# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:56:26 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-[(3S)-3-{[(2E)-but-2-enoyl]amino}piperidin-1-yl]-5-fluoro-2,3-dimethyl-1H-indole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C/C(=O)N[C@H]1CCCN(C1)c2c(F)cc(C(N)=O)c3[nH]c(C)c(C)c23
#
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
 LTJ  LTJ  4-[(3S)-3-{[(2E)-but-2-enoyl]amino}piperidin-1-yl]-5-fluoro-2,3-dimethyl-1H-indole-7-carboxamide  ligand  52  27  .  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_LTJ
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
 LTJ  C13  C  CH1   0  -0.076  -2.5121  -0.0501  -0.7964
 LTJ  C18  C  C1    0  -0.392  -5.6326   0.1674   1.2861
 LTJ  C17  C  CH3   0  -0.749   0.3734  -2.6270  -0.3615
 LTJ  C16  C  CH3   0  -0.742   2.9964  -3.7864   1.1221
 LTJ  C15  C  C     0   0.552  -4.6141  -0.4730   0.4201
 LTJ  C19  C  C1    0  -0.161  -6.7404  -0.4711   1.6577
 LTJ  C20  C  CH3   0  -0.713  -7.8086   0.1085   2.5153
 LTJ  C11  C  CH2   0  -0.447  -1.6232  -0.0523  -3.1395
 LTJ  C12  C  CH2   0  -0.436  -2.8241   0.2650  -2.2571
 LTJ  C1   C  CR6   0  -0.004   1.1433   0.5611  -0.7322
 LTJ  N1   N  NT    0  -0.500  -0.1427   0.3165  -1.2537
 LTJ  C2   C  CR6   0   0.558   1.7528   1.8078  -0.7367
 LTJ  C3   C  CR16  0  -0.528   3.0145   2.0582  -0.2177
 LTJ  C4   C  CR6   0  -0.068   3.7500   1.0398   0.3763
 LTJ  C5   C  CR56  0   0.323   3.1621  -0.2308   0.3907
 LTJ  C6   C  CR56  0   0.058   1.8745  -0.4826  -0.1462
 LTJ  C7   C  C     0   0.520   5.1010   1.2406   0.9648
 LTJ  O1   O  O     0  -0.494   5.8030   0.2786   1.2652
 LTJ  N2   N  NH2   0  -0.821   5.5118   2.5037   1.1465
 LTJ  F1   F  F     0  -0.322   1.0894   2.8548  -1.2694
 LTJ  N3   N  NR15  0  -0.725   3.6247  -1.4098   0.8800
 LTJ  C8   C  CR5   0   0.290   2.6984  -2.3994   0.6787
 LTJ  C9   C  CR5   0  -0.071   1.5979  -1.8775   0.0473
 LTJ  C10  C  CH2   0  -0.291  -0.3893   0.6821  -2.6399
 LTJ  C14  C  CH2   0  -0.290  -1.2297   0.6504  -0.3535
 LTJ  N4   N  NH1   0  -0.664  -3.5887   0.3350   0.0885
 LTJ  O2   O  O     0  -0.506  -4.6929  -1.6375   0.0441
 LTJ  H1   H  HCH1  0   0.246  -2.3606  -1.1265  -0.6918
 LTJ  H2   H  H     0   0.258  -5.4558   1.1880   1.6116
 LTJ  H3   H  HCH3  0   0.237   0.1907  -2.5536  -1.4335
 LTJ  H4   H  HCH3  0   0.233   0.4616  -3.6852  -0.1163
 LTJ  H5   H  HCH3  0   0.234  -0.5224  -2.2541   0.1370
 LTJ  H6   H  HCH3  0   0.255   3.2631  -3.8142   2.1800
 LTJ  H7   H  HCH3  0   0.255   2.1403  -4.4405   0.9796
 LTJ  H8   H  HCH3  0   0.256   3.8346  -4.2085   0.5642
 LTJ  H9   H  H     0   0.255  -6.8943  -1.4898   1.3148
