# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:00:56 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CNC(=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
 T1O  T1O  5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide  ligand  41  20  .  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_T1O
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
 T1O  O01  O  O     0  -0.524  -6.6799  -2.0175   0.6261
 T1O  C02  C  CR5   0   0.635  -5.8708  -1.2054   0.2069
 T1O  N03  N  NR15  0  -0.663  -4.5423  -1.4356  -0.0197
 T1O  C04  C  CR15  0  -0.046  -3.8792  -0.3061  -0.6277
 T1O  C05  C  CR15  0  -0.029  -4.9483   0.8157  -0.5217
 T1O  C06  C  CH2   0  -0.572  -4.4517   1.8611   0.4778
 T1O  S07  S  S2    0  -0.024  -2.6693   1.9475   0.1759
 T1O  N08  N  NR15  0  -0.667  -6.1235   0.0895  -0.1209
 T1O  C09  C  CH1   0  -0.371  -2.5988   0.1216   0.1130
 T1O  C10  C  CH2   0  -0.421  -1.3230  -0.3842  -0.5360
 T1O  C11  C  CH2   0  -0.424  -0.0480   0.0867   0.1505
 T1O  C12  C  CH2   0  -0.413   1.2025  -0.5373  -0.4556
 T1O  C13  C  CH2   0  -0.587   2.4682   0.0081   0.1845
 T1O  C14  C  C     0   0.569   3.7467  -0.5608  -0.3952
 T1O  N15  N  NH1   0  -0.651   4.8750  -0.0590   0.1360
 T1O  C16  C  CH2   0  -0.352   6.1800  -0.4781  -0.2833
 T1O  C17  C  C     0   0.361   7.2641   0.2520   0.4707
 T1O  C18  C  CH3   0  -0.772   8.6629  -0.0286   0.0116
 T1O  O19  O  O     0  -0.396   7.0057   1.0205   1.3686
 T1O  O20  O  O     0  -0.500   3.7643  -1.4082  -1.2768
 T1O  H1   H  HNR5  0   0.398  -4.2351  -2.3761  -0.2061
 T1O  H2   H  HCR5  0   0.271  -3.6386  -0.5061  -1.6762
 T1O  H3   H  HCR5  0   0.273  -5.0917   1.2997  -1.4890
 T1O  H4   H  HCH2  0   0.291  -4.9041   2.8395   0.3223
 T1O  H5   H  HCH2  0   0.272  -4.6438   1.5443   1.5054
 T1O  H6   H  HNR5  0   0.401  -6.9791   0.5427   0.1547
 T1O  H7   H  HCH1  0   0.281  -2.6599  -0.2427   1.1430
 T1O  H8   H  HCH2  0   0.239  -1.3558  -1.4790  -0.5272
 T1O  H9   H  HCH2  0   0.233  -1.3102  -0.0847  -1.5888
 T1O  H10  H  HCH2  0   0.221   0.0268   1.1774   0.0815
 T1O  H11  H  HCH2  0   0.222  -0.0994  -0.1468   1.2190
 T1O  H12  H  HCH2  0   0.225   1.1612  -1.6232  -0.3382
 T1O  H13  H  HCH2  0   0.224   1.2178  -0.3440  -1.5315
 T1O  H14  H  HCH2  0   0.264   2.4976   1.0982   0.0857
 T1O  H15  H  HCH2  0   0.267   2.4590  -0.1854   1.2623
 T1O  H16  H  HNH1  0   0.399   4.8206   0.6277   0.8726
 T1O  H17  H  HCH2  0   0.278   6.3330  -1.5521  -0.1243
 T1O  H18  H  HCH2  0   0.275   6.3361  -0.3123  -1.3551
 T1O  H19  H  HCH3  0   0.280   8.8743   0.5888  -0.8650
 T1O  H20  H  HCH3  0   0.270   9.3876   0.2178   0.7845
 T1O  H21  H  HCH3  0   0.262   8.7872  -1.0673  -0.2927

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
 T1O  C16  N15  single  1.433  0.020  1.433
 T1O  C16  C17  single  1.509  0.020  1.509
 T1O  C05  C04  single  1.553  0.020  1.553
 T1O  C05  N08  single  1.438  0.020  1.438
 T1O  C05  C06  single  1.529  0.020  1.529
