# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:02:39 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: N-(pyren-1-ylmethyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCc1ccc2ccc3cccc4ccc1c2c34
#
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
 JPY  JPY  N-(pyren-1-ylmethyl)acetamide  ligand  36  21  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JPY
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
 JPY  C1   C  CH3   0  -0.771  -4.6858   1.4453  -1.6180
 JPY  C4   C  C     0   0.531  -4.1410   1.0162  -0.2790
 JPY  O2   O  O     0  -0.513  -4.2689   1.7158   0.7188
 JPY  N1   N  NH1   0  -0.611  -3.4967  -0.1635  -0.2721
 JPY  C5   C  CH2   0  -0.395  -2.8806  -0.7596   0.8946
 JPY  C6   C  CR6   0   0.045  -1.4557  -1.1672   0.6200
 JPY  C21  C  CR66  0   0.087  -0.4291  -0.2186   0.4740
 JPY  C10  C  C     0   0.137   0.8845  -0.6583   0.1663
 JPY  C20  C  CR16  0  -0.357  -0.6507   1.1902   0.6302
 JPY  C19  C  CR16  0  -0.323   0.3520   2.0848   0.4751
 JPY  C12  C  CR66  0   0.089   1.6806   1.6680   0.1486
 JPY  C13  C  CR16  0  -0.341   2.7237   2.5805  -0.0206
 JPY  C14  C  CR16  0  -0.251   4.0011   2.1407  -0.3295
 JPY  C15  C  CR16  0  -0.341   4.2628   0.7861  -0.4742
 JPY  C16  C  CR66  0   0.093   3.2471  -0.1567  -0.3125
 JPY  C11  C  C     0   0.115   1.9369   0.2840   0.0014
 JPY  C17  C  CR16  0  -0.334   3.4890  -1.5616  -0.4563
 JPY  C18  C  CR16  0  -0.326   2.4923  -2.4598  -0.2962
 JPY  C9   C  CR66  0   0.064   1.1585  -2.0412   0.0188
 JPY  C8   C  CR16  0  -0.335   0.1210  -2.9552   0.1830
 JPY  C7   C  CR16  0  -0.317  -1.1602  -2.5170   0.4746
 JPY  H1   H  HCH3  0   0.265  -5.7387   1.7056  -1.5165
 JPY  H2   H  HCH3  0   0.268  -4.1592   2.3431  -1.9433
 JPY  H3   H  HCH3  0   0.249  -4.5865   0.6906  -2.3953
 JPY  H4   H  HNH1  0   0.401  -3.4502  -0.6910  -1.1288
 JPY  H5   H  HCH2  0   0.270  -2.9447  -0.0477   1.7166
 JPY  H6   H  HCH2  0   0.274  -3.4493  -1.6407   1.2007
 JPY  H7   H  HCR6  0   0.252  -1.6354   1.5524   0.8915
 JPY  H8   H  HCR6  0   0.259   0.1578   3.1428   0.6026
 JPY  H9   H  HCR6  0   0.260   2.5263   3.6395   0.0926
 JPY  H10  H  HCR6  0   0.262   4.7998   2.8590  -0.4587
 JPY  H11  H  HCR6  0   0.260   5.2637   0.4507  -0.7165
 JPY  H12  H  HCR6  0   0.258   4.4914  -1.8927  -0.6986
 JPY  H13  H  HCR6  0   0.258   2.6871  -3.5195  -0.4076
 JPY  H14  H  HCR6  0   0.259   0.3188  -4.0146   0.0756
 JPY  H15  H  HCR6  0   0.259  -1.9547  -3.2448   0.5869

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
 JPY  C17  C18  aromatic  1.351  0.020  1.351
 JPY  C17  C16  aromatic  1.433  0.020  1.433
 JPY  C18  C9   aromatic  1.433  0.020  1.433
