# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:33:03 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-[1-(piperidin-4-yl)-1H-indol-5-yl]thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=C(Nc1ccc2n(ccc2c1)C3CCNCC3)c4sccc4
#
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
 F2J  F2J  N-[1-(piperidin-4-yl)-1H-indol-5-yl]thiophene-2-carboximidamide  ligand  43  23  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F2J
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
 F2J  C02  C  CR5   0  -0.234   4.6636  -0.6308  -0.1884
 F2J  C03  C  CR15  0  -0.203   5.6585  -1.0608  -1.0194
 F2J  C04  C  CR15  0  -0.177   6.9531  -0.8382  -0.4877
 F2J  C05  C  CR15  0  -0.461   6.9191  -0.2500   0.7416
 F2J  C06  C  C     0   0.364   3.2142  -0.7164  -0.4272
 F2J  C11  C  CR6   0   0.287   1.0655   0.2756   0.1995
 F2J  C12  C  CR16  0  -0.315   0.2958  -0.8136   0.6535
 F2J  C13  C  CR16  0  -0.304  -1.0827  -0.7846   0.6136
 F2J  C14  C  CR56  0   0.366  -1.7007   0.3691   0.1317
 F2J  C15  C  CR56  0   0.056  -0.9439   1.4770  -0.3130
 F2J  C16  C  CR16  0  -0.411   0.4530   1.4151  -0.2857
 F2J  C17  C  CR15  0  -0.430  -1.8777   2.4663  -0.7399
 F2J  C18  C  CR15  0  -0.023  -3.1201   1.9373  -0.5423
 F2J  C22  C  CH2   0  -0.321  -5.9500  -1.6587  -0.6943
 F2J  C23  C  CH2   0  -0.436  -4.7699  -0.7435  -1.0217
 F2J  C24  C  CH1   0  -0.101  -4.1483  -0.2036   0.2644
 F2J  C25  C  CH2   0  -0.443  -5.2102   0.4656   1.1327
 F2J  C26  C  CH2   0  -0.322  -6.3696  -0.5031   1.3726
 F2J  N07  N  NH1   0  -0.751   2.4736   0.2073   0.2779
 F2J  N08  N  N     0  -0.631   2.7804  -1.6172  -1.2177
 F2J  N19  N  NR5   0  -0.535  -3.0269   0.6804  -0.0091
 F2J  N21  N  NH1   0  -0.573  -6.9538  -1.0418   0.1565
 F2J  S01  S  S2    0   0.234   5.3163   0.0360   1.2622
 F2J  H1   H  HCR5  0   0.267   5.4632  -1.5106  -1.9820
 F2J  H2   H  HCR5  0   0.272   7.8692  -1.1002  -0.9966
 F2J  H3   H  HCR5  0   0.302   7.7516   0.0232   1.3716
 F2J  H4   H  HCR6  0   0.268   0.7963  -1.6860   1.0531
 F2J  H5   H  HCR6  0   0.266  -1.6483  -1.6376   0.9647
 F2J  H6   H  HCR6  0   0.255   1.0486   2.2477  -0.6417
 F2J  H7   H  HCR5  0   0.248  -1.6581   3.4423  -1.1422
 F2J  H8   H  HCR5  0   0.285  -4.0822   2.3782  -0.7500
 F2J  H10  H  HCH2  0   0.221  -5.5806  -2.5573  -0.1882
 F2J  H11  H  HCH2  0   0.241  -4.0202  -1.2848  -1.6044
 F2J  H12  H  HCH2  0   0.226  -5.1194   0.0920  -1.6378
 F2J  H13  H  HCH1  0   0.256  -3.7453  -1.0480   0.8307
 F2J  H14  H  HCH2  0   0.245  -4.7748   0.7783   2.0849
 F2J  H15  H  HCH2  0   0.227  -5.5913   1.3651   0.6394
 F2J  H16  H  HCH2  0   0.221  -6.0147  -1.3431   1.9802
 F2J  H17  H  HCH2  0   0.244  -7.1506  -0.0094   1.9531
 F2J  H18  H  HNH1  0   0.400   2.9343   1.0815   0.4833
 F2J  H19  H  H     0   0.337   1.7770  -1.5395  -1.3597
