# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 11:25:17 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (4S,5R)-4-methyl-5-[6-oxo-6-(pyren-1-yl)hexyl]imidazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1NC(=O)N[C@@H]1CCCCCC(=O)c2ccc3ccc4cccc5ccc2c3c45
#
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
 D9P  D9P  (4S,5R)-4-methyl-5-[6-oxo-6-(pyren-1-yl)hexyl]imidazolidin-2-one  ligand  56  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D9P
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
 D9P  O11  O  O     0  -0.404   0.6023  -1.0699  -1.5391
 D9P  C11  C  C     0   0.370   0.6503  -0.0593  -0.8679
 D9P  C10  C  CH2   0  -0.587  -0.6234   0.6758  -0.5056
 D9P  C9   C  CH2   0  -0.414  -1.8880  -0.1411  -0.7234
 D9P  C8   C  CH2   0  -0.413  -3.1473   0.6715  -0.4490
 D9P  C7   C  CH2   0  -0.426  -4.4210  -0.1436  -0.6359
 D9P  C2   C  CH2   0  -0.425  -5.6823   0.6736  -0.3827
 D9P  C4   C  CR15  0  -0.084  -6.9666  -0.0916  -0.6901
 D9P  C5   C  CR15  0  -0.060  -8.2691   0.6600  -0.3379
 D9P  C6   C  CH3   0  -0.685  -8.2262   2.1691  -0.4491
 D9P  N1   N  NR15  0  -0.657  -8.4886   0.2014   1.0249
 D9P  N2   N  NR15  0  -0.655  -7.1360  -1.2802   0.1295
 D9P  C3   C  CR5   0   0.624  -7.9296  -1.0322   1.2102
 D9P  O3   O  O     0  -0.524  -8.1085  -1.7739   2.1642
 D9P  C1   C  CR6   0  -0.069   1.9470   0.5151  -0.4032
 D9P  C16  C  CR66  0   0.107   3.1370  -0.2448  -0.3010
 D9P  C15  C  C     0   0.125   4.3408   0.4152   0.0765
 D9P  C17  C  CR16  0  -0.357   3.2024  -1.6645  -0.5132
 D9P  C18  C  CR16  0  -0.306   4.3642  -2.3481  -0.3987
 D9P  C19  C  CR66  0   0.087   5.5897  -1.6991  -0.0636
 D9P  C20  C  C     0   0.122   5.5625  -0.3079   0.1839
 D9P  C24  C  CR16  0  -0.334   6.7954  -2.3957   0.0371
 D9P  C25  C  CR16  0  -0.251   7.9643  -1.7350   0.3784
 D9P  C26  C  CR16  0  -0.335   7.9489  -0.3712   0.6297
 D9P  C21  C  CR66  0   0.097   6.7622   0.3572   0.5403
 D9P  C22  C  CR16  0  -0.329   6.7255   1.7639   0.7998
 D9P  C23  C  CR16  0  -0.322   5.5689   2.4558   0.7078
 D9P  C14  C  CR66  0   0.072   4.3455   1.8073   0.3455
 D9P  C13  C  CR16  0  -0.332   3.1515   2.5186   0.2552
 D9P  C12  C  CR16  0  -0.313   1.9842   1.8784  -0.1035
 D9P  H1   H  HCH2  0   0.265  -0.5662   1.0200   0.5304
 D9P  H2   H  HCH2  0   0.273  -0.6634   1.5881  -1.1131
 D9P  H3   H  HCH2  0   0.224  -1.9199  -0.5167  -1.7484
 D9P  H4   H  HCH2  0   0.224  -1.8720  -1.0194  -0.0712
 D9P  H5   H  HCH2  0   0.215  -3.1185   1.0720   0.5698
 D9P  H6   H  HCH2  0   0.215  -3.1705   1.5386  -1.1176
 D9P  H7   H  HCH2  0   0.217  -4.4461  -0.5493  -1.6532
 D9P  H8   H  HCH2  0   0.212  -4.3887  -1.0054   0.0383
 D9P  H9   H  HCH2  0   0.224  -5.6947   1.0277   0.6531
 D9P  H10  H  HCH2  0   0.231  -5.6590   1.5633  -1.0185
 D9P  H11  H  HCR5  0   0.252  -6.9711  -0.3594  -1.7496
 D9P  H12  H  HCR5  0   0.248  -9.0656   0.2829  -0.9921
 D9P  H13  H  HCH3  0   0.234  -7.4782   2.6018   0.2143