 LTJ  H10  H  HCH3  0   0.250  -8.7591   0.1322   1.9777
 LTJ  H11  H  HCH3  0   0.250  -7.9714  -0.5120   3.3987
 LTJ  H12  H  HCH3  0   0.243  -7.5731   1.1203   2.8422
 LTJ  H13  H  HCH2  0   0.224  -1.4310  -1.1289  -3.1351
 LTJ  H14  H  HCH2  0   0.238  -1.8255   0.2363  -4.1729
 LTJ  H15  H  HCH2  0   0.244  -3.7027  -0.2992  -2.5772
 LTJ  H16  H  HCH2  0   0.216  -3.0755   1.3278  -2.3468
 LTJ  H17  H  HCR6  0   0.265   3.3959   3.0681  -0.2976
 LTJ  H18  H  HNH2  0   0.415   4.9125   3.3006   1.0278
 LTJ  H19  H  HNH2  0   0.407   6.4076   2.6724   1.5741
 LTJ  H20  H  HNR5  0   0.406   4.5333  -1.5280   1.2965
 LTJ  H21  H  HCH2  0   0.242   0.4837   0.4033  -3.2324
 LTJ  H22  H  HCH2  0   0.202  -0.5454   1.7619  -2.7735
 LTJ  H23  H  HCH2  0   0.211  -1.4065   1.7387  -0.3068
 LTJ  H24  H  HCH2  0   0.257  -0.9696   0.3226   0.6549
 LTJ  H25  H  HNH1  0   0.396  -3.6330   1.3021   0.3711

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
 LTJ  F1   C2   single    1.349  0.020  1.349
 LTJ  C10  C11  single    1.520  0.020  1.520
 LTJ  C10  N1   single    1.455  0.020  1.455
 LTJ  C12  C11  single    1.524  0.020  1.524
 LTJ  C12  C13  single    1.527  0.020  1.527
 LTJ  C2   C3   aromatic  1.387  0.020  1.387
 LTJ  C2   C1   aromatic  1.388  0.020  1.388
 LTJ  C3   C4   aromatic  1.390  0.020  1.390
 LTJ  C14  N1   single    1.450  0.020  1.450
 LTJ  C14  C13  single    1.527  0.020  1.527
 LTJ  N1   C1   single    1.409  0.020  1.409
 LTJ  N2   C7   single    1.341  0.020  1.341
 LTJ  N4   C13  single    1.446  0.020  1.446
 LTJ  N4   C15  single    1.347  0.020  1.347
 LTJ  C1   C6   aromatic  1.403  0.020  1.403
 LTJ  C4   C7   single    1.487  0.020  1.487
 LTJ  C4   C5   aromatic  1.400  0.020  1.400
 LTJ  C18  C15  single    1.482  0.020  1.482
 LTJ  C18  C19  double    1.332  0.020  1.332
 LTJ  C15  O2   double    1.226  0.020  1.226
 LTJ  C7   O1   double    1.228  0.020  1.228
 LTJ  C20  C19  single    1.487  0.020  1.487
 LTJ  C6   C5   aromatic  1.418  0.020  1.418
 LTJ  C6   C9   aromatic  1.435  0.020  1.435
 LTJ  C5   N3   aromatic  1.358  0.020  1.358
 LTJ  C9   C17  single    1.493  0.020  1.493
 LTJ  C9   C8   aromatic  1.372  0.020  1.372
 LTJ  N3   C8   aromatic  1.370  0.020  1.370
 LTJ  C8   C16  single    1.486  0.020  1.486
 LTJ  C13  H1   single    0.970  0.020  1.090
 LTJ  C18  H2   single    0.930  0.020  1.080
 LTJ  C17  H3   single    0.970  0.020  1.090
 LTJ  C17  H4   single    0.970  0.020  1.090
 LTJ  C17  H5   single    0.970  0.020  1.090
 LTJ  C16  H6   single    0.970  0.020  1.090
