# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:28:18 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 3-[5-[(3~{S})-1,2-dithiolan-3-yl]pentanoylamino]propane-1-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[S](=O)(=O)CCCNC(=O)CCCC[C@H]1CCSS1
#
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
 8NT  8NT  '3-[5-[(3~{S})-1,2-dithiolan-3-yl]pentanoylamino]propane-1-sulfonic acid'  ligand  39  19  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8NT
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
 8NT  C1   C  CH2    0  -0.411   4.1325   0.9701   0.1190
 8NT  C2   C  CH1    0  -0.373   5.4328   0.4501  -0.4728
 8NT  C10  C  C      0   0.561  -0.8999   1.3323  -0.3251
 8NT  C13  C  CH2    0  -0.233  -3.2727   0.9843   0.1868
 8NT  C14  C  CH2    0  -0.483  -4.2896  -0.1407   0.0729
 8NT  C15  C  CH2    0  -0.632  -5.6688   0.3227   0.5074
 8NT  C5   C  CH2    0  -0.546   7.9115   0.2016  -0.2505
 8NT  C6   C  CH2    0  -0.409   6.6654   0.8613   0.3197
 8NT  C7   C  CH2    0  -0.425   2.8835   0.5207  -0.6288
 8NT  C8   C  CH2    0  -0.416   1.6168   1.1678  -0.0847
 8NT  C9   C  CH2    0  -0.577   0.3729   0.6755  -0.8138
 8NT  N1   N  NH1    0  -0.645  -1.9661   0.5242  -0.2332
 8NT  O1   O  O      0  -0.510  -0.9584   2.5258  -0.0539
 8NT  O2   O  OS     0  -0.770  -6.9047  -1.4848  -0.9375
 8NT  O3   O  OS     0  -0.771  -6.4294  -2.0131   1.4202
 8NT  O4   O  OS    -1  -0.768  -8.1668  -0.3594   0.8555
 8NT  S1   S  S2     0  -0.060   5.4435  -1.3810  -0.4489
 8NT  S2   S  S2     0  -0.080   7.5032  -1.5038  -0.8139
 8NT  S3   S  S      0   1.403  -6.8956  -0.9958   0.4562
 8NT  H1   H  HCH2   0   0.234   4.0663   0.6764   1.1711
 8NT  H2   H  HCH2   0   0.246   4.1877   2.0632   0.1053
 8NT  H3   H  HCH1   0   0.282   5.5278   0.7754  -1.5129
 8NT  H4   H  HCH2   0   0.234  -3.5833   1.8312  -0.4308
 8NT  H5   H  HCH2   0   0.232  -3.2308   1.3444   1.2193
 8NT  H6   H  HCH2   0   0.245  -4.3304  -0.4941  -0.9597
 8NT  H7   H  HCH2   0   0.243  -3.9728  -0.9833   0.6928
 8NT  H8   H  HCH2   0   0.262  -5.6514   0.7014   1.5320
 8NT  H9   H  HCH2   0   0.263  -6.0311   1.1279  -0.1359
 8NT  H10  H  HCH2   0   0.281   8.2787   0.7434  -1.1203
 8NT  H11  H  HCH2   0   0.289   8.7086   0.1434   0.4885
 8NT  H12  H  HCH2   0   0.269   6.7866   1.9470   0.2849
 8NT  H13  H  HCH2   0   0.252   6.5293   0.5760   1.3647
 8NT  H14  H  HCH2   0   0.225   2.9892   0.7583  -1.6923
 8NT  H15  H  HCH2   0   0.222   2.7841  -0.5685  -0.5676
 8NT  H16  H  HCH2   0   0.227   1.5266   0.9506   0.9839
 8NT  H17  H  HCH2   0   0.228   1.6928   2.2536  -0.1762
 8NT  H18  H  HCH2   0   0.248   0.3010  -0.4122  -0.7348
 8NT  H19  H  HCH2   0   0.265   0.4659   0.8974  -1.8824
