# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:54:54 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 4-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
#
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
 SNR  SNR  '4-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]butanoic acid'  ligand  28  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SNR
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
 SNR  C1   C  CR5    0   0.643  -1.4170   0.2878  -3.1529
 SNR  N2   N  NR15   0  -0.660  -0.1653   0.3077  -3.6778
 SNR  C3   C  C      0  -0.064   0.7635  -0.5602  -3.0026
 SNR  C4   C  C      0  -0.035  -0.0894  -1.1159  -1.8215
 SNR  N5   N  NR15   0  -0.662  -1.3871  -0.5547  -2.0894
 SNR  C6   C  CR15   0  -0.367   0.5412  -0.6638  -0.4935
 SNR  S7   S  S2     0  -0.026   1.3722   0.9158  -0.8685
 SNR  C8   C  CH2    0  -0.560   1.9572   0.2006  -2.4252
 SNR  O11  O  O      0  -0.532  -2.3892   0.9023  -3.5670
 SNR  C12  C  CH2    0  -0.425  -0.4276  -0.5630   0.6706
 SNR  C13  C  CH2    0  -0.403   0.2510  -0.2716   2.0048
 SNR  C14  C  CH2    0  -0.584  -0.7402  -0.2484   3.1565
 SNR  C15  C  C      0   0.412  -0.1502   0.0385   4.5488
 SNR  O16  O  OC    -1  -0.634  -0.9672   0.0492   5.4942
 SNR  O17  O  O      0  -0.609   1.0773   0.2389   4.6329
 SNR  HN2  H  HNR5   0   0.399   0.0218   0.7052  -4.5822
 SNR  H3   H  H      0   0.280   1.1149  -1.3580  -3.6616
 SNR  H4   H  H      0   0.274  -0.1314  -2.2082  -1.8300
 SNR  HN5  H  HNR5   0   0.401  -2.1804  -0.6748  -1.4833
 SNR  H6   H  HCR5   0   0.272   1.3218  -1.3903  -0.2436
 SNR  H81  H  HCH2   0   0.288   2.3107   0.9830  -3.0958
 SNR  H82  H  HCH2   0   0.272   2.7857  -0.4826  -2.2298
 SNR  H11  H  HCH2   0   0.235  -0.9659  -1.5157   0.7406
 SNR  H21  H  HCH2   0   0.225  -1.1797   0.2037   0.4617
 SNR  H12  H  HCH2   0   0.211   0.7749   0.6869   1.9518
 SNR  H22  H  HCH2   0   0.209   1.0201  -1.0274   2.1868
 SNR  H13  H  HCH2   0   0.219  -1.2762  -1.2040   3.2013
 SNR  H23  H  HCH2   0   0.220  -1.5164   0.4998   2.9576

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
 SNR  C1   N2   single  1.357  0.020  1.357
 SNR  C1   N5   single  1.357  0.020  1.357
 SNR  C1   O11  double  1.222  0.020  1.222
 SNR  N2   C3   single  1.439  0.020  1.439
 SNR  N2   HN2  single  0.860  0.020  1.020
 SNR  C3   C4   single  1.559  0.020  1.559
 SNR  C3   C8   single  1.529  0.020  1.529
 SNR  C3   H3   single  0.970  0.020  1.090
 SNR  C4   N5   single  1.439  0.020  1.439
 SNR  C4   C6   single  1.538  0.020  1.538
 SNR  C4   H4   single  0.970  0.020  1.090
 SNR  N5   HN5  single  0.860  0.020  1.020
 SNR  C6   S7   single  1.824  0.020  1.824
 SNR  C6   C12  single  1.518  0.020  1.518
 SNR  C6   H6   single  0.970  0.020  1.090
 SNR  S7   C8   single  1.810  0.020  1.810
 SNR  C8   H81  single  0.970  0.020  1.090
 SNR  C8   H82  single  0.970  0.020  1.090
 SNR  C12  C13  single  1.525  0.020  1.525
 SNR  C12  H11  single  0.970  0.020  1.090
 SNR  C12  H21  single  0.970  0.020  1.090
 SNR  C13  C14  single  1.520  0.020  1.520
 SNR  C13  H12  single  0.970  0.020  1.090
 SNR  C13  H22  single  0.970  0.020  1.090
 SNR  C14  C15  single  1.539  0.020  1.539