 D9P  H14  H  HCH3  0   0.237  -8.0012   2.4753  -1.4711
 D9P  H15  H  HCH3  0   0.246  -9.1959   2.5944  -0.1871
 D9P  H16  H  HNR5  0   0.390  -9.3619   0.4047   1.4860
 D9P  H17  H  HNR5  0   0.393  -6.4177  -1.9832   0.1952
 D9P  H18  H  HCR6  0   0.265   2.3083  -2.2070  -0.7685
 D9P  H19  H  HCR6  0   0.261   4.3739  -3.4191  -0.5607
 D9P  H20  H  HCR6  0   0.263   6.8097  -3.4620  -0.1525
 D9P  H21  H  HCR6  0   0.264   8.8928  -2.2856   0.4517
 D9P  H22  H  HCR6  0   0.263   8.8642   0.1404   0.9003
 D9P  H23  H  HCR6  0   0.263   7.6452   2.2654   1.0744
 D9P  H24  H  HCR6  0   0.262   5.5471   3.5201   0.9067
 D9P  H25  H  HCR6  0   0.265   3.1422   3.5811   0.4625
 D9P  H26  H  HCR6  0   0.274   1.0827   2.4712  -0.1679

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
 D9P  C5   C6   single    1.514  0.020  1.514
 D9P  C5   N1   single    1.455  0.020  1.455
 D9P  C5   C4   single    1.544  0.020  1.544
 D9P  N1   C3   single    1.367  0.020  1.367
 D9P  C4   C2   single    1.526  0.020  1.526
 D9P  C4   N2   single    1.454  0.020  1.454
 D9P  C24  C25  aromatic  1.385  0.020  1.385
 D9P  C24  C19  aromatic  1.396  0.020  1.396
 D9P  C3   O3   double    1.222  0.020  1.222
 D9P  C3   N2   single    1.364  0.020  1.364
 D9P  C25  C26  aromatic  1.387  0.020  1.387
 D9P  C18  C19  aromatic  1.427  0.020  1.427
 D9P  C18  C17  aromatic  1.353  0.020  1.353
 D9P  C2   C7   single    1.524  0.020  1.524
 D9P  C19  C20  aromatic  1.413  0.020  1.413
 D9P  C7   C8   single    1.524  0.020  1.524
 D9P  C17  C16  aromatic  1.437  0.020  1.437
 D9P  C26  C21  aromatic  1.395  0.020  1.395
 D9P  O11  C11  double    1.214  0.020  1.214
 D9P  C20  C21  aromatic  1.417  0.020  1.417
 D9P  C20  C15  aromatic  1.424  0.020  1.424
 D9P  C16  C15  aromatic  1.424  0.020  1.424
 D9P  C16  C1   aromatic  1.416  0.020  1.416
 D9P  C21  C22  aromatic  1.431  0.020  1.431
 D9P  C8   C9   single    1.524  0.020  1.524
 D9P  C15  C14  aromatic  1.418  0.020  1.418
 D9P  C9   C10  single    1.521  0.020  1.521
 D9P  C11  C1   single    1.492  0.020  1.492
 D9P  C11  C10  single    1.515  0.020  1.515
 D9P  C1   C12  aromatic  1.396  0.020  1.396
 D9P  C22  C23  aromatic  1.351  0.020  1.351
 D9P  C14  C23  aromatic  1.431  0.020  1.431
 D9P  C14  C13  aromatic  1.393  0.020  1.393
 D9P  C12  C13  aromatic  1.379  0.020  1.379
 D9P  C10  H1   single    0.970  0.020  1.090
 D9P  C10  H2   single    0.970  0.020  1.090
 D9P  C9   H3   single    0.970  0.020  1.090
 D9P  C9   H4   single    0.970  0.020  1.090
 D9P  C8   H5   single    0.970  0.020  1.090
 D9P  C8   H6   single    0.970  0.020  1.090
 D9P  C7   H7   single    0.970  0.020  1.090
 D9P  C7   H8   single    0.970  0.020  1.090
 D9P  C2   H9   single    0.970  0.020  1.090
 D9P  C2   H10  single    0.970  0.020  1.090
 D9P  C4   H11  single    0.970  0.020  1.090
 D9P  C5   H12  single    0.970  0.020  1.090
 D9P  C6   H13  single    0.970  0.020  1.090
 D9P  C6   H14  single    0.970  0.020  1.090
