# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:56:38 2021
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-[(4~{R})-4-(2-methylpropyl)-2,5-bis(oxidanylidene)imidazolidin-1-yl]-~{N}-[4-(trifluoromethyl)phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H]1NC(=O)N(CC(=O)Nc2ccc(cc2)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
 7ZW  7ZW  2-[(4~{R})-4-(2-methylpropyl)-2,5-bis(oxidanylidene)imidazolidin-1-yl]-~{N}-[4-(trifluoromethyl)phenyl]ethanamide  ligand  43  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7ZW
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
 7ZW  F2   F  F     0  -0.316  -2.2305  -21.6336  -36.3592
 7ZW  C13  C  CT    0   1.052  -1.1841  -22.2539  -35.7882
 7ZW  F    F  F     0  -0.306  -1.5752  -22.6106  -34.5597
 7ZW  F1   F  F     0  -0.311  -0.9919  -23.3835  -36.4826
 7ZW  C12  C  CR6   0  -0.215   0.0332  -21.3903  -35.7715
 7ZW  C11  C  CR16  0  -0.265   0.3709  -20.6513  -34.6437
 7ZW  C10  C  CR16  0  -0.336   1.4786  -19.8272  -34.6619
 7ZW  C14  C  CR16  0  -0.260   0.8192  -21.2815  -36.9117
 7ZW  C15  C  CR16  0  -0.301   1.9316  -20.4574  -36.9398
 7ZW  C9   C  CR6   0   0.391   2.2740  -19.7192  -35.8053
 7ZW  N2   N  NH1   0  -0.748   3.3729  -18.8657  -35.7253
 7ZW  C    C  C     0   0.550   4.3134  -18.5890  -36.6602
 7ZW  O    O  O     0  -0.443   4.3385  -19.0362  -37.7871
 7ZW  C1   C  CH2   0  -0.462   5.3954  -17.6416  -36.1530
 7ZW  N    N  NR5   0  -0.536   6.2321  -17.2235  -37.2321
 7ZW  C8   C  CR5   0   0.712   5.8454  -16.2224  -38.1323
 7ZW  O1   O  O     0  -0.479   4.8709  -15.5181  -37.9887
 7ZW  N1   N  NR15  0  -0.672   6.7560  -16.2233  -39.1184
 7ZW  C3   C  CR15  0  -0.212   7.7578  -17.2509  -38.9714
 7ZW  C2   C  CR5   0   0.569   7.3297  -17.9046  -37.6719
 7ZW  O2   O  O     0  -0.434   7.8416  -18.8552  -37.1319
 7ZW  C4   C  CH2   0  -0.402   7.7663  -18.2685  -40.1111
 7ZW  C5   C  CH1   0  -0.253   8.0269  -17.6641  -41.4916
 7ZW  C7   C  CH3   0  -0.649   7.9348  -18.7563  -42.5521
 7ZW  C6   C  CH3   0  -0.661   9.3748  -16.9540  -41.5719
 7ZW  H1   H  HCR6  0   0.276  -0.2179  -20.7067  -33.7384
 7ZW  H2   H  HCR6  0   0.283   1.7317  -19.2600  -33.7742
 7ZW  H3   H  HCR6  0   0.277   0.5786  -21.8434  -37.8049
 7ZW  H4   H  HCR6  0   0.292   2.5176  -20.4021  -37.8416
 7ZW  H5   H  HNH1  0   0.428   3.4787  -18.3964  -34.8368
 7ZW  H6   H  HCH2  0   0.324   6.0032  -18.1532  -35.4041
 7ZW  H7   H  HCH2  0   0.315   4.9529  -16.7717  -35.6665
 7ZW  H8   H  HNR5  0   0.418   6.7402  -15.5478  -39.8640
 7ZW  H9   H  HCR5  0   0.310   8.7524  -16.8143  -38.8348
 7ZW  H10  H  HCH2  0   0.243   6.8038  -18.7897  -40.1214
