# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:18:52 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 1~{H}-indol-5-ylboronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1ccc2[nH]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
 JDN  JDN  '1~{H}-indol-5-ylboronic acid'  ligand  20  12  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JDN
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
 JDN  O01  O  OH1   0  -0.641   3.5168   0.8540  -0.0142
 JDN  B02  B  B     0   0.496   2.6526  -0.2017  -0.0051
 JDN  O03  O  OH1   0  -0.642   3.0478  -1.5079   0.0022
 JDN  C04  C  CR6   0  -0.101   1.1188   0.1028  -0.0005
 JDN  C05  C  CR16  0  -0.408   0.1921  -0.9340   0.0079
 JDN  C06  C  CR56  0   0.078  -1.1771  -0.6566   0.0151
 JDN  C07  C  CR56  0   0.333  -1.6044   0.6905   0.0148
 JDN  C08  C  CR16  0  -0.286  -0.6969   1.7503   0.0054
 JDN  C09  C  CR16  0  -0.344   0.6464   1.4367  -0.0021
 JDN  N10  N  NR15  0  -0.677  -2.9658   0.6862   0.0237
 JDN  C11  C  CR15  0  -0.030  -3.4181  -0.6052   0.0302
 JDN  C12  C  CR15  0  -0.417  -2.3589  -1.4641   0.0251
 JDN  H1   H  HOH1  0   0.481   4.4522   0.6294  -0.0197
 JDN  H2   H  HOH1  0   0.480   3.9983  -1.6555   0.0044
 JDN  H3   H  HCR6  0   0.241   0.5246  -1.9657   0.0083
 JDN  H4   H  HCR6  0   0.255  -1.0320   2.7801   0.0048
 JDN  H5   H  HCR6  0   0.244   1.3605   2.2504  -0.0097
 JDN  H6   H  HNR5  0   0.410  -3.5559   1.5011   0.0288
 JDN  H7   H  HCR5  0   0.281  -4.4762  -0.8112   0.0385
 JDN  H8   H  HCR5  0   0.247  -2.4130  -2.5410   0.0274

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
 JDN  O03  B02  single    1.365  0.020  1.365
 JDN  O01  B02  single    1.364  0.020  1.364
 JDN  B02  C04  single    1.564  0.020  1.564
 JDN  C04  C09  aromatic  1.415  0.020  1.415
 JDN  C04  C05  aromatic  1.391  0.020  1.391
 JDN  C09  C08  aromatic  1.379  0.020  1.379
 JDN  C05  C06  aromatic  1.397  0.020  1.397
 JDN  C08  C07  aromatic  1.395  0.020  1.395
 JDN  C06  C07  aromatic  1.413  0.020  1.413
 JDN  C06  C12  aromatic  1.431  0.020  1.431
 JDN  C07  N10  aromatic  1.361  0.020  1.361
 JDN  C12  C11  aromatic  1.364  0.020  1.364
 JDN  N10  C11  aromatic  1.368  0.020  1.368
 JDN  O01  H1   single    0.850  0.020  0.980
 JDN  O03  H2   single    0.850  0.020  0.980
 JDN  C05  H3   single    0.930  0.020  1.080
 JDN  C08  H4   single    0.930  0.020  1.080
 JDN  C09  H5   single    0.930  0.020  1.080
 JDN  N10  H6   single    0.860  0.020  1.020
 JDN  C11  H7   single    0.930  0.020  1.080
 JDN  C12  H8   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
 JDN  H1   O01  B02  115.80  3.000
 JDN  C04  B02  O03  118.06  3.000
 JDN  C04  B02  O01  118.08  3.000
 JDN  O03  B02  O01  123.86  3.000
 JDN  H2   O03  B02  115.66  3.000
