# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:16:41 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-{2,4-dimethyl-5-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(\C=C2/C(=O)Nc3ccccc23)c(C)c1CCC(O)=O
#
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
 SU6  SU6  '3-{2,4-dimethyl-5-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid'  ligand  40  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SU6
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
 SU6  C1   C  C      0   0.412   6.0197   0.7211   0.4931
 SU6  N1   N  NR15   0  -0.724   0.5354  -1.2011  -0.5472
 SU6  O1   O  OC    -1  -0.630   6.6458   0.5317   1.5573
 SU6  C2   C  CH2    0  -0.576   4.5323   0.3280   0.5103
 SU6  N2   N  NR15   0  -0.760  -3.9430  -1.8305   0.0405
 SU6  O2   O  O      0  -0.607   6.4831   1.2012  -0.5601
 SU6  C3   C  CH2    0  -0.521   3.7968   0.4483  -0.8226
 SU6  O3   O  O      0  -0.506  -1.7975  -2.5576  -0.2914
 SU6  C4   C  CR5    0  -0.009   2.3580   0.0580  -0.7092
 SU6  C5   C  CR5    0   0.312   1.8600  -1.2479  -0.7356
 SU6  C6   C  CH3    0  -0.744   2.5947  -2.5274  -0.9053
 SU6  C7   C  CR5    0  -0.014   1.2686   0.9080  -0.4876
 SU6  C8   C  CH3    0  -0.762   1.3380   2.3934  -0.3813
 SU6  C9   C  CR5    0   0.323   0.1198   0.0998  -0.3910
 SU6  C10  C  C1     0  -0.381  -1.2084   0.5110  -0.1890
 SU6  C11  C  CR5    0  -0.084  -2.3822  -0.1849  -0.0798
 SU6  C12  C  CR5    0   0.523  -2.6016  -1.6380  -0.1319
 SU6  C13  C  CR56   0   0.077  -3.6916   0.4110   0.1302
 SU6  C14  C  CR56   0   0.373  -4.6226  -0.6354   0.1997
 SU6  C15  C  CR16   0  -0.302  -5.9718  -0.4122   0.3958
 SU6  C16  C  CR16   0  -0.281  -6.3944   0.9089   0.5245
 SU6  C17  C  CR16   0  -0.261  -5.4868   1.9623   0.4576
 SU6  C18  C  CR16   0  -0.383  -4.1308   1.7202   0.2599
 SU6  H1   H  HNR5   0   0.424  -0.1228  -1.9812  -0.5119
 SU6  H3   H  HCH2   0   0.224   4.4457  -0.6969   0.8867
 SU6  H4   H  HNR5   0   0.409  -4.3688  -2.7443   0.0583
 SU6  H5   H  HCH2   0   0.228   3.8725   1.4735  -1.1902
 SU6  H6   H  HCH3   0   0.259   3.0190  -2.8690   0.0412
 SU6  H7   H  HCH3   0   0.258   1.9451  -3.3181  -1.2794
 SU6  H8   H  HCH3   0   0.255   3.4206  -2.4106  -1.6061
 SU6  H9   H  HCH3   0   0.249   1.6429   2.8462  -1.3270
 SU6  H10  H  HCH3   0   0.249   0.3849   2.8395  -0.1012
 SU6  H11  H  HCH3   0   0.247   2.0703   2.6989   0.3679
 SU6  H12  H  H      0   0.256  -1.3116   1.5883  -0.1034
 SU6  H15  H  HCR6   0   0.264  -6.6775  -1.2309   0.4471
 SU6  H16  H  HCR6   0   0.254  -7.4456   1.1150   0.6777
 SU6  H17  H  HCR6   0   0.251  -5.8384   2.9804   0.5612
 SU6  H18  H  HCR6   0   0.247  -3.4334   2.5478   0.2093
 SU6  H19  H  HCH2   0   0.228   4.0239   0.9454   1.2601
 SU6  H20  H  HCH2   0   0.225   4.2953  -0.1730  -1.5718

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
 SU6  O2   C1   deloc     1.247  0.020  1.247
 SU6  O1   C1   deloc     1.249  0.020  1.249
 SU6  C1   C2   single    1.539  0.020  1.539
 SU6  C2   C3   single    1.527  0.020  1.527
 SU6  C3   C4   single    1.495  0.020  1.495
 SU6  C4   C7   aromatic  1.399  0.020  1.399
 SU6  C4   C5   aromatic  1.398  0.020  1.398
 SU6  C8   C7   single    1.491  0.020  1.491
 SU6  C6   C5   single    1.485  0.020  1.485
 SU6  C7   C9   aromatic  1.408  0.020  1.408
