# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:25:37 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (3Z)-5-amino-3-[(3,5-dimethyl-1H-pyrrol-2-yl)methylidene]-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(\C=C\2C(=O)Nc3ccc(N)cc\23)c(C)c1
#
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
 X2K  X2K  (3Z)-5-amino-3-[(3,5-dimethyl-1H-pyrrol-2-yl)methylidene]-1,3-dihydro-2H-indol-2-one  ligand  34  19  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X2K
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
 X2K  CAB   C  CH3   0  -0.755   2.5735   3.0710   0.0827
 X2K  CAN   C  CR5   0   0.047   2.9176   1.6209   0.0128
 X2K  CAH   C  CR15  0  -0.428   4.2013   1.0684  -0.0323
 X2K  CAL   C  CR5   0   0.341   4.0726  -0.3158  -0.1143
 X2K  CAA   C  CH3   0  -0.743   5.1228  -1.3645  -0.1780
 X2K  NAJ   N  NR15  0  -0.708   2.7642  -0.6052  -0.1205
 X2K  CAO   C  CR5   0   0.300   2.0160   0.5458  -0.0436
 X2K  CAE   C  C1    0  -0.375   0.6087   0.6219  -0.0212
 X2K  CAQ   C  CR5   0  -0.084  -0.3678  -0.3299  -0.0798
 X2K  CAS   C  CR56  0   0.098  -1.7995  -0.0698  -0.0481
 X2K  CAI   C  CR16  0  -0.465  -2.5392   1.0983   0.0436
 X2K  CAM   C  CR6   0   0.306  -3.9378   1.0324   0.0470
 X2K  NAC   N  NH2   0  -0.864  -4.6957   2.1967   0.0785
 X2K  CAF   C  CR16  0  -0.349  -4.5608  -0.2193  -0.0403
 X2K  CAG   C  CR16  0  -0.292  -3.8238  -1.3963  -0.1320
 X2K  CAR   C  CR56  0   0.342  -2.4481  -1.3054  -0.1354
 X2K  NAK   N  NR15  0  -0.760  -1.4823  -2.3049  -0.2155
 X2K  CAP   C  CR5   0   0.523  -0.2217  -1.7958  -0.1883
 X2K  OAD   O  O     0  -0.507   0.7997  -2.4825  -0.2464
 X2K  HAB1  H  HCH3  0   0.250   2.2167   3.4472  -0.8781
 X2K  HAB2  H  HCH3  0   0.244   1.7944   3.2750   0.8179
 X2K  HAB3  H  HCH3  0   0.254   3.4474   3.6598   0.3576
 X2K  HAH   H  HCR5  0   0.251   5.1360   1.6083  -0.0063
 X2K  HAA1  H  HCH3  0   0.258   5.0588  -2.0436   0.6738
 X2K  HAA2  H  HCH3  0   0.258   5.0320  -1.9679  -1.0828
 X2K  HAA3  H  HCH3  0   0.257   6.1116  -0.9116  -0.1733
 X2K  HAJ   H  HNR5  0   0.427   2.3256  -1.5253  -0.1730
 X2K  HAE   H  H     0   0.259   0.2481   1.6435   0.0588
 X2K  HAI   H  HCR6  0   0.248  -2.0475   2.0626   0.1140
 X2K  HAC1  H  HNH2  0   0.373  -4.2405   2.9771   0.5257
 X2K  HAC2  H  HNH2  0   0.372  -5.6269   2.0780   0.4466
 X2K  HAF   H  HCR6  0   0.254  -5.6427  -0.2751  -0.0369
 X2K  HAG   H  HCR6  0   0.262  -4.3286  -2.3518  -0.1968
 X2K  HAK   H  HNR5  0   0.407  -1.6775  -3.2915  -0.2807

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
 X2K  CAB  CAN   single    1.492  0.020  1.492
 X2K  CAN  CAH   aromatic  1.398  0.020  1.398
 X2K  CAN  CAO   aromatic  1.404  0.020  1.404
 X2K  CAH  CAL   aromatic  1.393  0.020  1.393
 X2K  CAL  CAA   single    1.486  0.020  1.486
 X2K  CAL  NAJ   aromatic  1.340  0.020  1.340
 X2K  NAJ  CAO   aromatic  1.375  0.020  1.375
 X2K  CAO  CAE   single    1.410  0.020  1.410
 X2K  CAE  CAQ   double    1.365  0.020  1.365
 X2K  CAQ  CAS   single    1.455  0.020  1.455
