# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 11:23:48 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5-[(3aS,4R,6aR)-2-oxohexahydro-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(=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
 BTQ  BTQ  '5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid'  ligand  31  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BTQ
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
 BTQ  C11   C  C      0   0.411   5.5385   0.3045  -0.0771
 BTQ  O11   O  O      0  -0.609   5.5724   1.1546   0.8342
 BTQ  O12   O  OC    -1  -0.634   6.5259  -0.1855  -0.6664
 BTQ  C10   C  CH2    0  -0.584   4.1611  -0.2059  -0.5357
 BTQ  C9    C  CH2    0  -0.403   2.9554   0.3742   0.1850
 BTQ  C8    C  CH2    0  -0.417   1.6409  -0.2096  -0.3187
 BTQ  C7    C  CH2    0  -0.418   0.4288   0.3296   0.4295
 BTQ  C2    C  CH1    0  -0.370  -0.9027  -0.1745  -0.0983
 BTQ  S1    S  S2     0  -0.026  -1.0319  -1.9955  -0.0226
 BTQ  C6    C  CH2    0  -0.573  -2.8248  -1.8706  -0.2406
 BTQ  C5    C  CR15   0  -0.023  -3.2430  -0.7294   0.6887
 BTQ  N1    N  NR15   0  -0.670  -4.3874   0.0223   0.2527
 BTQ  C3    C  CR5    0   0.639  -4.1012   1.3029  -0.0932
 BTQ  O3    O  O      0  -0.527  -4.8935   2.1407  -0.4955
 BTQ  N2    N  NR15   0  -0.665  -2.7578   1.4831   0.0830
 BTQ  C4    C  CR15   0  -0.043  -2.1169   0.3427   0.6930
 BTQ  H101  H  HCH2   0   0.218   4.0694  -0.0202  -1.6124
 BTQ  H102  H  HCH2   0   0.217   4.1531  -1.2982  -0.4392
 BTQ  H91   H  HCH2   0   0.204   3.0418   0.1898   1.2598
 BTQ  H92   H  HCH2   0   0.204   2.9376   1.4618   0.0677
 BTQ  H81   H  HCH2   0   0.213   1.5307  -0.0034  -1.3889
 BTQ  H82   H  HCH2   0   0.213   1.6765  -1.3008  -0.2243
 BTQ  H71   H  HCH2   0   0.229   0.5100   0.0855   1.4937
 BTQ  H72   H  HCH2   0   0.236   0.4234   1.4231   0.3634
 BTQ  H2    H  HCH1   0   0.278  -1.0218   0.1209  -1.1458
 BTQ  H61   H  HCH2   0   0.272  -3.0590  -1.6334  -1.2806
 BTQ  H62   H  HCH2   0   0.290  -3.2986  -2.8164   0.0179
 BTQ  H5    H  HCR5   0   0.273  -3.3911  -1.1337   1.6916
 BTQ  HN1   H  HNR5   0   0.401  -5.3043  -0.3736   0.1329
 BTQ  HN2   H  HNR5   0   0.398  -2.3964   2.4147   0.2059
 BTQ  H4    H  HCR5   0   0.269  -1.8054   0.5652   1.7179

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
 BTQ  C11  O11   deloc   1.247  0.020  1.247
 BTQ  C11  O12   deloc   1.250  0.020  1.250
 BTQ  C11  C10   single  1.539  0.020  1.539
 BTQ  C10  C9    single  1.520  0.020  1.520
 BTQ  C10  H101  single  0.970  0.020  1.090
 BTQ  C10  H102  single  0.970  0.020  1.090
 BTQ  C9   C8    single  1.524  0.020  1.524
 BTQ  C9   H91   single  0.970  0.020  1.090
 BTQ  C9   H92   single  0.970  0.020  1.090
 BTQ  C8   C7    single  1.523  0.020  1.523
 BTQ  C8   H81   single  0.970  0.020  1.090
 BTQ  C8   H82   single  0.970  0.020  1.090
 BTQ  C7   C2    single  1.518  0.020  1.518
 BTQ  C7   H71   single  0.970  0.020  1.090
 BTQ  C7   H72   single  0.970  0.020  1.090
 BTQ  C2   S1    single  1.827  0.020  1.827
 BTQ  C2   C4    single  1.539  0.020  1.539
 BTQ  C2   H2    single  0.970  0.020  1.090
 BTQ  S1   C6    single  1.810  0.020  1.810
 BTQ  C6   C5    single  1.530  0.020  1.530
 BTQ  C6   H61   single  0.970  0.020  1.090
 BTQ  C6   H62   single  0.970  0.020  1.090
 BTQ  C5   N1    single  1.437  0.020  1.437
 BTQ  C5   C4    single  1.555  0.020  1.555
 BTQ  C5   H5    single  0.970  0.020  1.090
 BTQ  N1   C3    single  1.357  0.020  1.357
 BTQ  N1   HN1   single  0.860  0.020  1.020
