# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 07:34:32 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 6-iodanyl-1~{H}-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c2cc(I)ccc2c1
#
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
 Y6S  Y6S  "6-iodanyl-1~{H}-indole-2-carboxylic acid"  ligand  18  13  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y6S
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
 Y6S  C10  C  C      0   0.362  29.7153  -39.4226  -6.4453
 Y6S  C01  C  CR6    0  -0.251  23.9212  -38.4085  -7.6571
 Y6S  C02  C  CR16   0  -0.272  25.1515  -37.8021  -7.5100
 Y6S  C03  C  CR56   0   0.352  26.2243  -38.6379  -7.2006
 Y6S  C04  C  CR56   0   0.070  26.0782  -40.0377  -7.0421
 Y6S  C05  C  CR16   0  -0.337  24.8082  -40.6036  -7.2011
 Y6S  C06  C  CR16   0  -0.245  23.7339  -39.7921  -7.5080
 Y6S  C08  C  CR5    0   0.171  28.2329  -39.4845  -6.7149
 Y6S  C09  C  CR15   0  -0.430  27.3714  -40.5500  -6.7341
 Y6S  N07  N  NR15   0  -0.709  27.5333  -38.3420  -6.9957
 Y6S  O11  O  O      0  -0.594  30.2172  -38.2828  -6.4893
 Y6S  O12  O  OC    -1  -0.577  30.2747  -40.5065  -6.2086
 Y6S  H1   H  HCR6   0   0.278  25.2889  -36.7352  -7.6267
 Y6S  H2   H  HCR6   0   0.252  24.6604  -41.6702  -7.0864
 Y6S  H3   H  HCR6   0   0.266  22.7514  -40.2266  -7.6310
 Y6S  H4   H  HCR5   0   0.242  27.6321  -41.5795  -6.5479
 Y6S  H5   H  HNR5   0   0.396  27.9606  -37.4311  -7.0459
 Y6S  I13  I  I      0   0.026  22.2511  -37.2106  -8.1256

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
 Y6S  I13  C01  single    2.108  0.020  2.108
 Y6S  C01  C06  aromatic  1.404  0.020  1.404
 Y6S  C01  C02  aromatic  1.379  0.020  1.379
 Y6S  C06  C05  aromatic  1.381  0.020  1.381
 Y6S  C02  C03  aromatic  1.395  0.020  1.395
 Y6S  C05  C04  aromatic  1.399  0.020  1.399
 Y6S  C03  C04  aromatic  1.416  0.020  1.416
 Y6S  C03  N07  aromatic  1.358  0.020  1.358
 Y6S  O11  C10  deloc     1.246  0.020  1.246
 Y6S  C04  C09  aromatic  1.425  0.020  1.425
 Y6S  N07  C08  aromatic  1.369  0.020  1.369
 Y6S  C09  C08  aromatic  1.370  0.020  1.370
 Y6S  C08  C10  single    1.508  0.020  1.508
 Y6S  C10  O12  deloc     1.242  0.020  1.242
 Y6S  C02  H1   single    0.930  0.020  1.080
 Y6S  C05  H2   single    0.930  0.020  1.080
 Y6S  C06  H3   single    0.930  0.020  1.080
 Y6S  C09  H4   single    0.930  0.020  1.080
 Y6S  N07  H5   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
 Y6S  O12  C10  O11  128.56  3.000
 Y6S  O12  C10  C08  116.16  3.000
 Y6S  O11  C10  C08  115.28  3.000
 Y6S  I13  C01  C06  118.55  3.000
 Y6S  C06  C01  C02  122.74  3.000
 Y6S  I13  C01  C02  118.72  3.000
 Y6S  H1   C02  C03  121.14  3.000
 Y6S  H1   C02  C01  122.36  3.000
 Y6S  C03  C02  C01  116.50  3.000
 Y6S  N07  C03  C04  107.33  3.000
 Y6S  N07  C03  C02  130.13  3.000
 Y6S  C04  C03  C02  122.53  3.000
 Y6S  C09  C04  C05  134.66  3.000
 Y6S  C09  C04  C03  106.62  3.000
 Y6S  C05  C04  C03  118.72  3.000
 Y6S  H2   C05  C06  119.75  3.000
 Y6S  H2   C05  C04  120.67  3.000
 Y6S  C06  C05  C04  119.58  3.000