 T1O  C04  N03  single  1.444  0.020  1.444
 T1O  C04  C09  single  1.540  0.020  1.540
 T1O  N15  C14  single  1.344  0.020  1.344
 T1O  N08  C02  single  1.359  0.020  1.359
 T1O  C11  C10  single  1.523  0.020  1.523
 T1O  C11  C12  single  1.523  0.020  1.523
 T1O  C06  S07  single  1.810  0.020  1.810
 T1O  C10  C09  single  1.518  0.020  1.518
 T1O  N03  C02  single  1.367  0.020  1.367
 T1O  C18  C17  single  1.499  0.020  1.499
 T1O  C14  O20  double  1.223  0.020  1.223
 T1O  C14  C13  single  1.515  0.020  1.515
 T1O  S07  C09  single  1.828  0.020  1.828
 T1O  C17  O19  double  1.210  0.020  1.210
 T1O  C02  O01  double  1.221  0.020  1.221
 T1O  C13  C12  single  1.520  0.020  1.520
 T1O  N03  H1   single  0.890  0.020  1.040
 T1O  C04  H2   single  0.970  0.020  1.090
 T1O  C05  H3   single  0.970  0.020  1.090
 T1O  C06  H4   single  0.970  0.020  1.090
 T1O  C06  H5   single  0.970  0.020  1.090
 T1O  N08  H6   single  0.860  0.020  1.020
 T1O  C09  H7   single  0.970  0.020  1.090
 T1O  C10  H8   single  0.970  0.020  1.090
 T1O  C10  H9   single  0.970  0.020  1.090
 T1O  C11  H10  single  0.970  0.020  1.090
 T1O  C11  H11  single  0.970  0.020  1.090
 T1O  C12  H12  single  0.970  0.020  1.090
 T1O  C12  H13  single  0.970  0.020  1.090
 T1O  C13  H14  single  0.970  0.020  1.090
 T1O  C13  H15  single  0.970  0.020  1.090
 T1O  N15  H16  single  0.860  0.020  1.020
 T1O  C16  H17  single  0.970  0.020  1.090
 T1O  C16  H18  single  0.970  0.020  1.090
 T1O  C18  H19  single  0.970  0.020  1.090
 T1O  C18  H20  single  0.970  0.020  1.090
 T1O  C18  H21  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
 T1O  N08  C02  N03  107.52  3.000
 T1O  N03  C02  O01  126.08  3.000
 T1O  N08  C02  O01  126.39  3.000
 T1O  H1   N03  C04  120.84  3.000
 T1O  H1   N03  C02  118.98  3.000
 T1O  C04  N03  C02  112.60  3.000
 T1O  H2   C04  C09  109.21  3.000
 T1O  H2   C04  C05  110.41  3.000
 T1O  C09  C04  C05  109.81  3.000
 T1O  H2   C04  N03  111.19  3.000
 T1O  C09  C04  N03  113.36  3.000
 T1O  C05  C04  N03  102.71  3.000
 T1O  H3   C05  N08  111.32  3.000
 T1O  H3   C05  C06  108.60  3.000
 T1O  N08  C05  C06  115.36  3.000
 T1O  H3   C05  C04  110.51  3.000
 T1O  C06  C05  C04  108.35  3.000
 T1O  N08  C05  C04  102.52  3.000
 T1O  H5   C06  H4   108.77  3.000
 T1O  H5   C06  S07  110.12  3.000
 T1O  H4   C06  S07  110.02  3.000
 T1O  H5   C06  C05  111.07  3.000
 T1O  H4   C06  C05  112.70  3.000
 T1O  S07  C06  C05  104.09  3.000
 T1O  C09  S07  C06   89.77  3.000
 T1O  H6   N08  C05  122.92  3.000
 T1O  H6   N08  C02  121.39  3.000
 T1O  C05  N08  C02  113.34  3.000
 T1O  H7   C09  C10  109.77  3.000
 T1O  H7   C09  S07  107.34  3.000
 T1O  C10  C09  S07  112.33  3.000
 T1O  H7   C09  C04  108.30  3.000
 T1O  S07  C09  C04  105.18  3.000
 T1O  C10  C09  C04  113.61  3.000
 T1O  H9   C10  H8   106.35  3.000
 T1O  H9   C10  C11  109.82  3.000
 T1O  H8   C10  C11  109.30  3.000
 T1O  H9   C10  C09  109.26  3.000
