# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:17:14 2021
#   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  33  16  .  2021-08-11  2022-11-17
;
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   0.530  29.1643  14.3475   -9.4956
 IMI  O11   O  O     0  -0.438  28.0554  14.0910   -9.1037
 IMI  O12   O  OH1   0  -0.585  29.6113  13.7437  -10.5972
 IMI  C10   C  CH2   0  -0.606  30.1000  15.3302   -8.8360
 IMI  C9    C  CH2   0  -0.465  31.4969  14.7775   -8.5466
 IMI  C8    C  CH2   0  -0.418  31.4893  13.5571   -7.6344
 IMI  C7    C  CH2   0  -0.415  32.8997  13.0828   -7.3033
 IMI  C2    C  CH1   0  -0.364  32.9354  11.7737   -6.5385
 IMI  S1    S  S2    0  -0.031  32.1466  11.8773   -4.8977
 IMI  C6    C  CH2   0  -0.560  32.8489  10.2560   -4.5000
 IMI  C5    C  CH1   0  -0.065  34.2830  10.2826   -5.0312
 IMI  N1    N  NH1   0  -0.661  35.2023  10.8968   -4.1016
 IMI  C3    C  C     0   0.559  35.8949  11.9401   -4.6561
 IMI  N3    N  N     0  -0.720  36.9068  12.5785   -4.2039
 IMI  N2    N  NH1   0  -0.643  35.2757  12.2482   -5.8361
 IMI  C4    C  CH1   0  -0.054  34.3451  11.2327   -6.2620
 IMI  HO2   H  HOH1  0   0.487  30.5008  14.0344  -10.8359
 IMI  H101  H  HCH2  0   0.294  30.1834  16.2039   -9.4906
 IMI  H102  H  HCH2  0   0.269  29.6330  15.6688   -7.9117
 IMI  H91   H  HCH2  0   0.227  32.0262  14.5430   -9.4766
 IMI  H92   H  HCH2  0   0.256  32.0761  15.5782   -8.0820
 IMI  H81   H  HCH2  0   0.230  30.9492  13.8019   -6.7145
 IMI  H82   H  HCH2  0   0.225  30.9389  12.7370   -8.1068
 IMI  H71   H  HCH2  0   0.239  33.4548  12.9394   -8.2371
 IMI  H72   H  HCH2  0   0.236  33.4289  13.8560   -6.7412
 IMI  H2    H  HCH1  0   0.272  32.3948  11.0127   -7.1119
 IMI  H61   H  HCH2  0   0.286  32.8138  10.0791   -3.4259
 IMI  H62   H  HCH2  0   0.269  32.2702   9.4733   -4.9947
 IMI  H5    H  HCH1  0   0.276  34.5983   9.2682   -5.2892
 IMI  HN1   H  HNH1  0   0.393  35.6538  10.3276   -3.4052
 IMI  HN3   H  H     0   0.318  37.1932  12.2030   -3.3077
 IMI  HN2   H  HNH1  0   0.387  35.7922  12.7782   -6.5169
 IMI  H4    H  HCH1  0   0.273  34.7058  10.7144   -7.1560

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   double  1.204  0.020  1.204
 IMI  C11  O12   single  1.333  0.020  1.333
 IMI  C11  C10   single  1.509  0.020  1.509
 IMI  O12  HO2   single  0.850  0.020  0.980
 IMI  C10  C9    single  1.530  0.020  1.530
 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  1.824  0.020  1.824
 IMI  C2   C4    single  1.535  0.020  1.535
 IMI  C2   H2    single  0.970  0.020  1.090
 IMI  S1   C6    single  1.811  0.020  1.811
 IMI  C6   C5    single  1.530  0.020  1.530
 IMI  C6   H61   single  0.970  0.020  1.090
 IMI  C6   H62   single  0.970  0.020  1.090
 IMI  C5   N1    single  1.444  0.020  1.444
 IMI  C5   C4    single  1.556  0.020  1.556
 IMI  C5   H5    single  0.970  0.020  1.090
 IMI  N1   C3    single  1.370  0.020  1.370
 IMI  N1   HN1   single  0.890  0.020  1.040
