# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 02:55:16 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (3aS,4S,6aR)-4-[5-oxo-5-(pyren-1-yl)pentyl]tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@H]2CS[C@@H](CCCCC(=O)c3ccc4ccc5cccc6ccc3c4c56)[C@H]2N1
#
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
 B9P  B9P  (3aS,4S,6aR)-4-[5-oxo-5-(pyren-1-yl)pentyl]tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one  ligand  55  31  .  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_B9P
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
 B9P  O11  O  O     0  -0.404  -0.9406  -1.1471   1.5802
 B9P  C11  C  C     0   0.370  -0.9907  -0.0942   0.9780
 B9P  C10  C  CH2   0  -0.587   0.2799   0.6682   0.6663
 B9P  C9   C  CH2   0  -0.415   1.5476  -0.1504   0.8542
 B9P  C8   C  CH2   0  -0.419   2.8030   0.6777   0.6102
 B9P  C7   C  CH2   0  -0.421   4.0682  -0.1636   0.7268
 B9P  C2   C  CH1   0  -0.365   5.3516   0.6385   0.6269
 B9P  S1   S  S2    0  -0.025   5.5612   1.4598  -0.9878
 B9P  C6   C  CH2   0  -0.564   7.2764   1.8259  -0.5385
 B9P  C5   C  CR15  0  -0.052   7.8164   0.5560   0.1232
 B9P  N1   N  NR15  0  -0.661   8.2800  -0.4175  -0.8297
 B9P  C4   C  CR15  0  -0.051   6.6325  -0.1881   0.8141
 B9P  N2   N  NR15  0  -0.659   6.6067  -1.4498   0.1203
 B9P  C3   C  CR5   0   0.645   7.6131  -1.5968  -0.7825
 B9P  O3   O  O     0  -0.531   7.8602  -2.6005  -1.4343
 B9P  C1   C  CR6   0  -0.069  -2.2882   0.5029   0.5457
 B9P  C16  C  CR16  0  -0.312  -2.3402   1.8867   0.3673
 B9P  C15  C  CR16  0  -0.332  -3.5114   2.5402   0.0470
 B9P  C14  C  CR66  0   0.073  -4.6924   1.8232  -0.1285
 B9P  C30  C  CR16  0  -0.322  -5.9190   2.4842  -0.4559
 B9P  C31  C  CR16  0  -0.328  -7.0622   1.7871  -0.6349
 B9P  C32  C  CR66  0   0.096  -7.0812   0.3622  -0.5053
 B9P  C19  C  CR16  0  -0.335  -8.2530  -0.3726  -0.6892
 B9P  C18  C  CR16  0  -0.251  -8.2507  -1.7539  -0.5648
 B9P  C17  C  CR16  0  -0.334  -7.0789  -2.4256  -0.2570
 B9P  C34  C  CR66  0   0.088  -5.8878  -1.7232  -0.0645
 B9P  C33  C  C     0   0.122  -5.8785  -0.3149  -0.1838
 B9P  C13  C  C     0   0.125  -4.6711   0.4128   0.0148
 B9P  C35  C  CR16  0  -0.307  -4.6594  -2.3819   0.2391
 B9P  C36  C  CR16  0  -0.357  -3.5114  -1.6950   0.4403
 B9P  C12  C  CR66  0   0.106  -3.4643  -0.2613   0.3557
 B9P  H1   H  HCH2  0   0.266   0.2281   1.0622  -0.3524
 B9P  H2   H  HCH2  0   0.274   0.3091   1.5500   1.3174
 B9P  H3   H  HCH2  0   0.227   1.5806  -0.5643   1.8643
 B9P  H4   H  HCH2  0   0.226   1.5367  -1.0039   0.1698
 B9P  H5   H  HCH2  0   0.221   2.7545   1.1372  -0.3824
 B9P  H6   H  HCH2  0   0.221   2.8413   1.5036   1.3284
 B9P  H7   H  HCH2  0   0.239   4.0697  -0.6763   1.6955
 B9P  H8   H  HCH2  0   0.233   4.0593  -0.9449  -0.0377
 B9P  H9   H  HCH1  0   0.274   5.3459   1.4204   1.3944
 B9P  H10  H  HCH2  0   0.289   7.8497   2.1054  -1.4217
 B9P  H11  H  HCH2  0   0.272   7.3040   2.6608   0.1640
 B9P  H12  H  HCR5  0   0.279   8.6035   0.8165   0.8350