 SU6  C5   N1   aromatic  1.339  0.020  1.339
 SU6  C9   N1   aromatic  1.375  0.020  1.375
 SU6  C9   C10  single    1.405  0.020  1.405
 SU6  C10  C11  double    1.369  0.020  1.369
 SU6  O3   C12  double    1.232  0.020  1.232
 SU6  C11  C12  single    1.470  0.020  1.470
 SU6  C11  C13  single    1.454  0.020  1.454
 SU6  C12  N2   single    1.366  0.020  1.366
 SU6  C13  C18  aromatic  1.387  0.020  1.387
 SU6  C13  C14  aromatic  1.402  0.020  1.402
 SU6  C18  C17  aromatic  1.392  0.020  1.392
 SU6  N2   C14  single    1.384  0.020  1.384
 SU6  C14  C15  aromatic  1.382  0.020  1.382
 SU6  C17  C16  aromatic  1.392  0.020  1.392
 SU6  C15  C16  aromatic  1.393  0.020  1.393
 SU6  N1   H1   single    0.860  0.020  1.020
 SU6  C2   H3   single    0.970  0.020  1.090
 SU6  N2   H4   single    0.860  0.020  1.020
 SU6  C3   H5   single    0.970  0.020  1.090
 SU6  C6   H6   single    0.970  0.020  1.090
 SU6  C6   H7   single    0.970  0.020  1.090
 SU6  C6   H8   single    0.970  0.020  1.090
 SU6  C8   H9   single    0.970  0.020  1.090
 SU6  C8   H10  single    0.970  0.020  1.090
 SU6  C8   H11  single    0.970  0.020  1.090
 SU6  C10  H12  single    0.930  0.020  1.080
 SU6  C15  H15  single    0.930  0.020  1.080
 SU6  C16  H16  single    0.930  0.020  1.080
 SU6  C17  H17  single    0.930  0.020  1.080
 SU6  C18  H18  single    0.930  0.020  1.080
 SU6  C2   H19  single    0.970  0.020  1.090
 SU6  C3   H20  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
 SU6  O2   C1   C2   117.85  3.000
 SU6  C2   C1   O1   115.87  3.000
 SU6  O2   C1   O1   126.28  3.000
 SU6  H1   N1   C9   121.61  3.000
 SU6  H1   N1   C5   128.01  3.000
 SU6  C9   N1   C5   110.38  3.000
 SU6  H19  C2   H3   104.79  3.000
 SU6  H19  C2   C3   109.23  3.000
 SU6  H3   C2   C3   109.61  3.000
 SU6  H19  C2   C1   108.19  3.000
 SU6  H3   C2   C1   108.62  3.000
 SU6  C3   C2   C1   115.83  3.000
 SU6  H4   N2   C14  124.97  3.000
 SU6  H4   N2   C12  123.00  3.000
 SU6  C14  N2   C12  112.02  3.000
 SU6  H20  C3   H5   105.75  3.000
 SU6  H20  C3   C4   110.02  3.000
 SU6  H5   C3   C4   109.72  3.000
 SU6  H20  C3   C2   109.49  3.000
 SU6  H5   C3   C2   109.54  3.000
 SU6  C4   C3   C2   112.13  3.000
 SU6  C7   C4   C5   107.04  3.000
 SU6  C5   C4   C3   125.82  3.000
 SU6  C7   C4   C3   127.06  3.000
 SU6  C6   C5   C4   129.11  3.000
 SU6  C6   C5   N1   122.39  3.000
 SU6  C4   C5   N1   108.49  3.000
 SU6  H8   C6   H7   108.00  3.000
 SU6  H8   C6   H6   107.25  3.000
 SU6  H7   C6   H6   107.59  3.000
 SU6  H8   C6   C5   110.86  3.000
 SU6  H7   C6   C5   111.68  3.000
 SU6  H6   C6   C5   111.26  3.000
 SU6  C9   C7   C8   127.23  3.000
 SU6  C9   C7   C4   107.30  3.000
 SU6  C8   C7   C4   125.47  3.000
 SU6  H11  C8   H10  107.22  3.000
 SU6  H11  C8   H9   106.92  3.000
 SU6  H10  C8   H9   107.29  3.000
 SU6  H11  C8   C7   111.05  3.000
 SU6  H10  C8   C7   112.69  3.000
 SU6  H9   C8   C7   111.38  3.000
 SU6  C10  C9   C7   127.82  3.000
 SU6  C10  C9   N1   125.39  3.000
 SU6  C7   C9   N1   106.78  3.000
 SU6  H12  C10  C11  114.63  3.000
 SU6  H12  C10  C9   113.06  3.000
 SU6  C11  C10  C9   132.32  3.000
 SU6  C13  C11  C12  106.01  3.000
 SU6  C13  C11  C10  125.13  3.000
 SU6  C12  C11  C10  128.86  3.000
 SU6  C11  C12  O3   130.15  3.000
 SU6  C11  C12  N2   106.34  3.000
