# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:02:51 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (3Z)-5-amino-3-[(4-methoxyphenyl)methylidene]-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)\C=C\2C(=O)Nc3ccc(N)cc\23
#
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
 X2L  X2L  (3Z)-5-amino-3-[(4-methoxyphenyl)methylidene]-1,3-dihydro-2H-indol-2-one  ligand  34  20  .  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_X2L
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
 X2L  CAH   C  CR16  0  -0.288  -2.1240  -1.6834   0.0178
 X2L  CAO   C  CR16  0  -0.335  -3.4941  -1.8032   0.0477
 X2L  CAM   C  CR6   0   0.392  -4.2905  -0.6628   0.1937
 X2L  OAB   O  O2    0  -0.460  -5.6135  -0.8585   0.2077
 X2L  CAP   C  CR16  0  -0.358  -3.6751   0.5847   0.3134
 X2L  CAI   C  CR16  0  -0.327  -2.2956   0.6905   0.2796
 X2L  CAQ   C  CR6   0   0.129  -1.4794  -0.4366   0.1283
 X2L  CAF   C  C1    0  -0.346  -0.0330  -0.4600   0.0705
 X2L  CAS   C  CR5   0  -0.080   0.9580   0.4603   0.0985
 X2L  CAU   C  CR56  0   0.092   2.3771   0.1153   0.0032
 X2L  CAK   C  CR16  0  -0.459   3.0332  -1.0987  -0.1061
 X2L  CAN   C  CR6   0   0.310   4.4310  -1.1244  -0.1846
 X2L  CAG   C  CR16  0  -0.344   5.1337   0.0862  -0.1473
 X2L  CAJ   C  CR16  0  -0.294   4.4792   1.3094  -0.0385
 X2L  CAT   C  CR56  0   0.354   3.1025   1.3068   0.0359
 X2L  CAA   C  CH3   0  -0.441  -6.4707   0.2623   0.3359
 X2L  NAL   N  NR15  0  -0.765   2.2095   2.3680   0.1515
 X2L  CAR   C  CR5   0   0.512   0.9144   1.9512   0.2001
 X2L  NAB   N  NH2   0  -0.864   5.1035  -2.3270  -0.3550
 X2L  OAA   O  O     0  -0.462  -0.0451   2.6988   0.3056
 X2L  HAH   H  HCR6  0   0.264  -1.5267  -2.5798  -0.0994
 X2L  HAO   H  HCR6  0   0.269  -3.9613  -2.7757  -0.0435
 X2L  HAP   H  HCR6  0   0.284  -4.2592   1.4870   0.4328
 X2L  HAA1  H  HCH3  0   0.264  -7.4860  -0.1230   0.2962
 X2L  HAA2  H  HCH3  0   0.234  -6.3254   0.7775   1.2882
 X2L  HAA3  H  HCH3  0   0.235  -6.3292   0.9753  -0.4793
 X2L  HAI   H  HCR6  0   0.297  -1.8488   1.6674   0.3726
 X2L  HAF   H  H     0   0.257   0.3407  -1.4763  -0.0270
 X2L  HAK   H  HCR6  0   0.253   2.4773  -2.0300  -0.1312
 X2L  HAG   H  HCR6  0   0.258   6.2156   0.0724  -0.2037
 X2L  HAB1  H  HNH2  0   0.374   4.6311  -3.1311   0.0272
 X2L  HAB2  H  HNH2  0   0.373   6.0679  -2.3119  -0.0624
 X2L  HAJ   H  HCR6  0   0.264   5.0481   2.2297  -0.0101
 X2L  HAL   H  HNR5  0   0.408   2.4734   3.3398   0.2004

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
 X2L  CAH  CAO   aromatic  1.376  0.020  1.376
 X2L  CAH  CAQ   aromatic  1.408  0.020  1.408
 X2L  CAO  CAM   aromatic  1.399  0.020  1.399
 X2L  CAM  OAB   single    1.337  0.020  1.337
 X2L  CAM  CAP   aromatic  1.396  0.020  1.396
 X2L  OAB  CAA   single    1.417  0.020  1.417
 X2L  CAP  CAI   aromatic  1.384  0.020  1.384
 X2L  CAI  CAQ   aromatic  1.400  0.020  1.400
 X2L  CAQ  CAF   single    1.448  0.020  1.448
 X2L  CAF  CAS   double    1.353  0.020  1.353