 B9P  H13  H  HNR5  0   0.400   9.1256  -0.3048  -1.3618
 B9P  H14  H  HCR5  0   0.279   6.8107  -0.3309   1.8837
 B9P  H15  H  HNR5  0   0.399   6.1164  -2.2516   0.4774
 B9P  H16  H  HCR6  0   0.273  -1.4488   2.4829   0.5022
 B9P  H17  H  HCR6  0   0.265  -3.5155   3.6169  -0.0648
 B9P  H18  H  HCR6  0   0.262  -5.9107   3.5622  -0.5574
 B9P  H19  H  HCR6  0   0.263  -7.9840   2.2986  -0.8835
 B9P  H20  H  HCR6  0   0.263  -9.1705   0.1478  -0.9349
 B9P  H21  H  HCR6  0   0.264  -9.1674  -2.3092  -0.7127
 B9P  H22  H  HCR6  0   0.263  -7.0790  -3.5048  -0.1656
 B9P  H23  H  HCR6  0   0.261  -4.6549  -3.4631   0.3052
 B9P  H24  H  HCR6  0   0.264  -2.6152  -2.2464   0.6678

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
 B9P  C15  C16  aromatic  1.379  0.020  1.379
 B9P  C15  C14  aromatic  1.393  0.020  1.393
 B9P  C30  C14  aromatic  1.431  0.020  1.431
 B9P  C30  C31  aromatic  1.351  0.020  1.351
 B9P  C16  C1   aromatic  1.396  0.020  1.396
 B9P  C14  C13  aromatic  1.418  0.020  1.418
 B9P  C31  C32  aromatic  1.431  0.020  1.431
 B9P  C10  C9   single    1.521  0.020  1.521
 B9P  C10  C11  single    1.514  0.020  1.514
 B9P  C1   C11  single    1.492  0.020  1.492
 B9P  C1   C12  aromatic  1.415  0.020  1.415
 B9P  C13  C12  aromatic  1.424  0.020  1.424
 B9P  C13  C33  aromatic  1.424  0.020  1.424
 B9P  C32  C33  aromatic  1.417  0.020  1.417
 B9P  C32  C19  aromatic  1.395  0.020  1.395
 B9P  C9   C8   single    1.524  0.020  1.524
 B9P  C11  O11  double    1.214  0.020  1.214
 B9P  C12  C36  aromatic  1.437  0.020  1.437
 B9P  C33  C34  aromatic  1.413  0.020  1.413
 B9P  C19  C18  aromatic  1.387  0.020  1.387
 B9P  C36  C35  aromatic  1.353  0.020  1.353
 B9P  C34  C35  aromatic  1.427  0.020  1.427
 B9P  C34  C17  aromatic  1.396  0.020  1.396
 B9P  C18  C17  aromatic  1.385  0.020  1.385
 B9P  C8   C7   single    1.524  0.020  1.524
 B9P  C7   C2   single    1.517  0.020  1.517
 B9P  S1   C2   single    1.824  0.020  1.824
 B9P  S1   C6   single    1.810  0.020  1.810
 B9P  N2   C3   single    1.360  0.020  1.360
 B9P  N2   C4   single    1.440  0.020  1.440
 B9P  C2   C4   single    1.536  0.020  1.536
 B9P  O3   C3   double    1.222  0.020  1.222
 B9P  C3   N1   single    1.356  0.020  1.356
 B9P  C4   C5   single    1.560  0.020  1.560
 B9P  C6   C5   single    1.530  0.020  1.530
 B9P  N1   C5   single    1.439  0.020  1.439
 B9P  C10  H1   single    0.970  0.020  1.090
 B9P  C10  H2   single    0.970  0.020  1.090
 B9P  C9   H3   single    0.970  0.020  1.090
 B9P  C9   H4   single    0.970  0.020  1.090
 B9P  C8   H5   single    0.970  0.020  1.090
 B9P  C8   H6   single    0.970  0.020  1.090
 B9P  C7   H7   single    0.970  0.020  1.090
 B9P  C7   H8   single    0.970  0.020  1.090
 B9P  C2   H9   single    0.970  0.020  1.090
 B9P  C6   H10  single    0.970  0.020  1.090
 B9P  C6   H11  single    0.970  0.020  1.090
 B9P  C5   H12  single    0.970  0.020  1.090
 B9P  N1   H13  single    0.860  0.020  1.020
