# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 22:35:03 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (2,3-dihydro-1H-indol-1-yl)(1H-1,2,3-triazol-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(n1ccnn1)N2CCc3ccccc23
#
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
 KOK  KOK  (2,3-dihydro-1H-indol-1-yl)(1H-1,2,3-triazol-1-yl)methanone  ligand  26  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KOK
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
 KOK  OAB  O  O     0  -0.446  -0.6514   1.9665   0.4758
 KOK  CAA  C  C     0   0.738  -0.8352   0.8204   0.1370
 KOK  NAG  N  NR5   0  -0.604   0.1088  -0.1039  -0.0854
 KOK  CAF  C  CH2   0  -0.297  -0.0692  -1.5702  -0.1530
 KOK  CAE  C  CH2   0  -0.492   1.2702  -2.1273   0.3360
 KOK  CAD  C  CR56  0  -0.013   2.2099  -0.9794   0.1252
 KOK  CAC  C  CR56  0   0.415   1.4892   0.1929  -0.0780
 KOK  CAK  C  CR16  0  -0.282   2.1262   1.4081  -0.2812
 KOK  CAJ  C  CR16  0  -0.266   3.5179   1.4190  -0.2712
 KOK  CAI  C  CR16  0  -0.256   4.2479   0.2563  -0.0632
 KOK  CAH  C  CR16  0  -0.322   3.5912  -0.9544   0.1375
 KOK  H2   H  HCH2  0   0.275  -0.9036  -1.8885   0.4653
 KOK  H3   H  HCH2  0   0.271   1.2268  -2.3965   1.3942
 KOK  H4   H  HCR6  0   0.273   1.5817   2.3232  -0.4537
 KOK  H5   H  HCR6  0   0.261   4.0348   2.3555  -0.4355
 KOK  H6   H  HCR6  0   0.258   5.3292   0.2910  -0.0615
 KOK  H7   H  HCR6  0   0.258   4.1546  -1.8648   0.2993
 KOK  N1   N  NR5   0  -0.370  -2.1812   0.3796  -0.0489
 KOK  C2   C  CR15  0  -0.038  -3.2655   0.8576   0.6024
 KOK  C1   C  CR15  0  -0.179  -4.3105   0.2364  -0.0124
 KOK  N3   N  N     0  -0.267  -3.8166  -0.5519  -1.0002
 KOK  N2   N  N     0  -0.079  -2.5423  -0.4596  -1.0210
 KOK  H1   H  HCR5  0   0.326  -3.2088   1.5560   1.4183
 KOK  H8   H  HCR5  0   0.290  -5.3645   0.3095   0.1951
 KOK  H9   H  HCH2  0   0.275  -0.2638  -1.8660  -1.1822
 KOK  H10  H  HCH2  0   0.275   1.5547  -3.0211  -0.2178

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
 KOK  CAF  CAE  single    1.531  0.020  1.531
 KOK  CAF  NAG  single    1.479  0.020  1.479
 KOK  CAE  CAD  single    1.498  0.020  1.498
 KOK  NAG  CAA  single    1.340  0.020  1.340
 KOK  NAG  CAC  single    1.412  0.020  1.412
 KOK  CAA  OAB  double    1.209  0.020  1.209
 KOK  CAD  CAC  aromatic  1.391  0.020  1.391
 KOK  CAD  CAH  aromatic  1.382  0.020  1.382
 KOK  CAC  CAK  aromatic  1.387  0.020  1.387
 KOK  CAH  CAI  aromatic  1.392  0.020  1.392
 KOK  CAK  CAJ  aromatic  1.392  0.020  1.392
 KOK  CAI  CAJ  aromatic  1.389  0.020  1.389
 KOK  CAF  H2   single    0.970  0.020  1.090
 KOK  CAE  H3   single    0.970  0.020  1.090
 KOK  CAK  H4   single    0.930  0.020  1.080
 KOK  CAJ  H5   single    0.930  0.020  1.080
 KOK  CAI  H6   single    0.930  0.020  1.080
 KOK  CAH  H7   single    0.930  0.020  1.080
 KOK  CAA  N1   single    1.428  0.020  1.428
 KOK  N1   C2   aromatic  1.352  0.020  1.352
 KOK  C2   C1   aromatic  1.362  0.020  1.362
 KOK  C1   N3   aromatic  1.357  0.020  1.357
 KOK  N3   N2   aromatic  1.278  0.020  1.278
 KOK  N2   N1   aromatic  1.334  0.020  1.334
 KOK  C2   H1   single    0.930  0.020  1.080
 KOK  C1   H8   single    0.930  0.020  1.080
 KOK  CAF  H9   single    0.970  0.020  1.090
 KOK  CAE  H10  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
 KOK  N1   CAA  NAG  115.43  3.000
 KOK  N1   CAA  OAB  118.18  3.000
 KOK  NAG  CAA  OAB  126.39  3.000
 KOK  CAC  NAG  CAF  109.05  3.000
