32  21  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EQF
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
 EQF  F3   F   F     0  -0.301  -36.6030  70.3455  26.3691
 EQF  C12  C   CT    0   1.083  -35.3956  70.2723  26.9356
 EQF  F1   F   F     0  -0.310  -34.6277  69.5351  26.1237
 EQF  F2   F   F     0  -0.311  -35.5407  69.5707  28.0667
 EQF  C2   C   CR6   0  -0.264  -34.8242  71.6321  27.1803
 EQF  C1   C   CR6   0   0.153  -33.5603  71.8285  27.7189
 EQF  CL   CL  CL    0  -0.077  -32.5697  70.4778  28.1526
 EQF  C3   C   CR16  0  -0.155  -35.5452  72.7905  26.8777
 EQF  C4   C   CR16  0  -0.357  -35.0046  74.0323  27.1062
 EQF  C5   C   CR6   0   0.538  -33.7146  74.0904  27.6449
 EQF  N1   N   N     0  -0.441  -33.0216  73.0002  27.9416
 EQF  N2   N   NH1   0  -0.529  -33.1255  75.2924  27.9205
 EQF  N3   N   NT    0  -0.402  -31.8079  75.3217  28.2288
 EQF  C9   C   C     0   0.577  -31.3475  75.2339  29.5354
 EQF  O1   O   O     0  -0.398  -32.0540  75.2932  30.5048
 EQF  C8   C   CH1   0  -0.396  -29.8604  74.9798  29.4634
 EQF  C11  C   CH3   0  -0.667  -29.6043  73.5312  29.8836
 EQF  C7   C   CH1   0  -0.396  -29.4923  75.3002  28.0015
 EQF  C10  C   CH3   0  -0.668  -28.4004  74.4663  27.3540
 EQF  C6   C   C     0   0.597  -30.8077  75.2258  27.2697
 EQF  O2   O   O     0  -0.400  -31.0195  75.1313  26.0910
 EQF  H1   H   HCR6  0   0.293  -36.5388  72.7263  26.4567
 EQF  H2   H   HCR6  0   0.294  -35.5540  74.9337  26.8726
 EQF  H3   H   HNH1  0   0.428  -33.5227  76.1445  27.5529
 EQF  H4   H   HCH1  0   0.302  -29.3451  75.6476  30.1553
 EQF  H5   H   HCH3  0   0.256  -29.9341  73.3719  30.9093
 EQF  H6   H   HCH3  0   0.235  -30.1315  72.8224  29.2436
 EQF  H7   H   HCH3  0   0.256  -28.5405  73.3045  29.8389
 EQF  H8   H   HCH1  0   0.319  -29.1946  76.3547  27.9549
 EQF  H9   H   HCH3  0   0.250  -27.4721  74.5548  27.9170
 EQF  H10  H   HCH3  0   0.240  -28.6659  73.4112  27.3018
 EQF  H11  H   HCH3  0   0.252  -28.2070  74.8157  26.3410

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
 EQF  O2   C6   double    1.201  0.020  1.201
 EQF  F1   C12  single    1.339  0.020  1.339
 EQF  F3   C12  single    1.336  0.020  1.336
 EQF  C3   C2   aromatic  1.398  0.020  1.398
 EQF  C3   C4   aromatic  1.374  0.020  1.374
 EQF  C12  C2   single    1.495  0.020  1.495
 EQF  C12  F2   single    1.339  0.020  1.339
 EQF  C2   C1   aromatic  1.388  0.020  1.388
 EQF  C4   C5   aromatic  1.399  0.020  1.399
 EQF  C6   N3   single    1.389  0.020  1.389
 EQF  C6   C7   single    1.507  0.020  1.507
 EQF  C10  C7   single    1.519  0.020  1.519
 EQF  C5   N1   aromatic  1.325  0.020  1.325
 EQF  C5   N2   single    1.367  0.020  1.367
 EQF  C1   N1   aromatic  1.309  0.020  1.309
 EQF  C1   CL   single    1.730  0.020  1.730
 EQF  N2   N3   single    1.353  0.020  1.353
 EQF  N3   C9   single    1.388  0.020  1.388
 EQF  C7   C8   single    1.541  0.020  1.541
 EQF  C9   C8   single    1.510  0.020  1.510
 EQF  C9   O1   double    1.201  0.020  1.201
 EQF  C8   C11  single    1.530  0.020  1.530
 EQF  C3   H1   single    0.930  0.020  1.080
 EQF  C4   H2   single    0.930  0.020  1.080
 EQF  N2   H3   single    0.890  0.020  1.040
 EQF  C8   H4   single    0.970  0.020  1.090
 EQF  C11  H5   single    0.970  0.020  1.090
 EQF  C11  H6   single    0.970  0.020  1.090
 EQF  C11  H7   single    0.970  0.020  1.090
 EQF  C7   H8   single    0.970  0.020  1.090
 EQF  C10  H9   single    0.970  0.020  1.090
 EQF  C10  H10  single    0.970  0.020  1.090
 EQF  C10  H11  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
 EQF  C2   C12  F2   112.32  3.000
 EQF  F2   C12  F1   106.62  3.000
 EQF  C2   C12  F1   112.39  3.000
 EQF  F2   C12  F3   106.80  3.000
 EQF  C2   C12  F3   111.41  3.000
 EQF  F1   C12  F3   106.95  3.000
