# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:16:02 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCCCC(=O)NO)NC1=C(Nc2ccc(OC(F)(F)F)cc2)C(=O)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
 EL8  EL8  (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide  ligand  49  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EL8
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
 EL8  C4   C  C     0   0.248  -1.0981  -1.9816   1.5738
 EL8  C8   C  CH1   0  -0.130  -3.1593  -2.9447  -0.6743
 EL8  C9   C  CH2   0  -0.404  -4.3334  -1.9865  -0.8598
 EL8  O5   O  O     0  -0.432   1.0559  -1.0292   2.4527
 EL8  C10  C  CH2   0  -0.427  -4.3739  -0.8433   0.1444
 EL8  O6   O  O     0  -0.418  -1.8651  -2.4094   2.4054
 EL8  C11  C  CH2   0  -0.418  -5.5978   0.0424  -0.0507
 EL8  C12  C  CH2   0  -0.579  -5.6459   1.1868   0.9581
 EL8  C13  C  C     0   0.523  -6.8793   2.0402   0.7784
 EL8  C1   C  C     0   0.241   0.2622  -1.3353   1.5891
 EL8  C2   C  C     0   0.189   0.1859  -1.2708   0.1301
 EL8  C3   C  C     0   0.224  -1.0705  -1.8923   0.1045
 EL8  N7   N  NH1   0  -0.627  -1.8857  -2.2552  -0.8633
 EL8  N14  N  NH1   0  -0.375  -6.6081   3.3523   0.6316
 EL8  O15  O  O     0  -0.481  -8.0109   1.5876   0.7936
 EL8  O16  O  OH1   0  -0.546  -7.6038   4.2177   0.2888
 EL8  C17  C  CH3   0  -0.655  -3.2334  -4.1223  -1.6349
 EL8  N18  N  NH1   0  -0.758   0.9798  -0.8794  -0.8788
 EL8  C19  C  CR6   0   0.371   2.1567  -0.1376  -0.7883
 EL8  C20  C  CR16  0  -0.337   3.1097  -0.2849  -1.7962
 EL8  C21  C  CR16  0  -0.289   4.2831   0.4473  -1.7671
 EL8  C22  C  CR6   0   0.296   4.5077   1.3223  -0.7180
 EL8  C23  C  CR16  0  -0.295   3.5670   1.4919   0.2823
 EL8  C24  C  CR16  0  -0.290   2.3835   0.7732   0.2417
 EL8  O25  O  O2    0  -0.523   5.6633   2.0974  -0.7053
 EL8  C26  C  CT    0   1.072   6.7440   1.5889  -0.1020
 EL8  F27  F  F     0  -0.299   6.5349   1.3164   1.1875
 EL8  F28  F  F     0  -0.300   7.1703   0.4586  -0.6698
 EL8  F29  F  F     0  -0.277   7.7124   2.4872  -0.1863
 EL8  H1   H  HCH1  0   0.265  -3.1682  -3.3219   0.3495
 EL8  H2   H  HCH2  0   0.223  -4.3131  -1.5880  -1.8803
 EL8  H3   H  HCH2  0   0.231  -5.2537  -2.5729  -0.7797
 EL8  H4   H  HCH2  0   0.222  -4.3739  -1.2488   1.1615
 EL8  H5   H  HCH2  0   0.221  -3.4711  -0.2307   0.0568
 EL8  H6   H  HCH2  0   0.229  -5.5937   0.4510  -1.0660
 EL8  H7   H  HCH2  0   0.230  -6.5044  -0.5611   0.0377
 EL8  H8   H  HCH2  0   0.267  -5.6702   0.7811   1.9735
 EL8  H9   H  HCH2  0   0.250  -4.7353   1.7872   0.8864
 EL8  H10  H  HNH1  0   0.404  -1.6501  -2.0006  -1.8127
 EL8  H11  H  HNH1  0   0.414  -5.6769   3.6812   0.4214
