# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 23:41:24 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-benzyl-5-chloro-3-(2-fluorophenyl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1n(Cc2ccccc2)c3ccc(Cl)cc3c1c4ccccc4F
#
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
 058  058  '1-benzyl-5-chloro-3-(2-fluorophenyl)-1H-indole-2-carboxylic acid'  ligand  41  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_058
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
 058  C1   C   CR6    0  -0.050   1.0574   3.1405  -0.6153
 058  F1   F   F      0  -0.307   2.4537  -2.2241   1.8398
 058  N1   N   NR5    0  -0.568  -1.0066   0.0388   1.0609
 058  O1   O   OC    -1  -0.581  -1.0036  -2.6025   2.3353
 058  CL1  CL  CL     0  -0.147   2.0015   4.4182  -1.3269
 058  C2   C   CR16   0  -0.244  -0.1917   3.4629  -0.0685
 058  O2   O   O      0  -0.575  -0.0876  -3.3112   0.4253
 058  C3   C   CR16   0  -0.306  -0.9686   2.4793   0.5118
 058  C4   C   CR16   0  -0.348   1.5598   1.8574  -0.6115
 058  C5   C   CR5    0   0.160  -0.1584  -1.0150   0.8120
 058  C6   C   CR5    0  -0.026   0.9502  -0.5569   0.1368
 058  C7   C   CR56   0   0.075   0.7754   0.8513  -0.0391
 058  C8   C   CR56   0   0.366  -0.4691   1.1797   0.5329
 058  C9   C   CH2    0  -0.425  -2.3667  -0.0284   1.5533
 058  C10  C   C      0   0.383  -0.4482  -2.4416   1.2326
 058  C11  C   CR6    0  -0.153   2.1190  -1.3199  -0.3043
 058  C12  C   CR16   0  -0.305   2.5875  -1.2270  -1.6159
 058  C13  C   CR16   0  -0.261   3.7140  -1.9194  -2.0379
 058  C14  C   CR16   0  -0.254   4.4029  -2.7288  -1.1461
 058  C15  C   CR16   0  -0.410   3.9651  -2.8380   0.1675
 058  C16  C   CR6    0   0.501   2.8452  -2.1328   0.5583
 058  C17  C   CR6    0   0.122  -3.3855  -0.0019   0.4410
 058  C18  C   CR16   0  -0.318  -4.4462   0.8959   0.4816
 058  C19  C   CR16   0  -0.240  -5.4017   0.9135  -0.5277
 058  C20  C   CR16   0  -0.269  -5.3004   0.0331  -1.5948
 058  C21  C   CR16   0  -0.239  -4.2412  -0.8660  -1.6448
 058  C22  C   CR16   0  -0.287  -3.2922  -0.8851  -0.6334
 058  H2   H   HCR6   0   0.272  -0.5468   4.4837  -0.0973
 058  H3   H   HCR6   0   0.267  -1.9309   2.7323   0.9362
 058  H4   H   HCR6   0   0.266   2.5290   1.6358  -1.0389
 058  H9   H   HCH2   0   0.301  -2.4589  -0.9346   2.1468
 058  H9A  H   HCH2   0   0.274  -2.5303   0.8085   2.2348
 058  H12  H   HCR6   0   0.261   2.0461  -0.6082  -2.3207
 058  H13  H   HCR6   0   0.257   4.0471  -1.8301  -3.0632
 058  H14  H   HCR6   0   0.264   5.2806  -3.2750  -1.4649
 058  H15  H   HCR6   0   0.274   4.4909  -3.4579   0.8821
 058  H18  H   HCR6   0   0.252  -4.5282   1.5935   1.3073
 058  H19  H   HCR6   0   0.256  -6.2199   1.6204  -0.4815
 058  H20  H   HCR6   0   0.256  -6.0395   0.0470  -2.3851
 058  H21  H   HCR6   0   0.257  -4.1550  -1.5561  -2.4741
 058  H22  H   HCR6   0   0.249  -2.4733  -1.5934  -0.6902

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
 058  C1   C2   aromatic  1.401  0.020  1.401
