# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:06:04 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 5-[(2Z,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC[C@@H]1SC[C@@H]2NC(=N)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
 IMI  IMI  '5-[(2Z,3aS,4S,6aR)-2-iminohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid'  ligand  32  16  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IMI
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
 IMI  C11   C  C      0   0.410   0.0077   0.1050   5.3564
 IMI  O11   O  O      0  -0.609   1.2288   0.3567   5.3436
 IMI  O12   O  OC    -1  -0.635  -0.6872  -0.1214   6.3704
 IMI  C10   C  CH2    0  -0.582  -0.7351   0.0627   4.0092
 IMI  C9    C  CH2    0  -0.403   0.1054   0.3353   2.7731
 IMI  C8    C  CH2    0  -0.412  -0.7036   0.2657   1.4832
 IMI  C7    C  CH2    0  -0.414   0.1423   0.5525   0.2486
 IMI  C2    C  CH1    0  -0.359  -0.6492   0.5901  -1.0451
 IMI  S1    S  S2     0  -0.031  -1.3806  -1.0219  -1.4820
 IMI  C6    C  CH2    0  -0.567  -1.7710  -0.3677  -3.1250
 IMI  C5    C  CR15   0  -0.040  -0.5626   0.4747  -3.5511
 IMI  N1    N  NR15   0  -0.671   0.4625  -0.2901  -4.2083
 IMI  C3    C  CR5    0   0.570   1.6534  -0.3048  -3.5509
 IMI  N3    N  N      0  -0.727   2.7812  -0.7981  -3.9031
 IMI  N2    N  NR15   0  -0.644   1.4495   0.3200  -2.3469
 IMI  C4    C  CR15   0  -0.069   0.1707   0.9866  -2.2791
 IMI  H101  H  HCH2   0   0.216  -1.2170  -0.9183   3.9187
 IMI  H102  H  HCH2   0   0.216  -1.5643   0.7787   4.0549
 IMI  H91   H  HCH2   0   0.202   0.5712   1.3224   2.8512
 IMI  H92   H  HCH2   0   0.203   0.9299  -0.3817   2.7204
 IMI  H81   H  HCH2   0   0.211  -1.1645  -0.7245   1.3974
 IMI  H82   H  HCH2   0   0.209  -1.5321   0.9813   1.5285
 IMI  H71   H  HCH2   0   0.232   0.6290   1.5271   0.3698
 IMI  H72   H  HCH2   0   0.228   0.9446  -0.1856   0.1658
 IMI  H2    H  HCH1   0   0.268  -1.4689   1.3106  -0.9451
 IMI  H61   H  HCH2   0   0.285  -1.9673  -1.1821  -3.8215
 IMI  H62   H  HCH2   0   0.269  -2.6653   0.2557  -3.0685
 IMI  H5    H  HCR5   0   0.271  -0.9050   1.3014  -4.1793
 IMI  HN1   H  HNR5   0   0.395   0.3573  -0.6441  -5.1427
 IMI  HN3   H  H      0   0.316   2.7124  -1.2187  -4.8220
 IMI  HN2   H  HNR5   0   0.386   2.2482   0.7390  -1.9012
 IMI  H4    H  HCR5   0   0.273   0.2888   2.0748  -2.2904

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
 IMI  C11  O11   deloc   1.247  0.020  1.247
 IMI  C11  O12   deloc   1.250  0.020  1.250
 IMI  C11  C10   single  1.539  0.020  1.539
 IMI  C10  C9    single  1.519  0.020  1.519
 IMI  C10  H101  single  0.970  0.020  1.090
 IMI  C10  H102  single  0.970  0.020  1.090
 IMI  C9   C8    single  1.524  0.020  1.524
 IMI  C9   H91   single  0.970  0.020  1.090
 IMI  C9   H92   single  0.970  0.020  1.090
 IMI  C8   C7    single  1.524  0.020  1.524
 IMI  C8   H81   single  0.970  0.020  1.090
 IMI  C8   H82   single  0.970  0.020  1.090
 IMI  C7   C2    single  1.517  0.020  1.517
 IMI  C7   H71   single  0.970  0.020  1.090
 IMI  C7   H72   single  0.970  0.020  1.090
 IMI  C2   S1    single  1.823  0.020  1.823
 IMI  C2   C4    single  1.534  0.020  1.534
 IMI  C2   H2    single  0.970  0.020  1.090
 IMI  S1   C6    single  1.811  0.020  1.811
 IMI  C6   C5    single  1.533  0.020  1.533
 IMI  C6   H61   single  0.970  0.020  1.090
 IMI  C6   H62   single  0.970  0.020  1.090
 IMI  C5   N1    single  1.438  0.020  1.438
 IMI  C5   C4    single  1.555  0.020  1.555
 IMI  C5   H5    single  0.970  0.020  1.090
 IMI  N1   C3    single  1.360  0.020  1.360
 IMI  N1   HN1   single  0.860  0.020  1.020
 IMI  C3   N3    double  1.280  0.020  1.280
