# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 10:55:49 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (~{N}~{E})-~{N}-[1-[(6-chloranylpyridin-3-yl)methyl]pyridin-2-ylidene]-2,2,2-tris(fluoranyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)C(=O)N=C1C=CC=CN1Cc2ccc(Cl)nc2
#
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
 7OF  7OF  "(~{N}~{E})-~{N}-[1-[(6-chloranylpyridin-3-yl)methyl]pyridin-2-ylidene]-2,2,2-tris(fluoranyl)ethanamide"
  ligand  30  21  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7OF
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
 7OF  C1   C   C     0   0.256  59.1485  -16.6371   1.3513
 7OF  C2   C   CT    0   0.967  59.9242  -16.9439   0.0565
 7OF  N3   N   N     0  -0.385  55.1610  -13.2876  -1.5224
 7OF  C5   C   CR6   0   0.054  57.2426  -13.2589  -0.3417
 7OF  C6   C   CR16  0  -0.163  57.8631  -13.8597  -1.4298
 7OF  C8   C   CR6   0   0.156  55.7755  -13.8507  -2.5335
 7OF  C9   C   CR16  0  -0.082  55.8845  -12.9939  -0.4475
 7OF  C10  C   CR16  0   0.056  56.7956  -12.8920   2.9792
 7OF  C11  C   CR16  0  -0.372  56.3099  -13.4780   4.1079
 7OF  C12  C   CR16  0  -0.107  56.6220  -14.8237   4.3302
 7OF  C13  C   CR16  0  -0.406  57.3996  -15.5139   3.4393
 7OF  CL1  CL  CL    0  -0.103  54.8054  -14.2083  -3.9267
 7OF  C7   C   CR16  0  -0.265  57.1256  -14.1630  -2.5597
 7OF  N2   N   NR6   0  -0.481  57.5532  -13.5726   2.0917
 7OF  C3   C   CR6   0   0.575  57.8962  -14.8906   2.2691
 7OF  N1   N   N     0  -0.563  58.6478  -15.4044   1.3005
 7OF  O1   O   O     0  -0.458  59.1002  -17.5083   2.2049
 7OF  F1   F   F     0  -0.314  59.1148  -16.9087  -1.0096
 7OF  F2   F   F     0  -0.315  60.9029  -16.0559  -0.1551
 7OF  F3   F   F     0  -0.303  60.4812  -18.1524   0.0898
 7OF  H1   H   HCH2  0   0.309  59.0755  -13.0648   0.7524
 7OF  H2   H   HCH2  0   0.308  57.8988  -11.8028   1.0806
 7OF  H3   H   HCR6  0   0.280  58.9206  -14.0825  -1.3984
 7OF  H4   H   HCR6  0   0.275  55.3459  -12.5169   0.3650
 7OF  H5   H   HCR6  0   0.330  56.5988  -11.8576   2.7387
 7OF  H6   H   HCR6  0   0.292  55.7070  -12.9048   4.7953
 7OF  H7   H   HCR6  0   0.292  56.2515  -15.3268   5.2136
 7OF  H8   H   HCR6  0   0.306  57.6435  -16.5469   3.6170
 7OF  H9   H   HCR6  0   0.294  57.5802  -14.6259  -3.4236
 7OF  C4   C   CH2   0  -0.432  58.0151  -12.8684   0.8872

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
 7OF  CL1  C8   single    1.735  0.020  1.735
 7OF  C8   C7   aromatic  1.386  0.020  1.386
 7OF  C8   N3   aromatic  1.310  0.020  1.310
 7OF  C7   C6   aromatic  1.383  0.020  1.383
 7OF  N3   C9   aromatic  1.329  0.020  1.329
 7OF  C6   C5   aromatic  1.389  0.020  1.389
 7OF  F1   C2   single    1.339  0.020  1.339
 7OF  F3   C2   single    1.331  0.020  1.331
 7OF  C9   C5   aromatic  1.388  0.020  1.388
 7OF  C5   C4   single    1.503  0.020  1.503
 7OF  C2   F2   single    1.338  0.020  1.338
 7OF  C2   C1   single    1.540  0.020  1.540
 7OF  C4   N2   single    1.470  0.020  1.470
 7OF  C1   N1   single    1.331  0.020  1.331
 7OF  C1   O1   double    1.221  0.020  1.221