 7ZW  H11  H  HCH2  0   0.241   8.5326  -19.0174  -39.8907
 7ZW  H12  H  HCH1  0   0.222   7.2375  -16.9326  -41.6995
 7ZW  H13  H  HCH3  0   0.228   6.9704  -19.2662  -42.5210
 7ZW  H14  H  HCH3  0   0.230   8.0596  -18.3413  -43.5531
 7ZW  H15  H  HCH3  0   0.217   8.7147  -19.5064  -42.4038
 7ZW  H16  H  HCH3  0   0.231   9.4574  -16.1258  -40.8662
 7ZW  H17  H  HCH3  0   0.220  10.1935  -17.6484  -41.3673
 7ZW  H18  H  HCH3  0   0.235   9.5331  -16.5425  -42.5698

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
 7ZW  C7   C5   single    1.525  0.020  1.525
 7ZW  C6   C5   single    1.526  0.020  1.526
 7ZW  C5   C4   single    1.529  0.020  1.529
 7ZW  C4   C3   single    1.528  0.020  1.528
 7ZW  N1   C3   single    1.443  0.020  1.443
 7ZW  N1   C8   single    1.342  0.020  1.342
 7ZW  C3   C2   single    1.516  0.020  1.516
 7ZW  C8   O1   double    1.211  0.020  1.211
 7ZW  C8   N    single    1.401  0.020  1.401
 7ZW  C2   N    single    1.365  0.020  1.365
 7ZW  C2   O2   double    1.207  0.020  1.207
 7ZW  O    C    double    1.213  0.020  1.213
 7ZW  N    C1   single    1.428  0.020  1.428
 7ZW  C14  C15  aromatic  1.385  0.020  1.385
 7ZW  C14  C12  aromatic  1.389  0.020  1.389
 7ZW  C15  C9   aromatic  1.396  0.020  1.396
 7ZW  F2   C13  single    1.344  0.020  1.344
 7ZW  C    C1   single    1.525  0.020  1.525
 7ZW  C    N2   single    1.355  0.020  1.355
 7ZW  F1   C13  single    1.340  0.020  1.340
 7ZW  C13  C12  single    1.493  0.020  1.493
 7ZW  C13  F    single    1.338  0.020  1.338
 7ZW  C12  C11  aromatic  1.390  0.020  1.390
 7ZW  C9   N2   single    1.394  0.020  1.394
 7ZW  C9   C10  aromatic  1.397  0.020  1.397
 7ZW  C11  C10  aromatic  1.381  0.020  1.381
 7ZW  C11  H1   single    0.930  0.020  1.080
 7ZW  C10  H2   single    0.930  0.020  1.080
 7ZW  C14  H3   single    0.930  0.020  1.080
 7ZW  C15  H4   single    0.930  0.020  1.080
 7ZW  N2   H5   single    0.860  0.020  1.020
 7ZW  C1   H6   single    0.970  0.020  1.090
 7ZW  C1   H7   single    0.970  0.020  1.090
 7ZW  N1   H8   single    0.860  0.020  1.020
 7ZW  C3   H9   single    0.970  0.020  1.090
 7ZW  C4   H10  single    0.970  0.020  1.090
 7ZW  C4   H11  single    0.970  0.020  1.090
 7ZW  C5   H12  single    0.970  0.020  1.090
 7ZW  C7   H13  single    0.970  0.020  1.090
 7ZW  C7   H14  single    0.970  0.020  1.090
 7ZW  C7   H15  single    0.970  0.020  1.090
 7ZW  C6   H16  single    0.970  0.020  1.090
 7ZW  C6   H17  single    0.970  0.020  1.090
 7ZW  C6   H18  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
 7ZW  C12  C13  F1   112.12  3.000
 7ZW  C12  C13  F    112.48  3.000
