# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:29:24 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: [5-(aminomethyl)-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc2sc(cc2c1)[B-](O)(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
 HCQ  HCQ  '[5-(aminomethyl)-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide'  ligand  26  15  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HCQ
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
 HCQ  C14  C  CH2    0  -0.326   4.5546   0.5182   0.2436
 HCQ  C13  C  CR16   0  -0.327   2.9315  -1.4011   0.2460
 HCQ  C12  C  CR16   0  -0.270   1.6601  -1.9426   0.2408
 HCQ  C11  C  CR56   0  -0.252   0.5691  -1.0798   0.1802
 HCQ  C01  C  CR6    0   0.075   3.1418  -0.0125   0.2005
 HCQ  C02  C  CR16   0  -0.390   2.0491   0.8349   0.1416
 HCQ  C03  C  CR56   0   0.246   0.7482   0.3147   0.1301
 HCQ  C04  C  CR15   0  -0.348  -0.5104   1.0049   0.0712
 HCQ  C05  C  CR5    0  -0.343  -1.6047   0.1988   0.0688
 HCQ  B06  B  B     -1   0.459  -3.2015   0.5642  -0.0739
 HCQ  O07  O  OB     0  -0.750  -3.8912  -0.5240   0.6396
 HCQ  O08  O  OB     0  -0.740  -3.4782   1.8951   0.4643
 HCQ  O09  O  OB     0  -0.733  -3.5923   0.6580  -1.4858
 HCQ  S10  S  S2     0   0.106  -1.1200  -1.4741   0.1588
 HCQ  N15  N  NH2    0  -0.795   4.6745   1.8325  -0.3610
 HCQ  H1   H  HCH2   0   0.238   4.8637   0.6052   1.2901
 HCQ  H2   H  HCH2   0   0.210   5.2206  -0.2361  -0.1984
 HCQ  H4   H  HCR6   0   0.254   1.5222  -3.0161   0.2735
 HCQ  H5   H  HCR6   0   0.236   2.2017   1.9064   0.0964
 HCQ  H6   H  HCR5   0   0.233  -0.5839   2.0848   0.0259
 HCQ  H7   H  H      0   0.430  -4.8417  -0.4065   0.5499
 HCQ  H8   H  H      0   0.426  -3.1008   1.9675   1.3433
 HCQ  H9   H  H      0   0.424  -3.3482  -0.1496  -1.9429
 HCQ  H10  H  HNH2   0   0.354   5.6176   2.1747  -0.2312
 HCQ  H11  H  HNH2   0   0.342   4.5391   1.7583  -1.3615
 HCQ  H3   H  HCR6   0   0.241   3.7870  -2.0658   0.2804

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
 HCQ  N15  C14  single    1.452  0.020  1.452
 HCQ  C14  C01  single    1.510  0.020  1.510
 HCQ  C01  C13  aromatic  1.405  0.020  1.405
 HCQ  C01  C02  aromatic  1.384  0.020  1.384
 HCQ  C13  C12  aromatic  1.382  0.020  1.382
 HCQ  C02  C03  aromatic  1.401  0.020  1.401
 HCQ  C12  C11  aromatic  1.392  0.020  1.392
 HCQ  C03  C11  aromatic  1.407  0.020  1.407
 HCQ  C03  C04  aromatic  1.437  0.020  1.437
 HCQ  C11  S10  aromatic  1.735  0.020  1.735
 HCQ  C04  C05  aromatic  1.359  0.020  1.359
 HCQ  C05  S10  aromatic  1.744  0.020  1.744
 HCQ  C05  B06  single    1.644  0.020  1.644
 HCQ  O07  B06  single    1.473  0.020  1.473
 HCQ  B06  O09  single    1.468  0.020  1.468
 HCQ  B06  O08  single    1.462  0.020  1.462
 HCQ  C14  H1   single    0.970  0.020  1.090
 HCQ  C14  H2   single    0.970  0.020  1.090
 HCQ  C13  H3   single    0.930  0.020  1.080
 HCQ  C12  H4   single    0.930  0.020  1.080
 HCQ  C02  H5   single    0.930  0.020  1.080
 HCQ  C04  H6   single    0.930  0.020  1.080
 HCQ  O07  H7   single    0.850  0.020  0.980
 HCQ  O08  H8   single    0.850  0.020  0.980
 HCQ  O09  H9   single    0.850  0.020  0.980
 HCQ  N15  H10  single    0.890  0.020  1.040
 HCQ  N15  H11  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
 HCQ  H2   C14  H1   105.54  3.000
 HCQ  H2   C14  N15  113.82  3.000
