# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 09:45:15 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 1~{H}-indol-6-ylboronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1ccc2cc[nH]c2c1
#
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
 JB8  JB8  '1~{H}-indol-6-ylboronic acid'  ligand  20  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JB8
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
 JB8  C10  C  CR15  0  -0.026  -3.4335   0.5587  -0.0031
 JB8  O01  O  OH1   0  -0.641   2.9797   1.5292   0.0017
 JB8  B02  B  B     0   0.499   2.6175   0.2141   0.0073
 JB8  C03  C  CR6   0  -0.111   1.0904  -0.1286   0.0031
 JB8  C04  C  CR16  0  -0.370   0.1427   0.8892   0.0032
 JB8  C05  C  CR56  0   0.369  -1.2062   0.5493   0.0005
 JB8  C06  C  CR56  0   0.035  -1.6469  -0.7936  -0.0024
 JB8  C07  C  CR16  0  -0.320  -0.6864  -1.8140  -0.0025
 JB8  C08  C  CR16  0  -0.336   0.6497  -1.4735   0.0004
 JB8  C09  C  CR15  0  -0.418  -3.0739  -0.7602  -0.0048
 JB8  N11  N  NR15  0  -0.679  -2.3188   1.3428  -0.0000
 JB8  O12  O  OH1   0  -0.640   3.5053  -0.8209   0.0174
 JB8  H1   H  HCR5  0   0.281  -4.4155   1.0044  -0.0045
 JB8  H2   H  HOH1  0   0.481   3.9263   1.7013   0.0069
 JB8  H3   H  HCR6  0   0.254   0.4411   1.9309   0.0054
 JB8  H4   H  HCR6  0   0.241  -0.9882  -2.8545  -0.0045
 JB8  H5   H  HCR6  0   0.240   1.3849  -2.2682   0.0003
 JB8  H6   H  HCR5  0   0.249  -3.7483  -1.6013  -0.0072
 JB8  H7   H  HNR5  0   0.410  -2.3223   2.3489   0.0016
 JB8  H8   H  HOH1  0   0.481   4.4351  -0.5741   0.0209

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
 JB8  C10  C09  aromatic  1.367  0.020  1.367
 JB8  C10  N11  aromatic  1.363  0.020  1.363
 JB8  C09  C06  aromatic  1.427  0.020  1.427
 JB8  N11  C05  aromatic  1.367  0.020  1.367
 JB8  C06  C05  aromatic  1.413  0.020  1.413
 JB8  C06  C07  aromatic  1.401  0.020  1.401
 JB8  C05  C04  aromatic  1.391  0.020  1.391
 JB8  C07  C08  aromatic  1.379  0.020  1.379
 JB8  C04  C03  aromatic  1.391  0.020  1.391
 JB8  C08  C03  aromatic  1.415  0.020  1.415
 JB8  C03  B02  single    1.565  0.020  1.565
 JB8  O12  B02  single    1.364  0.020  1.364
 JB8  O01  B02  single    1.364  0.020  1.364
 JB8  C10  H1   single    0.930  0.020  1.080
 JB8  O01  H2   single    0.850  0.020  0.980
 JB8  C04  H3   single    0.930  0.020  1.080
 JB8  C07  H4   single    0.930  0.020  1.080
 JB8  C08  H5   single    0.930  0.020  1.080
 JB8  C09  H6   single    0.930  0.020  1.080
 JB8  N11  H7   single    0.860  0.020  1.020
 JB8  O12  H8   single    0.850  0.020  0.980

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
 JB8  H1   C10  N11  120.47  3.000
 JB8  H1   C10  C09  129.67  3.000
 JB8  N11  C10  C09  109.87  3.000
 JB8  H2   O01  B02  115.69  3.000
 JB8  O12  B02  C03  117.98  3.000