 X2L  CAS  CAU   single    1.464  0.020  1.464
 X2L  CAS  CAR   single    1.495  0.020  1.495
 X2L  CAU  CAK   aromatic  1.384  0.020  1.384
 X2L  CAU  CAT   aromatic  1.395  0.020  1.395
 X2L  CAK  CAN   aromatic  1.400  0.020  1.400
 X2L  CAN  CAG   aromatic  1.400  0.020  1.400
 X2L  CAN  NAB   single    1.388  0.020  1.388
 X2L  CAG  CAJ   aromatic  1.392  0.020  1.392
 X2L  CAJ  CAT   aromatic  1.379  0.020  1.379
 X2L  CAT  NAL   single    1.392  0.020  1.392
 X2L  NAL  CAR   single    1.361  0.020  1.361
 X2L  CAR  OAA   double    1.221  0.020  1.221
 X2L  CAH  HAH   single    0.930  0.020  1.080
 X2L  CAO  HAO   single    0.930  0.020  1.080
 X2L  CAP  HAP   single    0.930  0.020  1.080
 X2L  CAA  HAA1  single    0.970  0.020  1.090
 X2L  CAA  HAA2  single    0.970  0.020  1.090
 X2L  CAA  HAA3  single    0.970  0.020  1.090
 X2L  CAI  HAI   single    0.930  0.020  1.080
 X2L  CAF  HAF   single    0.930  0.020  1.080
 X2L  CAK  HAK   single    0.930  0.020  1.080
 X2L  CAG  HAG   single    0.930  0.020  1.080
 X2L  NAB  HAB1  single    0.890  0.020  1.040
 X2L  NAB  HAB2  single    0.890  0.020  1.040
 X2L  CAJ  HAJ   single    0.930  0.020  1.080
 X2L  NAL  HAL   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
 X2L  HAH   CAH  CAQ   119.26  3.000
 X2L  HAH   CAH  CAO   118.64  3.000
 X2L  CAQ   CAH  CAO   122.10  3.000
 X2L  HAO   CAO  CAM   119.69  3.000
 X2L  HAO   CAO  CAH   120.41  3.000
 X2L  CAM   CAO  CAH   119.89  3.000
 X2L  CAP   CAM  OAB   124.46  3.000
 X2L  CAP   CAM  CAO   119.11  3.000
 X2L  OAB   CAM  CAO   116.43  3.000
 X2L  CAA   OAB  CAM   118.93  3.000
 X2L  HAP   CAP  CAI   118.51  3.000
 X2L  HAP   CAP  CAM   121.12  3.000
 X2L  CAI   CAP  CAM   120.37  3.000
 X2L  HAI   CAI  CAQ   119.82  3.000
 X2L  HAI   CAI  CAP   118.69  3.000
 X2L  CAQ   CAI  CAP   121.49  3.000
 X2L  CAF   CAQ  CAI   126.86  3.000
 X2L  CAF   CAQ  CAH   116.10  3.000
 X2L  CAI   CAQ  CAH   117.04  3.000
 X2L  HAF   CAF  CAS   112.70  3.000
 X2L  HAF   CAF  CAQ   111.23  3.000
 X2L  CAS   CAF  CAQ   136.06  3.000
 X2L  CAR   CAS  CAU   105.53  3.000
 X2L  CAR   CAS  CAF   131.19  3.000
 X2L  CAU   CAS  CAF   123.28  3.000
 X2L  CAT   CAU  CAK   120.28  3.000
 X2L  CAT   CAU  CAS   107.54  3.000
 X2L  CAK   CAU  CAS   132.18  3.000
 X2L  HAK   CAK  CAN   119.63  3.000
 X2L  HAK   CAK  CAU   120.78  3.000
 X2L  CAN   CAK  CAU   119.58  3.000
 X2L  NAB   CAN  CAG   120.60  3.000
 X2L  NAB   CAN  CAK   120.42  3.000
 X2L  CAG   CAN  CAK   118.92  3.000
 X2L  HAG   CAG  CAJ   119.00  3.000
 X2L  HAG   CAG  CAN   119.26  3.000
 X2L  CAJ   CAG  CAN   121.74  3.000
 X2L  HAJ   CAJ  CAT   121.67  3.000
 X2L  HAJ   CAJ  CAG   120.15  3.000
 X2L  CAT   CAJ  CAG   118.17  3.000
 X2L  NAL   CAT  CAJ   130.07  3.000
 X2L  NAL   CAT  CAU   108.63  3.000
 X2L  CAJ   CAT  CAU   121.30  3.000
 X2L  HAA3  CAA  HAA2  108.99  3.000
 X2L  HAA3  CAA  HAA1  108.98  3.000
 X2L  HAA2  CAA  HAA1  108.87  3.000
 X2L  HAA3  CAA  OAB   111.75  3.000