 7OF  N1   C3   double    1.329  0.020  1.329
 7OF  N2   C3   single    1.373  0.020  1.373
 7OF  N2   C10  single    1.351  0.020  1.351
 7OF  C3   C13  single    1.416  0.020  1.416
 7OF  C10  C11  double    1.361  0.020  1.361
 7OF  C13  C12  double    1.369  0.020  1.369
 7OF  C11  C12  single    1.399  0.020  1.399
 7OF  C4   H1   single    0.970  0.020  1.090
 7OF  C4   H2   single    0.970  0.020  1.090
 7OF  C6   H3   single    0.930  0.020  1.080
 7OF  C9   H4   single    0.930  0.020  1.080
 7OF  C10  H5   single    0.930  0.020  1.080
 7OF  C11  H6   single    0.930  0.020  1.080
 7OF  C12  H7   single    0.930  0.020  1.080
 7OF  C13  H8   single    0.930  0.020  1.080
 7OF  C7   H9   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
 7OF  O1   C1   N1   132.27  3.000
 7OF  O1   C1   C2   117.75  3.000
 7OF  N1   C1   C2   109.98  3.000
 7OF  F3   C2   F2   107.48  3.000
 7OF  F2   C2   F1   107.38  3.000
 7OF  F3   C2   F1   107.26  3.000
 7OF  F2   C2   C1   111.66  3.000
 7OF  F3   C2   C1   111.75  3.000
 7OF  F1   C2   C1   111.08  3.000
 7OF  C9   N3   C8   117.64  3.000
 7OF  C9   C5   C6   117.38  3.000
 7OF  C9   C5   C4   121.04  3.000
 7OF  C6   C5   C4   121.54  3.000
 7OF  H3   C6   C7   120.01  3.000
 7OF  H3   C6   C5   120.22  3.000
 7OF  C7   C6   C5   119.77  3.000
 7OF  C7   C8   CL1  118.89  3.000
 7OF  C7   C8   N3   124.62  3.000
 7OF  CL1  C8   N3   116.49  3.000
 7OF  H4   C9   C5   120.84  3.000
 7OF  H4   C9   N3   115.63  3.000
 7OF  C5   C9   N3   123.53  3.000
 7OF  H5   C10  N2   116.00  3.000
 7OF  H5   C10  C11  122.13  3.000
 7OF  N2   C10  C11  121.86  3.000
 7OF  H6   C11  C12  122.29  3.000
 7OF  H6   C11  C10  119.92  3.000
 7OF  C12  C11  C10  117.79  3.000
 7OF  H7   C12  C13  119.42  3.000
 7OF  H7   C12  C11  120.04  3.000
 7OF  C13  C12  C11  120.54  3.000
 7OF  H8   C13  C3   118.66  3.000
 7OF  H8   C13  C12  120.34  3.000
 7OF  C3   C13  C12  121.00  3.000
 7OF  H9   C7   C8   121.43  3.000
 7OF  H9   C7   C6   121.52  3.000
 7OF  C8   C7   C6   117.04  3.000
 7OF  C3   N2   C10  122.59  3.000
 7OF  C10  N2   C4   118.25  3.000
 7OF  C3   N2   C4   119.16  3.000
 7OF  N1   C3   N2   114.71  3.000
 7OF  N2   C3   C13  116.21  3.000
 7OF  N1   C3   C13  129.08  3.000
 7OF  C3   N1   C1   122.86  3.000
 7OF  H2   C4   H1   107.64  3.000
 7OF  H2   C4   N2   106.84  3.000
 7OF  H1   C4   N2   108.76  3.000
 7OF  H2   C4   C5   110.15  3.000
 7OF  H1   C4   C5   110.67  3.000
 7OF  N2   C4   C5   112.58  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
 7OF  CONST_01  C6   C7   C8   N3      0.00   0.0  0
 7OF  CONST_02  C6   C5   C9   N3      0.00   0.0  0
 7OF  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 7OF  CONST_04  C8   N3   C9   C5      0.00   0.0  0
 7OF  CONST_05  C7   C8   N3   C9      0.00   0.0  0
 7OF  CONST_06  C7   C6   C5   C9      0.00   0.0  0
 7OF  CONST_07  C13  C3   N2   C10     0.00   0.0  0
 7OF  CONST_08  C4   C5   C9   N3    180.00   0.0  0
 7OF  CONST_09  C7   C6   C5   C4    180.00   0.0  0
 7OF  CONST_10  CL1  C8   C7   C6    180.00   0.0  0
 7OF  CONST_11  CL1  C8   N3   C9    180.00   0.0  0