 EL8  H12  H  HOH1  0   0.478  -7.8671   4.6593   1.1061
 EL8  H13  H  HCH3  0   0.228  -3.2014  -3.7822  -2.6721
 EL8  H14  H  HCH3  0   0.244  -2.4062  -4.8134  -1.4755
 EL8  H15  H  HCH3  0   0.241  -4.1651  -4.6690  -1.4933
 EL8  H16  H  HNH1  0   0.419   0.7357  -1.2026  -1.8037
 EL8  H17  H  HCR6  0   0.282   2.9349  -0.9812  -2.6067
 EL8  H18  H  HCR6  0   0.285   5.0085   0.3362  -2.5618
 EL8  H19  H  HCR6  0   0.284   3.7332   2.2060   1.0777
 EL8  H20  H  HCR6  0   0.280   1.6419   0.9439   1.0073

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
 EL8  F27  C26  single    1.334  0.020  1.334
 EL8  F29  C26  single    1.324  0.020  1.324
 EL8  C26  O25  single    1.338  0.020  1.338
 EL8  C26  F28  single    1.335  0.020  1.335
 EL8  O25  C22  single    1.392  0.020  1.392
 EL8  C23  C22  aromatic  1.384  0.020  1.384
 EL8  C23  C24  aromatic  1.385  0.020  1.385
 EL8  C22  C21  aromatic  1.384  0.020  1.384
 EL8  C24  C19  aromatic  1.394  0.020  1.394
 EL8  C21  C20  aromatic  1.383  0.020  1.383
 EL8  C19  C20  aromatic  1.395  0.020  1.395
 EL8  C19  N18  single    1.394  0.020  1.394
 EL8  N18  C2   single    1.342  0.020  1.342
 EL8  C2   C1   single    1.462  0.020  1.462
 EL8  C2   C3   double    1.402  0.020  1.402
 EL8  O5   C1   double    1.212  0.020  1.212
 EL8  C1   C4   single    1.506  0.020  1.506
 EL8  C3   N7   single    1.316  0.020  1.316
 EL8  C3   C4   single    1.472  0.020  1.472
 EL8  N7   C8   single    1.461  0.020  1.461
 EL8  C4   O6   double    1.209  0.020  1.209
 EL8  C12  C13  single    1.511  0.020  1.511
 EL8  C12  C11  single    1.526  0.020  1.526
 EL8  C10  C11  single    1.523  0.020  1.523
 EL8  C10  C9   single    1.522  0.020  1.522
 EL8  C8   C9   single    1.527  0.020  1.527
 EL8  C8   C17  single    1.521  0.020  1.521
 EL8  C13  O15  double    1.219  0.020  1.219
 EL8  C13  N14  single    1.348  0.020  1.348
 EL8  N14  O16  single    1.363  0.020  1.363
 EL8  C8   H1   single    0.970  0.020  1.090
 EL8  C9   H2   single    0.970  0.020  1.090
 EL8  C9   H3   single    0.970  0.020  1.090
 EL8  C10  H4   single    0.970  0.020  1.090
 EL8  C10  H5   single    0.970  0.020  1.090
 EL8  C11  H6   single    0.970  0.020  1.090
 EL8  C11  H7   single    0.970  0.020  1.090
 EL8  C12  H8   single    0.970  0.020  1.090
 EL8  C12  H9   single    0.970  0.020  1.090
 EL8  N7   H10  single    0.860  0.020  1.020
 EL8  N14  H11  single    0.890  0.020  1.040
 EL8  O16  H12  single    0.850  0.020  0.980
 EL8  C17  H13  single    0.970  0.020  1.090
 EL8  C17  H14  single    0.970  0.020  1.090
 EL8  C17  H15  single    0.970  0.020  1.090
 EL8  N18  H16  single    0.860  0.020  1.020
 EL8  C20  H17  single    0.930  0.020  1.080