 7ZW  F1   C13  F    107.04  3.000
 7ZW  F    C13  F2   106.60  3.000
 7ZW  C12  C13  F2   111.89  3.000
 7ZW  F1   C13  F2   106.30  3.000
 7ZW  C14  C12  C11  119.14  3.000
 7ZW  C11  C12  C13  120.98  3.000
 7ZW  C14  C12  C13  119.84  3.000
 7ZW  H1   C11  C10  118.58  3.000
 7ZW  H1   C11  C12  121.32  3.000
 7ZW  C10  C11  C12  120.10  3.000
 7ZW  H2   C10  C9   119.81  3.000
 7ZW  H2   C10  C11  119.28  3.000
 7ZW  C9   C10  C11  120.91  3.000
 7ZW  H3   C14  C15  118.09  3.000
 7ZW  H3   C14  C12  120.73  3.000
 7ZW  C15  C14  C12  121.18  3.000
 7ZW  H4   C15  C9   121.32  3.000
 7ZW  H4   C15  C14  118.99  3.000
 7ZW  C9   C15  C14  119.68  3.000
 7ZW  N2   C9   C15  124.32  3.000
 7ZW  N2   C9   C10  116.70  3.000
 7ZW  C15  C9   C10  118.98  3.000
 7ZW  H5   N2   C    116.06  3.000
 7ZW  H5   N2   C9   114.68  3.000
 7ZW  C    N2   C9   129.26  3.000
 7ZW  C1   C    O    121.56  3.000
 7ZW  C1   C    N2   112.95  3.000
 7ZW  O    C    N2   125.48  3.000
 7ZW  H7   C1   H6   107.08  3.000
 7ZW  H7   C1   N    109.96  3.000
 7ZW  H6   C1   N    109.23  3.000
 7ZW  H7   C1   C    110.86  3.000
 7ZW  H6   C1   C    109.39  3.000
 7ZW  N    C1   C    110.26  3.000
 7ZW  C2   N    C8   111.82  3.000
 7ZW  C2   N    C1   124.66  3.000
 7ZW  C8   N    C1   122.21  3.000
 7ZW  N1   C8   O1   129.31  3.000
 7ZW  O1   C8   N    124.17  3.000
 7ZW  N1   C8   N    106.52  3.000
 7ZW  H8   N1   C3   124.38  3.000
 7ZW  H8   N1   C8   122.22  3.000
 7ZW  C3   N1   C8   113.38  3.000
 7ZW  H9   C3   C4   110.71  3.000
 7ZW  H9   C3   C2   108.75  3.000
 7ZW  C4   C3   C2   110.71  3.000
 7ZW  H9   C3   N1   111.08  3.000
 7ZW  C2   C3   N1   101.44  3.000
 7ZW  C4   C3   N1   113.72  3.000
 7ZW  O2   C2   C3   127.09  3.000
 7ZW  O2   C2   N    126.16  3.000
 7ZW  C3   C2   N    106.75  3.000
 7ZW  H11  C4   H10  106.97  3.000
 7ZW  H11  C4   C5   109.46  3.000
 7ZW  H10  C4   C5   109.24  3.000
 7ZW  H11  C4   C3   108.03  3.000
 7ZW  H10  C4   C3   108.62  3.000
 7ZW  C5   C4   C3   114.27  3.000
 7ZW  H12  C5   C6   108.41  3.000
 7ZW  H12  C5   C7   107.61  3.000
 7ZW  C6   C5   C7   110.49  3.000
 7ZW  H12  C5   C4   108.20  3.000
 7ZW  C6   C5   C4   112.46  3.000
 7ZW  C7   C5   C4   109.53  3.000
 7ZW  H15  C7   H14  107.71  3.000
 7ZW  H15  C7   H13  107.83  3.000
 7ZW  H14  C7   H13  107.75  3.000
 7ZW  H15  C7   C5   110.75  3.000
 7ZW  H14  C7   C5   111.02  3.000
 7ZW  H13  C7   C5   111.60  3.000
 7ZW  H18  C6   H17  107.59  3.000
 7ZW  H18  C6   H16  107.11  3.000
 7ZW  H17  C6   H16  107.73  3.000
 7ZW  H18  C6   C5   110.61  3.000
 7ZW  H17  C6   C5   110.88  3.000
 7ZW  H16  C6   C5   112.71  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