 B9P  C4   H14  single    0.970  0.020  1.090
 B9P  N2   H15  single    0.860  0.020  1.020
 B9P  C16  H16  single    0.930  0.020  1.080
 B9P  C15  H17  single    0.930  0.020  1.080
 B9P  C30  H18  single    0.930  0.020  1.080
 B9P  C31  H19  single    0.930  0.020  1.080
 B9P  C19  H20  single    0.930  0.020  1.080
 B9P  C18  H21  single    0.930  0.020  1.080
 B9P  C17  H22  single    0.930  0.020  1.080
 B9P  C35  H23  single    0.930  0.020  1.080
 B9P  C36  H24  single    0.930  0.020  1.080

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
 B9P  C1   C11  C10  117.94  3.000
 B9P  C1   C11  O11  121.78  3.000
 B9P  C10  C11  O11  120.28  3.000
 B9P  H2   C10  H1   105.35  3.000
 B9P  H2   C10  C9   109.71  3.000
 B9P  H1   C10  C9   110.41  3.000
 B9P  H2   C10  C11  107.76  3.000
 B9P  H1   C10  C11  109.48  3.000
 B9P  C9   C10  C11  113.76  3.000
 B9P  H4   C9   H3   106.45  3.000
 B9P  H4   C9   C8   109.39  3.000
 B9P  H3   C9   C8   109.22  3.000
 B9P  H4   C9   C10  109.53  3.000
 B9P  H3   C9   C10  110.09  3.000
 B9P  C8   C9   C10  111.99  3.000
 B9P  H6   C8   H5   106.24  3.000
 B9P  H6   C8   C7   109.70  3.000
 B9P  H5   C8   C7   109.75  3.000
 B9P  H6   C8   C9   109.49  3.000
 B9P  H5   C8   C9   109.68  3.000
 B9P  C7   C8   C9   111.82  3.000
 B9P  H8   C7   H7   106.48  3.000
 B9P  H8   C7   C2   109.80  3.000
 B9P  H7   C7   C2   107.73  3.000
 B9P  H8   C7   C8   109.53  3.000
 B9P  H7   C7   C8   109.09  3.000
 B9P  C2   C7   C8   113.93  3.000
 B9P  H9   C2   C4   107.64  3.000
 B9P  H9   C2   S1   107.43  3.000
 B9P  C4   C2   S1   104.74  3.000
 B9P  H9   C2   C7   109.07  3.000
 B9P  C4   C2   C7   114.39  3.000
 B9P  S1   C2   C7   113.19  3.000
 B9P  C6   S1   C2    88.87  3.000
 B9P  H11  C6   H10  108.19  3.000
 B9P  H11  C6   C5   110.33  3.000
 B9P  H10  C6   C5   112.20  3.000
 B9P  H11  C6   S1   109.78  3.000
 B9P  H10  C6   S1   110.45  3.000
 B9P  C5   C6   S1   105.89  3.000
 B9P  H12  C5   C4   111.83  3.000
 B9P  H12  C5   N1   111.13  3.000
 B9P  C4   C5   N1   102.42  3.000
 B9P  H12  C5   C6   109.76  3.000
 B9P  N1   C5   C6   112.87  3.000
 B9P  C4   C5   C6   108.64  3.000
 B9P  H13  N1   C3   121.98  3.000
 B9P  H13  N1   C5   123.07  3.000
 B9P  C3   N1   C5   114.02  3.000
 B9P  H14  C4   N2   111.08  3.000
 B9P  H14  C4   C5   111.83  3.000
 B9P  N2   C4   C5   102.60  3.000
 B9P  H14  C4   C2   108.99  3.000
 B9P  C5   C4   C2   108.80  3.000
 B9P  N2   C4   C2   113.44  3.000
 B9P  H15  N2   C3   120.69  3.000
 B9P  H15  N2   C4   122.44  3.000
 B9P  C3   N2   C4   113.66  3.000
 B9P  O3   C3   N2   126.33  3.000
 B9P  O3   C3   N1   126.62  3.000
 B9P  N2   C3   N1   107.04  3.000
 B9P  C12  C1   C16  119.15  3.000
 B9P  C12  C1   C11  123.05  3.000
 B9P  C16  C1   C11  117.77  3.000
 B9P  H16  C16  C15  117.91  3.000
 B9P  H16  C16  C1   120.00  3.000
 B9P  C15  C16  C1   122.07  3.000
 B9P  H17  C15  C14  119.73  3.000
 B9P  H17  C15  C16  119.91  3.000
 B9P  C14  C15  C16  120.37  3.000
 B9P  C13  C14  C30  119.70  3.000