 D9P  C6   H15  single    0.970  0.020  1.090
 D9P  N1   H16  single    0.890  0.020  1.040
 D9P  N2   H17  single    0.890  0.020  1.040
 D9P  C17  H18  single    0.930  0.020  1.080
 D9P  C18  H19  single    0.930  0.020  1.080
 D9P  C24  H20  single    0.930  0.020  1.080
 D9P  C25  H21  single    0.930  0.020  1.080
 D9P  C26  H22  single    0.930  0.020  1.080
 D9P  C22  H23  single    0.930  0.020  1.080
 D9P  C23  H24  single    0.930  0.020  1.080
 D9P  C13  H25  single    0.930  0.020  1.080
 D9P  C12  H26  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
 D9P  C1   C11  C10  117.99  3.000
 D9P  C10  C11  O11  120.20  3.000
 D9P  C1   C11  O11  121.79  3.000
 D9P  H2   C10  H1   105.37  3.000
 D9P  H2   C10  C9   109.70  3.000
 D9P  H1   C10  C9   110.38  3.000
 D9P  H2   C10  C11  107.57  3.000
 D9P  H1   C10  C11  109.61  3.000
 D9P  C9   C10  C11  113.84  3.000
 D9P  H4   C9   H3   106.49  3.000
 D9P  H4   C9   C8   109.44  3.000
 D9P  H3   C9   C8   109.16  3.000
 D9P  H4   C9   C10  109.49  3.000
 D9P  H3   C9   C10  110.08  3.000
 D9P  C8   C9   C10  112.02  3.000
 D9P  H6   C8   H5   106.20  3.000
 D9P  H6   C8   C7   109.32  3.000
 D9P  H5   C8   C7   109.37  3.000
 D9P  H6   C8   C9   109.26  3.000
 D9P  H5   C8   C9   109.93  3.000
 D9P  C7   C8   C9   112.55  3.000
 D9P  H8   C7   H7   106.32  3.000
 D9P  H8   C7   C2   110.13  3.000
 D9P  H7   C7   C2   109.50  3.000
 D9P  H8   C7   C8   108.72  3.000
 D9P  H7   C7   C8   109.34  3.000
 D9P  C2   C7   C8   112.62  3.000
 D9P  H10  C2   H9   106.68  3.000
 D9P  H10  C2   C4   107.98  3.000
 D9P  H9   C2   C4   110.07  3.000
 D9P  H10  C2   C7   108.78  3.000
 D9P  H9   C2   C7   109.88  3.000
 D9P  C4   C2   C7   113.22  3.000
 D9P  H11  C4   N2   110.22  3.000
 D9P  H11  C4   C5   109.69  3.000
 D9P  N2   C4   C5    99.85  3.000
 D9P  H11  C4   C2   108.76  3.000
 D9P  N2   C4   C2   113.23  3.000
 D9P  C5   C4   C2   114.82  3.000
 D9P  H12  C5   N1   109.91  3.000
 D9P  H12  C5   C6   108.62  3.000
 D9P  N1   C5   C6   112.79  3.000
 D9P  H12  C5   C4   107.99  3.000
 D9P  N1   C5   C4   100.80  3.000
 D9P  C6   C5   C4   116.39  3.000
 D9P  H15  C6   H14  107.40  3.000
 D9P  H15  C6   H13  108.02  3.000
 D9P  H14  C6   H13  108.51  3.000
 D9P  H15  C6   C5   110.23  3.000
 D9P  H14  C6   C5   110.77  3.000
 D9P  H13  C6   C5   111.76  3.000
 D9P  H16  N1   C3   118.31  3.000
 D9P  H16  N1   C5   119.71  3.000
 D9P  C3   N1   C5   110.48  3.000
 D9P  H17  N2   C3   119.36  3.000
 D9P  H17  N2   C4   121.63  3.000
 D9P  C3   N2   C4   111.47  3.000
 D9P  O3   C3   N2   126.43  3.000
 D9P  N2   C3   N1   107.14  3.000
 D9P  O3   C3   N1   126.43  3.000
 D9P  C12  C1   C16  119.09  3.000
 D9P  C12  C1   C11  117.76  3.000
 D9P  C16  C1   C11  123.11  3.000
 D9P  C17  C16  C15  117.30  3.000
 D9P  C15  C16  C1   118.76  3.000
 D9P  C17  C16  C1   123.91  3.000
 D9P  C14  C15  C20  118.78  3.000
 D9P  C14  C15  C16  120.55  3.000