 KOK  CAC  NAG  CAA  122.89  3.000
 KOK  CAF  NAG  CAA  127.37  3.000
 KOK  H9   CAF  H2   108.74  3.000
 KOK  H9   CAF  CAE  111.07  3.000
 KOK  H2   CAF  CAE  112.56  3.000
 KOK  H9   CAF  NAG  109.52  3.000
 KOK  H2   CAF  NAG  110.92  3.000
 KOK  CAE  CAF  NAG  103.94  3.000
 KOK  H10  CAE  H3   107.49  3.000
 KOK  H10  CAE  CAD  113.16  3.000
 KOK  H3   CAE  CAD  110.47  3.000
 KOK  H10  CAE  CAF  111.40  3.000
 KOK  H3   CAE  CAF  111.36  3.000
 KOK  CAD  CAE  CAF  103.00  3.000
 KOK  CAH  CAD  CAC  120.27  3.000
 KOK  CAH  CAD  CAE  129.76  3.000
 KOK  CAC  CAD  CAE  109.95  3.000
 KOK  CAK  CAC  CAD  121.45  3.000
 KOK  CAK  CAC  NAG  129.23  3.000
 KOK  CAD  CAC  NAG  109.28  3.000
 KOK  H4   CAK  CAJ  119.96  3.000
 KOK  H4   CAK  CAC  122.33  3.000
 KOK  CAJ  CAK  CAC  117.71  3.000
 KOK  H5   CAJ  CAI  119.75  3.000
 KOK  H5   CAJ  CAK  118.90  3.000
 KOK  CAI  CAJ  CAK  121.35  3.000
 KOK  H6   CAI  CAH  119.95  3.000
 KOK  H6   CAI  CAJ  119.92  3.000
 KOK  CAH  CAI  CAJ  120.13  3.000
 KOK  H7   CAH  CAI  120.49  3.000
 KOK  H7   CAH  CAD  120.42  3.000
 KOK  CAI  CAH  CAD  119.09  3.000
 KOK  N2   N1   C2   110.87  3.000
 KOK  N2   N1   CAA  122.96  3.000
 KOK  C2   N1   CAA  125.72  3.000
 KOK  H1   C2   C1   132.76  3.000
 KOK  H1   C2   N1   123.55  3.000
 KOK  C1   C2   N1   103.68  3.000
 KOK  H8   C1   N3   122.42  3.000
 KOK  H8   C1   C2   129.26  3.000
 KOK  N3   C1   C2   108.32  3.000
 KOK  N2   N3   C1   109.44  3.000
 KOK  N3   N2   N1   107.67  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
 KOK  CONST_01  CAJ  CAK  CAC  CAD    0.00   0.0  0
 KOK  CONST_02  CAJ  CAI  CAH  CAD    0.00   0.0  0
 KOK  CONST_03  CAI  CAH  CAD  CAC    0.00   0.0  0
 KOK  CONST_04  CAI  CAJ  CAK  CAC    0.00   0.0  0
 KOK  CONST_05  CAH  CAD  CAC  CAK    0.00   0.0  0
 KOK  CONST_06  CAH  CAI  CAJ  CAK    0.00   0.0  0
 KOK  CONST_07  N3   C1   C2   N1     0.00   0.0  0
 KOK  CONST_08  C1   N3   N2   N1     0.00   0.0  0
 KOK  CONST_09  N3   N2   N1   C2     0.00   0.0  0
 KOK  CONST_10  N2   N3   C1   C2     0.00   0.0  0
 KOK  CONST_11  N2   N1   C2   C1     0.00   0.0  0
 KOK  CONST_12  C1   C2   N1   CAA  180.00   0.0  0
 KOK  CONST_13  N3   N2   N1   CAA  180.00   0.0  0
 KOK  CONST_17  N1   CAA  NAG  CAC  180.00   0.0  0
 KOK  CONST_18  H4   CAK  CAC  NAG    0.00   0.0  0
 KOK  CONST_19  H7   CAH  CAD  CAE    0.00   0.0  0
 KOK  CONST_20  H6   CAI  CAH  CAD  180.00   0.0  0
 KOK  CONST_21  H5   CAJ  CAK  CAC  180.00   0.0  0
 KOK  CONST_22  H8   C1   C2   N1   180.00   0.0  0
 KOK  CONST_23  H1   C2   C1   N3   180.00   0.0  0
 KOK  CONST_25  CAC  NAG  CAA  OAB    0.00   0.0  0
 KOK  Var_01    CAD  CAE  CAF  NAG  -20.97  30.0  1
 KOK  Var_02    CAC  CAD  CAE  CAF   15.29  30.0  1
 KOK  Var_03    CAD  CAC  NAG  CAF  -11.46  30.0  1
 KOK  Var_04    CAC  NAG  CAF  CAE   20.51  30.0  1

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
 KOK  plan-1  NAG  0.020
 KOK  plan-1  CAE  0.020
 KOK  plan-1  CAD  0.020
 KOK  plan-1  CAC  0.020
 KOK  plan-1  CAK  0.020
 KOK  plan-1  CAJ  0.020
 KOK  plan-1  CAI  0.020
 KOK  plan-1  CAH  0.020
 KOK  plan-1  H4   0.020
 KOK  plan-1  H5   0.020
 KOK  plan-1  H6   0.020
 KOK  plan-1  H7   0.020
 KOK  plan-2  OAB  0.020
 KOK  plan-2  CAA  0.020
 KOK  plan-2  NAG  0.020
 KOK  plan-2  CAF  0.020
 KOK  plan-2  CAC  0.020
 KOK  plan-2  N1   0.020
 KOK  plan-2  C2   0.020
 KOK  plan-2  C1   0.020
 KOK  plan-2  N3   0.020
 KOK  plan-2  N2   0.020
 KOK  plan-2  H1   0.020
 KOK  plan-2  H8   0.020