 BTQ  C3   O3    double  1.221  0.020  1.221
 BTQ  C3   N2    single  1.367  0.020  1.367
 BTQ  N2   C4    single  1.443  0.020  1.443
 BTQ  N2   HN2   single  0.890  0.020  1.040
 BTQ  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
 BTQ  C10   C11  O12   115.88  3.000
 BTQ  C10   C11  O11   117.92  3.000
 BTQ  O12   C11  O11   126.19  3.000
 BTQ  H102  C10  H101  104.74  3.000
 BTQ  H102  C10  C9    109.43  3.000
 BTQ  H101  C10  C9    109.55  3.000
 BTQ  H102  C10  C11   108.10  3.000
 BTQ  H101  C10  C11   108.14  3.000
 BTQ  C9    C10  C11   116.25  3.000
 BTQ  H92   C9   H91   105.91  3.000
 BTQ  H92   C9   C8    109.35  3.000
 BTQ  H91   C9   C8    109.17  3.000
 BTQ  H92   C9   C10   109.97  3.000
 BTQ  H91   C9   C10   109.81  3.000
 BTQ  C8    C9   C10   112.42  3.000
 BTQ  H82   C8   H81   105.96  3.000
 BTQ  H82   C8   C7    109.63  3.000
 BTQ  H81   C8   C7    109.46  3.000
 BTQ  H82   C8   C9    108.96  3.000
 BTQ  H81   C8   C9    109.73  3.000
 BTQ  C7    C8   C9    112.86  3.000
 BTQ  H72   C7   H71   106.35  3.000
 BTQ  H72   C7   C2    107.82  3.000
 BTQ  H71   C7   C2    109.20  3.000
 BTQ  H72   C7   C8    109.13  3.000
 BTQ  H71   C7   C8    109.85  3.000
 BTQ  C2    C7   C8    114.18  3.000
 BTQ  H2    C2   C4    108.39  3.000
 BTQ  H2    C2   S1    107.51  3.000
 BTQ  C4    C2   S1    104.94  3.000
 BTQ  H2    C2   C7    109.78  3.000
 BTQ  C4    C2   C7    113.68  3.000
 BTQ  S1    C2   C7    112.24  3.000
 BTQ  C6    S1   C2     89.79  3.000
 BTQ  H62   C6   H61   108.75  3.000
 BTQ  H62   C6   C5    112.63  3.000
 BTQ  H61   C6   C5    110.97  3.000
 BTQ  H62   C6   S1    110.02  3.000
 BTQ  H61   C6   S1    110.00  3.000
 BTQ  C5    C6   S1    104.42  3.000
 BTQ  H5    C5   C4    110.56  3.000
 BTQ  H5    C5   N1    111.38  3.000
 BTQ  C4    C5   N1    102.53  3.000
 BTQ  H5    C5   C6    108.60  3.000
 BTQ  C4    C5   C6    108.55  3.000
 BTQ  N1    C5   C6    115.06  3.000
 BTQ  HN1   N1   C3    122.23  3.000
 BTQ  HN1   N1   C5    123.80  3.000
 BTQ  C3    N1   C5    113.77  3.000
 BTQ  N2    C3   O3    126.13  3.000
 BTQ  N2    C3   N1    107.39  3.000
 BTQ  O3    C3   N1    126.48  3.000
 BTQ  HN2   N2   C4    121.34  3.000
 BTQ  HN2   N2   C3    119.38  3.000
 BTQ  C4    N2   C3    112.75  3.000
 BTQ  H4    C4   N2    111.20  3.000
 BTQ  H4    C4   C5    110.43  3.000
 BTQ  N2    C4   C5    102.83  3.000
 BTQ  H4    C4   C2    108.99  3.000
 BTQ  N2    C4   C2    113.49  3.000
 BTQ  C5    C4   C2    109.77  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
 BTQ  CONST_01  N2   C3   N1   C5      0.00   0.0  0
 BTQ  CONST_02  C4   N2   C3   N1      0.00   0.0  0
 BTQ  CONST_03  O3   C3   N1   C5    180.00   0.0  0
 BTQ  CONST_04  C4   N2   C3   O3    180.00   0.0  0
 BTQ  CONST_06  HN1  N1   C3   N2    180.00   0.0  0
 BTQ  Var_01    C5   C6   S1   C2    -43.89  30.0  1
 BTQ  Var_02    C2   C7   C8   C9    176.83  30.0  3
 BTQ  Var_03    C8   C9   C10  C11  -178.91  30.0  3
 BTQ  Var_04    C9   C10  C11  O11    -0.54  30.0  3
 BTQ  Var_05    C7   C8   C9   C10   178.03  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
 BTQ  chir_01  C2  C7  S1  C4  negativ
 BTQ  chir_02  C5  N1  C4  C6  positiv
 BTQ  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
 BTQ  plan-1  C5   0.020
 BTQ  plan-1  N1   0.020
 BTQ  plan-1  C3   0.020
 BTQ  plan-1  O3   0.020
 BTQ  plan-1  N2   0.020
 BTQ  plan-1  C4   0.020
 BTQ  plan-1  HN1  0.020
 BTQ  plan-1  HN2  0.020
 BTQ  plan-2  C11  0.020
 BTQ  plan-2  O11  0.020
 BTQ  plan-2  O12  0.020
 BTQ  plan-2  C10  0.020