 7OF  CONST_12  C13  C3   N2   C4    180.00   0.0  0
 7OF  CONST_13  N1   C3   N2   C10   180.00   0.0  0
 7OF  CONST_14  H9   C7   C8   N3    180.00   0.0  0
 7OF  CONST_15  H9   C7   C6   C5    180.00   0.0  0
 7OF  CONST_16  H4   C9   C5   C6    180.00   0.0  0
 7OF  CONST_17  H3   C6   C7   C8    180.00   0.0  0
 7OF  CONST_18  H4   C9   N3   C8    180.00   0.0  0
 7OF  CONST_19  H3   C6   C5   C9    180.00   0.0  0
 7OF  CONST_20  N2   C3   N1   C1    180.00   0.0  0
 7OF  CONST_21  C13  C3   N1   C1      0.00   0.0  0
 7OF  CONST_22  N1   C3   N2   C4      0.00   0.0  0
 7OF  CONST_23  C3   N1   C1   C2    180.00   0.0  0
 7OF  CONST_24  O1   C1   N1   C3      0.00   0.0  0
 7OF  Var_01    C13  C12  C11  C10     0.48  30.0  1
 7OF  Var_02    C3   N2   C10  C11    -0.64  30.0  1
 7OF  Var_03    C3   C13  C12  C11    -0.56  30.0  1
 7OF  Var_04    N2   C3   C13  C12     0.05  30.0  1
 7OF  Var_05    N2   C10  C11  C12     0.11  30.0  1
 7OF  Var_06    C11  C10  N2   C4    178.88  30.0  1
 7OF  Var_07    C3   N2   C4   C5     75.45  30.0  3
 7OF  Var_08    C10  N2   C4   C5   -104.09  30.0  3
 7OF  Var_09    N2   C4   C5   C6   -118.39  30.0  2
 7OF  Var_10    N2   C4   C5   C9     63.61  30.0  2
 7OF  Var_11    N1   C3   C13  C12  -179.42  30.0  1
 7OF  Var_12    H7   C12  C11  C10  -179.75  30.0  1
 7OF  Var_13    H8   C13  C12  C11   179.56  30.0  1
 7OF  Var_14    H5   C10  C11  C12  -179.94  30.0  1
 7OF  Var_15    H6   C11  C12  C13  -179.45  30.0  1
 7OF  Var_16    H8   C13  C3   N2    179.93  30.0  1
 7OF  Var_17    H6   C11  C10  N2   -179.96  30.0  1
 7OF  Var_18    H5   C10  N2   C3    179.40  30.0  1
 7OF  Var_19    H7   C12  C13  C3    179.66  30.0  1
 7OF  Var_20    H5   C10  N2   C4     -1.07  30.0  1
 7OF  Var_21    H1   C4   C5   C6      3.57  30.0  2
 7OF  Var_22    H2   C4   C5   C6    122.48  30.0  2
 7OF  Var_23    H1   C4   C5   C9   -174.43  30.0  2
 7OF  Var_24    H2   C4   C5   C9    -55.52  30.0  2
 7OF  Var_25    H1   C4   N2   C10   132.88  30.0  2
 7OF  Var_26    H2   C4   N2   C10    16.95  30.0  2
 7OF  Var_27    H1   C4   N2   C3    -47.58  30.0  2
 7OF  Var_28    H2   C4   N2   C3   -163.50  30.0  2
 7OF  Var_29    H8   C13  C3   N1      0.46  30.0  1
 7OF  Var_30    F1   C2   C1   N1    -62.50  30.0  3
 7OF  Var_31    F3   C2   C1   N1    177.76  30.0  3
 7OF  Var_32    F2   C2   C1   N1     57.34  30.0  3
 7OF  Var_33    F1   C2   C1   O1    117.72  30.0  3
 7OF  Var_34    F3   C2   C1   O1     -2.02  30.0  3
 7OF  Var_35    F2   C2   C1   O1   -122.44  30.0  3

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
 7OF  plan-1  N3   0.020
 7OF  plan-1  C5   0.020
 7OF  plan-1  C6   0.020
 7OF  plan-1  C8   0.020
 7OF  plan-1  C9   0.020
 7OF  plan-1  CL1  0.020
 7OF  plan-1  C7   0.020
 7OF  plan-1  H3   0.020
 7OF  plan-1  H4   0.020
 7OF  plan-1  H9   0.020
 7OF  plan-1  C4   0.020
 7OF  plan-2  C1   0.020
 7OF  plan-2  C2   0.020
 7OF  plan-2  C10  0.020
 7OF  plan-2  C13  0.020
 7OF  plan-2  N2   0.020
 7OF  plan-2  C3   0.020
 7OF  plan-2  N1   0.020
 7OF  plan-2  O1   0.020
 7OF  plan-2  C4   0.020

