# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:47:03 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: [5-(aminomethyl)-1-benzothiophen-2-yl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc2sc(cc2c1)B(O)O
#
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
 HD5  HD5  '[5-(aminomethyl)-1-benzothiophen-2-yl]boronic acid'  ligand  24  14  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HD5
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
 HD5  C14  C  CH2   0  -0.356   4.2273  -0.6902  -0.3809
 HD5  C13  C  CR16  0  -0.319   2.6354   1.2684  -0.2668
 HD5  C12  C  CR16  0  -0.259   1.3734   1.8250  -0.1805
 HD5  C11  C  CR56  0  -0.243   0.2791   0.9675  -0.1193
 HD5  C01  C  CR6   0   0.108   2.8345  -0.1212  -0.2978
 HD5  C02  C  CR16  0  -0.358   1.7388  -0.9625  -0.2261
 HD5  C03  C  CR56  0   0.234   0.4482  -0.4300  -0.1419
 HD5  C04  C  CR15  0  -0.277  -0.8087  -1.1123  -0.0689
 HD5  C05  C  CR5   0  -0.337  -1.8800  -0.2801   0.0040
 HD5  B06  B  B     0   0.536  -3.3929  -0.6459   0.0900
 HD5  O07  O  OH1   0  -0.626  -3.7150  -1.9646   0.1025
 HD5  O09  O  OH1   0  -0.631  -4.2632   0.3959   0.1442
 HD5  S10  S  S2    0   0.170  -1.3947   1.3914  -0.0122
 HD5  N15  N  NH2   0  -0.789   4.5513  -1.4381   0.8261
 HD5  H1   H  HCH2  0   0.235   4.2825  -1.3824  -1.2251
 HD5  H2   H  HCH2  0   0.214   4.9307   0.1228  -0.6040
 HD5  H4   H  HCR6  0   0.265   1.2454   2.8994  -0.1599
 HD5  H5   H  HCR6  0   0.247   1.8755  -2.0378  -0.2387
 HD5  H6   H  HCR5  0   0.264  -0.8969  -2.1906  -0.0736
 HD5  H7   H  HOH1  0   0.488  -4.6540  -2.1682   0.1587
 HD5  H8   H  HOH1  0   0.488  -5.1976   0.1700   0.1913
 HD5  H9   H  HNH2  0   0.350   5.4801  -1.8306   0.7347
 HD5  H10  H  HNH2  0   0.341   4.5963  -0.8020   1.6127
 HD5  H3   H  HCR6  0   0.255   3.4959   1.9250  -0.3142

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
 HD5  O09  B06  single    1.359  0.020  1.359
 HD5  C13  C12  aromatic  1.382  0.020  1.382
 HD5  C13  C01  aromatic  1.404  0.020  1.404
 HD5  C12  C11  aromatic  1.392  0.020  1.392
 HD5  C14  C01  single    1.507  0.020  1.507
 HD5  C14  N15  single    1.456  0.020  1.456
 HD5  C01  C02  aromatic  1.383  0.020  1.383
 HD5  C11  S10  aromatic  1.730  0.020  1.730
 HD5  C11  C03  aromatic  1.408  0.020  1.408
 HD5  S10  C05  aromatic  1.741  0.020  1.741
 HD5  C02  C03  aromatic  1.399  0.020  1.399
 HD5  C03  C04  aromatic  1.432  0.020  1.432
 HD5  C05  C04  aromatic  1.359  0.020  1.359
 HD5  C05  B06  single    1.559  0.020  1.559
 HD5  B06  O07  single    1.358  0.020  1.358
 HD5  C14  H1   single    0.970  0.020  1.090
 HD5  C14  H2   single    0.970  0.020  1.090
 HD5  C13  H3   single    0.930  0.020  1.080
 HD5  C12  H4   single    0.930  0.020  1.080
 HD5  C02  H5   single    0.930  0.020  1.080
 HD5  C04  H6   single    0.930  0.020  1.080
 HD5  O07  H7   single    0.850  0.020  0.980
 HD5  O09  H8   single    0.850  0.020  0.980
 HD5  N15  H9   single    0.890  0.020  1.040
 HD5  N15  H10  single    0.890  0.020  1.040

