# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:52:35 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: {1-[(5-chloro-2-methyl-1-benzothiophen-3-yl)methyl]-6-(3,5-diaminophenyl)-1H-indol-3-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc2ccc(Cl)cc2c1Cn3cc(CC(O)=O)c4ccc(cc34)c5cc(N)cc(N)c5
#
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
 I79  I79  '{1-[(5-chloro-2-methyl-1-benzothiophen-3-yl)methyl]-6-(3,5-diaminophenyl)-1H-indol-3-yl}acetic acid'  ligand  55  33  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I79
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
 I79  C1    C   CR16  0  -0.433  -5.2454   0.0300  -0.5844
 I79  C2    C   CR6   0   0.108  -3.9146   0.4362  -0.5411
 I79  C3    C   CR16  0  -0.427  -3.5598   1.7132  -0.9678
 I79  C4    C   CR6   0   0.337  -4.5369   2.5982  -1.4365
 I79  C5    C   CR16  0  -0.418  -5.8700   2.1857  -1.4729
 I79  C6    C   CR6   0   0.336  -6.2324   0.9047  -1.0523
 I79  N7    N   NH2   0  -0.865  -7.5603   0.5254  -1.0386
 I79  N8    N   NH2   0  -0.866  -4.1750   3.8390  -1.9194
 I79  C9    C   CR6   0   0.053  -2.8686  -0.4873  -0.0522
 I79  C10   C   CR16  0  -0.318  -2.9007  -1.8527  -0.4053
 I79  C11   C   CR16  0  -0.361  -1.9212  -2.7307   0.0087
 I79  C12   C   CR56  0   0.037  -0.8698  -2.2578   0.7984
 I79  C13   C   CR56  0   0.412  -0.8435  -0.8922   1.1520
 I79  C14   C   CR16  0  -0.389  -1.8391  -0.0076   0.7457
 I79  C15   C   CR5   0   0.037   0.2847  -2.8666   1.3819
 I79  C16   C   CR15  0  -0.067   0.9430  -1.8721   2.0424
 I79  N17   N   NR5   0  -0.537   0.2732  -0.6832   1.9163
 I79  C18   C   CH2   0  -0.727   0.6651  -4.3023   1.3223
 I79  C19   C   C     0   0.552   1.0888  -4.7604  -0.0521
 I79  O20   O   O     0  -0.432   1.1849  -4.0564  -1.0234
 I79  O21   O   OH1   0  -0.595   1.3543  -6.0632  -0.0631
 I79  C22   C   CH2   0  -0.465   0.7450   0.5768   2.4571
 I79  C23   C   CR5   0   0.203   2.0258   1.0224   1.8176
 I79  C24   C   CR56  0   0.213   2.0851   1.5684   0.4845
 I79  C25   C   CR56  0  -0.223   3.3960   1.8859   0.0967
 I79  S26   S   S2    0   0.223   4.5222   1.5127   1.3561
 I79  C27   C   CR5   0  -0.265   3.2512   0.9367   2.3971
 I79  C28   C   CH3   0  -0.724   3.6305   0.4307   3.7462
 I79  C29   C   CR16  0  -0.282   3.6795   2.4350  -1.1486
 I79  C30   C   CR16  0  -0.232   2.6370   2.6771  -2.0222
 I79  C31   C   CR6   0  -0.045   1.3309   2.3669  -1.6375
 I79  C32   C   CR16  0  -0.278   1.0391   1.8163  -0.4083
 I79  CL33  CL  CL    0  -0.123   0.0326   2.6898  -2.7424
 I79  H1    H   HCR6  0   0.243  -5.5287  -0.9533  -0.2282
 I79  H3    H   HCR6  0   0.232  -2.5184   2.0128  -0.9832
 I79  H5    H   HCR6  0   0.250  -6.6333   2.8671  -1.8347
 I79  HN7   H   HNH2  0   0.376  -7.7224  -0.4685  -1.0761
 I79  HN7A  H   HNH2  0   0.376  -8.1575   1.0178  -1.6836
 I79  HN8   H   HNH2  0   0.374  -3.3118   4.2116  -1.5578
 I79  HN8A  H   HNH2  0   0.376  -4.9033   4.5347  -1.9292
 I79  H10   H   HCR6  0   0.244  -3.7011  -2.2133  -1.0385
 I79  H11   H   HCR6  0   0.241  -1.9682  -3.7718  -0.2862
 I79  H14   H   HCR6  0   0.270  -1.8364   1.0290   1.0605
 I79  H16   H   HCR5  0   0.290   1.8580  -1.9250   2.6134