 058  C4   C1   aromatic  1.378  0.020  1.378
 058  C1   CL1  single    1.741  0.020  1.741
 058  F1   C16  single    1.343  0.020  1.343
 058  C9   N1   single    1.448  0.020  1.448
 058  C5   N1   aromatic  1.375  0.020  1.375
 058  N1   C8   aromatic  1.367  0.020  1.367
 058  C10  O1   deloc     1.245  0.020  1.245
 058  C2   C3   aromatic  1.381  0.020  1.381
 058  C2   H2   single    0.930  0.020  1.080
 058  O2   C10  deloc     1.240  0.020  1.240
 058  C8   C3   aromatic  1.392  0.020  1.392
 058  C3   H3   single    0.930  0.020  1.080
 058  C7   C4   aromatic  1.398  0.020  1.398
 058  C4   H4   single    0.930  0.020  1.080
 058  C5   C6   aromatic  1.376  0.020  1.376
 058  C10  C5   single    1.515  0.020  1.515
 058  C6   C11  single    1.464  0.020  1.464
 058  C6   C7   aromatic  1.430  0.020  1.430
 058  C8   C7   aromatic  1.409  0.020  1.409
 058  C17  C9   single    1.509  0.020  1.509
 058  C9   H9   single    0.970  0.020  1.090
 058  C9   H9A  single    0.970  0.020  1.090
 058  C16  C11  aromatic  1.390  0.020  1.390
 058  C11  C12  aromatic  1.396  0.020  1.396
 058  C12  C13  aromatic  1.388  0.020  1.388
 058  C12  H12  single    0.930  0.020  1.080
 058  C14  C13  aromatic  1.387  0.020  1.387
 058  C13  H13  single    0.930  0.020  1.080
 058  C15  C14  aromatic  1.389  0.020  1.389
 058  C14  H14  single    0.930  0.020  1.080
 058  C16  C15  aromatic  1.380  0.020  1.380
 058  C15  H15  single    0.930  0.020  1.080
 058  C18  C17  aromatic  1.390  0.020  1.390
 058  C17  C22  aromatic  1.394  0.020  1.394
 058  C19  C18  aromatic  1.390  0.020  1.390
 058  C18  H18  single    0.930  0.020  1.080
 058  C19  C20  aromatic  1.387  0.020  1.387
 058  C19  H19  single    0.930  0.020  1.080
 058  C20  C21  aromatic  1.390  0.020  1.390
 058  C20  H20  single    0.930  0.020  1.080
 058  C21  C22  aromatic  1.387  0.020  1.387
 058  C21  H21  single    0.930  0.020  1.080
 058  C22  H22  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
 058  C4   C1   C2   122.56  3.000
 058  C4   C1   CL1  119.14  3.000
 058  C2   C1   CL1  118.30  3.000
 058  C9   N1   C8   122.63  3.000
 058  C8   N1   C5   109.09  3.000
 058  C9   N1   C5   127.24  3.000
 058  H2   C2   C3   119.92  3.000
 058  H2   C2   C1   119.98  3.000
 058  C3   C2   C1   120.10  3.000
 058  H3   C3   C8   122.10  3.000
 058  H3   C3   C2   119.91  3.000
 058  C8   C3   C2   117.99  3.000
 058  H4   C4   C7   121.11  3.000
 058  H4   C4   C1   121.07  3.000
 058  C7   C4   C1   117.82  3.000
 058  C10  C5   C6   127.13  3.000
 058  C10  C5   N1   123.58  3.000
 058  C6   C5   N1   109.29  3.000
 058  C11  C6   C7   125.02  3.000
 058  C7   C6   C5   106.84  3.000
 058  C11  C6   C5   128.12  3.000
 058  C8   C7   C6   106.72  3.000
 058  C8   C7   C4   119.61  3.000
 058  C6   C7   C4   133.67  3.000
 058  C7   C8   C3   121.90  3.000
 058  C7   C8   N1   108.03  3.000
 058  C3   C8   N1   130.07  3.000
 058  H9A  C9   H9   106.59  3.000
