# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:58:22 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  42  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  -0.051   1.4027   3.3784   0.3181
 058  F1   F   F     0  -0.306   2.1483  -2.4577   1.3678
 058  N1   N   NR5   0  -0.587  -1.1008   0.2299   1.0832
 058  O1   O   OH1   0  -0.586  -1.5316  -2.5476   1.5922
 058  CL1  CL  CL    0  -0.134   2.5171   4.6689  -0.0111
 058  C2   C   CR16  0  -0.227   0.1672   3.6979   0.9056
 058  O2   O   O     0  -0.422  -0.3965  -2.9997  -0.2783
 058  C3   C   CR16  0  -0.310  -0.7476   2.7113   1.1970
 058  C4   C   CR16  0  -0.328   1.7500   2.0882  -0.0006
 058  C5   C   CR5   0   0.206  -0.3479  -0.8077   0.5773
 058  C6   C   CR5   0   0.042   0.8384  -0.3317   0.0728
 058  C7   C   CR56  0   0.065   0.8209   1.0785   0.2765
 058  C8   C   CR56  0   0.370  -0.4080   1.3917   0.8881
 058  C9   C   CH2   0  -0.390  -2.4973   0.1723   1.4833
 058  C10  C   C     0   0.485  -0.7598  -2.2222   0.5682
 058  C11  C   CR6   0  -0.186   1.9495  -1.0786  -0.5227
 058  C12  C   CR16  0  -0.289   2.4456  -0.7348  -1.7802
 058  C13  C   CR16  0  -0.259   3.5232  -1.4069  -2.3382
 058  C14  C   CR16  0  -0.246   4.1298  -2.4418  -1.6402
 058  C15  C   CR16  0  -0.406   3.6602  -2.8020  -0.3842
 058  C16  C   CR6   0   0.511   2.5880  -2.1148   0.1462
 058  C17  C   CR6   0   0.094  -3.4020  -0.2772   0.3636
 058  C18  C   CR16  0  -0.279  -3.2786   0.2679  -0.9124
 058  C19  C   CR16  0  -0.239  -4.1297  -0.1309  -1.9323
 058  C20  C   CR16  0  -0.266  -5.1173  -1.0774  -1.6873
 058  C21  C   CR16  0  -0.242  -5.2467  -1.6226  -0.4179
 058  C22  C   CR16  0  -0.301  -4.3890  -1.2265   0.6007
 058  HO1  H   HOH1  0   0.494  -1.8101  -3.4737   1.5208
 058  H2   H   HCR6  0   0.282  -0.0680   4.7281   1.1345
 058  H3   H   HCR6  0   0.282  -1.6897   2.9766   1.6569
 058  H4   H   HCR6  0   0.275   2.7065   1.8579  -0.4511
 058  H9   H   HCH2  0   0.291  -2.6114  -0.4684   2.3550
 058  H9A  H   HCH2  0   0.294  -2.7786   1.1751   1.8031
 058  H12  H   HCR6  0   0.268   1.9666   0.0634  -2.3332
 058  H13  H   HCR6  0   0.264   3.8834  -1.1249  -3.3181
 058  H14  H   HCR6  0   0.269   4.9691  -2.9732  -2.0684
 058  H15  H   HCR6  0   0.280   4.1230  -3.6009   0.1802
 058  H18  H   HCR6  0   0.253  -2.5168   1.0117  -1.1160
 058  H19  H   HCR6  0   0.258  -4.0240   0.3000  -2.9196
 058  H20  H   HCR6  0   0.258  -5.7811  -1.3888  -2.4835
 058  H21  H   HCR6  0   0.258  -6.0113  -2.3630  -0.2209
 058  H22  H   HCR6  0   0.254  -4.4872  -1.6631   1.5874

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  1.405  0.020  1.405
 058  C4   C1   aromatic  1.374  0.020  1.374
 058  C1   CL1  single    1.737  0.020  1.737
 058  F1   C16  single    1.343  0.020  1.343
 058  C9   N1   single    1.454  0.020  1.454
 058  C5   N1   aromatic  1.378  0.020  1.378
 058  N1   C8   aromatic  1.367  0.020  1.367
 058  C10  O1   single    1.323  0.020  1.323
 058  O1   HO1  single    0.850  0.020  0.980
 058  C2   C3   aromatic  1.377  0.020  1.377
 058  C2   H2   single    0.930  0.020  1.080
 058  O2   C10  double    1.205  0.020  1.205
 058  C8   C3   aromatic  1.397  0.020  1.397
 058  C3   H3   single    0.930  0.020  1.080
 058  C7   C4   aromatic  1.400  0.020  1.400
 058  C4   H4   single    0.930  0.020  1.080
 058  C5   C6   aromatic  1.374  0.020  1.374
 058  C10  C5   single    1.473  0.020  1.473
 058  C6   C11  single    1.465  0.020  1.465
 058  C6   C7   aromatic  1.425  0.020  1.425
 058  C8   C7   aromatic  1.408  0.020  1.408
 058  C17  C9   single    1.508  0.020  1.508
 058  C9   H9   single    0.970  0.020  1.090
 058  C9   H9A  single    0.970  0.020  1.090