 JPY  C15  C16  aromatic  1.395  0.020  1.395
 JPY  C15  C14  aromatic  1.387  0.020  1.387
 JPY  C16  C11  aromatic  1.417  0.020  1.417
 JPY  C9   C8   aromatic  1.392  0.020  1.392
 JPY  C9   C10  aromatic  1.417  0.020  1.417
 JPY  C8   C7   aromatic  1.385  0.020  1.385
 JPY  C14  C13  aromatic  1.386  0.020  1.386
 JPY  C11  C10  aromatic  1.422  0.020  1.422
 JPY  C11  C12  aromatic  1.415  0.020  1.415
 JPY  C10  C21  aromatic  1.419  0.020  1.419
 JPY  C7   C6   aromatic  1.389  0.020  1.389
 JPY  C13  C12  aromatic  1.396  0.020  1.396
 JPY  C12  C19  aromatic  1.430  0.020  1.430
 JPY  C21  C6   aromatic  1.405  0.020  1.405
 JPY  C21  C20  aromatic  1.435  0.020  1.435
 JPY  C6   C5   single    1.507  0.020  1.507
 JPY  C19  C20  aromatic  1.353  0.020  1.353
 JPY  C5   N1   single    1.448  0.020  1.448
 JPY  N1   C4   single    1.344  0.020  1.344
 JPY  C4   O2   double    1.225  0.020  1.225
 JPY  C4   C1   single    1.508  0.020  1.508
 JPY  C1   H1   single    0.970  0.020  1.090
 JPY  C1   H2   single    0.970  0.020  1.090
 JPY  C1   H3   single    0.970  0.020  1.090
 JPY  N1   H4   single    0.860  0.020  1.020
 JPY  C5   H5   single    0.970  0.020  1.090
 JPY  C5   H6   single    0.970  0.020  1.090
 JPY  C20  H7   single    0.930  0.020  1.080
 JPY  C19  H8   single    0.930  0.020  1.080
 JPY  C13  H9   single    0.930  0.020  1.080
 JPY  C14  H10  single    0.930  0.020  1.080
 JPY  C15  H11  single    0.930  0.020  1.080
 JPY  C17  H12  single    0.930  0.020  1.080
 JPY  C18  H13  single    0.930  0.020  1.080
 JPY  C8   H14  single    0.930  0.020  1.080
 JPY  C7   H15  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
 JPY  H3   C1   H2   108.30  3.000
 JPY  H3   C1   H1   108.69  3.000
 JPY  H2   C1   H1   107.32  3.000
 JPY  H3   C1   C4   113.83  3.000
 JPY  H2   C1   C4   108.95  3.000
 JPY  H1   C1   C4   109.54  3.000
 JPY  N1   C4   O2   123.15  3.000
 JPY  O2   C4   C1   121.53  3.000
 JPY  N1   C4   C1   115.31  3.000
 JPY  H4   N1   C5   116.75  3.000
 JPY  H4   N1   C4   118.51  3.000
 JPY  C5   N1   C4   124.71  3.000
 JPY  H6   C5   H5   106.56  3.000
 JPY  H6   C5   C6   108.97  3.000
 JPY  H5   C5   C6   111.71  3.000
 JPY  H6   C5   N1   109.66  3.000
 JPY  H5   C5   N1   108.29  3.000
 JPY  C6   C5   N1   111.52  3.000
 JPY  C7   C6   C21  119.30  3.000
 JPY  C21  C6   C5   121.80  3.000
 JPY  C7   C6   C5   118.87  3.000
 JPY  C20  C21  C10  118.09  3.000
 JPY  C20  C21  C6   122.59  3.000
 JPY  C10  C21  C6   119.31  3.000
 JPY  C9   C10  C11  119.42  3.000
 JPY  C11  C10  C21  120.32  3.000
 JPY  C9   C10  C21  120.25  3.000
 JPY  H7   C20  C19  118.77  3.000
 JPY  H7   C20  C21  119.73  3.000
