# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 06:49:22 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 6-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCC[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
 SHM  SHM  '6-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]hexanoic acid'  ligand  35  17  .  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_SHM
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
 SHM  C1    C  CR15  0  -0.070   0.6467  -0.4098  -4.0736
 SHM  C2    C  CR15  0  -0.032  -0.0913  -1.0896  -2.8810
 SHM  N3    N  NR15  0  -0.661  -1.4243  -0.5651  -3.0114
 SHM  C4    C  CR5   0   0.643  -1.5515   0.3890  -3.9667
 SHM  N5    N  NR15  0  -0.658  -0.3393   0.5161  -4.5657
 SHM  C6    C  CH1   0  -0.373   0.6218  -0.7139  -1.5662
 SHM  S7    S  S2    0  -0.025   1.4343   0.8877  -1.8877
 SHM  C8    C  CH2   0  -0.558   1.8890   0.2969  -3.5361
 SHM  C9    C  CH2   0  -0.428  -0.2847  -0.6718  -0.3485
 SHM  C10   C  CH2   0  -0.415   0.4521  -0.4029   0.9582
 SHM  C11   C  CH2   0  -0.416  -0.4866  -0.4080   2.1575
 SHM  C12   C  CH2   0  -0.419   0.2282  -0.1240   3.4731
 SHM  C13   C  CH2   0  -0.580  -0.7425  -0.1041   4.6419
 SHM  C14   C  C     0   0.550  -0.0987   0.1930   5.9676
 SHM  O15   O  O     0  -0.446   1.0759   0.4028   6.1419
 SHM  O16   O  OH1   0  -0.599  -0.9886   0.1999   6.9575
 SHM  O17   O  O     0  -0.532  -2.5651   1.0168  -4.2373
 SHM  H11   H  HCR5  0   0.281   0.9330  -1.1326  -4.8422
 SHM  H12   H  HCR5  0   0.277  -0.0940  -2.1782  -2.9726
 SHM  HN3   H  HNR5  0   0.400  -2.1725  -0.7838  -2.3759
 SHM  HN5   H  HNR5  0   0.399  -0.2392   0.9914  -5.4463
 SHM  H6    H  HCH1  0   0.276   1.4078  -1.4575  -1.4001
 SHM  H81   H  HCH2  0   0.289   2.1954   1.1298  -4.1689
 SHM  H82   H  HCH2  0   0.273   2.7223  -0.4037  -3.4616
 SHM  H11A  H  HCH2  0   0.241  -0.7998  -1.6374  -0.2770
 SHM  H21   H  HCH2  0   0.230  -1.0607   0.0851  -0.4927
 SHM  H12A  H  HCH2  0   0.220   0.9629   0.5642   0.9056
 SHM  H22   H  HCH2  0   0.220   1.2339  -1.1559   1.0989
 SHM  H13   H  HCH2  0   0.216  -0.9901  -1.3792   2.2159
 SHM  H23   H  HCH2  0   0.216  -1.2765   0.3349   2.0048
 SHM  H14   H  HCH2  0   0.226   0.7474   0.8362   3.4070
 SHM  H24   H  HCH2  0   0.226   0.9974  -0.8828   3.6404
 SHM  H15   H  HCH2  0   0.276  -1.2640  -1.0632   4.7257
 SHM  H25   H  HCH2  0   0.275  -1.5287   0.6389   4.4740
 SHM  H16   H  HOH1  0   0.478  -0.5450   0.3865   7.7981

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
 SHM  C1   C2    single  1.559  0.020  1.559
 SHM  C1   N5    single  1.439  0.020  1.439
 SHM  C1   C8    single  1.527  0.020  1.527
 SHM  C1   H11   single  0.970  0.020  1.090
 SHM  C2   N3    single  1.438  0.020  1.438
 SHM  C2   C6    single  1.542  0.020  1.542
 SHM  C2   H12   single  0.970  0.020  1.090
 SHM  N3   C4    single  1.356  0.020  1.356
 SHM  N3   HN3   single  0.860  0.020  1.020
 SHM  C4   N5    single  1.358  0.020  1.358
 SHM  C4   O17   double  1.223  0.020  1.223
 SHM  N5   HN5   single  0.860  0.020  1.020
 SHM  C6   S7    single  1.824  0.020  1.824
 SHM  C6   C9    single  1.519  0.020  1.519
 SHM  C6   H6    single  0.970  0.020  1.090
 SHM  S7   C8    single  1.809  0.020  1.809
 SHM  C8   H81   single  0.970  0.020  1.090
 SHM  C8   H82   single  0.970  0.020  1.090
 SHM  C9   C10   single  1.524  0.020  1.524
 SHM  C9   H11A  single  0.970  0.020  1.090
 SHM  C9   H21   single  0.970  0.020  1.090
 SHM  C10  C11   single  1.523  0.020  1.523
 SHM  C10  H12A  single  0.970  0.020  1.090
 SHM  C10  H22   single  0.970  0.020  1.090
 SHM  C11  C12   single  1.524  0.020  1.524
 SHM  C11  H13   single  0.970  0.020  1.090
 SHM  C11  H23   single  0.970  0.020  1.090
 SHM  C12  C13   single  1.519  0.020  1.519
 SHM  C12  H14   single  0.970  0.020  1.090
 SHM  C12  H24   single  0.970  0.020  1.090
 SHM  C13  C14   single  1.503  0.020  1.503
 SHM  C13  H15   single  0.970  0.020  1.090
