# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 10:33:28 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-amino-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1sc2CCCCc2c1C(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
 QAB  QAB  '2-amino-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid'  ligand  23  13  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QAB
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
 QAB  C1    C  CR5    0  -0.149  -0.9471   0.1477   0.0777
 QAB  O1    O  O      0  -0.585  -1.7554   2.3382  -0.2638
 QAB  S1    S  S2     0   0.136   0.2843  -2.1157   0.2714
 QAB  C2    C  C      0   0.409  -2.0589   1.1462  -0.0655
 QAB  N3    N  NH2    0  -0.838  -2.3866  -1.8516   0.3516
 QAB  C5    C  CR5    0   0.169   0.4714   0.4324   0.0437
 QAB  C6    C  CR5    0  -0.275   1.2492  -0.6783   0.1187
 QAB  C7    C  CR5    0  -0.002  -1.1883  -1.2032   0.2053
 QAB  C10   C  CH2    0  -0.472   1.1067   1.7907  -0.0722
 QAB  C11   C  CH2    0  -0.447   2.5982   1.7513   0.2512
 QAB  C12   C  CH2    0  -0.442   3.2958   0.5862  -0.4379
 QAB  C13   C  CH2    0  -0.470   2.7423  -0.7425   0.0694
 QAB  OXT   O  OC    -1  -0.615  -3.2358   0.7070   0.0113
 QAB  HN3   H  HNH2   0   0.374  -2.4667  -2.7447  -0.1092
 QAB  HN3A  H  HNH2   0   0.384  -3.1499  -1.2117   0.1516
 QAB  H10   H  HCH2   0   0.221   0.9551   2.1769  -1.0849
 QAB  H10A  H  HCH2   0   0.234   0.6007   2.4967   0.5849
 QAB  H11   H  HCH2   0   0.229   3.0582   2.6977  -0.0421
 QAB  H11A  H  HCH2   0   0.215   2.7365   1.6607   1.3337
 QAB  H12   H  HCH2   0   0.220   3.1428   0.6577  -1.5192
 QAB  H12A  H  HCH2   0   0.232   4.3738   0.6255  -0.2687
 QAB  H13   H  HCH2   0   0.234   3.1516  -0.9590   1.0626
 QAB  H13A  H  HCH2   0   0.241   3.0748  -1.5600  -0.5765

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
 QAB  C5   C1    aromatic  1.447  0.020  1.447
 QAB  C7   C1    aromatic  1.378  0.020  1.378
 QAB  C1   C2    single    1.501  0.020  1.501
 QAB  O1   C2    deloc     1.246  0.020  1.246
 QAB  C6   S1    aromatic  1.738  0.020  1.738
 QAB  S1   C7    aromatic  1.734  0.020  1.734
 QAB  C2   OXT   deloc     1.259  0.020  1.259
 QAB  C7   N3    single    1.370  0.020  1.370
 QAB  N3   HN3   single    0.890  0.020  1.040
 QAB  N3   HN3A  single    0.890  0.020  1.040
 QAB  C6   C5    aromatic  1.358  0.020  1.358
 QAB  C10  C5    single    1.504  0.020  1.504
 QAB  C13  C6    single    1.495  0.020  1.495
 QAB  C11  C10   single    1.527  0.020  1.527
 QAB  C10  H10   single    0.970  0.020  1.090
 QAB  C10  H10A  single    0.970  0.020  1.090
 QAB  C12  C11   single    1.523  0.020  1.523
 QAB  C11  H11   single    0.970  0.020  1.090
 QAB  C11  H11A  single    0.970  0.020  1.090
 QAB  C12  C13   single    1.526  0.020  1.526
 QAB  C12  H12   single    0.970  0.020  1.090
 QAB  C12  H12A  single    0.970  0.020  1.090
 QAB  C13  H13   single    0.970  0.020  1.090
 QAB  C13  H13A  single    0.970  0.020  1.090