 JB8  O12  B02  O01  123.98  3.000
 JB8  C03  B02  O01  118.04  3.000
 JB8  C08  C03  C04  118.90  3.000
 JB8  C08  C03  B02  120.79  3.000
 JB8  C04  C03  B02  120.31  3.000
 JB8  H3   C04  C05  120.13  3.000
 JB8  H3   C04  C03  121.06  3.000
 JB8  C05  C04  C03  118.82  3.000
 JB8  N11  C05  C06  107.33  3.000
 JB8  C06  C05  C04  122.31  3.000
 JB8  N11  C05  C04  130.36  3.000
 JB8  C09  C06  C07  134.61  3.000
 JB8  C07  C06  C05  118.56  3.000
 JB8  C09  C06  C05  106.82  3.000
 JB8  H4   C07  C08  120.48  3.000
 JB8  H4   C07  C06  120.55  3.000
 JB8  C08  C07  C06  118.97  3.000
 JB8  H5   C08  C07  118.47  3.000
 JB8  H5   C08  C03  119.08  3.000
 JB8  C07  C08  C03  122.44  3.000
 JB8  H6   C09  C06  127.38  3.000
 JB8  H6   C09  C10  126.02  3.000
 JB8  C06  C09  C10  106.60  3.000
 JB8  H7   N11  C05  125.70  3.000
 JB8  H7   N11  C10  124.92  3.000
 JB8  C05  N11  C10  109.38  3.000
 JB8  H8   O12  B02  115.76  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
 JB8  CONST_01  C05  C06  C09  C10    0.00   0.0  0
 JB8  CONST_02  C07  C06  C09  C10  180.00   0.0  0
 JB8  CONST_03  C06  C05  N11  C10    0.00   0.0  0
 JB8  CONST_04  C04  C05  N11  C10  180.00   0.0  0
 JB8  CONST_05  N11  C05  C04  C03  180.00   0.0  0
 JB8  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 JB8  CONST_07  C06  C07  C08  C03    0.00   0.0  0
 JB8  CONST_08  C09  C06  C05  C04  180.00   0.0  0
 JB8  CONST_09  C07  C06  C05  C04    0.00   0.0  0
 JB8  CONST_10  C07  C08  C03  C04    0.00   0.0  0
 JB8  CONST_11  C09  C10  N11  C05    0.00   0.0  0
 JB8  CONST_12  C08  C07  C06  C05    0.00   0.0  0
 JB8  CONST_13  C08  C03  C04  C05    0.00   0.0  0
 JB8  CONST_14  N11  C10  C09  C06    0.00   0.0  0
 JB8  CONST_15  N11  C05  C06  C07  180.00   0.0  0
 JB8  CONST_16  C09  C06  C07  C08  180.00   0.0  0
 JB8  CONST_17  N11  C05  C06  C09    0.00   0.0  0
 JB8  CONST_18  C05  C04  C03  B02  180.00   0.0  0
 JB8  CONST_19  C07  C08  C03  B02  180.00   0.0  0
 JB8  CONST_20  H4   C07  C08  C03  180.00   0.0  0
 JB8  CONST_21  H7   N11  C05  C04    0.00   0.0  0
 JB8  CONST_22  H5   C08  C03  C04  180.00   0.0  0
 JB8  CONST_23  H1   C10  N11  C05  180.00   0.0  0
 JB8  CONST_24  H6   C09  C06  C05  180.00   0.0  0
 JB8  CONST_25  H3   C04  C05  C06  180.00   0.0  0
 JB8  Var_01    C04  C03  B02  O01   -0.44  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
 JB8  plan-1  C10  0.020
 JB8  plan-1  B02  0.020
 JB8  plan-1  C03  0.020
 JB8  plan-1  C04  0.020
 JB8  plan-1  C05  0.020
 JB8  plan-1  C06  0.020
 JB8  plan-1  C07  0.020
 JB8  plan-1  C08  0.020
 JB8  plan-1  C09  0.020
 JB8  plan-1  N11  0.020
 JB8  plan-1  H1   0.020
 JB8  plan-1  H3   0.020
 JB8  plan-1  H4   0.020
 JB8  plan-1  H5   0.020
 JB8  plan-1  H6   0.020
 JB8  plan-1  H7   0.020