 HCQ  H1   C14  N15  107.63  3.000
 HCQ  H2   C14  C01  108.32  3.000
 HCQ  H1   C14  C01  108.63  3.000
 HCQ  N15  C14  C01  112.56  3.000
 HCQ  H3   C13  C01  119.26  3.000
 HCQ  H3   C13  C12  119.08  3.000
 HCQ  C01  C13  C12  121.65  3.000
 HCQ  H4   C12  C11  121.05  3.000
 HCQ  H4   C12  C13  120.37  3.000
 HCQ  C11  C12  C13  118.58  3.000
 HCQ  S10  C11  C03  110.42  3.000
 HCQ  S10  C11  C12  128.52  3.000
 HCQ  C03  C11  C12  121.07  3.000
 HCQ  C02  C01  C13  119.23  3.000
 HCQ  C02  C01  C14  121.65  3.000
 HCQ  C13  C01  C14  119.11  3.000
 HCQ  H5   C02  C03  119.85  3.000
 HCQ  H5   C02  C01  119.75  3.000
 HCQ  C03  C02  C01  120.40  3.000
 HCQ  C04  C03  C02  129.44  3.000
 HCQ  C04  C03  C11  111.48  3.000
 HCQ  C02  C03  C11  119.08  3.000
 HCQ  H6   C04  C05  122.45  3.000
 HCQ  H6   C04  C03  122.69  3.000
 HCQ  C05  C04  C03  114.86  3.000
 HCQ  S10  C05  B06  119.18  3.000
 HCQ  B06  C05  C04  130.56  3.000
 HCQ  S10  C05  C04  110.19  3.000
 HCQ  O09  B06  O08  104.21  3.000
 HCQ  O08  B06  O07  113.93  3.000
 HCQ  O09  B06  O07  112.86  3.000
 HCQ  O08  B06  C05  110.74  3.000
 HCQ  O09  B06  C05  110.87  3.000
 HCQ  O07  B06  C05  104.39  3.000
 HCQ  H7   O07  B06  109.10  3.000
 HCQ  H8   O08  B06  109.36  3.000
 HCQ  H9   O09  B06  109.67  3.000
 HCQ  C05  S10  C11   93.05  3.000
 HCQ  H11  N15  H10  106.04  3.000
 HCQ  H11  N15  C14  109.53  3.000
 HCQ  H10  N15  C14  109.25  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
 HCQ  CONST_01  C03  C02  C01  C13     0.00   0.0  0
 HCQ  CONST_02  C03  C11  C12  C13     0.00   0.0  0
 HCQ  CONST_03  S10  C11  C12  C13   180.00   0.0  0
 HCQ  CONST_04  C02  C01  C13  C12     0.00   0.0  0
 HCQ  CONST_05  C02  C03  C11  C12     0.00   0.0  0
 HCQ  CONST_06  C04  C03  C11  C12   180.00   0.0  0
 HCQ  CONST_07  C05  S10  C11  C12   180.00   0.0  0
 HCQ  CONST_08  C01  C13  C12  C11     0.00   0.0  0
 HCQ  CONST_09  C01  C02  C03  C11     0.00   0.0  0
 HCQ  CONST_10  C05  C04  C03  C11     0.00   0.0  0
 HCQ  CONST_11  C04  C05  S10  C11     0.00   0.0  0
 HCQ  CONST_12  C04  C03  C02  C01   180.00   0.0  0
 HCQ  CONST_13  S10  C11  C03  C02   180.00   0.0  0
 HCQ  CONST_14  C05  C04  C03  C02   180.00   0.0  0
 HCQ  CONST_15  C05  S10  C11  C03     0.00   0.0  0
 HCQ  CONST_16  S10  C05  C04  C03     0.00   0.0  0
 HCQ  CONST_17  S10  C11  C03  C04     0.00   0.0  0
 HCQ  CONST_18  C12  C13  C01  C14   180.00   0.0  0
 HCQ  CONST_19  C03  C02  C01  C14   180.00   0.0  0
 HCQ  CONST_20  B06  C05  S10  C11   180.00   0.0  0
 HCQ  CONST_21  B06  C05  C04  C03   180.00   0.0  0
 HCQ  CONST_22  H5   C02  C01  C13   180.00   0.0  0
 HCQ  CONST_23  H3   C13  C12  C11   180.00   0.0  0
 HCQ  CONST_24  H6   C04  C03  C11   180.00   0.0  0
 HCQ  CONST_25  H4   C12  C13  C01   180.00   0.0  0
 HCQ  Var_01    N15  C14  C01  C13   155.45  30.0  2
 HCQ  Var_02    O07  B06  C05  C04  -152.51  30.0  2
 HCQ  Var_03    H10  N15  C14  C01   174.93  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
 HCQ  plan-1  C14  0.020
 HCQ  plan-1  C13  0.020
 HCQ  plan-1  C12  0.020
 HCQ  plan-1  C11  0.020
 HCQ  plan-1  C01  0.020
 HCQ  plan-1  C02  0.020
 HCQ  plan-1  C03  0.020
 HCQ  plan-1  C04  0.020
 HCQ  plan-1  C05  0.020
 HCQ  plan-1  B06  0.020
 HCQ  plan-1  S10  0.020
 HCQ  plan-1  H4   0.020
 HCQ  plan-1  H5   0.020
 HCQ  plan-1  H6   0.020
 HCQ  plan-1  H3   0.020