 058  H9A  C9   C17  110.22  3.000
 058  H9   C9   C17  111.09  3.000
 058  H9A  C9   N1   108.52  3.000
 058  H9   C9   N1   107.70  3.000
 058  C17  C9   N1   112.51  3.000
 058  C5   C10  O2   115.08  3.000
 058  C5   C10  O1   116.93  3.000
 058  O2   C10  O1   127.99  3.000
 058  C16  C11  C12  116.53  3.000
 058  C12  C11  C6   121.10  3.000
 058  C16  C11  C6   122.34  3.000
 058  H12  C12  C13  119.53  3.000
 058  H12  C12  C11  118.80  3.000
 058  C13  C12  C11  121.66  3.000
 058  H13  C13  C14  120.30  3.000
 058  H13  C13  C12  119.80  3.000
 058  C14  C13  C12  119.90  3.000
 058  H14  C14  C15  119.66  3.000
 058  H14  C14  C13  120.53  3.000
 058  C15  C14  C13  119.82  3.000
 058  H15  C15  C16  120.00  3.000
 058  H15  C15  C14  121.09  3.000
 058  C16  C15  C14  118.92  3.000
 058  C15  C16  C11  123.17  3.000
 058  C15  C16  F1   118.17  3.000
 058  C11  C16  F1   118.65  3.000
 058  C22  C17  C18  118.87  3.000
 058  C22  C17  C9   120.79  3.000
 058  C18  C17  C9   120.33  3.000
 058  H18  C18  C19  119.54  3.000
 058  H18  C18  C17  119.70  3.000
 058  C19  C18  C17  120.76  3.000
 058  H19  C19  C20  120.17  3.000
 058  H19  C19  C18  119.80  3.000
 058  C20  C19  C18  120.03  3.000
 058  H20  C20  C21  120.16  3.000
 058  H20  C20  C19  120.25  3.000
 058  C21  C20  C19  119.59  3.000
 058  H21  C21  C22  119.70  3.000
 058  H21  C21  C20  120.04  3.000
 058  C22  C21  C20  120.26  3.000
 058  H22  C22  C21  119.18  3.000
 058  H22  C22  C17  120.32  3.000
 058  C21  C22  C17  120.50  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
 058  CONST_01  C8   C3   C2   C1      0.00   0.0  0
 058  CONST_02  C6   C7   C4   C1    180.00   0.0  0
 058  CONST_03  C8   C7   C4   C1      0.00   0.0  0
 058  CONST_04  C11  C6   C5   N1    180.00   0.0  0
 058  CONST_05  C7   C6   C5   N1      0.00   0.0  0
 058  CONST_06  C2   C3   C8   N1    180.00   0.0  0
 058  CONST_07  C4   C7   C8   N1    180.00   0.0  0
 058  CONST_08  C6   C7   C8   N1      0.00   0.0  0
 058  CONST_09  C7   C4   C1   C2      0.00   0.0  0
 058  CONST_10  C7   C8   C3   C2      0.00   0.0  0
 058  CONST_11  C4   C1   C2   C3      0.00   0.0  0
 058  CONST_12  C5   N1   C8   C3    180.00   0.0  0
 058  CONST_13  C4   C7   C8   C3      0.00   0.0  0
 058  CONST_14  C6   C7   C8   C3    180.00   0.0  0
 058  CONST_15  C5   C6   C7   C4    180.00   0.0  0
 058  CONST_16  C11  C6   C7   C4      0.00   0.0  0
 058  CONST_17  C7   C8   N1   C5      0.00   0.0  0
 058  CONST_20  C8   C7   C6   C5      0.00   0.0  0
 058  CONST_21  C8   N1   C5   C6      0.00   0.0  0
 058  CONST_22  C15  C16  C11  C6    180.00   0.0  0
 058  CONST_23  C13  C12  C11  C6    180.00   0.0  0
 058  CONST_26  C11  C6   C7   C8    180.00   0.0  0
 058  CONST_27  C14  C15  C16  C11     0.00   0.0  0
 058  CONST_28  C14  C13  C12  C11     0.00   0.0  0
 058  CONST_29  C15  C16  C11  C12     0.00   0.0  0
 058  CONST_30  C15  C14  C13  C12     0.00   0.0  0
 058  CONST_31  C16  C11  C12  C13     0.00   0.0  0