 058  C16  C11  aromatic  1.389  0.020  1.389
 058  C11  C12  aromatic  1.395  0.020  1.395
 058  C12  C13  aromatic  1.387  0.020  1.387
 058  C12  H12  single    0.930  0.020  1.080
 058  C14  C13  aromatic  1.388  0.020  1.388
 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  1.379  0.020  1.379
 058  C15  H15  single    0.930  0.020  1.080
 058  C18  C17  aromatic  1.393  0.020  1.393
 058  C17  C22  aromatic  1.390  0.020  1.390
 058  C19  C18  aromatic  1.387  0.020  1.387
 058  C18  H18  single    0.930  0.020  1.080
 058  C19  C20  aromatic  1.390  0.020  1.390
 058  C19  H19  single    0.930  0.020  1.080
 058  C20  C21  aromatic  1.388  0.020  1.388
 058  C20  H20  single    0.930  0.020  1.080
 058  C21  C22  aromatic  1.389  0.020  1.389
 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   122.21  3.000
 058  C4   C1   CL1  119.45  3.000
 058  C2   C1   CL1  118.33  3.000
 058  C9   N1   C8   124.05  3.000
 058  C8   N1   C5   108.10  3.000
 058  C9   N1   C5   126.58  3.000
 058  HO1  O1   C10  110.21  3.000
 058  H2   C2   C3   119.57  3.000
 058  H2   C2   C1   119.77  3.000
 058  C3   C2   C1   120.66  3.000
 058  H3   C3   C8   122.51  3.000
 058  H3   C3   C2   119.55  3.000
 058  C8   C3   C2   117.94  3.000
 058  H4   C4   C7   121.04  3.000
 058  H4   C4   C1   121.34  3.000
 058  C7   C4   C1   117.63  3.000
 058  C10  C5   C6   124.87  3.000
 058  C10  C5   N1   124.91  3.000
 058  C6   C5   N1   110.22  3.000
 058  C11  C6   C7   124.88  3.000
 058  C7   C6   C5   106.25  3.000
 058  C11  C6   C5   128.85  3.000
 058  C8   C7   C6   107.04  3.000
 058  C8   C7   C4   120.32  3.000
 058  C6   C7   C4   132.64  3.000
 058  C7   C8   C3   121.22  3.000
 058  C7   C8   N1   108.38  3.000
 058  C3   C8   N1   130.40  3.000
 058  H9A  C9   H9   106.25  3.000
 058  H9A  C9   C17  109.71  3.000
 058  H9   C9   C17  110.89  3.000
 058  H9A  C9   N1   107.00  3.000
 058  H9   C9   N1   110.16  3.000
 058  C17  C9   N1   112.56  3.000
 058  C5   C10  O2   122.64  3.000
 058  C5   C10  O1   113.23  3.000
 058  O2   C10  O1   124.11  3.000
 058  C16  C11  C12  117.04  3.000
 058  C12  C11  C6   120.70  3.000
 058  C16  C11  C6   122.22  3.000
 058  H12  C12  C13  119.70  3.000
 058  H12  C12  C11  119.00  3.000
 058  C13  C12  C11  121.30  3.000
 058  H13  C13  C14  120.30  3.000
 058  H13  C13  C12  119.79  3.000
 058  C14  C13  C12  119.90  3.000
 058  H14  C14  C15  119.54  3.000
 058  H14  C14  C13  120.42  3.000
 058  C15  C14  C13  120.04  3.000
 058  H15  C15  C16  119.98  3.000
 058  H15  C15  C14  121.24  3.000
 058  C16  C15  C14  118.78  3.000
 058  C15  C16  C11  122.94  3.000
 058  C15  C16  F1   118.50  3.000
 058  C11  C16  F1   118.56  3.000
 058  C22  C17  C18  119.11  3.000
 058  C22  C17  C9   120.19  3.000
 058  C18  C17  C9   120.69  3.000
 058  H18  C18  C19  119.37  3.000
 058  H18  C18  C17  120.18  3.000
 058  C19  C18  C17  120.45  3.000
 058  H19  C19  C20  120.09  3.000
 058  H19  C19  C18  119.76  3.000
 058  C20  C19  C18  120.15  3.000
 058  H20  C20  C21  120.18  3.000
 058  H20  C20  C19  120.14  3.000
 058  C21  C20  C19  119.68  3.000
 058  H21  C21  C22  119.85  3.000
 058  H21  C21  C20  120.07  3.000
 058  C22  C21  C20  120.08  3.000
 058  H22  C22  C21  119.79  3.000
 058  H22  C22  C17  119.67  3.000
 058  C21  C22  C17  120.54  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  CONST_64  HO1  O1   C10  C5   180.00   0.0  0
 058  Var_01    C18  C17  C9   N1   -46.31  30.0  3
 058  Var_02    C17  C9   N1   C5   -57.56  30.0  2
 058  Var_03    O1   C10  C5   N1   -31.36  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
 058  plan-4  HO1  0.020

