# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 09:51:40 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  29  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   0.642  -1.3833   0.2728  -3.2644
 SNR  N2   N  NR15  0  -0.661  -0.1526   0.1124  -3.8120
 SNR  C3   C  CR15  0  -0.043   0.7712  -0.6022  -2.9712
 SNR  C4   C  CR15  0  -0.065  -0.1372  -1.0531  -1.7892
 SNR  N5   N  NR15  0  -0.656  -1.3747  -0.3677  -2.0630
 SNR  C6   C  CH1   0  -0.363   0.5153  -0.6139  -0.4738
 SNR  S7   S  S2    0  -0.022   1.3048   0.9809  -0.8671
 SNR  C8   C  CH2   0  -0.571   1.9071   0.2694  -2.4204
 SNR  O11  O  O     0  -0.529  -2.3271   0.8698  -3.7593
 SNR  C12  C  CH2   0  -0.422  -0.4416  -0.5279   0.7008
 SNR  C13  C  CH2   0  -0.420   0.2558  -0.2375   2.0244
 SNR  C14  C  CH2   0  -0.582  -0.7363  -0.2259   3.1754
 SNR  C15  C  C     0   0.551  -0.1064   0.0375   4.5146
 SNR  O16  O  OH1   0  -0.598  -1.0070   0.0290   5.4935
 SNR  O17  O  O     0  -0.445   1.0676   0.2365   4.7053
 SNR  HN2  H  HNR5  0   0.399   0.1382   0.6343  -4.6214
 SNR  H3   H  HCR5  0   0.278   1.1985  -1.4570  -3.4992
 SNR  H4   H  HCR5  0   0.281  -0.2799  -2.1375  -1.7762
 SNR  HN5  H  HNR5  0   0.399  -2.2398  -0.6367  -1.6254
 SNR  H6   H  HCH1  0   0.276   1.3087  -1.3325  -0.2411
 SNR  H81  H  HCH2  0   0.289   2.1924   1.0615  -3.1120
 SNR  H82  H  HCH2  0   0.275   2.7882  -0.3435  -2.2249
 SNR  H11  H  HCH2  0   0.244  -0.9691  -1.4858   0.7734
 SNR  H21  H  HCH2  0   0.236  -1.2008   0.2336   0.5034
 SNR  H12  H  HCH2  0   0.234   0.7687   0.7261   1.9721
 SNR  H22  H  HCH2  0   0.234   1.0258  -0.9926   2.2006
 SNR  H13  H  HCH2  0   0.278  -1.2730  -1.1787   3.2315
 SNR  H23  H  HCH2  0   0.279  -1.5070   0.5333   3.0097
 SNR  H16  H  HOH1  0   0.478  -0.5735   0.1947   6.3440

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  1.361  0.020  1.361
 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  1.557  0.020  1.557
 SNR  C3   C8   single  1.534  0.020  1.534
 SNR  C3   H3   single  0.970  0.020  1.090
 SNR  C4   N5   single  1.441  0.020  1.441
 SNR  C4   C6   single  1.533  0.020  1.533
 SNR  C4   H4   single  0.970  0.020  1.090
 SNR  N5   HN5  single  0.890  0.020  1.040
 SNR  C6   S7   single  1.823  0.020  1.823
 SNR  C6   C12  single  1.517  0.020  1.517
 SNR  C6   H6   single  0.970  0.020  1.090
 SNR  S7   C8   single  1.812  0.020  1.812
 SNR  C8   H81  single  0.970  0.020  1.090
 SNR  C8   H82  single  0.970  0.020  1.090
 SNR  C12  C13  single  1.524  0.020  1.524
 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  1.503  0.020  1.503
 SNR  C14  H13  single  0.970  0.020  1.090
 SNR  C14  H23  single  0.970  0.020  1.090
 SNR  C15  O16  single  1.330  0.020  1.330
 SNR  C15  O17  double  1.206  0.020  1.206
 SNR  O16  H16  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
 SNR  O11  C1   N5   126.32  3.000
 SNR  O11  C1   N2   126.52  3.000
 SNR  N5   C1   N2   107.15  3.000
 SNR  HN2  N2   C3   122.83  3.000
 SNR  HN2  N2   C1   121.72  3.000
 SNR  C3   N2   C1   113.91  3.000
 SNR  H3   C3   C8   109.18  3.000
 SNR  H3   C3   C4   111.63  3.000
 SNR  C8   C3   C4   108.90  3.000
 SNR  H3   C3   N2   110.95  3.000
 SNR  C8   C3   N2   113.77  3.000
 SNR  C4   C3   N2   102.29  3.000
 SNR  H4   C4   C6   109.24  3.000
 SNR  H4   C4   N5   111.21  3.000
 SNR  C6   C4   N5   113.11  3.000
 SNR  H4   C4   C3   111.85  3.000
 SNR  C6   C4   C3   108.67  3.000
 SNR  N5   C4   C3   102.65  3.000
 SNR  HN5  N5   C4   121.91  3.000
 SNR  HN5  N5   C1   120.28  3.000
 SNR  C4   N5   C1   113.38  3.000
 SNR  H6   C6   C12  109.23  3.000
 SNR  H6   C6   S7   107.82  3.000
 SNR  C12  C6   S7   112.99  3.000
 SNR  H6   C6   C4   107.62  3.000
 SNR  C12  C6   C4   114.34  3.000
 SNR  S7   C6   C4   104.48  3.000
 SNR  C8   S7   C6    89.16  3.000
 SNR  H82  C8   H81  108.10  3.000
 SNR  H82  C8   S7   109.60  3.000
 SNR  H81  C8   S7   110.23  3.000
 SNR  H82  C8   C3   110.07  3.000
 SNR  H81  C8   C3   112.28  3.000
 SNR  S7   C8   C3   106.55  3.000
 SNR  H21  C12  H11  106.65  3.000
 SNR  H21  C12  C13  109.99  3.000
 SNR  H11  C12  C13  109.22  3.000
 SNR  H21  C12  C6   109.73  3.000
 SNR  H11  C12  C6   107.77  3.000
 SNR  C13  C12  C6   113.23  3.000
 SNR  H22  C13  H12  106.64  3.000
 SNR  H22  C13  C14  110.07  3.000
 SNR  H12  C13  C14  109.62  3.000
 SNR  H22  C13  C12  109.32  3.000
 SNR  H12  C13  C12  109.95  3.000
 SNR  C14  C13  C12  111.13  3.000
 SNR  H23  C14  H13  105.44  3.000
 SNR  H23  C14  C15  107.97  3.000
 SNR  H13  C14  C15  108.19  3.000
 SNR  H23  C14  C13  110.51  3.000
 SNR  H13  C14  C13  110.62  3.000
 SNR  C15  C14  C13  113.74  3.000
 SNR  O17  C15  O16  122.95  3.000
 SNR  O17  C15  C14  125.29  3.000
 SNR  O16  C15  C14  111.76  3.000
 SNR  H16  O16  C15  110.00  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_06  HN2  N2   C1   N5    180.00   0.0  0
 SNR  CONST_07  H16  O16  C15  C14   180.00   0.0  0
 SNR  Var_01    H81  C8   S7   C6    161.87  30.0  1
 SNR  Var_02    C14  C13  C12  C6   -177.35  30.0  3
 SNR  Var_03    C15  C14  C13  C12   179.22  30.0  3
 SNR  Var_04    O16  C15  C14  C13  -179.52  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
 SNR  plan-2  H16  0.020