 SU6  O3   C12  N2   123.51  3.000
 SU6  C18  C13  C14  119.31  3.000
 SU6  C14  C13  C11  107.41  3.000
 SU6  C18  C13  C11  133.28  3.000
 SU6  C15  C14  C13  122.34  3.000
 SU6  C15  C14  N2   129.45  3.000
 SU6  C13  C14  N2   108.22  3.000
 SU6  H15  C15  C16  121.02  3.000
 SU6  H15  C15  C14  121.42  3.000
 SU6  C16  C15  C14  117.56  3.000
 SU6  H16  C16  C17  119.74  3.000
 SU6  H16  C16  C15  119.24  3.000
 SU6  C17  C16  C15  121.02  3.000
 SU6  H17  C17  C18  119.60  3.000
 SU6  H17  C17  C16  119.70  3.000
 SU6  C18  C17  C16  120.70  3.000
 SU6  H18  C18  C17  120.06  3.000
 SU6  H18  C18  C13  120.86  3.000
 SU6  C17  C18  C13  119.08  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
 SU6  CONST_01  C7   C4   C5   N1      0.00   0.0  0
 SU6  CONST_02  C4   C7   C9   N1      0.00   0.0  0
 SU6  CONST_03  C9   N1   C5   C4      0.00   0.0  0
 SU6  CONST_04  C9   C7   C4   C5      0.00   0.0  0
 SU6  CONST_05  C7   C9   N1   C5      0.00   0.0  0
 SU6  CONST_06  C16  C17  C18  C13     0.00   0.0  0
 SU6  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 SU6  CONST_08  C17  C18  C13  C14     0.00   0.0  0
 SU6  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 SU6  CONST_10  C18  C13  C14  C15     0.00   0.0  0
 SU6  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 SU6  CONST_12  C14  N2   C12  C11     0.00   0.0  0
 SU6  CONST_13  C3   C4   C5   N1    180.00   0.0  0
 SU6  CONST_14  C8   C7   C9   N1    180.00   0.0  0
 SU6  CONST_15  C9   C7   C4   C3    180.00   0.0  0
 SU6  CONST_16  C10  C9   C7   C4    180.00   0.0  0
 SU6  CONST_17  C8   C7   C4   C5    180.00   0.0  0
 SU6  CONST_18  C10  C9   N1   C5    180.00   0.0  0
 SU6  CONST_19  C7   C4   C5   C6    180.00   0.0  0
 SU6  CONST_20  C9   N1   C5   C6    180.00   0.0  0
 SU6  CONST_21  C14  N2   C12  O3    180.00   0.0  0
 SU6  CONST_22  H15  C15  C14  N2      0.00   0.0  0
 SU6  CONST_23  H1   N1   C5   C4    180.00   0.0  0
 SU6  CONST_24  H18  C18  C13  C11     0.00   0.0  0
 SU6  CONST_25  H17  C17  C18  C13   180.00   0.0  0
 SU6  CONST_26  H16  C16  C15  C14   180.00   0.0  0
 SU6  CONST_27  H4   N2   C12  C11   180.00   0.0  0
 SU6  Var_01    C11  C10  C9   N1      0.82  30.0  2
 SU6  Var_02    C12  C11  C10  C9      0.70  30.0  2
 SU6  Var_03    C7   C4   C3   C2     94.46  30.0  2
 SU6  Var_04    H6   C6   C5   N1    -95.77  30.0  2
 SU6  Var_05    H9   C8   C7   C4     65.54  30.0  2
 SU6  Var_06    C4   C3   C2   C1   -179.51  30.0  3
 SU6  Var_07    C3   C2   C1   O1   -175.01  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
 SU6  plan-1  N1   0.020
 SU6  plan-1  C3   0.020
 SU6  plan-1  C4   0.020
 SU6  plan-1  C5   0.020
 SU6  plan-1  C6   0.020
 SU6  plan-1  C7   0.020
 SU6  plan-1  C8   0.020
 SU6  plan-1  C9   0.020
 SU6  plan-1  C10  0.020
 SU6  plan-1  H1   0.020
 SU6  plan-2  N2   0.020
 SU6  plan-2  O3   0.020
 SU6  plan-2  C10  0.020
 SU6  plan-2  C11  0.020
 SU6  plan-2  C12  0.020
 SU6  plan-2  C13  0.020
 SU6  plan-2  C14  0.020
 SU6  plan-2  C15  0.020
 SU6  plan-2  C16  0.020
 SU6  plan-2  C17  0.020
 SU6  plan-2  C18  0.020
 SU6  plan-2  H4   0.020
 SU6  plan-2  H15  0.020
 SU6  plan-2  H16  0.020
 SU6  plan-2  H17  0.020
 SU6  plan-2  H18  0.020
 SU6  plan-3  C1   0.020
 SU6  plan-3  O1   0.020
 SU6  plan-3  C2   0.020
 SU6  plan-3  O2   0.020