 7ZW  CONST_01  C9   C15  C14  C12     0.00   0.0  0
 7ZW  CONST_02  C9   C10  C11  C12     0.00   0.0  0
 7ZW  CONST_03  C15  C14  C12  C11     0.00   0.0  0
 7ZW  CONST_04  C15  C9   C10  C11     0.00   0.0  0
 7ZW  CONST_05  C14  C15  C9   C10     0.00   0.0  0
 7ZW  CONST_06  C14  C12  C11  C10     0.00   0.0  0
 7ZW  CONST_07  C3   N1   C8   N       0.00   0.0  0
 7ZW  CONST_08  C3   C2   N    C8      0.00   0.0  0
 7ZW  CONST_09  C2   N    C8   N1      0.00   0.0  0
 7ZW  CONST_10  C15  C14  C12  C13   180.00   0.0  0
 7ZW  CONST_11  C10  C11  C12  C13   180.00   0.0  0
 7ZW  CONST_12  N2   C9   C10  C11   180.00   0.0  0
 7ZW  CONST_13  N2   C9   C15  C14   180.00   0.0  0
 7ZW  CONST_14  N1   C8   N    C1    180.00   0.0  0
 7ZW  CONST_15  C3   C2   N    C1    180.00   0.0  0
 7ZW  CONST_16  C3   N1   C8   O1    180.00   0.0  0
 7ZW  CONST_17  C2   N    C8   O1    180.00   0.0  0
 7ZW  CONST_18  H4   C15  C14  C12   180.00   0.0  0
 7ZW  CONST_19  H2   C10  C11  C12   180.00   0.0  0
 7ZW  CONST_20  H3   C14  C12  C11   180.00   0.0  0
 7ZW  CONST_21  H1   C11  C12  C14   180.00   0.0  0
 7ZW  CONST_22  H8   N1   C8   N     180.00   0.0  0
 7ZW  CONST_23  C    N2   C9   C10   180.00   0.0  0
 7ZW  CONST_24  C    N2   C9   C15     0.00   0.0  0
 7ZW  CONST_25  O1   C8   N    C1      0.00   0.0  0
 7ZW  CONST_26  H5   N2   C9   C10     0.00   0.0  0
 7ZW  CONST_27  O    C    N2   C9      0.00   0.0  0
 7ZW  CONST_28  C1   C    N2   C9    180.00   0.0  0
 7ZW  Var_01    C14  C12  C13  F2    -80.72  30.0  2
 7ZW  Var_02    C8   N    C1   C      79.09  30.0  1
 7ZW  Var_03    N    C1   C    N2   -170.92  30.0  3
 7ZW  Var_04    C7   C5   C4   C3   -176.86  30.0  1
 7ZW  Var_05    H13  C7   C5   C4     56.47  30.0  3
 7ZW  Var_06    H16  C6   C5   C4    -60.61  30.0  3

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
 7ZW  chir_01  C3  C4  N1  C2  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
 7ZW  plan-1  C13  0.020
 7ZW  plan-1  C12  0.020
 7ZW  plan-1  C11  0.020
 7ZW  plan-1  C10  0.020
 7ZW  plan-1  C14  0.020
 7ZW  plan-1  C15  0.020
 7ZW  plan-1  C9   0.020
 7ZW  plan-1  N2   0.020
 7ZW  plan-1  H1   0.020
 7ZW  plan-1  H2   0.020
 7ZW  plan-1  H3   0.020
 7ZW  plan-1  H4   0.020
 7ZW  plan-2  C9   0.020
 7ZW  plan-2  N2   0.020
 7ZW  plan-2  C    0.020
 7ZW  plan-2  O    0.020
 7ZW  plan-2  C1   0.020
 7ZW  plan-2  H5   0.020
 7ZW  plan-3  C1   0.020
 7ZW  plan-3  N    0.020
 7ZW  plan-3  C8   0.020
 7ZW  plan-3  O1   0.020
 7ZW  plan-3  N1   0.020
 7ZW  plan-3  C3   0.020
 7ZW  plan-3  C2   0.020
 7ZW  plan-3  O2   0.020
 7ZW  plan-3  H8   0.020