 JDN  C09  C04  C05  118.71  3.000
 JDN  C05  C04  B02  120.56  3.000
 JDN  C09  C04  B02  120.73  3.000
 JDN  H3   C05  C06  119.32  3.000
 JDN  H3   C05  C04  120.35  3.000
 JDN  C06  C05  C04  120.34  3.000
 JDN  C12  C06  C07  106.75  3.000
 JDN  C12  C06  C05  134.20  3.000
 JDN  C07  C06  C05  119.05  3.000
 JDN  N10  C07  C08  130.75  3.000
 JDN  N10  C07  C06  107.41  3.000
 JDN  C08  C07  C06  121.83  3.000
 JDN  H4   C08  C09  121.17  3.000
 JDN  H4   C08  C07  121.40  3.000
 JDN  C09  C08  C07  117.43  3.000
 JDN  H5   C09  C08  118.13  3.000
 JDN  H5   C09  C04  119.23  3.000
 JDN  C08  C09  C04  122.64  3.000
 JDN  H6   N10  C11  124.78  3.000
 JDN  H6   N10  C07  125.73  3.000
 JDN  C11  N10  C07  109.49  3.000
 JDN  H7   C11  C12  129.94  3.000
 JDN  H7   C11  N10  120.32  3.000
 JDN  C12  C11  N10  109.73  3.000
 JDN  H8   C12  C11  126.16  3.000
 JDN  H8   C12  C06  127.22  3.000
 JDN  C11  C12  C06  106.62  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
 JDN  CONST_01  C07  C08  C09  C04    0.00   0.0  0
 JDN  CONST_02  C07  C06  C05  C04    0.00   0.0  0
 JDN  CONST_03  C12  C06  C05  C04  180.00   0.0  0
 JDN  CONST_04  C08  C09  C04  C05    0.00   0.0  0
 JDN  CONST_05  C08  C07  C06  C05    0.00   0.0  0
 JDN  CONST_06  N10  C07  C06  C05  180.00   0.0  0
 JDN  CONST_07  C11  C12  C06  C05  180.00   0.0  0
 JDN  CONST_08  C09  C04  C05  C06    0.00   0.0  0
 JDN  CONST_09  C09  C08  C07  C06    0.00   0.0  0
 JDN  CONST_10  C11  N10  C07  C06    0.00   0.0  0
 JDN  CONST_11  N10  C11  C12  C06    0.00   0.0  0
 JDN  CONST_12  C11  C12  C06  C07    0.00   0.0  0
 JDN  CONST_13  C12  C11  N10  C07    0.00   0.0  0
 JDN  CONST_14  C12  C06  C07  C08  180.00   0.0  0
 JDN  CONST_15  C11  N10  C07  C08  180.00   0.0  0
 JDN  CONST_16  N10  C07  C08  C09  180.00   0.0  0
 JDN  CONST_17  C12  C06  C07  N10    0.00   0.0  0
 JDN  CONST_18  C08  C09  C04  B02  180.00   0.0  0
 JDN  CONST_19  C06  C05  C04  B02  180.00   0.0  0
 JDN  CONST_20  H4   C08  C09  C04  180.00   0.0  0
 JDN  CONST_21  H5   C09  C04  C05  180.00   0.0  0
 JDN  CONST_22  H8   C12  C06  C05    0.00   0.0  0
 JDN  CONST_23  H6   N10  C07  C06  180.00   0.0  0
 JDN  CONST_24  H7   C11  C12  C06  180.00   0.0  0
 JDN  CONST_25  H3   C05  C06  C07  180.00   0.0  0
 JDN  Var_01    C09  C04  B02  O01   -0.17  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
 JDN  plan-1  B02  0.020
 JDN  plan-1  C04  0.020
 JDN  plan-1  C05  0.020
 JDN  plan-1  C06  0.020
 JDN  plan-1  C07  0.020
 JDN  plan-1  C08  0.020
 JDN  plan-1  C09  0.020
 JDN  plan-1  N10  0.020
 JDN  plan-1  C11  0.020
 JDN  plan-1  C12  0.020
 JDN  plan-1  H3   0.020
 JDN  plan-1  H4   0.020
 JDN  plan-1  H5   0.020
 JDN  plan-1  H6   0.020
 JDN  plan-1  H7   0.020
 JDN  plan-1  H8   0.020