 I79  H18   H   HCH2  0   0.306   1.4863  -4.5110   2.0141
 I79  H18A  H   HCH2  0   0.293  -0.1603  -4.9424   1.6519
 I79  HO21  H   HOH1  0   0.480   1.6293  -6.3388  -0.9503
 I79  H22   H   HCH2  0   0.293  -0.0334   1.3258   2.3092
 I79  H22A  H   HCH2  0   0.296   0.8632   0.4795   3.5362
 I79  H28   H   HCH3  0   0.271   4.1078   1.2121   4.3388
 I79  H28A  H   HCH3  0   0.257   2.7638   0.0778   4.3013
 I79  H28B  H   HCH3  0   0.267   4.3361  -0.3974   3.6697
 I79  H29   H   HCR6  0   0.280   4.6944   2.6733  -1.4374
 I79  H30   H   HCR6  0   0.284   2.8338   3.1064  -2.9948
 I79  H32   H   HCR6  0   0.263   0.0152   1.5863  -0.1485

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
 I79  C1    C6    aromatic  1.399  0.020  1.399
 I79  C1    C2    aromatic  1.392  0.020  1.392
 I79  C1    H1    single    0.930  0.020  1.080
 I79  C9    C2    single    1.479  0.020  1.479
 I79  C2    C3    aromatic  1.392  0.020  1.392
 I79  C3    C4    aromatic  1.399  0.020  1.399
 I79  C3    H3    single    0.930  0.020  1.080
 I79  C5    C4    aromatic  1.396  0.020  1.396
 I79  C4    N8    single    1.380  0.020  1.380
 I79  C6    C5    aromatic  1.396  0.020  1.396
 I79  C5    H5    single    0.930  0.020  1.080
 I79  N7    C6    single    1.381  0.020  1.381
 I79  N7    HN7   single    0.890  0.020  1.040
 I79  N7    HN7A  single    0.890  0.020  1.040
 I79  N8    HN8   single    0.890  0.020  1.040
 I79  N8    HN8A  single    0.890  0.020  1.040
 I79  C14   C9    aromatic  1.388  0.020  1.388
 I79  C9    C10   aromatic  1.411  0.020  1.411
 I79  C11   C10   aromatic  1.379  0.020  1.379
 I79  C10   H10   single    0.930  0.020  1.080
 I79  C12   C11   aromatic  1.397  0.020  1.397
 I79  C11   H11   single    0.930  0.020  1.080
 I79  C13   C12   aromatic  1.411  0.020  1.411
 I79  C15   C12   aromatic  1.430  0.020  1.430
 I79  N17   C13   aromatic  1.369  0.020  1.369
 I79  C13   C14   aromatic  1.392  0.020  1.392
 I79  C14   H14   single    0.930  0.020  1.080
 I79  C16   C15   aromatic  1.363  0.020  1.363
 I79  C15   C18   single    1.486  0.020  1.486
 I79  N17   C16   aromatic  1.370  0.020  1.370
 I79  C16   H16   single    0.930  0.020  1.080
 I79  C22   N17   single    1.450  0.020  1.450
 I79  C18   C19   single    1.509  0.020  1.509
 I79  C18   H18   single    0.970  0.020  1.090
 I79  C18   H18A  single    0.970  0.020  1.090
 I79  O20   C19   double    1.203  0.020  1.203
 I79  C19   O21   single    1.330  0.020  1.330
 I79  O21   HO21  single    0.850  0.020  0.980
 I79  C23   C22   single    1.499  0.020  1.499
 I79  C22   H22   single    0.970  0.020  1.090
 I79  C22   H22A  single    0.970  0.020  1.090
 I79  C24   C23   aromatic  1.442  0.020  1.442
 I79  C27   C23   aromatic  1.358  0.020  1.358
 I79  C25   C24   aromatic  1.403  0.020  1.403
 I79  C32   C24   aromatic  1.397  0.020  1.397
 I79  C29   C25   aromatic  1.390  0.020  1.390
 I79  C25   S26   aromatic  1.730  0.020  1.730
 I79  S26   C27   aromatic  1.741  0.020  1.741
 I79  C27   C28   single    1.490  0.020  1.490
 I79  C28   H28   single    0.970  0.020  1.090
 I79  C28   H28A  single    0.970  0.020  1.090
 I79  C28   H28B  single    0.970  0.020  1.090
 I79  C30   C29   aromatic  1.381  0.020  1.381
