# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 16:23:48 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 5-[(3~{S})-1,2-dithiolan-3-yl]-~{N}-(3-oxidanylpropyl)pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCNC(=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
 8NW  8NW  5-[(3~{S})-1,2-dithiolan-3-yl]-~{N}-(3-oxidanylpropyl)pentanamide  ligand  37  16  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8NW
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
 8NW  C1   C  CH2   0  -0.418  -2.2010   0.9874   0.1640
 8NW  C2   C  CR15  0  -0.370  -3.5556   0.5723   0.7158
 8NW  N1   N  NH1   0  -0.621   3.6242  -0.5578  -0.4241
 8NW  O1   O  O     0  -0.505   3.1081   1.5088   0.3116
 8NW  S1   S  S2    0  -0.068  -4.0210  -1.1475   0.2046
 8NW  S2   S  S2    0  -0.050  -5.5951  -0.5819  -1.0350
 8NW  O3   O  OH1   0  -0.660   8.3000  -0.0396   0.7973
 8NW  C5   C  CH2   0  -0.553  -5.9880   0.8285   0.0391
 8NW  C6   C  CH2   0  -0.396  -4.6696   1.5405   0.2869
 8NW  C7   C  CH2   0  -0.410  -1.0361   0.1473   0.6655
 8NW  C8   C  CH2   0  -0.409   0.3030   0.6427   0.1363
 8NW  C9   C  CH2   0  -0.550   1.4702  -0.2106   0.6231
 8NW  C10  C  C     0   0.557   2.8050   0.3312   0.1604
 8NW  C13  C  CH2   0  -0.265   4.9593  -0.2319  -0.8727
 8NW  C14  C  CH2   0  -0.456   6.0007  -0.3118   0.2385
 8NW  C15  C  CH2   0  -0.121   7.3794   0.0650  -0.2674
 8NW  H1   H  HCH2  0   0.245  -2.2415   0.9645  -0.9295
 8NW  H2   H  HCH2  0   0.256  -2.0384   2.0340   0.4465
 8NW  H3   H  HCR5  0   0.305  -3.5091   0.5184   1.8057
 8NW  H4   H  HNH1  0   0.386   3.3303  -1.5178  -0.4900
 8NW  H5   H  HOH1  0   0.429   9.1668   0.2162   0.4699
 8NW  H6   H  HCH2  0   0.279  -6.6997   1.4635  -0.4894
 8NW  H7   H  HCH2  0   0.267  -6.4477   0.4711   0.9609
 8NW  H8   H  HCH2  0   0.257  -4.7906   2.3102   1.0520
 8NW  H9   H  HCH2  0   0.245  -4.3670   2.0412  -0.6350
 8NW  H10  H  HCH2  0   0.208  -1.0226   0.1593   1.7606
 8NW  H11  H  HCH2  0   0.211  -1.1818  -0.8969   0.3703
 8NW  H12  H  HCH2  0   0.221   0.2850   0.6417  -0.9579
 8NW  H13  H  HCH2  0   0.228   0.4553   1.6797   0.4437
 8NW  H14  H  HCH2  0   0.249   1.4832  -0.2195   1.7177
 8NW  H15  H  HCH2  0   0.225   1.3335  -1.2475   0.3071
 8NW  H16  H  HCH2  0   0.231   5.2138  -0.9236  -1.6768
 8NW  H17  H  HCH2  0   0.230   4.9492   0.7684  -1.3087
 8NW  H18  H  HCH2  0   0.229   5.7130   0.3589   1.0522
 8NW  H19  H  HCH2  0   0.228   6.0219  -1.3270   0.6446
 8NW  H20  H  HCH2  0   0.186   7.3502   1.0858  -0.6720
 8NW  H21  H  HCH2  0   0.184   7.6556  -0.5941  -1.1017

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
 8NW  C5   S2   single  1.816  0.020  1.816
 8NW  C5   C6   single  1.519  0.020  1.519
 8NW  S2   S1   single  2.082  0.020  2.082
 8NW  C6   C2   single  1.537  0.020  1.537
 8NW  S1   C2   single  1.853  0.020  1.853
 8NW  C2   C1   single  1.520  0.020  1.520
 8NW  C8   C9   single  1.526  0.020  1.526
 8NW  C8   C7   single  1.523  0.020  1.523
 8NW  C9   C10  single  1.513  0.020  1.513
 8NW  C7   C1   single  1.521  0.020  1.521
 8NW  C10  N1   single  1.343  0.020  1.343
 8NW  C10  O1   double  1.225  0.020  1.225
 8NW  N1   C13  single  1.446  0.020  1.446
 8NW  C13  C14  single  1.525  0.020  1.525
 8NW  C14  C15  single  1.516  0.020  1.516
 8NW  C15  O3   single  1.411  0.020  1.411
 8NW  C1   H1   single  0.970  0.020  1.090
 8NW  C1   H2   single  0.970  0.020  1.090
 8NW  C2   H3   single  0.970  0.020  1.090
 8NW  N1   H4   single  0.860  0.020  1.020
 8NW  O3   H5   single  0.850  0.020  0.980
 8NW  C5   H6   single  0.970  0.020  1.090
 8NW  C5   H7   single  0.970  0.020  1.090
 8NW  C6   H8   single  0.970  0.020  1.090
 8NW  C6   H9   single  0.970  0.020  1.090
 8NW  C7   H10  single  0.970  0.020  1.090
 8NW  C7   H11  single  0.970  0.020  1.090