 Y6S  H3   C06  C05  119.74  3.000
 Y6S  H3   C06  C01  120.33  3.000
 Y6S  C05  C06  C01  119.93  3.000
 Y6S  N07  C08  C09  108.95  3.000
 Y6S  C09  C08  C10  130.73  3.000
 Y6S  N07  C08  C10  120.32  3.000
 Y6S  H4   C09  C08  126.01  3.000
 Y6S  H4   C09  C04  126.89  3.000
 Y6S  C08  C09  C04  107.10  3.000
 Y6S  H5   N07  C08  123.24  3.000
 Y6S  H5   N07  C03  126.76  3.000
 Y6S  C08  N07  C03  109.99  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
 Y6S  CONST_01  C04  C05  C06  C01     0.00   0.0  0
 Y6S  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 Y6S  CONST_03  N07  C03  C02  C01   180.00   0.0  0
 Y6S  CONST_04  C05  C06  C01  C02     0.00   0.0  0
 Y6S  CONST_05  C05  C04  C03  C02     0.00   0.0  0
 Y6S  CONST_06  C09  C04  C03  C02   180.00   0.0  0
 Y6S  CONST_07  C08  N07  C03  C02   180.00   0.0  0
 Y6S  CONST_08  C06  C01  C02  C03     0.00   0.0  0
 Y6S  CONST_09  C06  C05  C04  C03     0.00   0.0  0
 Y6S  CONST_10  C08  C09  C04  C03     0.00   0.0  0
 Y6S  CONST_11  C09  C08  N07  C03     0.00   0.0  0
 Y6S  CONST_12  C08  N07  C03  C04     0.00   0.0  0
 Y6S  CONST_13  N07  C08  C09  C04     0.00   0.0  0
 Y6S  CONST_14  N07  C03  C04  C05   180.00   0.0  0
 Y6S  CONST_15  C08  C09  C04  C05   180.00   0.0  0
 Y6S  CONST_16  C09  C04  C05  C06   180.00   0.0  0
 Y6S  CONST_17  N07  C03  C04  C09     0.00   0.0  0
 Y6S  CONST_18  C03  N07  C08  C10   180.00   0.0  0
 Y6S  CONST_19  C04  C09  C08  C10   180.00   0.0  0
 Y6S  CONST_20  I13  C01  C02  C03   180.00   0.0  0
 Y6S  CONST_21  I13  C01  C06  C05   180.00   0.0  0
 Y6S  CONST_22  H2   C05  C06  C01   180.00   0.0  0
 Y6S  CONST_23  H3   C06  C01  C02   180.00   0.0  0
 Y6S  CONST_24  H5   N07  C03  C02     0.00   0.0  0
 Y6S  CONST_25  H2   C05  C04  C03   180.00   0.0  0
 Y6S  CONST_26  H4   C09  C04  C03   180.00   0.0  0
 Y6S  CONST_27  H3   C06  C05  C04   180.00   0.0  0
 Y6S  CONST_28  H1   C02  C03  C04   180.00   0.0  0
 Y6S  CONST_29  H5   N07  C03  C04   180.00   0.0  0
 Y6S  CONST_30  H4   C09  C04  C05     0.00   0.0  0
 Y6S  CONST_31  H1   C02  C01  C06   180.00   0.0  0
 Y6S  CONST_32  H2   C05  C04  C09     0.00   0.0  0
 Y6S  CONST_33  H5   N07  C08  C09   180.00   0.0  0
 Y6S  CONST_34  H1   C02  C03  N07     0.00   0.0  0
 Y6S  CONST_35  H4   C09  C08  N07   180.00   0.0  0
 Y6S  Var_01    O11  C10  C08  C09  -179.30  30.0  2
 Y6S  Var_02    O12  C10  C08  C09     0.65  30.0  2
 Y6S  Var_03    O11  C10  C08  N07     0.56  30.0  2
 Y6S  Var_04    O12  C10  C08  N07  -179.49  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
 Y6S  plan-1  C10  0.020
 Y6S  plan-1  C01  0.020
 Y6S  plan-1  C02  0.020
 Y6S  plan-1  C03  0.020
 Y6S  plan-1  C04  0.020
 Y6S  plan-1  C05  0.020
 Y6S  plan-1  C06  0.020
 Y6S  plan-1  C08  0.020
 Y6S  plan-1  C09  0.020
 Y6S  plan-1  N07  0.020
 Y6S  plan-1  H1   0.020
 Y6S  plan-1  H2   0.020
 Y6S  plan-1  H3   0.020
 Y6S  plan-1  H4   0.020
 Y6S  plan-1  H5   0.020
 Y6S  plan-1  I13  0.020
 Y6S  plan-2  C10  0.020
 Y6S  plan-2  C08  0.020
 Y6S  plan-2  O11  0.020
 Y6S  plan-2  O12  0.020