 JPY  C19  C20  C21  121.50  3.000
 JPY  H8   C19  C12  118.56  3.000
 JPY  H8   C19  C20  119.97  3.000
 JPY  C12  C19  C20  121.47  3.000
 JPY  C11  C12  C13  119.42  3.000
 JPY  C13  C12  C19  122.09  3.000
 JPY  C11  C12  C19  118.49  3.000
 JPY  H9   C13  C14  120.10  3.000
 JPY  H9   C13  C12  119.35  3.000
 JPY  C14  C13  C12  120.55  3.000
 JPY  H10  C14  C15  119.77  3.000
 JPY  H10  C14  C13  119.76  3.000
 JPY  C15  C14  C13  120.47  3.000
 JPY  H11  C15  C16  119.30  3.000
 JPY  H11  C15  C14  120.01  3.000
 JPY  C16  C15  C14  120.69  3.000
 JPY  C17  C16  C11  118.89  3.000
 JPY  C11  C16  C15  119.24  3.000
 JPY  C17  C16  C15  121.87  3.000
 JPY  C16  C11  C12  119.63  3.000
 JPY  C12  C11  C10  120.12  3.000
 JPY  C16  C11  C10  120.24  3.000
 JPY  H12  C17  C18  120.40  3.000
 JPY  H12  C17  C16  118.58  3.000
 JPY  C18  C17  C16  121.02  3.000
 JPY  H13  C18  C9   118.41  3.000
 JPY  H13  C18  C17  120.36  3.000
 JPY  C9   C18  C17  121.22  3.000
 JPY  C8   C9   C18  121.84  3.000
 JPY  C8   C9   C10  118.96  3.000
 JPY  C18  C9   C10  119.20  3.000
 JPY  H14  C8   C7   119.95  3.000
 JPY  H14  C8   C9   119.63  3.000
 JPY  C7   C8   C9   120.42  3.000
 JPY  H15  C7   C8   119.19  3.000
 JPY  H15  C7   C6   119.06  3.000
 JPY  C8   C7   C6   121.75  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
 JPY  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 JPY  CONST_02  C9   C10  C21  C6      0.00   0.0  0
 JPY  CONST_03  C11  C10  C21  C6    180.00   0.0  0
 JPY  CONST_04  C19  C20  C21  C6    180.00   0.0  0
 JPY  CONST_05  C18  C9   C10  C21   180.00   0.0  0
 JPY  CONST_06  C8   C9   C10  C21     0.00   0.0  0
 JPY  CONST_07  C16  C11  C10  C21   180.00   0.0  0
 JPY  CONST_08  C12  C11  C10  C21     0.00   0.0  0
 JPY  CONST_09  C8   C7   C6   C21     0.00   0.0  0
 JPY  CONST_10  C12  C19  C20  C21     0.00   0.0  0
 JPY  CONST_11  C17  C18  C9   C10     0.00   0.0  0
 JPY  CONST_12  C7   C8   C9   C10     0.00   0.0  0
 JPY  CONST_13  C17  C16  C11  C10     0.00   0.0  0
 JPY  CONST_14  C15  C16  C11  C10   180.00   0.0  0
 JPY  CONST_15  C13  C12  C11  C10   180.00   0.0  0
 JPY  CONST_16  C19  C12  C11  C10     0.00   0.0  0
 JPY  CONST_17  C7   C6   C21  C10     0.00   0.0  0
 JPY  CONST_18  C19  C20  C21  C10     0.00   0.0  0
 JPY  CONST_19  C9   C10  C21  C20   180.00   0.0  0
 JPY  CONST_20  C11  C10  C21  C20     0.00   0.0  0
 JPY  CONST_21  C7   C6   C21  C20   180.00   0.0  0
 JPY  CONST_22  C11  C12  C19  C20     0.00   0.0  0
 JPY  CONST_23  C13  C12  C19  C20   180.00   0.0  0
 JPY  CONST_24  C16  C11  C12  C19   180.00   0.0  0
 JPY  CONST_25  C14  C13  C12  C19   180.00   0.0  0