 I79  C29   H29   single    0.930  0.020  1.080
 I79  C30   C31   aromatic  1.396  0.020  1.396
 I79  C30   H30   single    0.930  0.020  1.080
 I79  CL33  C31   single    1.735  0.020  1.735
 I79  C31   C32   aromatic  1.378  0.020  1.378
 I79  C32   H32   single    0.930  0.020  1.080

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
 I79  H1    C1   C6    119.52  3.000
 I79  H1    C1   C2    120.30  3.000
 I79  C6    C1   C2    120.16  3.000
 I79  C9    C2   C3    119.59  3.000
 I79  C3    C2   C1    120.11  3.000
 I79  C9    C2   C1    120.29  3.000
 I79  H3    C3   C4    119.43  3.000
 I79  H3    C3   C2    120.19  3.000
 I79  C4    C3   C2    120.32  3.000
 I79  N8    C4   C5    120.47  3.000
 I79  N8    C4   C3    120.19  3.000
 I79  C5    C4   C3    119.25  3.000
 I79  H5    C5   C6    119.60  3.000
 I79  H5    C5   C4    119.65  3.000
 I79  C6    C5   C4    120.74  3.000
 I79  N7    C6   C5    120.30  3.000
 I79  N7    C6   C1    120.21  3.000
 I79  C5    C6   C1    119.41  3.000
 I79  HN7A  N7   HN7   111.28  3.000
 I79  HN7A  N7   C6    115.43  3.000
 I79  HN7   N7   C6    115.16  3.000
 I79  HN8A  N8   HN8   111.57  3.000
 I79  HN8A  N8   C4    115.78  3.000
 I79  HN8   N8   C4    115.58  3.000
 I79  C14   C9   C10   119.69  3.000
 I79  C10   C9   C2    120.38  3.000
 I79  C14   C9   C2    119.93  3.000
 I79  H10   C10  C11   119.26  3.000
 I79  H10   C10  C9    119.06  3.000
 I79  C11   C10  C9    121.66  3.000
 I79  H11   C11  C12   120.79  3.000
 I79  H11   C11  C10   119.96  3.000
 I79  C12   C11  C10   119.25  3.000
 I79  C15   C12  C13   107.14  3.000
 I79  C15   C12  C11   133.95  3.000
 I79  C13   C12  C11   118.90  3.000
 I79  N17   C13  C14   130.47  3.000
 I79  C14   C13  C12   121.90  3.000
 I79  N17   C13  C12   107.63  3.000
 I79  H14   C14  C13   121.42  3.000
 I79  H14   C14  C9    119.97  3.000
 I79  C13   C14  C9    118.59  3.000
 I79  C18   C15  C16   126.90  3.000
 I79  C18   C15  C12   126.99  3.000
 I79  C16   C15  C12   106.08  3.000
 I79  H16   C16  N17   120.35  3.000
 I79  H16   C16  C15   129.02  3.000
 I79  N17   C16  C15   110.63  3.000
 I79  C22   N17  C16   124.10  3.000
 I79  C22   N17  C13   127.31  3.000
 I79  C16   N17  C13   108.51  3.000
 I79  H18A  C18  H18   105.30  3.000
 I79  H18A  C18  C19   107.95  3.000
 I79  H18   C18  C19   107.89  3.000
 I79  H18A  C18  C15   111.07  3.000
 I79  H18   C18  C15   110.55  3.000
 I79  C19   C18  C15   113.67  3.000
 I79  O21   C19  O20   123.40  3.000
 I79  O21   C19  C18   111.16  3.000
 I79  O20   C19  C18   125.44  3.000
 I79  HO21  O21  C19   110.06  3.000
 I79  H22A  C22  H22   105.85  3.000
 I79  H22A  C22  C23   110.86  3.000
 I79  H22   C22  C23   110.35  3.000
 I79  H22A  C22  N17   109.09  3.000
 I79  H22   C22  N17   108.31  3.000
 I79  C23   C22  N17   112.15  3.000
 I79  C27   C23  C24   112.41  3.000
 I79  C27   C23  C22   124.75  3.000
 I79  C24   C23  C22   122.82  3.000
 I79  C32   C24  C25   118.85  3.000
 I79  C32   C24  C23   128.84  3.000
 I79  C25   C24  C23   112.31  3.000
 I79  C29   C25  S26   127.19  3.000
 I79  S26   C25  C24   110.98  3.000
 I79  C29   C25  C24   121.83  3.000
 I79  C27   S26  C25    91.80  3.000
 I79  C28   C27  S26   117.90  3.000