 D9P  C20  C15  C16  120.67  3.000
 D9P  H18  C17  C18  118.60  3.000
 D9P  H18  C17  C16  119.68  3.000
 D9P  C18  C17  C16  121.72  3.000
 D9P  H19  C18  C19  118.50  3.000
 D9P  H19  C18  C17  119.65  3.000
 D9P  C19  C18  C17  121.85  3.000
 D9P  C24  C19  C20  119.68  3.000
 D9P  C20  C19  C18  118.19  3.000
 D9P  C24  C19  C18  122.12  3.000
 D9P  C21  C20  C19  119.32  3.000
 D9P  C21  C20  C15  120.47  3.000
 D9P  C19  C20  C15  120.21  3.000
 D9P  H20  C24  C25  120.09  3.000
 D9P  H20  C24  C19  119.35  3.000
 D9P  C25  C24  C19  120.56  3.000
 D9P  H21  C25  C26  119.85  3.000
 D9P  H21  C25  C24  119.87  3.000
 D9P  C26  C25  C24  120.28  3.000
 D9P  H22  C26  C21  119.23  3.000
 D9P  H22  C26  C25  120.03  3.000
 D9P  C21  C26  C25  120.75  3.000
 D9P  C22  C21  C26  121.56  3.000
 D9P  C22  C21  C20  119.02  3.000
 D9P  C26  C21  C20  119.41  3.000
 D9P  H23  C22  C23  120.48  3.000
 D9P  H23  C22  C21  118.65  3.000
 D9P  C23  C22  C21  120.87  3.000
 D9P  H24  C23  C14  118.33  3.000
 D9P  H24  C23  C22  120.54  3.000
 D9P  C14  C23  C22  121.13  3.000
 D9P  C13  C14  C23  121.18  3.000
 D9P  C13  C14  C15  119.09  3.000
 D9P  C23  C14  C15  119.72  3.000
 D9P  H25  C13  C12  119.89  3.000
 D9P  H25  C13  C14  119.75  3.000
 D9P  C12  C13  C14  120.37  3.000
 D9P  H26  C12  C13  117.84  3.000
 D9P  H26  C12  C1   120.03  3.000
 D9P  C13  C12  C1   122.12  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
 D9P  CONST_01  C18  C17  C16  C1    180.00   0.0  0
 D9P  CONST_02  C20  C15  C16  C1    180.00   0.0  0
 D9P  CONST_03  C14  C15  C16  C1      0.00   0.0  0
 D9P  CONST_04  C14  C13  C12  C1      0.00   0.0  0
 D9P  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 D9P  CONST_06  C19  C20  C15  C16     0.00   0.0  0
 D9P  CONST_07  C21  C20  C15  C16   180.00   0.0  0
 D9P  CONST_08  C23  C14  C15  C16   180.00   0.0  0
 D9P  CONST_09  C13  C14  C15  C16     0.00   0.0  0
 D9P  CONST_10  C13  C12  C1   C16     0.00   0.0  0
 D9P  CONST_11  C24  C19  C20  C15   180.00   0.0  0
 D9P  CONST_12  C18  C19  C20  C15     0.00   0.0  0
 D9P  CONST_13  C26  C21  C20  C15   180.00   0.0  0
 D9P  CONST_14  C22  C21  C20  C15     0.00   0.0  0
 D9P  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 D9P  CONST_16  C12  C1   C16  C15     0.00   0.0  0
 D9P  CONST_17  C22  C23  C14  C15     0.00   0.0  0
 D9P  CONST_18  C12  C13  C14  C15     0.00   0.0  0
 D9P  CONST_19  C24  C19  C18  C17   180.00   0.0  0
 D9P  CONST_20  C20  C19  C18  C17     0.00   0.0  0
 D9P  CONST_21  C20  C15  C16  C17     0.00   0.0  0
 D9P  CONST_22  C14  C15  C16  C17   180.00   0.0  0
 D9P  CONST_23  C12  C1   C16  C17   180.00   0.0  0
 D9P  CONST_24  C25  C24  C19  C18   180.00   0.0  0
 D9P  CONST_25  C21  C20  C19  C18   180.00   0.0  0
 D9P  CONST_26  C26  C25  C24  C19     0.00   0.0  0
 D9P  CONST_27  C26  C21  C20  C19     0.00   0.0  0
 D9P  CONST_28  C22  C21  C20  C19   180.00   0.0  0
 D9P  CONST_29  C14  C15  C20  C19   180.00   0.0  0