 058  CONST_32  C16  C15  C14  C13     0.00   0.0  0
 058  CONST_33  C20  C19  C18  C17     0.00   0.0  0
 058  CONST_34  C20  C21  C22  C17     0.00   0.0  0
 058  CONST_35  C21  C22  C17  C18     0.00   0.0  0
 058  CONST_36  C21  C20  C19  C18     0.00   0.0  0
 058  CONST_37  C22  C17  C18  C19     0.00   0.0  0
 058  CONST_38  C22  C21  C20  C19     0.00   0.0  0
 058  CONST_39  C6   C11  C16  F1      0.00   0.0  0
 058  CONST_40  C12  C11  C16  F1    180.00   0.0  0
 058  CONST_41  C14  C15  C16  F1    180.00   0.0  0
 058  CONST_42  C3   C2   C1   CL1   180.00   0.0  0
 058  CONST_43  C7   C4   C1   CL1   180.00   0.0  0
 058  CONST_44  C9   N1   C8   C3      0.00   0.0  0
 058  CONST_45  C9   N1   C5   C6    180.00   0.0  0
 058  CONST_46  C10  C5   C6   C7    180.00   0.0  0
 058  CONST_47  C9   N1   C8   C7    180.00   0.0  0
 058  CONST_48  C10  C5   N1   C8    180.00   0.0  0
 058  CONST_49  C19  C18  C17  C9    180.00   0.0  0
 058  CONST_50  C21  C22  C17  C9    180.00   0.0  0
 058  CONST_51  C11  C6   C5   C10     0.00   0.0  0
 058  CONST_52  H3   C3   C2   C1    180.00   0.0  0
 058  CONST_53  H4   C4   C1   C2    180.00   0.0  0
 058  CONST_54  H2   C2   C1   C4    180.00   0.0  0
 058  CONST_55  H12  C12  C11  C6      0.00   0.0  0
 058  CONST_56  H15  C15  C16  C11   180.00   0.0  0
 058  CONST_57  H13  C13  C12  C11   180.00   0.0  0
 058  CONST_58  H14  C14  C13  C12   180.00   0.0  0
 058  CONST_59  H19  C19  C18  C17   180.00   0.0  0
 058  CONST_60  H21  C21  C22  C17   180.00   0.0  0
 058  CONST_61  H22  C22  C17  C18   180.00   0.0  0
 058  CONST_62  H20  C20  C19  C18   180.00   0.0  0
 058  CONST_63  H18  C18  C19  C20   180.00   0.0  0
 058  Var_01    C18  C17  C9   N1   -129.14  30.0  2
 058  Var_02    C17  C9   N1   C5    -95.06  30.0  2
 058  Var_03    O1   C10  C5   N1    -37.82  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
 058  plan-1  F1   0.020
 058  plan-1  C6   0.020
 058  plan-1  C11  0.020
 058  plan-1  C12  0.020
 058  plan-1  C13  0.020
 058  plan-1  C14  0.020
 058  plan-1  C15  0.020
 058  plan-1  C16  0.020
 058  plan-1  H12  0.020
 058  plan-1  H13  0.020
 058  plan-1  H14  0.020
 058  plan-1  H15  0.020
 058  plan-2  C9   0.020
 058  plan-2  C17  0.020
 058  plan-2  C18  0.020
 058  plan-2  C19  0.020
 058  plan-2  C20  0.020
 058  plan-2  C21  0.020
 058  plan-2  C22  0.020
 058  plan-2  H18  0.020
 058  plan-2  H19  0.020
 058  plan-2  H20  0.020
 058  plan-2  H21  0.020
 058  plan-2  H22  0.020
 058  plan-3  C1   0.020
 058  plan-3  N1   0.020
 058  plan-3  CL1  0.020
 058  plan-3  C2   0.020
 058  plan-3  C3   0.020
 058  plan-3  C4   0.020
 058  plan-3  C5   0.020
 058  plan-3  C6   0.020
 058  plan-3  C7   0.020
 058  plan-3  C8   0.020
 058  plan-3  C9   0.020
 058  plan-3  C10  0.020
 058  plan-3  C11  0.020
 058  plan-3  H2   0.020
 058  plan-3  H3   0.020
 058  plan-3  H4   0.020
 058  plan-4  O1   0.020
 058  plan-4  O2   0.020
 058  plan-4  C5   0.020
 058  plan-4  C10  0.020