 8NT  H20  H  HNH1   0   0.400  -1.8500  -0.4558  -0.4335

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
 8NT  C5   C6   single  1.521  0.020  1.521
 8NT  C5   S2   single  1.842  0.020  1.842
 8NT  C6   C2   single  1.522  0.020  1.522
 8NT  C2   C1   single  1.520  0.020  1.520
 8NT  C2   S1   single  1.831  0.020  1.831
 8NT  C1   C7   single  1.523  0.020  1.523
 8NT  S2   S1   single  2.095  0.020  2.095
 8NT  C7   C8   single  1.523  0.020  1.523
 8NT  C8   C9   single  1.524  0.020  1.524
 8NT  C9   C10  single  1.513  0.020  1.513
 8NT  C10  N1   single  1.341  0.020  1.341
 8NT  C10  O1   double  1.225  0.020  1.225
 8NT  N1   C13  single  1.448  0.020  1.448
 8NT  C13  C14  single  1.521  0.020  1.521
 8NT  C15  C14  single  1.518  0.020  1.518
 8NT  C15  S3   single  1.802  0.020  1.802
 8NT  O3   S3   deloc   1.477  0.020  1.477
 8NT  O2   S3   deloc   1.477  0.020  1.477
 8NT  S3   O4   deloc   1.477  0.020  1.477
 8NT  C1   H1   single  0.970  0.020  1.090
 8NT  C1   H2   single  0.970  0.020  1.090
 8NT  C2   H3   single  0.970  0.020  1.090
 8NT  C13  H4   single  0.970  0.020  1.090
 8NT  C13  H5   single  0.970  0.020  1.090
 8NT  C14  H6   single  0.970  0.020  1.090
 8NT  C14  H7   single  0.970  0.020  1.090
 8NT  C15  H8   single  0.970  0.020  1.090
 8NT  C15  H9   single  0.970  0.020  1.090
 8NT  C5   H10  single  0.970  0.020  1.090
 8NT  C5   H11  single  0.970  0.020  1.090
 8NT  C6   H12  single  0.970  0.020  1.090
 8NT  C6   H13  single  0.970  0.020  1.090
 8NT  C7   H14  single  0.970  0.020  1.090
 8NT  C7   H15  single  0.970  0.020  1.090
 8NT  C8   H16  single  0.970  0.020  1.090
 8NT  C8   H17  single  0.970  0.020  1.090
 8NT  C9   H18  single  0.970  0.020  1.090
 8NT  C9   H19  single  0.970  0.020  1.090
 8NT  N1   H20  single  0.860  0.020  1.020

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
 8NT  H2   C1   H1   106.45  3.000
 8NT  H2   C1   C7   109.26  3.000
 8NT  H1   C1   C7   110.07  3.000
 8NT  H2   C1   C2   107.07  3.000
 8NT  H1   C1   C2   109.52  3.000
 8NT  C7   C1   C2   114.16  3.000
 8NT  H3   C2   S1   108.01  3.000
 8NT  H3   C2   C6   110.15  3.000
 8NT  S1   C2   C6   104.99  3.000
 8NT  H3   C2   C1   110.04  3.000
 8NT  S1   C2   C1   109.99  3.000
 8NT  C6   C2   C1   113.43  3.000
 8NT  O1   C10  N1   122.27  3.000
 8NT  O1   C10  C9   122.30  3.000
 8NT  N1   C10  C9   115.42  3.000
 8NT  H5   C13  H4   106.80  3.000
 8NT  H5   C13  N1   110.11  3.000
 8NT  H4   C13  N1   109.80  3.000
 8NT  H5   C13  C14  109.86  3.000
 8NT  H4   C13  C14  109.93  3.000
 8NT  N1   C13  C14  110.29  3.000
 8NT  H7   C14  H6   107.32  3.000
 8NT  H7   C14  C15  109.65  3.000
 8NT  H6   C14  C15  109.59  3.000