 JPY  CONST_26  C17  C16  C11  C12   180.00   0.0  0
 JPY  CONST_27  C15  C16  C11  C12     0.00   0.0  0
 JPY  CONST_28  C9   C10  C11  C12   180.00   0.0  0
 JPY  CONST_29  C15  C14  C13  C12     0.00   0.0  0
 JPY  CONST_30  C16  C15  C14  C13     0.00   0.0  0
 JPY  CONST_31  C16  C11  C12  C13     0.00   0.0  0
 JPY  CONST_32  C17  C16  C15  C14   180.00   0.0  0
 JPY  CONST_33  C11  C16  C15  C14     0.00   0.0  0
 JPY  CONST_34  C11  C12  C13  C14     0.00   0.0  0
 JPY  CONST_35  C18  C17  C16  C15   180.00   0.0  0
 JPY  CONST_36  C9   C18  C17  C16     0.00   0.0  0
 JPY  CONST_37  C9   C10  C11  C16     0.00   0.0  0
 JPY  CONST_38  C18  C17  C16  C11     0.00   0.0  0
 JPY  CONST_39  C18  C9   C10  C11     0.00   0.0  0
 JPY  CONST_40  C8   C9   C10  C11   180.00   0.0  0
 JPY  CONST_41  C8   C9   C18  C17   180.00   0.0  0
 JPY  CONST_42  C7   C8   C9   C18   180.00   0.0  0
 JPY  CONST_43  C8   C7   C6   C5    180.00   0.0  0
 JPY  CONST_44  C10  C21  C6   C5    180.00   0.0  0
 JPY  CONST_45  C20  C21  C6   C5      0.00   0.0  0
 JPY  CONST_46  H14  C8   C7   C6    180.00   0.0  0
 JPY  CONST_47  H7   C20  C21  C6      0.00   0.0  0
 JPY  CONST_48  H15  C7   C6   C21   180.00   0.0  0
 JPY  CONST_49  H8   C19  C20  C21   180.00   0.0  0
 JPY  CONST_50  H13  C18  C9   C10   180.00   0.0  0
 JPY  CONST_51  H9   C13  C12  C19     0.00   0.0  0
 JPY  CONST_52  H10  C14  C13  C12   180.00   0.0  0
 JPY  CONST_53  H11  C15  C14  C13   180.00   0.0  0
 JPY  CONST_54  H12  C17  C16  C15     0.00   0.0  0
 JPY  CONST_55  C5   N1   C4   C1    180.00   0.0  0
 JPY  CONST_56  C5   N1   C4   O2      0.00   0.0  0
 JPY  CONST_57  H4   N1   C4   C1      0.00   0.0  0
 JPY  Var_01    C7   C6   C5   N1   -106.33  30.0  2
 JPY  Var_02    C6   C5   N1   C4   -128.94  30.0  2
 JPY  Var_03    H1   C1   C4   O2    -52.59  30.0  3

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
 JPY  plan-1  C5   0.020
 JPY  plan-1  C6   0.020
 JPY  plan-1  C21  0.020
 JPY  plan-1  C10  0.020
 JPY  plan-1  C20  0.020
 JPY  plan-1  C19  0.020
 JPY  plan-1  C12  0.020
 JPY  plan-1  C13  0.020
 JPY  plan-1  C14  0.020
 JPY  plan-1  C15  0.020
 JPY  plan-1  C16  0.020
 JPY  plan-1  C11  0.020
 JPY  plan-1  C17  0.020
 JPY  plan-1  C18  0.020
 JPY  plan-1  C9   0.020
 JPY  plan-1  C8   0.020
 JPY  plan-1  C7   0.020
 JPY  plan-1  H7   0.020
 JPY  plan-1  H8   0.020
 JPY  plan-1  H9   0.020
 JPY  plan-1  H10  0.020
 JPY  plan-1  H11  0.020
 JPY  plan-1  H12  0.020
 JPY  plan-1  H13  0.020
 JPY  plan-1  H14  0.020
 JPY  plan-1  H15  0.020
 JPY  plan-2  C1   0.020
 JPY  plan-2  C4   0.020
 JPY  plan-2  O2   0.020
 JPY  plan-2  N1   0.020
 JPY  plan-2  C5   0.020
 JPY  plan-2  H4   0.020