 B9P  C13  C14  C15  119.12  3.000
 B9P  C30  C14  C15  121.18  3.000
 B9P  H18  C30  C31  120.52  3.000
 B9P  H18  C30  C14  118.34  3.000
 B9P  C31  C30  C14  121.15  3.000
 B9P  H19  C31  C32  118.67  3.000
 B9P  H19  C31  C30  120.46  3.000
 B9P  C32  C31  C30  120.87  3.000
 B9P  C33  C32  C19  119.41  3.000
 B9P  C19  C32  C31  121.58  3.000
 B9P  C33  C32  C31  119.01  3.000
 B9P  H20  C19  C18  120.02  3.000
 B9P  H20  C19  C32  119.23  3.000
 B9P  C18  C19  C32  120.75  3.000
 B9P  H21  C18  C17  119.88  3.000
 B9P  H21  C18  C19  119.84  3.000
 B9P  C17  C18  C19  120.28  3.000
 B9P  H22  C17  C34  119.33  3.000
 B9P  H22  C17  C18  120.12  3.000
 B9P  C34  C17  C18  120.55  3.000
 B9P  C35  C34  C33  118.19  3.000
 B9P  C35  C34  C17  122.12  3.000
 B9P  C33  C34  C17  119.69  3.000
 B9P  C13  C33  C34  120.21  3.000
 B9P  C34  C33  C32  119.31  3.000
 B9P  C13  C33  C32  120.48  3.000
 B9P  C12  C13  C33  120.68  3.000
 B9P  C33  C13  C14  118.79  3.000
 B9P  C12  C13  C14  120.53  3.000
 B9P  H23  C35  C36  119.62  3.000
 B9P  H23  C35  C34  118.51  3.000
 B9P  C36  C35  C34  121.87  3.000
 B9P  H24  C36  C12  119.75  3.000
 B9P  H24  C36  C35  118.54  3.000
 B9P  C12  C36  C35  121.71  3.000
 B9P  C36  C12  C13  117.31  3.000
 B9P  C36  C12  C1   123.92  3.000
 B9P  C13  C12  C1   118.74  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
 B9P  CONST_01  C14  C15  C16  C1      0.00   0.0  0
 B9P  CONST_02  C14  C13  C12  C1      0.00   0.0  0
 B9P  CONST_03  C33  C13  C12  C1    180.00   0.0  0
 B9P  CONST_04  C35  C36  C12  C1    180.00   0.0  0
 B9P  CONST_05  C30  C14  C15  C16   180.00   0.0  0
 B9P  CONST_06  C13  C14  C15  C16     0.00   0.0  0
 B9P  CONST_07  C13  C12  C1   C16     0.00   0.0  0
 B9P  CONST_08  C36  C12  C1   C16   180.00   0.0  0
 B9P  CONST_09  C12  C1   C16  C15     0.00   0.0  0
 B9P  CONST_10  C31  C30  C14  C15   180.00   0.0  0
 B9P  CONST_11  C12  C13  C14  C15     0.00   0.0  0
 B9P  CONST_12  C33  C13  C14  C15   180.00   0.0  0
 B9P  CONST_13  C32  C31  C30  C14     0.00   0.0  0
 B9P  CONST_14  C36  C12  C13  C14   180.00   0.0  0
 B9P  CONST_15  C32  C33  C13  C14     0.00   0.0  0
 B9P  CONST_16  C34  C33  C13  C14   180.00   0.0  0
 B9P  CONST_17  C12  C13  C14  C30   180.00   0.0  0
 B9P  CONST_18  C33  C13  C14  C30     0.00   0.0  0
 B9P  CONST_19  C33  C32  C31  C30     0.00   0.0  0
 B9P  CONST_20  C19  C32  C31  C30   180.00   0.0  0
 B9P  CONST_21  C13  C14  C30  C31     0.00   0.0  0
 B9P  CONST_22  C13  C33  C32  C31     0.00   0.0  0
 B9P  CONST_23  C34  C33  C32  C31   180.00   0.0  0
 B9P  CONST_24  C18  C19  C32  C31   180.00   0.0  0
 B9P  CONST_25  C12  C13  C33  C32   180.00   0.0  0
 B9P  CONST_26  C35  C34  C33  C32   180.00   0.0  0
 B9P  CONST_27  C17  C34  C33  C32     0.00   0.0  0
 B9P  CONST_28  C17  C18  C19  C32     0.00   0.0  0
 B9P  CONST_29  C13  C33  C32  C19   180.00   0.0  0
 B9P  CONST_30  C34  C33  C32  C19     0.00   0.0  0
 B9P  CONST_31  C34  C17  C18  C19     0.00   0.0  0