 I79  C28   C27  C23   129.60  3.000
 I79  S26   C27  C23   112.50  3.000
 I79  H28B  C28  H28A  107.75  3.000
 I79  H28B  C28  H28   107.40  3.000
 I79  H28A  C28  H28   107.68  3.000
 I79  H28B  C28  C27   111.04  3.000
 I79  H28A  C28  C27   111.67  3.000
 I79  H28   C28  C27   111.11  3.000
 I79  H29   C29  C30   120.04  3.000
 I79  H29   C29  C25   121.16  3.000
 I79  C30   C29  C25   118.80  3.000
 I79  H30   C30  C31   120.41  3.000
 I79  H30   C30  C29   120.07  3.000
 I79  C31   C30  C29   119.52  3.000
 I79  CL33  C31  C32   118.94  3.000
 I79  C32   C31  C30   122.18  3.000
 I79  CL33  C31  C30   118.89  3.000
 I79  H32   C32  C31   120.00  3.000
 I79  H32   C32  C24   121.17  3.000
 I79  C31   C32  C24   118.83  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
 I79  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 I79  CONST_04  C4    C3   C2   C1      0.00   0.0  0
 I79  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 I79  CONST_06  C13   C14  C9   C2    180.00   0.0  0
 I79  CONST_07  C11   C10  C9   C2    180.00   0.0  0
 I79  CONST_08  C5    C4   C3   C2      0.00   0.0  0
 I79  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 I79  CONST_12  C6    C5   C4   C3      0.00   0.0  0
 I79  CONST_13  C9    C2   C3   C4    180.00   0.0  0
 I79  CONST_14  C9    C2   C1   C6    180.00   0.0  0
 I79  CONST_15  C12   C13  C14  C9      0.00   0.0  0
 I79  CONST_16  N17   C13  C14  C9    180.00   0.0  0
 I79  CONST_17  C12   C11  C10  C9      0.00   0.0  0
 I79  CONST_18  C13   C14  C9   C10     0.00   0.0  0
 I79  CONST_19  C13   C12  C11  C10     0.00   0.0  0
 I79  CONST_20  C15   C12  C11  C10   180.00   0.0  0
 I79  CONST_21  C14   C9   C10  C11     0.00   0.0  0
 I79  CONST_22  N17   C13  C12  C11   180.00   0.0  0
 I79  CONST_23  C14   C13  C12  C11     0.00   0.0  0
 I79  CONST_24  C16   C15  C12  C11   180.00   0.0  0
 I79  CONST_25  C16   N17  C13  C12     0.00   0.0  0
 I79  CONST_26  N17   C16  C15  C12     0.00   0.0  0
 I79  CONST_27  C16   C15  C12  C13     0.00   0.0  0
 I79  CONST_28  C15   C16  N17  C13     0.00   0.0  0
 I79  CONST_29  C15   C12  C13  C14   180.00   0.0  0
 I79  CONST_30  C16   N17  C13  C14   180.00   0.0  0
 I79  CONST_31  N17   C13  C12  C15     0.00   0.0  0
 I79  CONST_32  C29   C25  C24  C23   180.00   0.0  0
 I79  CONST_33  S26   C25  C24  C23     0.00   0.0  0
 I79  CONST_34  C31   C32  C24  C23   180.00   0.0  0
 I79  CONST_35  C25   S26  C27  C23     0.00   0.0  0
 I79  CONST_36  S26   C27  C23  C24     0.00   0.0  0
 I79  CONST_37  C30   C29  C25  C24     0.00   0.0  0
 I79  CONST_38  C27   S26  C25  C24     0.00   0.0  0
 I79  CONST_39  C30   C31  C32  C24     0.00   0.0  0
 I79  CONST_40  C27   C23  C24  C25     0.00   0.0  0
 I79  CONST_41  C31   C32  C24  C25     0.00   0.0  0
 I79  CONST_42  C31   C30  C29  C25     0.00   0.0  0
 I79  CONST_43  C32   C24  C25  S26   180.00   0.0  0
 I79  CONST_44  C30   C29  C25  S26   180.00   0.0  0
 I79  CONST_45  C32   C24  C23  C27   180.00   0.0  0
 I79  CONST_46  C29   C25  S26  C27   180.00   0.0  0
 I79  CONST_47  C32   C24  C25  C29     0.00   0.0  0
 I79  CONST_48  C32   C31  C30  C29     0.00   0.0  0
 I79  CONST_49  N7    C6   C1   C2    180.00   0.0  0