 T1O  H8   C10  C09  107.73  3.000
 T1O  C11  C10  C09  114.07  3.000
 T1O  H11  C11  H10  106.09  3.000
 T1O  H11  C11  C12  109.85  3.000
 T1O  H10  C11  C12  109.08  3.000
 T1O  H11  C11  C10  109.55  3.000
 T1O  H10  C11  C10  109.67  3.000
 T1O  C12  C11  C10  112.41  3.000
 T1O  H13  C12  H12  106.38  3.000
 T1O  H13  C12  C13  109.84  3.000
 T1O  H12  C12  C13  110.05  3.000
 T1O  H13  C12  C11  109.31  3.000
 T1O  H12  C12  C11  109.46  3.000
 T1O  C13  C12  C11  111.66  3.000
 T1O  H15  C13  H14  105.37  3.000
 T1O  H15  C13  C14  108.51  3.000
 T1O  H14  C13  C14  108.46  3.000
 T1O  H15  C13  C12  110.13  3.000
 T1O  H14  C13  C12  109.98  3.000
 T1O  C14  C13  C12  114.01  3.000
 T1O  O20  C14  N15  122.10  3.000
 T1O  O20  C14  C13  123.25  3.000
 T1O  N15  C14  C13  114.65  3.000
 T1O  H16  N15  C16  117.51  3.000
 T1O  H16  N15  C14  119.84  3.000
 T1O  C16  N15  C14  122.65  3.000
 T1O  H18  C16  H17  105.68  3.000
 T1O  H18  C16  C17  108.25  3.000
 T1O  H17  C16  C17  107.53  3.000
 T1O  H18  C16  N15  111.82  3.000
 T1O  H17  C16  N15  111.78  3.000
 T1O  C17  C16  N15  111.50  3.000
 T1O  O19  C17  C18  123.07  3.000
 T1O  O19  C17  C16  121.65  3.000
 T1O  C18  C17  C16  115.27  3.000
 T1O  H21  C18  H20  109.78  3.000
 T1O  H21  C18  H19  107.01  3.000
 T1O  H20  C18  H19  108.24  3.000
 T1O  H21  C18  C17  111.75  3.000
 T1O  H20  C18  C17  111.20  3.000
 T1O  H19  C18  C17  108.69  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
 T1O  CONST_01  C05  N08  C02  N03     0.00   0.0  0
 T1O  CONST_02  N08  C02  N03  C04     0.00   0.0  0
 T1O  CONST_03  C05  N08  C02  O01   180.00   0.0  0
 T1O  CONST_04  C04  N03  C02  O01   180.00   0.0  0
 T1O  CONST_05  H6   N08  C02  N03   180.00   0.0  0
 T1O  CONST_07  C16  N15  C14  C13   180.00   0.0  0
 T1O  CONST_08  O20  C14  N15  C16     0.00   0.0  0
 T1O  CONST_09  H16  N15  C14  C13     0.00   0.0  0
 T1O  Var_01    H4   C06  S07  C09  -165.50  30.0  1
 T1O  Var_02    C12  C11  C10  C09   175.06  30.0  1
 T1O  Var_03    C13  C12  C11  C10   176.51  30.0  3
 T1O  Var_04    C14  C13  C12  C11  -179.05  30.0  2
 T1O  Var_05    N15  C14  C13  C12   178.22  30.0  1
 T1O  Var_06    C17  C16  N15  C14   179.63  30.0  1
 T1O  Var_07    C18  C17  C16  N15  -174.61  30.0  3
 T1O  Var_08    H19  C18  C17  C16    81.59  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
 T1O  chir_01  C04  C05  N03  C09  positiv
 T1O  chir_02  C05  N08  C04  C06  positiv
 T1O  chir_03  C09  S07  C10  C04  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
 T1O  plan-1  C13  0.020
 T1O  plan-1  C14  0.020
 T1O  plan-1  N15  0.020
 T1O  plan-1  C16  0.020
 T1O  plan-1  O20  0.020
 T1O  plan-1  H16  0.020
 T1O  plan-2  C16  0.020
 T1O  plan-2  C17  0.020
 T1O  plan-2  C18  0.020
 T1O  plan-2  O19  0.020
 T1O  plan-3  O01  0.020
 T1O  plan-3  C02  0.020
 T1O  plan-3  N03  0.020
 T1O  plan-3  C04  0.020
 T1O  plan-3  C05  0.020
 T1O  plan-3  N08  0.020
 T1O  plan-3  H1   0.020
 T1O  plan-3  H6   0.020