 EL8  C21  H18  single    0.930  0.020  1.080
 EL8  C23  H19  single    0.930  0.020  1.080
 EL8  C24  H20  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
 EL8  C3   C4   C1    88.12  3.000
 EL8  C3   C4   O6   136.02  3.000
 EL8  C1   C4   O6   135.85  3.000
 EL8  H1   C8   C17  108.93  3.000
 EL8  H1   C8   N7   106.96  3.000
 EL8  C17  C8   N7   109.04  3.000
 EL8  H1   C8   C9   108.94  3.000
 EL8  C17  C8   C9   111.81  3.000
 EL8  N7   C8   C9   111.01  3.000
 EL8  H3   C9   H2   106.18  3.000
 EL8  H3   C9   C10  109.38  3.000
 EL8  H2   C9   C10  109.99  3.000
 EL8  H3   C9   C8   107.55  3.000
 EL8  H2   C9   C8   109.09  3.000
 EL8  C10  C9   C8   114.31  3.000
 EL8  H5   C10  H4   106.35  3.000
 EL8  H5   C10  C11  109.09  3.000
 EL8  H4   C10  C11  109.53  3.000
 EL8  H5   C10  C9   110.22  3.000
 EL8  H4   C10  C9   109.55  3.000
 EL8  C11  C10  C9   111.94  3.000
 EL8  H7   C11  H6   106.52  3.000
 EL8  H7   C11  C12  109.55  3.000
 EL8  H6   C11  C12  109.47  3.000
 EL8  H7   C11  C10  109.58  3.000
 EL8  H6   C11  C10  109.44  3.000
 EL8  C12  C11  C10  112.12  3.000
 EL8  H9   C12  H8   106.45  3.000
 EL8  H9   C12  C13  111.23  3.000
 EL8  H8   C12  C13  107.57  3.000
 EL8  H9   C12  C11  110.01  3.000
 EL8  H8   C12  C11  109.64  3.000
 EL8  C13  C12  C11  111.76  3.000
 EL8  O15  C13  N14  123.34  3.000
 EL8  N14  C13  C12  113.49  3.000
 EL8  O15  C13  C12  123.15  3.000
 EL8  C2   C1   O5   137.21  3.000
 EL8  O5   C1   C4   134.99  3.000
 EL8  C2   C1   C4    87.80  3.000
 EL8  N18  C2   C3   130.21  3.000
 EL8  C3   C2   C1    92.61  3.000
 EL8  N18  C2   C1   137.05  3.000
 EL8  N7   C3   C2   133.68  3.000
 EL8  N7   C3   C4   134.86  3.000
 EL8  C2   C3   C4    91.46  3.000
 EL8  H10  N7   C3   118.48  3.000
 EL8  H10  N7   C8   116.34  3.000
 EL8  C3   N7   C8   125.10  3.000
 EL8  H11  N14  O16  114.49  3.000
 EL8  H11  N14  C13  121.69  3.000
 EL8  O16  N14  C13  119.90  3.000
 EL8  H12  O16  N14  106.07  3.000
 EL8  H15  C17  H14  108.17  3.000
 EL8  H15  C17  H13  107.74  3.000
 EL8  H14  C17  H13  108.31  3.000
 EL8  H15  C17  C8   110.37  3.000
 EL8  H14  C17  C8   111.20  3.000
 EL8  H13  C17  C8   110.93  3.000
 EL8  H16  N18  C19  115.71  3.000
 EL8  H16  N18  C2   116.89  3.000
 EL8  C19  N18  C2   127.28  3.000
 EL8  C24  C19  C20  119.46  3.000
 EL8  C20  C19  N18  118.27  3.000
 EL8  C24  C19  N18  122.22  3.000
 EL8  H17  C20  C21  119.54  3.000
 EL8  H17  C20  C19  119.90  3.000
 EL8  C21  C20  C19  120.56  3.000
 EL8  H18  C21  C22  120.85  3.000
 EL8  H18  C21  C20  119.93  3.000
 EL8  C22  C21  C20  119.22  3.000
 EL8  O25  C22  C23  119.33  3.000
 EL8  C23  C22  C21  121.00  3.000
 EL8  O25  C22  C21  119.59  3.000