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
 QAB  C7    C1   C5   111.50  3.000
 QAB  C7    C1   C2   122.08  3.000
 QAB  C5    C1   C2   126.36  3.000
 QAB  C7    S1   C6    91.89  3.000
 QAB  OXT   C2   O1   124.84  3.000
 QAB  OXT   C2   C1   117.04  3.000
 QAB  O1    C2   C1   118.11  3.000
 QAB  HN3A  N3   HN3  114.10  3.000
 QAB  HN3A  N3   C7   109.76  3.000
 QAB  HN3   N3   C7   116.09  3.000
 QAB  C10   C5   C6   120.07  3.000
 QAB  C10   C5   C1   126.40  3.000
 QAB  C6    C5   C1   113.53  3.000
 QAB  C13   C6   C5   127.24  3.000
 QAB  C13   C6   S1   121.45  3.000
 QAB  C5    C6   S1   111.31  3.000
 QAB  N3    C7   S1   119.32  3.000
 QAB  N3    C7   C1   128.81  3.000
 QAB  S1    C7   C1   111.76  3.000
 QAB  H10A  C10  H10  105.38  3.000
 QAB  H10A  C10  C11  110.05  3.000
 QAB  H10   C10  C11  109.90  3.000
 QAB  H10A  C10  C5   110.04  3.000
 QAB  H10   C10  C5   109.36  3.000
 QAB  C11   C10  C5   111.90  3.000
 QAB  H11A  C11  H11  106.50  3.000
 QAB  H11A  C11  C12  109.04  3.000
 QAB  H11   C11  C12  110.40  3.000
 QAB  H11A  C11  C10  109.56  3.000
 QAB  H11   C11  C10  109.40  3.000
 QAB  C12   C11  C10  111.80  3.000
 QAB  H12A  C12  H12  106.79  3.000
 QAB  H12A  C12  C13  109.74  3.000
 QAB  H12   C12  C13  109.55  3.000
 QAB  H12A  C12  C11  110.77  3.000
 QAB  H12   C12  C11  109.46  3.000
 QAB  C13   C12  C11  110.46  3.000
 QAB  H13A  C13  H13  105.91  3.000
 QAB  H13A  C13  C12  110.13  3.000
 QAB  H13   C13  C12  109.75  3.000
 QAB  H13A  C13  C6   110.80  3.000
 QAB  H13   C13  C6   110.58  3.000
 QAB  C12   C13  C6   109.62  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
 QAB  CONST_01  S1    C6   C5   C1     0.00   0.0  0
 QAB  CONST_02  C6    S1   C7   C1     0.00   0.0  0
 QAB  CONST_03  C5    C1   C7   S1     0.00   0.0  0
 QAB  CONST_04  C7    S1   C6   C5     0.00   0.0  0
 QAB  CONST_05  C7    C1   C5   C6     0.00   0.0  0
 QAB  CONST_06  C2    C1   C7   S1   180.00   0.0  0
 QAB  CONST_07  C6    C5   C1   C2   180.00   0.0  0
 QAB  CONST_08  C10   C5   C1   C2     0.00   0.0  0
 QAB  CONST_09  C5    C1   C7   N3   180.00   0.0  0
 QAB  CONST_10  C6    S1   C7   N3   180.00   0.0  0
 QAB  CONST_12  HN3A  N3   C7   C1     0.00   0.0  0
 QAB  Var_01    C11   C10  C5   C1   166.51  30.0  1
 QAB  Var_02    C12   C13  C6   S1   164.79  30.0  1
 QAB  Var_03    C12   C11  C10  C5    45.74  30.0  1
 QAB  Var_04    C11   C12  C13  C6    45.14  30.0  1
 QAB  Var_05    C13   C12  C11  C10  -63.27  30.0  1
 QAB  Var_06    C5    C1   C2   O1     1.74  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
 QAB  plan-1  C1    0.020
 QAB  plan-1  S1    0.020
 QAB  plan-1  C2    0.020
 QAB  plan-1  N3    0.020
 QAB  plan-1  C5    0.020
 QAB  plan-1  C6    0.020
 QAB  plan-1  C7    0.020
 QAB  plan-1  C10   0.020
 QAB  plan-1  C13   0.020
 QAB  plan-2  N3    0.020
 QAB  plan-2  C7    0.020
 QAB  plan-2  HN3   0.020
 QAB  plan-2  HN3A  0.020
 QAB  plan-3  C1    0.020
 QAB  plan-3  O1    0.020
 QAB  plan-3  C2    0.020
 QAB  plan-3  OXT   0.020