 I79  CONST_50  N8    C4   C3   C2    180.00   0.0  0
 I79  CONST_51  N7    C6   C5   C4    180.00   0.0  0
 I79  CONST_52  N8    C4   C5   C6    180.00   0.0  0
 I79  CONST_53  C18   C15  C12  C11     0.00   0.0  0
 I79  CONST_54  C22   N17  C13  C12   180.00   0.0  0
 I79  CONST_55  C18   C15  C12  C13   180.00   0.0  0
 I79  CONST_56  C22   N17  C13  C14     0.00   0.0  0
 I79  CONST_57  C22   N17  C16  C15   180.00   0.0  0
 I79  CONST_58  C18   C15  C16  N17   180.00   0.0  0
 I79  CONST_59  C25   C24  C23  C22   180.00   0.0  0
 I79  CONST_60  C32   C24  C23  C22     0.00   0.0  0
 I79  CONST_61  S26   C27  C23  C22   180.00   0.0  0
 I79  CONST_62  C28   C27  C23  C24   180.00   0.0  0
 I79  CONST_63  CL33  C31  C32  C24   180.00   0.0  0
 I79  CONST_64  C28   C27  S26  C25   180.00   0.0  0
 I79  CONST_65  CL33  C31  C30  C29   180.00   0.0  0
 I79  CONST_66  H5    C5   C6   C1    180.00   0.0  0
 I79  CONST_67  H3    C3   C2   C1    180.00   0.0  0
 I79  CONST_68  H14   C14  C9   C2      0.00   0.0  0
 I79  CONST_69  H10   C10  C9   C2      0.00   0.0  0
 I79  CONST_70  H1    C1   C2   C3    180.00   0.0  0
 I79  CONST_71  H11   C11  C10  C9    180.00   0.0  0
 I79  CONST_72  H16   C16  C15  C12   180.00   0.0  0
 I79  CONST_73  H32   C32  C24  C23     0.00   0.0  0
 I79  CONST_74  H29   C29  C25  C24   180.00   0.0  0
 I79  CONST_75  H30   C30  C29  C25   180.00   0.0  0
 I79  CONST_80  HO21  O21  C19  C18   180.00   0.0  0
 I79  Var_01    C23   C22  N17  C13  -111.95  30.0  1
 I79  Var_02    C24   C23  C22  N17    74.59  30.0  2
 I79  Var_03    C19   C18  C15  C12    69.42  30.0  2
 I79  Var_04    H28   C28  C27  C23  -119.31  30.0  2
 I79  Var_05    O20   C19  C18  C15     3.29  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
 I79  plan-1  C1    0.020
 I79  plan-1  C2    0.020
 I79  plan-1  C3    0.020
 I79  plan-1  C4    0.020
 I79  plan-1  C5    0.020
 I79  plan-1  C6    0.020
 I79  plan-1  N7    0.020
 I79  plan-1  N8    0.020
 I79  plan-1  C9    0.020
 I79  plan-1  H1    0.020
 I79  plan-1  H3    0.020
 I79  plan-1  H5    0.020
 I79  plan-2  C2    0.020
 I79  plan-2  C9    0.020
 I79  plan-2  C10   0.020
 I79  plan-2  C11   0.020
 I79  plan-2  C12   0.020
 I79  plan-2  C13   0.020
 I79  plan-2  C14   0.020
 I79  plan-2  C15   0.020
 I79  plan-2  C16   0.020
 I79  plan-2  N17   0.020
 I79  plan-2  C18   0.020
 I79  plan-2  C22   0.020
 I79  plan-2  H10   0.020
 I79  plan-2  H11   0.020
 I79  plan-2  H14   0.020
 I79  plan-2  H16   0.020
 I79  plan-3  C22   0.020
 I79  plan-3  C23   0.020
 I79  plan-3  C24   0.020
 I79  plan-3  C25   0.020
 I79  plan-3  S26   0.020
 I79  plan-3  C27   0.020
 I79  plan-3  C28   0.020
 I79  plan-3  C29   0.020
 I79  plan-3  C30   0.020
 I79  plan-3  C31   0.020
 I79  plan-3  C32   0.020
 I79  plan-3  CL33  0.020
 I79  plan-3  H29   0.020
 I79  plan-3  H30   0.020
 I79  plan-3  H32   0.020
 I79  plan-4  C6    0.020
 I79  plan-4  N7    0.020
 I79  plan-4  HN7   0.020
 I79  plan-4  HN7A  0.020
 I79  plan-5  C4    0.020
 I79  plan-5  N8    0.020
 I79  plan-5  HN8   0.020
 I79  plan-5  HN8A  0.020
 I79  plan-6  C18   0.020
 I79  plan-6  C19   0.020
 I79  plan-6  O20   0.020
 I79  plan-6  O21   0.020
 I79  plan-6  HO21  0.020