 F2J  H20  H  HNH1  0   0.341  -7.4033  -0.2914  -0.3560
 F2J  H9   H  HCH2  0   0.243  -6.4258  -1.9961  -1.6167

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
 F2J  C04  C05  aromatic  1.363  0.020  1.363
 F2J  C04  C03  aromatic  1.417  0.020  1.417
 F2J  C05  S01  aromatic  1.709  0.020  1.709
 F2J  C03  C02  aromatic  1.366  0.020  1.366
 F2J  S01  C02  aromatic  1.725  0.020  1.725
 F2J  C02  C06  single    1.471  0.020  1.471
 F2J  N08  C06  double    1.275  0.020  1.275
 F2J  C06  N07  single    1.378  0.020  1.378
 F2J  N07  C11  single    1.412  0.020  1.412
 F2J  C12  C11  aromatic  1.409  0.020  1.409
 F2J  C12  C13  aromatic  1.379  0.020  1.379
 F2J  C11  C16  aromatic  1.382  0.020  1.382
 F2J  C13  C14  aromatic  1.395  0.020  1.395
 F2J  C16  C15  aromatic  1.399  0.020  1.399
 F2J  C14  C15  aromatic  1.413  0.020  1.413
 F2J  C14  N19  aromatic  1.369  0.020  1.369
 F2J  C15  C17  aromatic  1.426  0.020  1.426
 F2J  N19  C24  single    1.454  0.020  1.454
 F2J  N19  C18  aromatic  1.368  0.020  1.368
 F2J  C24  C23  single    1.527  0.020  1.527
 F2J  C24  C25  single    1.526  0.020  1.526
 F2J  C17  C18  aromatic  1.365  0.020  1.365
 F2J  C23  C22  single    1.529  0.020  1.529
 F2J  C22  N21  single    1.453  0.020  1.453
 F2J  C25  C26  single    1.530  0.020  1.530
 F2J  C26  N21  single    1.453  0.020  1.453
 F2J  C03  H1   single    0.930  0.020  1.080
 F2J  C04  H2   single    0.930  0.020  1.080
 F2J  C05  H3   single    0.930  0.020  1.080
 F2J  C12  H4   single    0.930  0.020  1.080
 F2J  C13  H5   single    0.930  0.020  1.080
 F2J  C16  H6   single    0.930  0.020  1.080
 F2J  C17  H7   single    0.930  0.020  1.080
 F2J  C18  H8   single    0.930  0.020  1.080
 F2J  C22  H9   single    0.970  0.020  1.090
 F2J  C22  H10  single    0.970  0.020  1.090
 F2J  C23  H11  single    0.970  0.020  1.090
 F2J  C23  H12  single    0.970  0.020  1.090
 F2J  C24  H13  single    0.970  0.020  1.090
 F2J  C25  H14  single    0.970  0.020  1.090
 F2J  C25  H15  single    0.970  0.020  1.090
 F2J  C26  H16  single    0.970  0.020  1.090
 F2J  C26  H17  single    0.970  0.020  1.090
 F2J  N07  H18  single    0.890  0.020  1.040
 F2J  N08  H19  single    0.890  0.020  1.040
 F2J  N21  H20  single    0.890  0.020  1.040

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
 F2J  S01  C02  C06  122.13  3.000
 F2J  C06  C02  C03  126.90  3.000
 F2J  S01  C02  C03  110.96  3.000
 F2J  H1   C03  C04  124.39  3.000
 F2J  H1   C03  C02  122.79  3.000
 F2J  C04  C03  C02  112.81  3.000
 F2J  H2   C04  C05  123.41  3.000
 F2J  H2   C04  C03  124.05  3.000
 F2J  C05  C04  C03  112.54  3.000
 F2J  H3   C05  S01  120.22  3.000
 F2J  H3   C05  C04  128.05  3.000
 F2J  S01  C05  C04  111.73  3.000
 F2J  N08  C06  N07  127.46  3.000
 F2J  N07  C06  C02  114.04  3.000