 B9P  CONST_32  C33  C32  C19  C18     0.00   0.0  0
 B9P  CONST_33  C33  C34  C17  C18     0.00   0.0  0
 B9P  CONST_34  C35  C34  C17  C18   180.00   0.0  0
 B9P  CONST_35  C13  C33  C34  C17   180.00   0.0  0
 B9P  CONST_36  C36  C35  C34  C17   180.00   0.0  0
 B9P  CONST_37  C12  C13  C33  C34     0.00   0.0  0
 B9P  CONST_38  C12  C36  C35  C34     0.00   0.0  0
 B9P  CONST_39  C36  C12  C13  C33     0.00   0.0  0
 B9P  CONST_40  C36  C35  C34  C33     0.00   0.0  0
 B9P  CONST_41  C35  C36  C12  C13     0.00   0.0  0
 B9P  CONST_42  C35  C34  C33  C13     0.00   0.0  0
 B9P  CONST_43  N2   C3   N1   C5      0.00   0.0  0
 B9P  CONST_44  C4   N2   C3   N1      0.00   0.0  0
 B9P  CONST_45  C15  C16  C1   C11   180.00   0.0  0
 B9P  CONST_46  C13  C12  C1   C11   180.00   0.0  0
 B9P  CONST_47  C36  C12  C1   C11     0.00   0.0  0
 B9P  CONST_48  O3   C3   N1   C5    180.00   0.0  0
 B9P  CONST_49  O3   C3   N2   C4    180.00   0.0  0
 B9P  CONST_50  H17  C15  C16  C1    180.00   0.0  0
 B9P  CONST_51  H24  C36  C12  C1      0.00   0.0  0
 B9P  CONST_52  H18  C30  C14  C15     0.00   0.0  0
 B9P  CONST_53  H16  C16  C15  C14   180.00   0.0  0
 B9P  CONST_54  H19  C31  C30  C14   180.00   0.0  0
 B9P  CONST_55  H20  C19  C32  C31     0.00   0.0  0
 B9P  CONST_56  H21  C18  C19  C32   180.00   0.0  0
 B9P  CONST_57  H22  C17  C18  C19   180.00   0.0  0
 B9P  CONST_58  H23  C35  C34  C17     0.00   0.0  0
 B9P  CONST_59  H15  N2   C3   N1    180.00   0.0  0
 B9P  CONST_60  H13  N1   C3   N2    180.00   0.0  0
 B9P  Var_01    C5   C6   S1   C2     42.36  30.0  1
 B9P  Var_02    C16  C1   C11  O11   154.54  30.0  2
 B9P  Var_03    C1   C11  C10  C9   -166.81  30.0  3
 B9P  Var_04    C2   C7   C8   C9   -174.35  30.0  3
 B9P  Var_05    C8   C9   C10  C11  -176.62  30.0  3
 B9P  Var_06    C7   C8   C9   C10  -176.97  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
 B9P  chir_01  C2  C7  S1  C4  positiv
 B9P  chir_02  C5  N1  C6  C4  negativ
 B9P  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
 B9P  plan-1  C11  0.020
 B9P  plan-1  C1   0.020
 B9P  plan-1  C16  0.020
 B9P  plan-1  C15  0.020
 B9P  plan-1  C14  0.020
 B9P  plan-1  C30  0.020
 B9P  plan-1  C31  0.020
 B9P  plan-1  C32  0.020
 B9P  plan-1  C19  0.020
 B9P  plan-1  C18  0.020
 B9P  plan-1  C17  0.020
 B9P  plan-1  C34  0.020
 B9P  plan-1  C33  0.020
 B9P  plan-1  C13  0.020
 B9P  plan-1  C35  0.020
 B9P  plan-1  C36  0.020
 B9P  plan-1  C12  0.020
 B9P  plan-1  H16  0.020
 B9P  plan-1  H17  0.020
 B9P  plan-1  H18  0.020
 B9P  plan-1  H19  0.020
 B9P  plan-1  H20  0.020
 B9P  plan-1  H21  0.020
 B9P  plan-1  H22  0.020
 B9P  plan-1  H23  0.020
 B9P  plan-1  H24  0.020
 B9P  plan-2  C5   0.020
 B9P  plan-2  N1   0.020
 B9P  plan-2  C4   0.020
 B9P  plan-2  N2   0.020
 B9P  plan-2  C3   0.020
 B9P  plan-2  O3   0.020
 B9P  plan-2  H13  0.020
 B9P  plan-2  H15  0.020
 B9P  plan-3  O11  0.020
 B9P  plan-3  C11  0.020
 B9P  plan-3  C10  0.020
 B9P  plan-3  C1   0.020