 X2L  HAA2  CAA  OAB   111.81  3.000
 X2L  HAA1  CAA  OAB   106.35  3.000
 X2L  HAL   NAL  CAR   122.85  3.000
 X2L  HAL   NAL  CAT   124.83  3.000
 X2L  CAR   NAL  CAT   112.32  3.000
 X2L  OAA   CAR  NAL   124.28  3.000
 X2L  OAA   CAR  CAS   129.74  3.000
 X2L  NAL   CAR  CAS   105.97  3.000
 X2L  HAB2  NAB  HAB1  110.51  3.000
 X2L  HAB2  NAB  CAN   114.51  3.000
 X2L  HAB1  NAB  CAN   114.67  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
 X2L  CONST_01  CAP   CAM  CAO  CAH     0.00   0.0  0
 X2L  CONST_02  CAP   CAI  CAQ  CAH     0.00   0.0  0
 X2L  CONST_03  CAI   CAQ  CAH  CAO     0.00   0.0  0
 X2L  CONST_04  CAI   CAP  CAM  CAO     0.00   0.0  0
 X2L  CONST_05  CAQ   CAH  CAO  CAM     0.00   0.0  0
 X2L  CONST_06  CAQ   CAI  CAP  CAM     0.00   0.0  0
 X2L  CONST_07  CAG   CAN  CAK  CAU     0.00   0.0  0
 X2L  CONST_08  CAG   CAJ  CAT  CAU     0.00   0.0  0
 X2L  CONST_09  CAJ   CAT  CAU  CAK     0.00   0.0  0
 X2L  CONST_10  CAJ   CAG  CAN  CAK     0.00   0.0  0
 X2L  CONST_11  CAT   CAU  CAK  CAN     0.00   0.0  0
 X2L  CONST_12  CAT   CAJ  CAG  CAN     0.00   0.0  0
 X2L  CONST_13  CAT   NAL  CAR  CAS     0.00   0.0  0
 X2L  CONST_14  OAB   CAM  CAO  CAH   180.00   0.0  0
 X2L  CONST_15  CAF   CAQ  CAH  CAO   180.00   0.0  0
 X2L  CONST_16  CAI   CAP  CAM  OAB   180.00   0.0  0
 X2L  CONST_17  CAF   CAQ  CAI  CAP   180.00   0.0  0
 X2L  CONST_18  NAB   CAN  CAK  CAU   180.00   0.0  0
 X2L  CONST_19  NAB   CAN  CAG  CAJ   180.00   0.0  0
 X2L  CONST_20  OAA   CAR  NAL  CAT   180.00   0.0  0
 X2L  CONST_21  HAI   CAI  CAQ  CAH   180.00   0.0  0
 X2L  CONST_22  HAP   CAP  CAM  CAO   180.00   0.0  0
 X2L  CONST_23  HAH   CAH  CAO  CAM   180.00   0.0  0
 X2L  CONST_24  HAO   CAO  CAM  CAP   180.00   0.0  0
 X2L  CONST_25  HAK   CAK  CAU  CAS     0.00   0.0  0
 X2L  CONST_26  HAJ   CAJ  CAT  CAU   180.00   0.0  0
 X2L  CONST_27  HAG   CAG  CAN  CAK   180.00   0.0  0
 X2L  CONST_28  HAL   NAL  CAR  CAS   180.00   0.0  0
 X2L  Var_01    CAS   CAF  CAQ  CAH   177.94  30.0  2
 X2L  Var_02    CAU   CAS  CAF  CAQ  -179.29  30.0  2
 X2L  Var_03    HAA1  CAA  OAB  CAM   178.47  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
 X2L  plan-1  CAH   0.020
 X2L  plan-1  CAO   0.020
 X2L  plan-1  CAM   0.020
 X2L  plan-1  OAB   0.020
 X2L  plan-1  CAP   0.020
 X2L  plan-1  CAI   0.020
 X2L  plan-1  CAQ   0.020
 X2L  plan-1  CAF   0.020
 X2L  plan-1  HAH   0.020
 X2L  plan-1  HAO   0.020
 X2L  plan-1  HAP   0.020
 X2L  plan-1  HAI   0.020
 X2L  plan-2  CAF   0.020
 X2L  plan-2  CAS   0.020
 X2L  plan-2  CAU   0.020
 X2L  plan-2  CAK   0.020
 X2L  plan-2  CAN   0.020
 X2L  plan-2  CAG   0.020
 X2L  plan-2  CAJ   0.020
 X2L  plan-2  CAT   0.020
 X2L  plan-2  NAL   0.020
 X2L  plan-2  CAR   0.020
 X2L  plan-2  NAB   0.020
 X2L  plan-2  OAA   0.020
 X2L  plan-2  HAK   0.020
 X2L  plan-2  HAG   0.020
 X2L  plan-2  HAJ   0.020
 X2L  plan-2  HAL   0.020
 X2L  plan-3  CAN   0.020
 X2L  plan-3  NAB   0.020
 X2L  plan-3  HAB1  0.020
 X2L  plan-3  HAB2  0.020