 F2J  N08  C06  C02  118.49  3.000
 F2J  N07  C11  C16  120.10  3.000
 F2J  C16  C11  C12  120.57  3.000
 F2J  N07  C11  C12  119.31  3.000
 F2J  H4   C12  C13  119.33  3.000
 F2J  H4   C12  C11  119.31  3.000
 F2J  C13  C12  C11  121.36  3.000
 F2J  H5   C13  C14  122.18  3.000
 F2J  H5   C13  C12  119.76  3.000
 F2J  C14  C13  C12  118.05  3.000
 F2J  N19  C14  C15  107.94  3.000
 F2J  N19  C14  C13  130.74  3.000
 F2J  C15  C14  C13  121.32  3.000
 F2J  C17  C15  C16  133.68  3.000
 F2J  C17  C15  C14  106.70  3.000
 F2J  C16  C15  C14  119.60  3.000
 F2J  H6   C16  C15  120.56  3.000
 F2J  H6   C16  C11  120.35  3.000
 F2J  C15  C16  C11  119.09  3.000
 F2J  H7   C17  C18  126.18  3.000
 F2J  H7   C17  C15  127.33  3.000
 F2J  C18  C17  C15  106.49  3.000
 F2J  H8   C18  N19  120.75  3.000
 F2J  H8   C18  C17  128.74  3.000
 F2J  N19  C18  C17  110.52  3.000
 F2J  H10  C22  H9   106.49  3.000
 F2J  H10  C22  N21  108.10  3.000
 F2J  H9   C22  N21  108.96  3.000
 F2J  H10  C22  C23  109.25  3.000
 F2J  H9   C22  C23  109.91  3.000
 F2J  N21  C22  C23  113.85  3.000
 F2J  H12  C23  H11  107.26  3.000
 F2J  H12  C23  C24  109.51  3.000
 F2J  H11  C23  C24  110.17  3.000
 F2J  H12  C23  C22  109.32  3.000
 F2J  H11  C23  C22  110.31  3.000
 F2J  C24  C23  C22  110.21  3.000
 F2J  H13  C24  N19  106.42  3.000
 F2J  H13  C24  C25  107.47  3.000
 F2J  N19  C24  C25  112.15  3.000
 F2J  H13  C24  C23  108.25  3.000
 F2J  C25  C24  C23  110.54  3.000
 F2J  N19  C24  C23  111.75  3.000
 F2J  H15  C25  H14  107.25  3.000
 F2J  H15  C25  C26  109.10  3.000
 F2J  H14  C25  C26  110.28  3.000
 F2J  H15  C25  C24  110.26  3.000
 F2J  H14  C25  C24  110.12  3.000
 F2J  C26  C25  C24  109.81  3.000
 F2J  H17  C26  H16  106.48  3.000
 F2J  H17  C26  N21  108.99  3.000
 F2J  H16  C26  N21  108.07  3.000
 F2J  H17  C26  C25  109.83  3.000
 F2J  H16  C26  C25  109.08  3.000
 F2J  N21  C26  C25  114.10  3.000
 F2J  H18  N07  C11  115.13  3.000
 F2J  H18  N07  C06  116.06  3.000
 F2J  C11  N07  C06  122.68  3.000
 F2J  H19  N08  C06  111.63  3.000
 F2J  C24  N19  C18  125.40  3.000
 F2J  C18  N19  C14  108.35  3.000
 F2J  C24  N19  C14  126.11  3.000
 F2J  H20  N21  C26  109.09  3.000
 F2J  H20  N21  C22  108.94  3.000
 F2J  C26  N21  C22  111.70  3.000
 F2J  C05  S01  C02   91.95  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
 F2J  CONST_01  C05  C04  C03  C02    0.00   0.0  0
 F2J  CONST_02  C04  C05  S01  C02    0.00   0.0  0
 F2J  CONST_03  S01  C05  C04  C03    0.00   0.0  0
 F2J  CONST_04  C05  S01  C02  C03    0.00   0.0  0
 F2J  CONST_05  S01  C02  C03  C04    0.00   0.0  0
 F2J  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 F2J  CONST_07  C14  C15  C16  C11    0.00   0.0  0
 F2J  CONST_08  C17  C15  C16  C11  180.00   0.0  0
 F2J  CONST_09  C15  C16  C11  C12    0.00   0.0  0