 X2K  CAQ  CAP   single    1.477  0.020  1.477
 X2K  CAS  CAI   aromatic  1.386  0.020  1.386
 X2K  CAS  CAR   aromatic  1.398  0.020  1.398
 X2K  CAI  CAM   aromatic  1.400  0.020  1.400
 X2K  CAM  NAC   single    1.390  0.020  1.390
 X2K  CAM  CAF   aromatic  1.401  0.020  1.401
 X2K  CAF  CAG   aromatic  1.392  0.020  1.392
 X2K  CAG  CAR   aromatic  1.379  0.020  1.379
 X2K  CAR  NAK   single    1.392  0.020  1.392
 X2K  NAK  CAP   single    1.360  0.020  1.360
 X2K  CAP  OAD   double    1.232  0.020  1.232
 X2K  CAB  HAB1  single    0.970  0.020  1.090
 X2K  CAB  HAB2  single    0.970  0.020  1.090
 X2K  CAB  HAB3  single    0.970  0.020  1.090
 X2K  CAH  HAH   single    0.930  0.020  1.080
 X2K  CAA  HAA1  single    0.970  0.020  1.090
 X2K  CAA  HAA2  single    0.970  0.020  1.090
 X2K  CAA  HAA3  single    0.970  0.020  1.090
 X2K  NAJ  HAJ   single    0.860  0.020  1.020
 X2K  CAE  HAE   single    0.930  0.020  1.080
 X2K  CAI  HAI   single    0.930  0.020  1.080
 X2K  NAC  HAC1  single    0.890  0.020  1.040
 X2K  NAC  HAC2  single    0.890  0.020  1.040
 X2K  CAF  HAF   single    0.930  0.020  1.080
 X2K  CAG  HAG   single    0.930  0.020  1.080
 X2K  NAK  HAK   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
 X2K  HAB3  CAB  HAB2  107.58  3.000
 X2K  HAB3  CAB  HAB1  107.34  3.000
 X2K  HAB2  CAB  HAB1  107.18  3.000
 X2K  HAB3  CAB  CAN   110.63  3.000
 X2K  HAB2  CAB  CAN   112.22  3.000
 X2K  HAB1  CAB  CAN   111.66  3.000
 X2K  CAO   CAN  CAH   106.60  3.000
 X2K  CAO   CAN  CAB   126.72  3.000
 X2K  CAH   CAN  CAB   126.67  3.000
 X2K  HAH   CAH  CAL   125.34  3.000
 X2K  HAH   CAH  CAN   126.61  3.000
 X2K  CAL   CAH  CAN   108.05  3.000
 X2K  NAJ   CAL  CAA   122.52  3.000
 X2K  NAJ   CAL  CAH   107.76  3.000
 X2K  CAA   CAL  CAH   129.72  3.000
 X2K  HAA3  CAA  HAA2  108.03  3.000
 X2K  HAA3  CAA  HAA1  108.00  3.000
 X2K  HAA2  CAA  HAA1  107.35  3.000
 X2K  HAA3  CAA  CAL   110.40  3.000
 X2K  HAA2  CAA  CAL   111.53  3.000
 X2K  HAA1  CAA  CAL   111.37  3.000
 X2K  HAJ   NAJ  CAO   121.58  3.000
 X2K  HAJ   NAJ  CAL   127.92  3.000
 X2K  CAO   NAJ  CAL   110.51  3.000
 X2K  CAE   CAO  NAJ   126.11  3.000
 X2K  CAE   CAO  CAN   126.81  3.000
 X2K  NAJ   CAO  CAN   107.08  3.000
 X2K  HAE   CAE  CAQ   114.93  3.000
 X2K  HAE   CAE  CAO   112.54  3.000
 X2K  CAQ   CAE  CAO   132.53  3.000
 X2K  CAP   CAQ  CAS   106.04  3.000
 X2K  CAP   CAQ  CAE   128.64  3.000
 X2K  CAS   CAQ  CAE   125.32  3.000
 X2K  CAR   CAS  CAI   120.09  3.000
 X2K  CAR   CAS  CAQ   107.28  3.000
 X2K  CAI   CAS  CAQ   132.63  3.000
 X2K  HAI   CAI  CAM   119.63  3.000
 X2K  HAI   CAI  CAS   120.78  3.000
 X2K  CAM   CAI  CAS   119.59  3.000
 X2K  CAF   CAM  NAC   120.49  3.000
 X2K  CAF   CAM  CAI   119.09  3.000
 X2K  NAC   CAM  CAI   120.36  3.000
 X2K  HAC2  NAC  HAC1  110.26  3.000
 X2K  HAC2  NAC  CAM   114.41  3.000
 X2K  HAC1  NAC  CAM   114.36  3.000
 X2K  HAF   CAF  CAG   119.04  3.000
 X2K  HAF   CAF  CAM   119.34  3.000
 X2K  CAG   CAF  CAM   121.62  3.000