 IMI  C3   N2    single  1.372  0.020  1.372
 IMI  N3   HN3   single  0.890  0.020  1.040
 IMI  N2   C4    single  1.444  0.020  1.444
 IMI  N2   HN2   single  0.890  0.020  1.040
 IMI  C4   H4    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
 IMI  C10   C11  O12   115.90  3.000
 IMI  C10   C11  O11   117.98  3.000
 IMI  O12   C11  O11   126.11  3.000
 IMI  H102  C10  H101  104.78  3.000
 IMI  H102  C10  C9    109.58  3.000
 IMI  H101  C10  C9    109.66  3.000
 IMI  H102  C10  C11   108.09  3.000
 IMI  H101  C10  C11   107.99  3.000
 IMI  C9    C10  C11   116.12  3.000
 IMI  H92   C9   H91   105.89  3.000
 IMI  H92   C9   C8    109.22  3.000
 IMI  H91   C9   C8    109.12  3.000
 IMI  H92   C9   C10   109.79  3.000
 IMI  H91   C9   C10   109.83  3.000
 IMI  C8    C9   C10   112.75  3.000
 IMI  H82   C8   H81   105.99  3.000
 IMI  H82   C8   C7    109.28  3.000
 IMI  H81   C8   C7    109.89  3.000
 IMI  H82   C8   C9    109.66  3.000
 IMI  H81   C8   C9    109.32  3.000
 IMI  C7    C8   C9    112.49  3.000
 IMI  H72   C7   H71   106.42  3.000
 IMI  H72   C7   C2    109.57  3.000
 IMI  H71   C7   C2    107.70  3.000
 IMI  H72   C7   C8    109.98  3.000
 IMI  H71   C7   C8    108.92  3.000
 IMI  C2    C7   C8    113.95  3.000
 IMI  H2    C2   C4    107.66  3.000
 IMI  H2    C2   S1    107.65  3.000
 IMI  C4    C2   S1    104.49  3.000
 IMI  H2    C2   C7    109.19  3.000
 IMI  C4    C2   C7    114.43  3.000
 IMI  S1    C2   C7    113.06  3.000
 IMI  C6    S1   C2     89.11  3.000
 IMI  H62   C6   H61   108.20  3.000
 IMI  H62   C6   C5    110.26  3.000
 IMI  H61   C6   C5    112.02  3.000
 IMI  H62   C6   S1    109.63  3.000
 IMI  H61   C6   S1    110.41  3.000
 IMI  C5    C6   S1    106.30  3.000
 IMI  H5    C5   C4    111.64  3.000
 IMI  H5    C5   N1    111.28  3.000
 IMI  C4    C5   N1    102.28  3.000
 IMI  H5    C5   C6    109.16  3.000
 IMI  C4    C5   C6    108.97  3.000
 IMI  N1    C5   C6    113.37  3.000
 IMI  HN1   N1   C3    122.50  3.000
 IMI  HN1   N1   C5    122.53  3.000
 IMI  C3    N1   C5    114.14  3.000
 IMI  N2    C3   N3    123.22  3.000
 IMI  N2    C3   N1    106.80  3.000
 IMI  N3    C3   N1    129.97  3.000
 IMI  HN3   N3   C3    110.47  3.000
 IMI  HN2   N2   C4    119.35  3.000
 IMI  HN2   N2   C3    117.42  3.000
 IMI  C4    N2   C3    112.53  3.000
 IMI  H4    C4   N2    111.29  3.000
 IMI  H4    C4   C5    111.69  3.000
 IMI  N2    C4   C5    103.14  3.000
 IMI  H4    C4   C2    108.85  3.000
 IMI  N2    C4   C2    113.08  3.000
 IMI  C5    C4   C2    108.72  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
 IMI  CONST_01  N2   C3   N1   C5      0.00   0.0  0
 IMI  CONST_02  C4   N2   C3   N1      0.00   0.0  0
 IMI  CONST_03  N3   C3   N1   C5    180.00   0.0  0
 IMI  CONST_04  C4   N2   C3   N3    180.00   0.0  0
 IMI  CONST_06  HN1  N1   C3   N2    180.00   0.0  0
 IMI  CONST_07  HN3  N3   C3   N1      0.00   0.0  0
 IMI  Var_01    C5   C6   S1   C2     40.40  30.0  1
 IMI  Var_02    C2   C7   C8   C9   -175.85  30.0  3
 IMI  Var_03    C8   C9   C10  C11   179.63  30.0  3
 IMI  Var_04    C9   C10  C11  O11     0.05  30.0  3
 IMI  Var_05    C7   C8   C9   C10   179.47  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
 IMI  chir_01  C2  C7  S1  C4  positiv
 IMI  chir_02  C5  N1  C6  C4  negativ
 IMI  chir_03  C4  N2  C2  C5  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
 IMI  plan-1  C5   0.020
 IMI  plan-1  N1   0.020
 IMI  plan-1  C3   0.020
 IMI  plan-1  N3   0.020
 IMI  plan-1  N2   0.020
 IMI  plan-1  C4   0.020
 IMI  plan-1  HN1  0.020
 IMI  plan-1  HN3  0.020
 IMI  plan-1  HN2  0.020
 IMI  plan-2  C11  0.020
 IMI  plan-2  O11  0.020
 IMI  plan-2  O12  0.020
 IMI  plan-2  C10  0.020