 F2J  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 F2J  CONST_11  N19  C14  C13  C12  180.00   0.0  0
 F2J  CONST_12  C16  C11  C12  C13    0.00   0.0  0
 F2J  CONST_13  C16  C15  C14  C13    0.00   0.0  0
 F2J  CONST_14  C17  C15  C14  C13  180.00   0.0  0
 F2J  CONST_15  C18  N19  C14  C13  180.00   0.0  0
 F2J  CONST_16  C18  C17  C15  C14    0.00   0.0  0
 F2J  CONST_17  C17  C18  N19  C14    0.00   0.0  0
 F2J  CONST_18  C18  N19  C14  C15    0.00   0.0  0
 F2J  CONST_19  N19  C18  C17  C15    0.00   0.0  0
 F2J  CONST_20  N19  C14  C15  C16  180.00   0.0  0
 F2J  CONST_21  C18  C17  C15  C16  180.00   0.0  0
 F2J  CONST_22  N19  C14  C15  C17    0.00   0.0  0
 F2J  CONST_23  C24  N19  C14  C13    0.00   0.0  0
 F2J  CONST_24  C24  N19  C14  C15  180.00   0.0  0
 F2J  CONST_25  C24  N19  C18  C17  180.00   0.0  0
 F2J  CONST_26  C06  C02  C03  C04  180.00   0.0  0
 F2J  CONST_27  C06  C02  S01  C05  180.00   0.0  0
 F2J  CONST_28  N07  C11  C12  C13  180.00   0.0  0
 F2J  CONST_29  N07  C11  C16  C15  180.00   0.0  0
 F2J  CONST_30  H2   C04  C03  C02  180.00   0.0  0
 F2J  CONST_31  H3   C05  S01  C02  180.00   0.0  0
 F2J  CONST_32  H1   C03  C04  C05  180.00   0.0  0
 F2J  CONST_33  H5   C13  C12  C11  180.00   0.0  0
 F2J  CONST_34  H6   C16  C11  C12  180.00   0.0  0
 F2J  CONST_35  H4   C12  C13  C14  180.00   0.0  0
 F2J  CONST_36  H7   C17  C15  C14  180.00   0.0  0
 F2J  CONST_37  H8   C18  N19  C14  180.00   0.0  0
 F2J  CONST_38  C11  N07  C06  C02  180.00   0.0  0
 F2J  CONST_42  N08  C06  N07  C11    0.00   0.0  0
 F2J  CONST_43  H19  N08  C06  C02  180.00   0.0  0
 F2J  Var_01    C25  C26  N21  C22   54.09  30.0  1
 F2J  Var_02    C26  N21  C22  C23  -53.74  30.0  1
 F2J  Var_03    N21  C22  C23  C24   54.23  30.0  1
 F2J  Var_04    N21  C26  C25  C24  -54.60  30.0  1
 F2J  Var_05    N08  C06  C02  C03   24.72  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
 F2J  chir_01  C24  N19  C23  C25  positiv

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
 F2J  plan-1  C02  0.020
 F2J  plan-1  C03  0.020
 F2J  plan-1  C04  0.020
 F2J  plan-1  C05  0.020
 F2J  plan-1  C06  0.020
 F2J  plan-1  S01  0.020
 F2J  plan-1  H1   0.020
 F2J  plan-1  H2   0.020
 F2J  plan-1  H3   0.020
 F2J  plan-2  C11  0.020
 F2J  plan-2  C12  0.020
 F2J  plan-2  C13  0.020
 F2J  plan-2  C14  0.020
 F2J  plan-2  C15  0.020
 F2J  plan-2  C16  0.020
 F2J  plan-2  C17  0.020
 F2J  plan-2  C18  0.020
 F2J  plan-2  C24  0.020
 F2J  plan-2  N07  0.020
 F2J  plan-2  N19  0.020
 F2J  plan-2  H4   0.020
 F2J  plan-2  H5   0.020
 F2J  plan-2  H6   0.020
 F2J  plan-2  H7   0.020
 F2J  plan-2  H8   0.020
 F2J  plan-3  C02  0.020
 F2J  plan-3  C06  0.020
 F2J  plan-3  C11  0.020
 F2J  plan-3  N07  0.020
 F2J  plan-3  N08  0.020
 F2J  plan-3  H18  0.020
 F2J  plan-3  H19  0.020