 SNR  C14  H13  single  0.970  0.020  1.090
 SNR  C14  H23  single  0.970  0.020  1.090
 SNR  C15  O16  deloc   1.250  0.020  1.250
 SNR  C15  O17  deloc   1.247  0.020  1.247

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
 SNR  O11  C1   N5   126.52  3.000
 SNR  O11  C1   N2   126.51  3.000
 SNR  N5   C1   N2   106.97  3.000
 SNR  HN2  N2   C3   122.70  3.000
 SNR  HN2  N2   C1   121.68  3.000
 SNR  C3   N2   C1   113.88  3.000
 SNR  H3   C3   C8   109.88  3.000
 SNR  H3   C3   C4   111.88  3.000
 SNR  C8   C3   C4   108.56  3.000
 SNR  H3   C3   N2   111.39  3.000
 SNR  C8   C3   N2   112.39  3.000
 SNR  C4   C3   N2   102.55  3.000
 SNR  H4   C4   C6   108.43  3.000
 SNR  H4   C4   N5   110.71  3.000
 SNR  C6   C4   N5   114.57  3.000
 SNR  H4   C4   C3   111.79  3.000
 SNR  C6   C4   C3   108.97  3.000
 SNR  N5   C4   C3   102.31  3.000
 SNR  HN5  N5   C4   123.55  3.000
 SNR  HN5  N5   C1   121.95  3.000
 SNR  C4   N5   C1   114.07  3.000
 SNR  H6   C6   C12  108.90  3.000
 SNR  H6   C6   S7   107.26  3.000
 SNR  C12  C6   S7   113.01  3.000
 SNR  H6   C6   C4   107.11  3.000
 SNR  C12  C6   C4   114.84  3.000
 SNR  S7   C6   C4   105.30  3.000
 SNR  C8   S7   C6    88.96  3.000
 SNR  H82  C8   H81  108.26  3.000
 SNR  H82  C8   S7   109.80  3.000
 SNR  H81  C8   S7   110.52  3.000
 SNR  H82  C8   C3   110.41  3.000
 SNR  H81  C8   C3   112.22  3.000
 SNR  S7   C8   C3   105.61  3.000
 SNR  H21  C12  H11  106.47  3.000
 SNR  H21  C12  C13  109.82  3.000
 SNR  H11  C12  C13  109.19  3.000
 SNR  H21  C12  C6   109.81  3.000
 SNR  H11  C12  C6   107.73  3.000
 SNR  C13  C12  C6   113.56  3.000
 SNR  H22  C13  H12  106.07  3.000
 SNR  H22  C13  C14  110.07  3.000
 SNR  H12  C13  C14  109.62  3.000
 SNR  H22  C13  C12  109.06  3.000
 SNR  H12  C13  C12  109.77  3.000
 SNR  C14  C13  C12  112.07  3.000
 SNR  H23  C14  H13  104.84  3.000
 SNR  H23  C14  C15  107.96  3.000
 SNR  H13  C14  C15  108.23  3.000
 SNR  H23  C14  C13  109.56  3.000
 SNR  H13  C14  C13  109.66  3.000
 SNR  C15  C14  C13  116.00  3.000
 SNR  O17  C15  O16  126.25  3.000
 SNR  O17  C15  C14  117.93  3.000
 SNR  O16  C15  C14  115.81  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
 SNR  CONST_01  C4   N5   C1   N2      0.00   0.0  0
 SNR  CONST_02  N5   C1   N2   C3      0.00   0.0  0
 SNR  CONST_03  O11  C1   N2   C3    180.00   0.0  0
 SNR  CONST_04  O11  C1   N5   C4    180.00   0.0  0
 SNR  CONST_05  HN5  N5   C1   N2    180.00   0.0  0
 SNR  CONST_06  HN2  N2   C1   N5    180.00   0.0  0
 SNR  Var_01    H81  C8   S7   C6    164.59  30.0  1
 SNR  Var_02    C14  C13  C12  C6   -177.07  30.0  3
 SNR  Var_03    C15  C14  C13  C12   179.99  30.0  3
 SNR  Var_04    O16  C15  C14  C13  -179.61  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
 SNR  chir_01  C3  N2  C4  C8   positiv
 SNR  chir_02  C4  N5  C6  C3   positiv
 SNR  chir_03  C6  S7  C4  C12  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
 SNR  plan-1  C1   0.020
 SNR  plan-1  N2   0.020
 SNR  plan-1  C3   0.020
 SNR  plan-1  C4   0.020
 SNR  plan-1  N5   0.020
 SNR  plan-1  O11  0.020
 SNR  plan-1  HN2  0.020
 SNR  plan-1  HN5  0.020
 SNR  plan-2  C14  0.020
 SNR  plan-2  C15  0.020
 SNR  plan-2  O16  0.020
 SNR  plan-2  O17  0.020