 LTJ  C16  H7   single    0.970  0.020  1.090
 LTJ  C16  H8   single    0.970  0.020  1.090
 LTJ  C19  H9   single    0.930  0.020  1.080
 LTJ  C20  H10  single    0.970  0.020  1.090
 LTJ  C20  H11  single    0.970  0.020  1.090
 LTJ  C20  H12  single    0.970  0.020  1.090
 LTJ  C11  H13  single    0.970  0.020  1.090
 LTJ  C11  H14  single    0.970  0.020  1.090
 LTJ  C12  H15  single    0.970  0.020  1.090
 LTJ  C12  H16  single    0.970  0.020  1.090
 LTJ  C3   H17  single    0.930  0.020  1.080
 LTJ  N2   H18  single    0.860  0.020  1.020
 LTJ  N2   H19  single    0.860  0.020  1.020
 LTJ  N3   H20  single    0.860  0.020  1.020
 LTJ  C10  H21  single    0.970  0.020  1.090
 LTJ  C10  H22  single    0.970  0.020  1.090
 LTJ  C14  H23  single    0.970  0.020  1.090
 LTJ  C14  H24  single    0.970  0.020  1.090
 LTJ  N4   H25  single    0.860  0.020  1.020

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
 LTJ  H1   C13  N4   107.89  3.000
 LTJ  H1   C13  C14  107.94  3.000
 LTJ  N4   C13  C14  109.01  3.000
 LTJ  H1   C13  C12  108.87  3.000
 LTJ  N4   C13  C12  112.24  3.000
 LTJ  C14  C13  C12  110.77  3.000
 LTJ  H2   C18  C19  120.17  3.000
 LTJ  H2   C18  C15  117.99  3.000
 LTJ  C19  C18  C15  121.83  3.000
 LTJ  H5   C17  H4   107.20  3.000
 LTJ  H5   C17  H3   106.79  3.000
 LTJ  H4   C17  H3   107.47  3.000
 LTJ  H5   C17  C9   112.14  3.000
 LTJ  H4   C17  C9   111.07  3.000
 LTJ  H3   C17  C9   111.90  3.000
 LTJ  H8   C16  H7   107.76  3.000
 LTJ  H8   C16  H6   107.33  3.000
 LTJ  H7   C16  H6   107.71  3.000
 LTJ  H8   C16  C8   111.24  3.000
 LTJ  H7   C16  C8   111.38  3.000
 LTJ  H6   C16  C8   111.22  3.000
 LTJ  O2   C15  N4   122.90  3.000
 LTJ  O2   C15  C18  123.04  3.000
 LTJ  N4   C15  C18  114.06  3.000
 LTJ  H9   C19  C20  116.48  3.000
 LTJ  H9   C19  C18  118.66  3.000
 LTJ  C20  C19  C18  124.85  3.000
 LTJ  H12  C20  H11  108.50  3.000
 LTJ  H12  C20  H10  108.41  3.000
 LTJ  H11  C20  H10  106.31  3.000
 LTJ  H12  C20  C19  112.32  3.000
 LTJ  H11  C20  C19  110.62  3.000
 LTJ  H10  C20  C19  110.46  3.000
 LTJ  H14  C11  H13  107.25  3.000
 LTJ  H14  C11  C10  109.49  3.000
 LTJ  H13  C11  C10  109.37  3.000
 LTJ  H14  C11  C12  110.31  3.000
 LTJ  H13  C11  C12  109.95  3.000
 LTJ  C10  C11  C12  110.41  3.000
 LTJ  H16  C12  H15  107.01  3.000
 LTJ  H16  C12  C11  109.60  3.000
 LTJ  H15  C12  C11  110.90  3.000
 LTJ  H16  C12  C13  108.99  3.000
 LTJ  H15  C12  C13  109.77  3.000
 LTJ  C11  C12  C13  110.49  3.000
 LTJ  C6   C1   C2   116.16  3.000
 LTJ  C6   C1   N1   120.08  3.000
 LTJ  C2   C1   N1   123.75  3.000
 LTJ  C14  N1   C10  113.99  3.000