 SHM  C13  H25   single  0.970  0.020  1.090
 SHM  C14  O15   double  1.206  0.020  1.206
 SHM  C14  O16   single  1.331  0.020  1.331
 SHM  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
 SHM  H11   C1   C8    109.90  3.000
 SHM  H11   C1   N5    111.37  3.000
 SHM  C8    C1   N5    112.33  3.000
 SHM  H11   C1   C2    111.94  3.000
 SHM  C8    C1   C2    108.53  3.000
 SHM  N5    C1   C2    102.58  3.000
 SHM  H12   C2   C6    108.39  3.000
 SHM  H12   C2   N3    110.70  3.000
 SHM  C6    C2   N3    114.65  3.000
 SHM  H12   C2   C1    111.81  3.000
 SHM  C6    C2   C1    109.10  3.000
 SHM  N3    C2   C1    102.14  3.000
 SHM  HN3   N3   C4    121.89  3.000
 SHM  HN3   N3   C2    123.56  3.000
 SHM  C4    N3   C2    114.04  3.000
 SHM  O17   C4   N5    126.46  3.000
 SHM  O17   C4   N3    126.51  3.000
 SHM  N5    C4   N3    107.02  3.000
 SHM  HN5   N5   C4    121.28  3.000
 SHM  HN5   N5   C1    122.36  3.000
 SHM  C4    N5   C1    113.61  3.000
 SHM  H6    C6   C9    109.01  3.000
 SHM  H6    C6   S7    107.65  3.000
 SHM  C9    C6   S7    112.51  3.000
 SHM  H6    C6   C2    107.21  3.000
 SHM  C9    C6   C2    114.48  3.000
 SHM  S7    C6   C2    105.64  3.000
 SHM  C8    S7   C6     89.19  3.000
 SHM  H82   C8   H81   108.40  3.000
 SHM  H82   C8   S7    109.84  3.000
 SHM  H81   C8   S7    110.49  3.000
 SHM  H82   C8   C1    110.38  3.000
 SHM  H81   C8   C1    112.21  3.000
 SHM  S7    C8   C1    105.51  3.000
 SHM  H21   C9   H11A  106.54  3.000
 SHM  H21   C9   C10   109.51  3.000
 SHM  H11A  C9   C10   109.06  3.000
 SHM  H21   C9   C6    109.69  3.000
 SHM  H11A  C9   C6    107.95  3.000
 SHM  C10   C9   C6    113.82  3.000
 SHM  H22   C10  H12A  106.29  3.000
 SHM  H22   C10  C11   109.68  3.000
 SHM  H12A  C10  C11   109.17  3.000
 SHM  H22   C10  C9    109.52  3.000
 SHM  H12A  C10  C9    109.89  3.000
 SHM  C11   C10  C9    112.13  3.000
 SHM  H23   C11  H13   106.10  3.000
 SHM  H23   C11  C12   109.41  3.000
 SHM  H13   C11  C12   109.56  3.000
 SHM  H23   C11  C10   109.42  3.000
 SHM  H13   C11  C10   109.16  3.000
 SHM  C12   C11  C10   112.96  3.000
 SHM  H24   C12  H14   106.54  3.000
 SHM  H24   C12  C13   109.92  3.000
 SHM  H14   C12  C13   109.78  3.000
 SHM  H24   C12  C11   109.43  3.000
 SHM  H14   C12  C11   109.52  3.000
 SHM  C13   C12  C11   111.52  3.000
 SHM  H25   C13  H15   105.31  3.000
 SHM  H25   C13  C14   107.98  3.000
 SHM  H15   C13  C14   108.04  3.000
 SHM  H25   C13  C12   110.47  3.000
 SHM  H15   C13  C12   110.59  3.000
 SHM  C14   C13  C12   114.04  3.000
 SHM  O16   C14  O15   122.88  3.000
 SHM  O16   C14  C13   111.75  3.000
 SHM  O15   C14  C13   125.38  3.000
 SHM  H16   O16  C14   109.89  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
 SHM  CONST_01  N3   C4   N5   C1      0.00   0.0  0
 SHM  CONST_02  N5   C4   N3   C2      0.00   0.0  0
 SHM  CONST_03  O17  C4   N5   C1    180.00   0.0  0
 SHM  CONST_04  O17  C4   N3   C2    180.00   0.0  0
 SHM  CONST_06  HN3  N3   C4   N5    180.00   0.0  0
 SHM  CONST_07  H16  O16  C14  C13   180.00   0.0  0
 SHM  Var_01    H81  C8   S7   C6    164.66  30.0  1
 SHM  Var_02    C11  C10  C9   C6   -178.38  30.0  3
 SHM  Var_03    C12  C11  C10  C9   -179.30  30.0  3
 SHM  Var_04    C13  C12  C11  C10   178.65  30.0  3
 SHM  Var_05    C14  C13  C12  C11  -179.10  30.0  3
 SHM  Var_06    O15  C14  C13  C12    -0.05  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
 SHM  chir_01  C1  C2  N5  C8  negativ
 SHM  chir_02  C2  N3  C6  C1  positiv
 SHM  chir_03  C6  S7  C2  C9  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
 SHM  plan-1  C1   0.020
 SHM  plan-1  C2   0.020
 SHM  plan-1  N3   0.020
 SHM  plan-1  C4   0.020
 SHM  plan-1  N5   0.020
 SHM  plan-1  O17  0.020
 SHM  plan-1  HN3  0.020
 SHM  plan-1  HN5  0.020
 SHM  plan-2  C13  0.020
 SHM  plan-2  C14  0.020
 SHM  plan-2  O15  0.020
 SHM  plan-2  O16  0.020
 SHM  plan-2  H16  0.020