 EQF  C3   C2   C1   115.88  3.000
 EQF  C1   C2   C12  122.70  3.000
 EQF  C3   C2   C12  121.42  3.000
 EQF  N1   C1   CL   114.88  3.000
 EQF  CL   C1   C2   120.54  3.000
 EQF  N1   C1   C2   124.58  3.000
 EQF  H1   C3   C4   118.71  3.000
 EQF  H1   C3   C2   120.61  3.000
 EQF  C4   C3   C2   120.68  3.000
 EQF  H2   C4   C5   121.13  3.000
 EQF  H2   C4   C3   121.18  3.000
 EQF  C5   C4   C3   117.68  3.000
 EQF  N2   C5   N1   116.93  3.000
 EQF  N2   C5   C4   120.77  3.000
 EQF  N1   C5   C4   122.28  3.000
 EQF  C5   N1   C1   118.89  3.000
 EQF  H3   N2   N3   116.60  3.000
 EQF  H3   N2   C5   119.96  3.000
 EQF  N3   N2   C5   118.99  3.000
 EQF  C6   N3   C9   114.00  3.000
 EQF  C9   N3   N2   122.41  3.000
 EQF  C6   N3   N2   122.83  3.000
 EQF  C8   C9   O1   128.75  3.000
 EQF  O1   C9   N3   124.16  3.000
 EQF  C8   C9   N3   107.00  3.000
 EQF  H4   C8   C7   111.19  3.000
 EQF  H4   C8   C11  109.04  3.000
 EQF  C7   C8   C11  114.67  3.000
 EQF  H4   C8   C9   109.38  3.000
 EQF  C11  C8   C9   108.12  3.000
 EQF  C7   C8   C9   104.21  3.000
 EQF  H7   C11  H6   108.23  3.000
 EQF  H7   C11  H5   107.71  3.000
 EQF  H6   C11  H5   108.12  3.000
 EQF  H7   C11  C8   110.46  3.000
 EQF  H6   C11  C8   111.92  3.000
 EQF  H5   C11  C8   110.28  3.000
 EQF  H8   C7   C6   105.30  3.000
 EQF  H8   C7   C10  108.34  3.000
 EQF  C6   C7   C10  113.16  3.000
 EQF  H8   C7   C8   107.76  3.000
 EQF  C10  C7   C8   117.51  3.000
 EQF  C6   C7   C8   103.99  3.000
 EQF  H11  C10  H10  108.03  3.000
 EQF  H11  C10  H9   107.66  3.000
 EQF  H10  C10  H9   108.13  3.000
 EQF  H11  C10  C7   110.37  3.000
 EQF  H10  C10  C7   112.15  3.000
 EQF  H9   C10  C7   110.35  3.000
 EQF  O2   C6   C7   129.36  3.000
 EQF  C7   C6   N3   106.85  3.000
 EQF  O2   C6   N3   123.78  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
 EQF  CONST_01  C5  C4  C3   C2     0.00   0.0  0
 EQF  CONST_02  C5  N1  C1   C2     0.00   0.0  0
 EQF  CONST_03  C4  C3  C2   C1     0.00   0.0  0
 EQF  CONST_04  C4  C5  N1   C1     0.00   0.0  0
 EQF  CONST_05  N1  C1  C2   C3     0.00   0.0  0
 EQF  CONST_06  N1  C5  C4   C3     0.00   0.0  0
 EQF  CONST_07  C6  N3  C9   C8     0.00   0.0  0
 EQF  CONST_08  C4  C3  C2   C12  180.00   0.0  0
 EQF  CONST_09  N1  C1  C2   C12  180.00   0.0  0
 EQF  CONST_10  N2  C5  N1   C1   180.00   0.0  0
 EQF  CONST_11  C3  C2  C1   CL   180.00   0.0  0
 EQF  CONST_12  C5  N1  C1   CL   180.00   0.0  0
 EQF  CONST_13  N2  C5  C4   C3   180.00   0.0  0
 EQF  CONST_14  N3  N2  C5   C4   180.00   0.0  0
 EQF  CONST_17  N3  N2  C5   N1     0.00   0.0  0
 EQF  CONST_18  C8  C9  N3   N2   180.00   0.0  0
 EQF  CONST_19  C6  N3  C9   O1   180.00   0.0  0
 EQF  CONST_20  H2  C4  C3   C2   180.00   0.0  0
 EQF  CONST_21  H1  C3  C2   C1   180.00   0.0  0
 EQF  CONST_22  O1  C9  N3   N2     0.00   0.0  0
 EQF  CONST_23  H3  N2  C5   C4     0.00   0.0  0
 EQF  Var_01    C7  C6  N3   C9    -9.92  30.0  1
 EQF  Var_02    C3  C2  C12  F3     2.36  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
 EQF  chir_01  C8  C7  C9   C11  negativ
 EQF  chir_02  C7  C8  C10  C6   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
 EQF  plan-1  C12  0.020
 EQF  plan-1  C2   0.020
 EQF  plan-1  C1   0.020
 EQF  plan-1  CL   0.020
 EQF  plan-1  C3   0.020
 EQF  plan-1  C4   0.020
 EQF  plan-1  C5   0.020
 EQF  plan-1  N1   0.020
 EQF  plan-1  N2   0.020
 EQF  plan-1  H1   0.020
 EQF  plan-1  H2   0.020
 EQF  plan-2  C5   0.020
 EQF  plan-2  N2   0.020
 EQF  plan-2  N3   0.020
 EQF  plan-2  H3   0.020
 EQF  plan-3  N3   0.020
 EQF  plan-3  C7   0.020
 EQF  plan-3  C6   0.020
 EQF  plan-3  O2   0.020
 EQF  plan-4  N2   0.020
 EQF  plan-4  N3   0.020
 EQF  plan-4  C9   0.020
 EQF  plan-4  O1   0.020
 EQF  plan-4  C8   0.020
 EQF  plan-4  C6   0.020