 8NW  C8   H12  single  0.970  0.020  1.090
 8NW  C8   H13  single  0.970  0.020  1.090
 8NW  C9   H14  single  0.970  0.020  1.090
 8NW  C9   H15  single  0.970  0.020  1.090
 8NW  C13  H16  single  0.970  0.020  1.090
 8NW  C13  H17  single  0.970  0.020  1.090
 8NW  C14  H18  single  0.970  0.020  1.090
 8NW  C14  H19  single  0.970  0.020  1.090
 8NW  C15  H20  single  0.970  0.020  1.090
 8NW  C15  H21  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
 8NW  H2   C1   H1   106.44  3.000
 8NW  H2   C1   C7   109.19  3.000
 8NW  H1   C1   C7   110.25  3.000
 8NW  H2   C1   C2   107.42  3.000
 8NW  H1   C1   C2   108.90  3.000
 8NW  C7   C1   C2   114.32  3.000
 8NW  H3   C2   C6   109.90  3.000
 8NW  H3   C2   S1   103.90  3.000
 8NW  C6   C2   S1   109.00  3.000
 8NW  H3   C2   C1   109.73  3.000
 8NW  S1   C2   C1   112.14  3.000
 8NW  C6   C2   C1   111.87  3.000
 8NW  H4   N1   C13  117.68  3.000
 8NW  H4   N1   C10  118.82  3.000
 8NW  C13  N1   C10  123.32  3.000
 8NW  S2   S1   C2    95.85  3.000
 8NW  C5   S2   S1    91.28  3.000
 8NW  H5   O3   C15  108.16  3.000
 8NW  H7   C5   H6   108.99  3.000
 8NW  H7   C5   C6   112.45  3.000
 8NW  H6   C5   C6   111.88  3.000
 8NW  H7   C5   S2   109.68  3.000
 8NW  H6   C5   S2   107.87  3.000
 8NW  C6   C5   S2   105.83  3.000
 8NW  H9   C6   H8   107.40  3.000
 8NW  H9   C6   C5   108.53  3.000
 8NW  H8   C6   C5   110.40  3.000
 8NW  H9   C6   C2   108.88  3.000
 8NW  H8   C6   C2   109.20  3.000
 8NW  C5   C6   C2   112.30  3.000
 8NW  H11  C7   H10  106.36  3.000
 8NW  H11  C7   C8   109.49  3.000
 8NW  H10  C7   C8   109.45  3.000
 8NW  H11  C7   C1   109.62  3.000
 8NW  H10  C7   C1   109.45  3.000
 8NW  C8   C7   C1   112.28  3.000
 8NW  H13  C8   H12  106.53  3.000
 8NW  H13  C8   C9   109.55  3.000
 8NW  H12  C8   C9   109.34  3.000
 8NW  H13  C8   C7   109.49  3.000
 8NW  H12  C8   C7   109.43  3.000
 8NW  C9   C8   C7   112.33  3.000
 8NW  H15  C9   H14  106.44  3.000
 8NW  H15  C9   C10  111.21  3.000
 8NW  H14  C9   C10  107.35  3.000
 8NW  H15  C9   C8   110.05  3.000
 8NW  H14  C9   C8   109.43  3.000
 8NW  C10  C9   C8   112.16  3.000
 8NW  C9   C10  O1   121.64  3.000
 8NW  O1   C10  N1   122.62  3.000
 8NW  C9   C10  N1   115.74  3.000
 8NW  H17  C13  H16  106.79  3.000
 8NW  H17  C13  C14  110.21  3.000
 8NW  H16  C13  C14  110.16  3.000
 8NW  H17  C13  N1   108.78  3.000
 8NW  H16  C13  N1   107.54  3.000
 8NW  C14  C13  N1   113.13  3.000
 8NW  H19  C14  H18  107.36  3.000
 8NW  H19  C14  C15  109.69  3.000
 8NW  H18  C14  C15  109.59  3.000
 8NW  H19  C14  C13  109.41  3.000
 8NW  H18  C14  C13  109.30  3.000
 8NW  C15  C14  C13  111.40  3.000
 8NW  H21  C15  H20  106.53  3.000
 8NW  H21  C15  C14  109.45  3.000
 8NW  H20  C15  C14  109.25  3.000
 8NW  H21  C15  O3   111.37  3.000
 8NW  H20  C15  O3   111.35  3.000
 8NW  C14  C15  O3   108.85  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
 8NW  CONST_01  C13  N1   C10  O1      0.00   0.0  0
 8NW  CONST_02  C13  N1   C10  C9    180.00   0.0  0
 8NW  CONST_03  H4   N1   C10  O1    180.00   0.0  0
 8NW  Var_01    S2   C5   C6   C2    -48.95  30.0  1
 8NW  Var_02    C6   C5   S2   S1     48.90  30.0  1
 8NW  Var_03    C8   C7   C1   C2   -177.32  30.0  1
 8NW  Var_04    C9   C8   C7   C1   -179.21  30.0  2
 8NW  Var_05    C8   C9   C10  N1   -129.83  30.0  1
 8NW  Var_06    C15  C14  C13  N1   -178.81  30.0  3
 8NW  Var_07    C13  C14  C15  O3   -179.43  30.0  1
 8NW  Var_08    C10  C9   C8   C7   -176.72  30.0  3
 8NW  Var_09    C14  C13  N1   C10    83.90  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
 8NW  chir_01  C2  C6  S1  C1  negativ

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
 8NW  plan-1  N1   0.020
 8NW  plan-1  O1   0.020
 8NW  plan-1  C9   0.020
 8NW  plan-1  C10  0.020
 8NW  plan-1  C13  0.020
 8NW  plan-1  H4   0.020