 EL8  H19  C23  C24  119.68  3.000
 EL8  H19  C23  C22  120.54  3.000
 EL8  C24  C23  C22  119.74  3.000
 EL8  H20  C24  C23  118.96  3.000
 EL8  H20  C24  C19  121.05  3.000
 EL8  C23  C24  C19  119.99  3.000
 EL8  C26  O25  C22  117.59  3.000
 EL8  F29  C26  F28  108.30  3.000
 EL8  F28  C26  F27  106.75  3.000
 EL8  F29  C26  F27  108.35  3.000
 EL8  F28  C26  O25  112.82  3.000
 EL8  F29  C26  O25  107.71  3.000
 EL8  F27  C26  O25  112.76  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
 EL8  CONST_01  C22  C23  C24  C19     0.00   0.0  0
 EL8  CONST_02  C22  C21  C20  C19     0.00   0.0  0
 EL8  CONST_03  C23  C22  C21  C20     0.00   0.0  0
 EL8  CONST_04  C23  C24  C19  C20     0.00   0.0  0
 EL8  CONST_05  C24  C23  C22  C21     0.00   0.0  0
 EL8  CONST_06  C24  C19  C20  C21     0.00   0.0  0
 EL8  CONST_07  C23  C24  C19  N18   180.00   0.0  0
 EL8  CONST_08  C21  C20  C19  N18   180.00   0.0  0
 EL8  CONST_09  O25  C22  C21  C20   180.00   0.0  0
 EL8  CONST_10  O25  C22  C23  C24   180.00   0.0  0
 EL8  CONST_11  C19  N18  C2   C1      0.00   0.0  0
 EL8  CONST_14  C19  N18  C2   C3    180.00   0.0  0
 EL8  CONST_15  H19  C23  C24  C19   180.00   0.0  0
 EL8  CONST_16  H18  C21  C20  C19   180.00   0.0  0
 EL8  CONST_17  H20  C24  C19  C20   180.00   0.0  0
 EL8  CONST_18  H17  C20  C21  C22   180.00   0.0  0
 EL8  CONST_20  O16  N14  C13  C12   180.00   0.0  0
 EL8  CONST_21  O16  N14  C13  O15     0.00   0.0  0
 EL8  Var_01    C3   C2   C1   C4     -0.93  30.0  1
 EL8  Var_02    C8   N7   C3   C4     -1.51  30.0  2
 EL8  Var_03    F27  C26  O25  C22   -59.55  30.0  3
 EL8  Var_04    C11  C10  C9   C8   -177.47  30.0  1
 EL8  Var_05    C12  C11  C10  C9    179.75  30.0  3
 EL8  Var_06    C13  C12  C11  C10  -178.64  30.0  2
 EL8  Var_07    O15  C13  C12  C11    55.22  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
 EL8  chir_01  C8  N7  C9  C17  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
 EL8  plan-1  N18  0.020
 EL8  plan-1  C19  0.020
 EL8  plan-1  C20  0.020
 EL8  plan-1  C21  0.020
 EL8  plan-1  C22  0.020
 EL8  plan-1  C23  0.020
 EL8  plan-1  C24  0.020
 EL8  plan-1  O25  0.020
 EL8  plan-1  H17  0.020
 EL8  plan-1  H18  0.020
 EL8  plan-1  H19  0.020
 EL8  plan-1  H20  0.020
 EL8  plan-2  C2   0.020
 EL8  plan-2  N18  0.020
 EL8  plan-2  C19  0.020
 EL8  plan-2  H16  0.020
 EL8  plan-3  C4   0.020
 EL8  plan-3  O6   0.020
 EL8  plan-3  C1   0.020
 EL8  plan-3  C3   0.020
 EL8  plan-4  C12  0.020
 EL8  plan-4  C13  0.020
 EL8  plan-4  N14  0.020
 EL8  plan-4  O15  0.020
 EL8  plan-4  O16  0.020
 EL8  plan-4  H11  0.020
 EL8  plan-5  C4   0.020
 EL8  plan-5  O5   0.020
 EL8  plan-5  C1   0.020
 EL8  plan-5  C2   0.020