 LTJ  C14  N1   C1   114.48  3.000
 LTJ  C10  N1   C1   117.63  3.000
 LTJ  F1   C2   C3   117.06  3.000
 LTJ  C3   C2   C1   124.09  3.000
 LTJ  F1   C2   C1   118.85  3.000
 LTJ  H17  C3   C4   121.92  3.000
 LTJ  H17  C3   C2   117.47  3.000
 LTJ  C4   C3   C2   120.61  3.000
 LTJ  C7   C4   C5   119.99  3.000
 LTJ  C5   C4   C3   116.56  3.000
 LTJ  C7   C4   C3   123.44  3.000
 LTJ  N3   C5   C6   106.96  3.000
 LTJ  N3   C5   C4   130.44  3.000
 LTJ  C6   C5   C4   122.60  3.000
 LTJ  C9   C6   C5   107.26  3.000
 LTJ  C9   C6   C1   132.77  3.000
 LTJ  C5   C6   C1   119.97  3.000
 LTJ  N2   C7   O1   121.98  3.000
 LTJ  O1   C7   C4   120.68  3.000
 LTJ  N2   C7   C4   117.34  3.000
 LTJ  H19  N2   H18  116.63  3.000
 LTJ  H19  N2   C7   119.21  3.000
 LTJ  H18  N2   C7   123.29  3.000
 LTJ  H20  N3   C8   125.89  3.000
 LTJ  H20  N3   C5   123.96  3.000
 LTJ  C8   N3   C5   110.11  3.000
 LTJ  C9   C8   N3   109.58  3.000
 LTJ  N3   C8   C16  119.63  3.000
 LTJ  C9   C8   C16  130.78  3.000
 LTJ  C8   C9   C6   106.09  3.000
 LTJ  C8   C9   C17  126.37  3.000
 LTJ  C6   C9   C17  127.53  3.000
 LTJ  H22  C10  H21  107.37  3.000
 LTJ  H22  C10  N1   112.75  3.000
 LTJ  H21  C10  N1   108.52  3.000
 LTJ  H22  C10  C11  108.63  3.000
 LTJ  H21  C10  C11  110.33  3.000
 LTJ  N1   C10  C11  109.23  3.000
 LTJ  H24  C14  H23  107.17  3.000
 LTJ  H24  C14  N1   109.00  3.000
 LTJ  H23  C14  N1   111.92  3.000
 LTJ  H24  C14  C13  109.29  3.000
 LTJ  H23  C14  C13  109.28  3.000
 LTJ  N1   C14  C13  110.11  3.000
 LTJ  H25  N4   C15  118.22  3.000
 LTJ  H25  N4   C13  117.36  3.000
 LTJ  C15  N4   C13  123.90  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
 LTJ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 LTJ  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 LTJ  CONST_03  N3   C5   C6   C1    180.00   0.0  0
 LTJ  CONST_04  C8   C9   C6   C1    180.00   0.0  0
 LTJ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 LTJ  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 LTJ  CONST_07  C9   C6   C1   C2    180.00   0.0  0
 LTJ  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 LTJ  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 LTJ  CONST_10  N3   C5   C4   C3    180.00   0.0  0
 LTJ  CONST_11  C9   C6   C5   C4    180.00   0.0  0
 LTJ  CONST_12  C8   N3   C5   C4    180.00   0.0  0
 LTJ  CONST_13  C8   C9   C6   C5      0.00   0.0  0
 LTJ  CONST_14  C9   C8   N3   C5      0.00   0.0  0
 LTJ  CONST_15  C8   N3   C5   C6      0.00   0.0  0
 LTJ  CONST_16  N3   C8   C9   C6      0.00   0.0  0
 LTJ  CONST_17  C9   C6   C5   N3      0.00   0.0  0
