# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 12:47:09 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  24  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  -0.131  -0.9753   0.1263   0.0575
 QAB  O1    O  O     0  -0.493  -3.2676   0.7013   0.0832
 QAB  S1    S  S2    0   0.181   0.2752  -2.1245  -0.1101
 QAB  C2    C  C     0   0.516  -2.0949   1.0434   0.0702
 QAB  N3    N  NH2   0  -0.825  -2.3741  -1.9079  -0.0101
 QAB  C5    C  CR5   0   0.209   0.4429   0.4373   0.0717
 QAB  C6    C  CR5   0  -0.279   1.2227  -0.6632  -0.0252
 QAB  C7    C  CR5   0   0.088  -1.2089  -1.2445  -0.0231
 QAB  C10   C  CH2   0  -0.488   1.0664   1.8003   0.1942
 QAB  C11   C  CH2   0  -0.449   2.5618   1.7184   0.4954
 QAB  C12   C  CH2   0  -0.444   3.2629   0.6780  -0.3668
 QAB  C13   C  CH2   0  -0.472   2.7153  -0.7147  -0.0685
 QAB  OXT   O  OH1   0  -0.602  -1.7558   2.3309   0.0515
 QAB  HN3   H  HNH2  0   0.405  -2.4149  -2.8751  -0.2808
 QAB  HN3A  H  HNH2  0   0.413  -3.2217  -1.3683  -0.0819
 QAB  H10   H  HCH2  0   0.236   0.9031   2.3659  -0.7282
 QAB  H10A  H  HCH2  0   0.244   0.5746   2.3692   0.9837
 QAB  H11   H  HCH2  0   0.236   3.0101   2.7026   0.3476
 QAB  H11A  H  HCH2  0   0.222   2.7074   1.4641   1.5499
 QAB  H12   H  HCH2  0   0.224   3.1121   0.9123  -1.4248
 QAB  H12A  H  HCH2  0   0.238   4.3398   0.6951  -0.1896
 QAB  H13   H  HCH2  0   0.243   3.1129  -1.0753   0.8863
 QAB  H13A  H  HCH2  0   0.249   3.0549  -1.4255  -0.8265
 QAB  HOXT  H  HOH1  0   0.479  -2.5606   2.8694   0.0613

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  1.452  0.020  1.452
 QAB  C7   C1    aromatic  1.393  0.020  1.393
 QAB  C1   C2    single    1.447  0.020  1.447
 QAB  O1   C2    double    1.222  0.020  1.222
 QAB  C6   S1    aromatic  1.744  0.020  1.744
 QAB  S1   C7    aromatic  1.728  0.020  1.728
 QAB  C2   OXT   single    1.332  0.020  1.332
 QAB  C7   N3    single    1.341  0.020  1.341
 QAB  N3   HN3   single    0.890  0.020  1.040
 QAB  N3   HN3A  single    0.890  0.020  1.040
 QAB  C6   C5    aromatic  1.352  0.020  1.352
 QAB  C10  C5    single    1.504  0.020  1.504
 QAB  C13  C6    single    1.494  0.020  1.494
 QAB  C11  C10   single    1.528  0.020  1.528
 QAB  C10  H10   single    0.970  0.020  1.090
 QAB  C10  H10A  single    0.970  0.020  1.090
 QAB  C12  C11   single    1.522  0.020  1.522
 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
 QAB  OXT  HOXT  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
 QAB  C7    C1   C5   112.03  3.000
 QAB  C7    C1   C2   119.63  3.000
 QAB  C5    C1   C2   128.30  3.000
 QAB  C7    S1   C6    92.15  3.000
 QAB  OXT   C2   O1   121.02  3.000
 QAB  OXT   C2   C1   114.56  3.000
 QAB  O1    C2   C1   124.42  3.000
 QAB  HN3A  N3   HN3  117.52  3.000
 QAB  HN3A  N3   C7   117.74  3.000
 QAB  HN3   N3   C7   120.58  3.000
 QAB  C10   C5   C6   120.29  3.000
 QAB  C10   C5   C1   126.86  3.000
 QAB  C6    C5   C1   112.85  3.000
 QAB  C13   C6   C5   127.32  3.000
 QAB  C13   C6   S1   120.83  3.000
 QAB  C5    C6   S1   111.85  3.000
 QAB  N3    C7   S1   119.67  3.000
 QAB  N3    C7   C1   129.20  3.000
 QAB  S1    C7   C1   111.11  3.000
 QAB  H10A  C10  H10  105.87  3.000
 QAB  H10A  C10  C11  109.07  3.000
 QAB  H10   C10  C11  109.88  3.000
 QAB  H10A  C10  C5   110.17  3.000
 QAB  H10   C10  C5   109.75  3.000
 QAB  C11   C10  C5   111.92  3.000
 QAB  H11A  C11  H11  106.57  3.000
 QAB  H11A  C11  C12  109.00  3.000
 QAB  H11   C11  C12  110.51  3.000
 QAB  H11A  C11  C10  109.43  3.000
 QAB  H11   C11  C10  109.09  3.000
 QAB  C12   C11  C10  112.07  3.000
 QAB  H12A  C12  H12  106.83  3.000
 QAB  H12A  C12  C13  109.68  3.000
 QAB  H12   C12  C13  109.58  3.000
 QAB  H12A  C12  C11  110.59  3.000
 QAB  H12   C12  C11  109.74  3.000
 QAB  C13   C12  C11  110.35  3.000
 QAB  H13A  C13  H13  106.12  3.000
 QAB  H13A  C13  C12  110.27  3.000
 QAB  H13   C13  C12  109.91  3.000
 QAB  H13A  C13  C6   110.66  3.000
 QAB  H13   C13  C6   110.41  3.000
 QAB  C12   C13  C6   109.43  3.000
 QAB  HOXT  OXT  C2   109.02  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_11  HN3   N3   C7   C1    180.00   0.0  0
 QAB  CONST_12  HN3A  N3   C7   C1      0.00   0.0  0
 QAB  CONST_13  HOXT  OXT  C2   C1    180.00   0.0  0
 QAB  Var_01    C11   C10  C5   C1    166.80  30.0  1
 QAB  Var_02    C12   C13  C6   S1    164.39  30.0  1
 QAB  Var_03    C12   C11  C10  C5     44.33  30.0  1
 QAB  Var_04    C11   C12  C13  C6     45.85  30.0  1
 QAB  Var_05    C13   C12  C11  C10   -62.99  30.0  1
 QAB  Var_06    C5    C1   C2   O1   -178.49  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
 QAB  plan-3  HOXT  0.020