 X2K  HAG   CAG  CAR   121.55  3.000
 X2K  HAG   CAG  CAF   120.23  3.000
 X2K  CAR   CAG  CAF   118.22  3.000
 X2K  NAK   CAR  CAG   130.17  3.000
 X2K  NAK   CAR  CAS   108.43  3.000
 X2K  CAG   CAR  CAS   121.40  3.000
 X2K  HAK   NAK  CAP   123.18  3.000
 X2K  HAK   NAK  CAR   124.90  3.000
 X2K  CAP   NAK  CAR   111.91  3.000
 X2K  OAD   CAP  NAK   123.98  3.000
 X2K  OAD   CAP  CAQ   129.68  3.000
 X2K  NAK   CAP  CAQ   106.34  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
 X2K  CONST_01  NAJ   CAL  CAH  CAN     0.00   0.0  0
 X2K  CONST_02  CAL   NAJ  CAO  CAN     0.00   0.0  0
 X2K  CONST_03  NAJ   CAO  CAN  CAH     0.00   0.0  0
 X2K  CONST_04  CAO   NAJ  CAL  CAH     0.00   0.0  0
 X2K  CONST_05  CAO   CAN  CAH  CAL     0.00   0.0  0
 X2K  CONST_06  CAF   CAM  CAI  CAS     0.00   0.0  0
 X2K  CONST_07  CAF   CAG  CAR  CAS     0.00   0.0  0
 X2K  CONST_08  CAG   CAR  CAS  CAI     0.00   0.0  0
 X2K  CONST_09  CAG   CAF  CAM  CAI     0.00   0.0  0
 X2K  CONST_10  CAR   CAS  CAI  CAM     0.00   0.0  0
 X2K  CONST_11  CAR   CAG  CAF  CAM     0.00   0.0  0
 X2K  CONST_12  CAR   NAK  CAP  CAQ     0.00   0.0  0
 X2K  CONST_13  CAL   CAH  CAN  CAB   180.00   0.0  0
 X2K  CONST_14  NAJ   CAO  CAN  CAB   180.00   0.0  0
 X2K  CONST_15  CAA   CAL  CAH  CAN   180.00   0.0  0
 X2K  CONST_16  CAE   CAO  CAN  CAH   180.00   0.0  0
 X2K  CONST_17  CAE   CAO  NAJ  CAL   180.00   0.0  0
 X2K  CONST_18  CAO   NAJ  CAL  CAA   180.00   0.0  0
 X2K  CONST_19  NAC   CAM  CAI  CAS   180.00   0.0  0
 X2K  CONST_20  CAG   CAF  CAM  NAC   180.00   0.0  0
 X2K  CONST_21  OAD   CAP  NAK  CAR   180.00   0.0  0
 X2K  CONST_22  HAJ   NAJ  CAO  CAN   180.00   0.0  0
 X2K  CONST_23  HAH   CAH  CAL  NAJ   180.00   0.0  0
 X2K  CONST_24  HAI   CAI  CAS  CAQ     0.00   0.0  0
 X2K  CONST_25  HAG   CAG  CAR  CAS   180.00   0.0  0
 X2K  CONST_26  HAF   CAF  CAM  CAI   180.00   0.0  0
 X2K  CONST_27  HAK   NAK  CAP  CAQ   180.00   0.0  0
 X2K  Var_01    CAQ   CAE  CAO  CAN   179.38  30.0  2
 X2K  Var_02    CAS   CAQ  CAE  CAO  -179.78  30.0  2
 X2K  Var_03    HAB1  CAB  CAN  CAH   104.56  30.0  2
 X2K  Var_04    HAA1  CAA  CAL  CAH   118.80  30.0  2

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
 X2K  plan-1  CAB   0.020
 X2K  plan-1  CAN   0.020
 X2K  plan-1  CAH   0.020
 X2K  plan-1  CAL   0.020
 X2K  plan-1  CAA   0.020
 X2K  plan-1  NAJ   0.020
 X2K  plan-1  CAO   0.020
 X2K  plan-1  CAE   0.020
 X2K  plan-1  HAH   0.020
 X2K  plan-1  HAJ   0.020
 X2K  plan-2  CAE   0.020
 X2K  plan-2  CAQ   0.020
 X2K  plan-2  CAS   0.020
 X2K  plan-2  CAI   0.020
 X2K  plan-2  CAM   0.020
 X2K  plan-2  NAC   0.020
 X2K  plan-2  CAF   0.020
 X2K  plan-2  CAG   0.020
 X2K  plan-2  CAR   0.020
 X2K  plan-2  NAK   0.020
 X2K  plan-2  CAP   0.020
 X2K  plan-2  OAD   0.020
 X2K  plan-2  HAI   0.020
 X2K  plan-2  HAF   0.020
 X2K  plan-2  HAG   0.020
 X2K  plan-2  HAK   0.020
 X2K  plan-3  CAM   0.020
 X2K  plan-3  NAC   0.020
 X2K  plan-3  HAC1  0.020
 X2K  plan-3  HAC2  0.020