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
 HD5  H2   C14  H1   106.24  3.000
 HD5  H2   C14  N15  113.96  3.000
 HD5  H1   C14  N15  107.68  3.000
 HD5  H2   C14  C01  108.89  3.000
 HD5  H1   C14  C01  109.17  3.000
 HD5  N15  C14  C01  110.72  3.000
 HD5  H3   C13  C01  119.09  3.000
 HD5  H3   C13  C12  118.94  3.000
 HD5  C01  C13  C12  121.97  3.000
 HD5  H4   C12  C11  121.19  3.000
 HD5  H4   C12  C13  120.60  3.000
 HD5  C11  C12  C13  118.20  3.000
 HD5  S10  C11  C03  111.12  3.000
 HD5  C03  C11  C12  121.10  3.000
 HD5  S10  C11  C12  127.77  3.000
 HD5  C02  C01  C13  119.24  3.000
 HD5  C02  C01  C14  120.36  3.000
 HD5  C13  C01  C14  120.39  3.000
 HD5  H5   C02  C03  119.65  3.000
 HD5  H5   C02  C01  120.18  3.000
 HD5  C03  C02  C01  120.17  3.000
 HD5  C04  C03  C02  129.17  3.000
 HD5  C04  C03  C11  111.51  3.000
 HD5  C02  C03  C11  119.32  3.000
 HD5  H6   C04  C05  123.12  3.000
 HD5  H6   C04  C03  123.11  3.000
 HD5  C05  C04  C03  113.77  3.000
 HD5  S10  C05  B06  119.76  3.000
 HD5  B06  C05  C04  128.65  3.000
 HD5  S10  C05  C04  111.58  3.000
 HD5  O09  B06  O07  126.34  3.000
 HD5  O07  B06  C05  117.31  3.000
 HD5  O09  B06  C05  116.36  3.000
 HD5  H7   O07  B06  115.95  3.000
 HD5  H8   O09  B06  116.35  3.000
 HD5  C05  S10  C11   92.01  3.000
 HD5  H10  N15  H9   105.84  3.000
 HD5  H10  N15  C14  109.33  3.000
 HD5  H9   N15  C14  109.17  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
 HD5  CONST_01  S10  C11  C12  C13   180.00   0.0  0
 HD5  CONST_02  C03  C11  C12  C13     0.00   0.0  0
 HD5  CONST_03  C03  C02  C01  C13     0.00   0.0  0
 HD5  CONST_04  C02  C01  C13  C12     0.00   0.0  0
 HD5  CONST_05  C05  S10  C11  C12   180.00   0.0  0
 HD5  CONST_06  C02  C03  C11  C12     0.00   0.0  0
 HD5  CONST_07  C04  C03  C11  C12   180.00   0.0  0
 HD5  CONST_08  C01  C13  C12  C11     0.00   0.0  0
 HD5  CONST_09  C04  C05  S10  C11     0.00   0.0  0
 HD5  CONST_10  C01  C02  C03  C11     0.00   0.0  0
 HD5  CONST_11  C05  C04  C03  C11     0.00   0.0  0
 HD5  CONST_12  C04  C03  C02  C01   180.00   0.0  0
 HD5  CONST_13  S10  C11  C03  C02   180.00   0.0  0
 HD5  CONST_14  C05  C04  C03  C02   180.00   0.0  0
 HD5  CONST_15  C05  S10  C11  C03     0.00   0.0  0
 HD5  CONST_16  S10  C05  C04  C03     0.00   0.0  0
 HD5  CONST_17  S10  C11  C03  C04     0.00   0.0  0
 HD5  CONST_18  C12  C13  C01  C14   180.00   0.0  0
 HD5  CONST_19  C03  C02  C01  C14   180.00   0.0  0
 HD5  CONST_20  B06  C05  S10  C11   180.00   0.0  0
 HD5  CONST_21  B06  C05  C04  C03   180.00   0.0  0
 HD5  CONST_22  H5   C02  C01  C13   180.00   0.0  0
 HD5  CONST_23  H3   C13  C12  C11   180.00   0.0  0
 HD5  CONST_24  H6   C04  C03  C11   180.00   0.0  0
 HD5  CONST_25  H4   C12  C13  C01   180.00   0.0  0
 HD5  Var_01    N15  C14  C01  C13   115.12  30.0  2
 HD5  Var_02    O09  B06  C05  C04  -179.58  30.0  2
 HD5  Var_03    H9   N15  C14  C01   178.45  30.0  3

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
 HD5  plan-1  C14  0.020
 HD5  plan-1  C13  0.020
 HD5  plan-1  C12  0.020
 HD5  plan-1  C11  0.020
 HD5  plan-1  C01  0.020
 HD5  plan-1  C02  0.020
 HD5  plan-1  C03  0.020
 HD5  plan-1  C04  0.020
 HD5  plan-1  C05  0.020
 HD5  plan-1  B06  0.020
 HD5  plan-1  S10  0.020
 HD5  plan-1  H4   0.020
 HD5  plan-1  H5   0.020
 HD5  plan-1  H6   0.020
 HD5  plan-1  H3   0.020