 D9P  CONST_30  C25  C24  C19  C20     0.00   0.0  0
 D9P  CONST_31  C25  C26  C21  C20     0.00   0.0  0
 D9P  CONST_32  C23  C22  C21  C20     0.00   0.0  0
 D9P  CONST_33  C23  C14  C15  C20     0.00   0.0  0
 D9P  CONST_34  C13  C14  C15  C20   180.00   0.0  0
 D9P  CONST_35  C21  C26  C25  C24     0.00   0.0  0
 D9P  CONST_36  C21  C20  C19  C24     0.00   0.0  0
 D9P  CONST_37  C22  C21  C26  C25   180.00   0.0  0
 D9P  CONST_38  C23  C22  C21  C26   180.00   0.0  0
 D9P  CONST_39  C14  C15  C20  C21     0.00   0.0  0
 D9P  CONST_40  C14  C23  C22  C21     0.00   0.0  0
 D9P  CONST_41  C13  C14  C23  C22   180.00   0.0  0
 D9P  CONST_42  C12  C13  C14  C23   180.00   0.0  0
 D9P  CONST_43  N1   C3   N2   C4      0.00   0.0  0
 D9P  CONST_44  N2   C3   N1   C5      0.00   0.0  0
 D9P  CONST_45  C17  C16  C1   C11     0.00   0.0  0
 D9P  CONST_46  C15  C16  C1   C11   180.00   0.0  0
 D9P  CONST_47  C13  C12  C1   C11   180.00   0.0  0
 D9P  CONST_48  O3   C3   N2   C4    180.00   0.0  0
 D9P  CONST_49  O3   C3   N1   C5    180.00   0.0  0
 D9P  CONST_50  H18  C17  C16  C1      0.00   0.0  0
 D9P  CONST_51  H25  C13  C12  C1    180.00   0.0  0
 D9P  CONST_52  H19  C18  C17  C16   180.00   0.0  0
 D9P  CONST_53  H26  C12  C1   C16   180.00   0.0  0
 D9P  CONST_54  H24  C23  C14  C15   180.00   0.0  0
 D9P  CONST_55  H20  C24  C19  C18     0.00   0.0  0
 D9P  CONST_56  H21  C25  C24  C19   180.00   0.0  0
 D9P  CONST_57  H22  C26  C21  C20   180.00   0.0  0
 D9P  CONST_58  H23  C22  C21  C20   180.00   0.0  0
 D9P  Var_01    C16  C1   C11  O11   -21.71  30.0  2
 D9P  Var_02    C1   C11  C10  C9   -166.06  30.0  1
 D9P  Var_03    C4   C2   C7   C8    174.70  30.0  1
 D9P  Var_04    C8   C9   C10  C11  -175.60  30.0  1
 D9P  Var_05    C7   C8   C9   C10  -178.83  30.0  1
 D9P  Var_06    C2   C7   C8   C9   -179.12  30.0  1

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
 D9P  chir_01  C4  C5  C2  N2  negativ
 D9P  chir_02  C5  N1  C4  C6  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
 D9P  plan-1  C11  0.020
 D9P  plan-1  C1   0.020
 D9P  plan-1  C16  0.020
 D9P  plan-1  C15  0.020
 D9P  plan-1  C17  0.020
 D9P  plan-1  C18  0.020
 D9P  plan-1  C19  0.020
 D9P  plan-1  C20  0.020
 D9P  plan-1  C24  0.020
 D9P  plan-1  C25  0.020
 D9P  plan-1  C26  0.020
 D9P  plan-1  C21  0.020
 D9P  plan-1  C22  0.020
 D9P  plan-1  C23  0.020
 D9P  plan-1  C14  0.020
 D9P  plan-1  C13  0.020
 D9P  plan-1  C12  0.020
 D9P  plan-1  H18  0.020
 D9P  plan-1  H19  0.020
 D9P  plan-1  H20  0.020
 D9P  plan-1  H21  0.020
 D9P  plan-1  H22  0.020
 D9P  plan-1  H23  0.020
 D9P  plan-1  H24  0.020
 D9P  plan-1  H25  0.020
 D9P  plan-1  H26  0.020
 D9P  plan-2  C4   0.020
 D9P  plan-2  C5   0.020
 D9P  plan-2  N1   0.020
 D9P  plan-2  N2   0.020
 D9P  plan-2  C3   0.020
 D9P  plan-2  O3   0.020
 D9P  plan-2  H16  0.020
 D9P  plan-2  H17  0.020
 D9P  plan-3  O11  0.020
 D9P  plan-3  C11  0.020
 D9P  plan-3  C10  0.020
 D9P  plan-3  C1   0.020