 LTJ  CONST_18  C3   C2   C1   N1    180.00   0.0  0
 LTJ  CONST_19  C5   C6   C1   N1    180.00   0.0  0
 LTJ  CONST_20  C9   C6   C1   N1      0.00   0.0  0
 LTJ  CONST_21  C1   C6   C9   C17     0.00   0.0  0
 LTJ  CONST_22  C5   C6   C9   C17   180.00   0.0  0
 LTJ  CONST_23  N3   C8   C9   C17   180.00   0.0  0
 LTJ  CONST_24  C6   C9   C8   C16   180.00   0.0  0
 LTJ  CONST_25  C5   N3   C8   C16   180.00   0.0  0
 LTJ  CONST_26  F1   C2   C1   N1      0.00   0.0  0
 LTJ  CONST_27  C7   C4   C3   C2    180.00   0.0  0
 LTJ  CONST_28  F1   C2   C3   C4    180.00   0.0  0
 LTJ  CONST_29  F1   C2   C1   C6    180.00   0.0  0
 LTJ  CONST_30  C7   C4   C5   C6    180.00   0.0  0
 LTJ  CONST_31  N3   C5   C4   C7      0.00   0.0  0
 LTJ  CONST_32  H17  C3   C2   C1    180.00   0.0  0
 LTJ  CONST_33  H20  N3   C5   C4      0.00   0.0  0
 LTJ  CONST_34  C18  C15  N4   C13   180.00   0.0  0
 LTJ  CONST_35  O2   C15  N4   C13     0.00   0.0  0
 LTJ  CONST_36  H18  N2   C7   C4      0.00   0.0  0
 LTJ  CONST_37  H19  N2   C7   C4    180.00   0.0  0
 LTJ  CONST_38  H25  N4   C15  C18     0.00   0.0  0
 LTJ  Var_01    C10  C11  C12  C13   -55.07  30.0  1
 LTJ  Var_02    C10  N1   C14  C13    58.89  30.0  1
 LTJ  Var_03    C14  N1   C10  C11   -60.33  30.0  1
 LTJ  Var_04    N1   C10  C11  C12    57.10  30.0  1
 LTJ  Var_05    N2   C7   C4   C3     12.62  30.0  2
 LTJ  Var_06    H3   C17  C9   C6     57.71  30.0  2
 LTJ  Var_07    H6   C16  C8   N3     54.70  30.0  2
 LTJ  Var_08    C20  C19  C18  C15  -179.57   0.0  2
 LTJ  Var_09    N4   C15  C18  C19   176.96  30.0  2
 LTJ  Var_10    H10  C20  C19  C18   119.32  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
 LTJ  chir_01  C13  C12  C14  N4  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
 LTJ  plan-1  C17  0.020
 LTJ  plan-1  C16  0.020
 LTJ  plan-1  C1   0.020
 LTJ  plan-1  N1   0.020
 LTJ  plan-1  C2   0.020
 LTJ  plan-1  C3   0.020
 LTJ  plan-1  C4   0.020
 LTJ  plan-1  C5   0.020
 LTJ  plan-1  C6   0.020
 LTJ  plan-1  C7   0.020
 LTJ  plan-1  F1   0.020
 LTJ  plan-1  N3   0.020
 LTJ  plan-1  C8   0.020
 LTJ  plan-1  C9   0.020
 LTJ  plan-1  H17  0.020
 LTJ  plan-1  H20  0.020
 LTJ  plan-2  C4   0.020
 LTJ  plan-2  C7   0.020
 LTJ  plan-2  O1   0.020
 LTJ  plan-2  N2   0.020
 LTJ  plan-2  H18  0.020
 LTJ  plan-2  H19  0.020
 LTJ  plan-3  C13  0.020
 LTJ  plan-3  C18  0.020
 LTJ  plan-3  C15  0.020
 LTJ  plan-3  N4   0.020
 LTJ  plan-3  O2   0.020
 LTJ  plan-3  H25  0.020
 LTJ  plan-4  C18  0.020
 LTJ  plan-4  C15  0.020
 LTJ  plan-4  C19  0.020
 LTJ  plan-4  C20  0.020
 LTJ  plan-4  H2   0.020
 LTJ  plan-4  H9   0.020