 8NT  H7   C14  C13  109.52  3.000
 8NT  H6   C14  C13  109.58  3.000
 8NT  C15  C14  C13  111.11  3.000
 8NT  H9   C15  H8   107.58  3.000
 8NT  H9   C15  S3   107.27  3.000
 8NT  H8   C15  S3   106.93  3.000
 8NT  H9   C15  C14  110.96  3.000
 8NT  H8   C15  C14  111.08  3.000
 8NT  S3   C15  C14  112.77  3.000
 8NT  H11  C5   H10  108.79  3.000
 8NT  H11  C5   S2   108.69  3.000
 8NT  H10  C5   S2   106.93  3.000
 8NT  H11  C5   C6   111.63  3.000
 8NT  H10  C5   C6   111.10  3.000
 8NT  S2   C5   C6   109.56  3.000
 8NT  H13  C6   H12  107.69  3.000
 8NT  H13  C6   C5   110.34  3.000
 8NT  H12  C6   C5   109.15  3.000
 8NT  H13  C6   C2   109.08  3.000
 8NT  H12  C6   C2   109.97  3.000
 8NT  C5   C6   C2   110.55  3.000
 8NT  H15  C7   H14  106.19  3.000
 8NT  H15  C7   C8   109.09  3.000
 8NT  H14  C7   C8   109.58  3.000
 8NT  H15  C7   C1   109.89  3.000
 8NT  H14  C7   C1   109.49  3.000
 8NT  C8   C7   C1   112.41  3.000
 8NT  H17  C8   H16  106.55  3.000
 8NT  H17  C8   C9   109.75  3.000
 8NT  H16  C8   C9   109.63  3.000
 8NT  H17  C8   C7   109.54  3.000
 8NT  H16  C8   C7   109.46  3.000
 8NT  C9   C8   C7   111.77  3.000
 8NT  H19  C9   H18  106.12  3.000
 8NT  H19  C9   C8   109.39  3.000
 8NT  H18  C9   C8   109.92  3.000
 8NT  H19  C9   C10  107.37  3.000
 8NT  H18  C9   C10  110.69  3.000
 8NT  C8   C9   C10  113.07  3.000
 8NT  H20  N1   C13  118.11  3.000
 8NT  H20  N1   C10  118.77  3.000
 8NT  C13  N1   C10  123.09  3.000
 8NT  S2   S1   C2    93.56  3.000
 8NT  S1   S2   C5    96.34  3.000
 8NT  O4   S3   O3   113.09  3.000
 8NT  O4   S3   O2   113.11  3.000
 8NT  O3   S3   O2   112.94  3.000
 8NT  O4   S3   C15  105.25  3.000
 8NT  O2   S3   C15  105.86  3.000
 8NT  O3   S3   C15  105.69  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
 8NT  CONST_01  C9   C10  N1   C13   180.00   0.0  0
 8NT  CONST_02  O1   C10  N1   C13     0.00   0.0  0
 8NT  CONST_03  H20  N1   C10  C9      0.00   0.0  0
 8NT  Var_01    S2   C5   C6   C2    -36.81  30.0  1
 8NT  Var_02    C8   C7   C1   C2   -174.59  30.0  3
 8NT  Var_03    C9   C8   C7   C1   -178.22  30.0  3
 8NT  Var_04    C7   C8   C9   C10  -178.21  30.0  1
 8NT  Var_05    C14  C13  N1   C10   175.17  30.0  3
 8NT  Var_06    S3   C15  C14  C13  -177.58  30.0  1
 8NT  Var_07    O3   S3   C15  C14    62.14  30.0  3
 8NT  Var_08    N1   C13  C14  C15  -179.92  30.0  1
 8NT  Var_09    N1   C10  C9   C8   -140.68  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8NT  chir_01  C2  C6  C1  S1  positiv

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
 8NT  plan-1  C10  0.020
 8NT  plan-1  C13  0.020
 8NT  plan-1  C9   0.020
 8NT  plan-1  N1   0.020
 8NT  plan-1  O1   0.020
 8NT  plan-1  H20  0.020