 IMI  C3   N3    double  1.279  0.020  1.279
 IMI  C3   N2    single  1.368  0.020  1.368
 IMI  N3   HN3   single  0.890  0.020  1.040
 IMI  N2   C4    single  1.442  0.020  1.442
 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   116.63  3.000
 IMI  C10   C11  O11   124.60  3.000
 IMI  O12   C11  O11   118.77  3.000
 IMI  HO2   O12  C11   112.13  3.000
 IMI  H102  C10  H101  106.97  3.000
 IMI  H102  C10  C9    110.07  3.000
 IMI  H101  C10  C9    109.39  3.000
 IMI  H102  C10  C11   107.90  3.000
 IMI  H101  C10  C11   107.79  3.000
 IMI  C9    C10  C11   114.43  3.000
 IMI  H92   C9   H91   105.18  3.000
 IMI  H92   C9   C8    109.59  3.000
 IMI  H91   C9   C8    109.83  3.000
 IMI  H92   C9   C10   107.45  3.000
 IMI  H91   C9   C10   110.97  3.000
 IMI  C8    C9   C10   113.46  3.000
 IMI  H82   C8   H81   106.38  3.000
 IMI  H82   C8   C7    109.01  3.000
 IMI  H81   C8   C7    110.10  3.000
 IMI  H82   C8   C9    110.13  3.000
 IMI  H81   C8   C9    109.06  3.000
 IMI  C7    C8   C9    112.00  3.000
 IMI  H72   C7   H71   106.60  3.000
 IMI  H72   C7   C2    109.87  3.000
 IMI  H71   C7   C2    107.75  3.000
 IMI  H72   C7   C8    109.86  3.000
 IMI  H71   C7   C8    108.93  3.000
 IMI  C2    C7   C8    113.57  3.000
 IMI  H2    C2   C4    107.61  3.000
 IMI  H2    C2   S1    107.28  3.000
 IMI  C4    C2   S1    104.79  3.000
 IMI  H2    C2   C7    108.91  3.000
 IMI  C4    C2   C7    114.62  3.000
 IMI  S1    C2   C7    113.24  3.000
 IMI  C6    S1   C2     88.79  3.000
 IMI  H62   C6   H61   108.25  3.000
 IMI  H62   C6   C5    110.61  3.000
 IMI  H61   C6   C5    112.06  3.000
 IMI  H62   C6   S1    109.68  3.000
 IMI  H61   C6   S1    110.46  3.000
 IMI  C5    C6   S1    105.77  3.000
 IMI  H5    C5   C4    111.62  3.000
 IMI  H5    C5   N1    111.28  3.000
 IMI  C4    C5   N1    102.94  3.000
 IMI  H5    C5   C6    109.65  3.000
 IMI  C4    C5   C6    108.82  3.000
 IMI  N1    C5   C6    112.37  3.000
 IMI  HN1   N1   C3    118.96  3.000
 IMI  HN1   N1   C5    119.36  3.000
 IMI  C3    N1   C5    112.66  3.000
 IMI  N2    C3   N3    123.42  3.000
 IMI  N2    C3   N1    106.97  3.000
 IMI  N3    C3   N1    129.58  3.000
 IMI  HN3   N3   C3    110.57  3.000
 IMI  HN2   N2   C4    120.18  3.000
 IMI  HN2   N2   C3    118.05  3.000
 IMI  C4    N2   C3    112.86  3.000
 IMI  H4    C4   N2    111.23  3.000
 IMI  H4    C4   C5    111.72  3.000
 IMI  N2    C4   C5    102.84  3.000
 IMI  H4    C4   C2    108.81  3.000
 IMI  N2    C4   C2    113.44  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_07  HN3  N3   C3   N1      0.00   0.0  0
 IMI  CONST_08  HO2  O12  C11  O11   180.00   0.0  0
 IMI  Var_01    C5   C6   S1   C2     42.32  30.0  1
 IMI  Var_02    C2   C7   C8   C9   -172.95  30.0  3
 IMI  Var_03    C8   C9   C10  C11   -59.19  30.0  3
 IMI  Var_04    C9   C10  C11  O11   128.61  30.0  3
 IMI  Var_05    C7   C8   C9   C10  -176.71  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
 IMI  plan-2  HO2  0.020

