# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:27:06 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: pyren-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2ccc3cccc4ccc1c2c34
#
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
 AP  AP  'pyren-1-amine            '  ligand  28  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AP
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
 AP  N1   N  NH2   0  -0.856   1.4180   0.1053   3.7548
 AP  C1   C  CR6   0   0.246   0.4539   0.0545   2.7803
 AP  C2   C  CR16  0  -0.339  -0.8995   0.0623   3.1437
 AP  C3   C  CR16  0  -0.336  -1.8996   0.0511   2.1951
 AP  C3A  C  CR66  0   0.047  -1.6052   0.0256   0.8303
 AP  C4   C  CR16  0  -0.321  -2.6249  -0.0008  -0.1702
 AP  C5   C  CR16  0  -0.352  -2.3172  -0.0253  -1.4877
 AP  C5A  C  CR66  0   0.096  -0.9530  -0.0207  -1.9222
 AP  C6   C  CR16  0  -0.351  -0.6107  -0.0404  -3.2761
 AP  C7   C  CR16  0  -0.249   0.7179  -0.0306  -3.6716
 AP  C8   C  CR16  0  -0.351   1.7341  -0.0002  -2.7292
 AP  C8A  C  CR66  0   0.095   1.4348   0.0188  -1.3651
 AP  C9   C  CR16  0  -0.331   2.4557   0.0594  -0.3642
 AP  C10  C  CR16  0  -0.322   2.1463   0.0767   0.9532
 AP  C1A  C  CR66  0   0.036   0.7894   0.0490   1.4073
 AP  C11  C  C     0   0.124  -0.2448   0.0259   0.4376
 AP  C12  C  C     0   0.096   0.0799   0.0070  -0.9488
 AP  HN1  H  HNH2  0   0.391   2.3083  -0.3200   3.5562
 AP  HN2  H  HNH2  0   0.388   1.1051  -0.1066   4.6884
 AP  H2   H  HCR6  0   0.263  -1.1599   0.0708   4.1956
 AP  H3   H  HCR6  0   0.257  -2.9344   0.0530   2.5169
 AP  H4   H  HCR6  0   0.252  -3.6610  -0.0015   0.1478
 AP  H5   H  HCR6  0   0.251  -3.0999  -0.0460  -2.2358
 AP  H6   H  HCR6  0   0.255  -1.3973  -0.0618  -4.0204
 AP  H7   H  HCR6  0   0.257   0.9624  -0.0448  -4.7259
 AP  H8   H  HCR6  0   0.254   2.7697   0.0104  -3.0471
 AP  H9   H  HCR6  0   0.254   3.4921   0.0835  -0.6781
 AP  H10  H  HCR6  0   0.248   2.9561   0.1232   1.6691

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
 AP  N1   C1   single    1.372  0.020  1.372
 AP  N1   HN1  single    0.890  0.020  1.040
 AP  N1   HN2  single    0.890  0.020  1.040
 AP  C1   C2   aromatic  1.401  0.020  1.401
 AP  C1   C1A  aromatic  1.413  0.020  1.413
 AP  C2   C3   aromatic  1.378  0.020  1.378
 AP  C2   H2   single    0.930  0.020  1.080
 AP  C3   C3A  aromatic  1.396  0.020  1.396
 AP  C3   H3   single    0.930  0.020  1.080
 AP  C3A  C4   aromatic  1.429  0.020  1.429
 AP  C3A  C11  aromatic  1.416  0.020  1.416
 AP  C4   C5   aromatic  1.353  0.020  1.353
 AP  C4   H4   single    0.930  0.020  1.080
 AP  C5   C5A  aromatic  1.432  0.020  1.432
 AP  C5   H5   single    0.930  0.020  1.080
 AP  C5A  C6   aromatic  1.397  0.020  1.397
 AP  C5A  C12  aromatic  1.420  0.020  1.420
 AP  C6   C7   aromatic  1.386  0.020  1.386
 AP  C6   H6   single    0.930  0.020  1.080
 AP  C7   C8   aromatic  1.386  0.020  1.386
 AP  C7   H7   single    0.930  0.020  1.080
 AP  C8   C8A  aromatic  1.397  0.020  1.397
 AP  C8   H8   single    0.930  0.020  1.080
 AP  C8A  C9   aromatic  1.430  0.020  1.430
 AP  C8A  C12  aromatic  1.417  0.020  1.417
 AP  C9   C10  aromatic  1.353  0.020  1.353
 AP  C9   H9   single    0.930  0.020  1.080
 AP  C10  C1A  aromatic  1.431  0.020  1.431
 AP  C10  H10  single    0.930  0.020  1.080
 AP  C1A  C11  aromatic  1.418  0.020  1.418
 AP  C11  C12  aromatic  1.424  0.020  1.424

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
 AP  HN2  N1   HN1  111.64  3.000
 AP  HN2  N1   C1   115.62  3.000
 AP  HN1  N1   C1   117.77  3.000
 AP  C1A  C1   C2   118.76  3.000
 AP  C1A  C1   N1   121.56  3.000
 AP  C2   C1   N1   119.63  3.000
 AP  H2   C2   C3   119.58  3.000
 AP  H2   C2   C1   118.94  3.000
 AP  C3   C2   C1   121.48  3.000
 AP  H3   C3   C3A  119.44  3.000
 AP  H3   C3   C2   119.24  3.000
 AP  C3A  C3   C2   121.31  3.000
 AP  C11  C3A  C4   119.44  3.000
 AP  C11  C3A  C3   118.27  3.000
 AP  C4   C3A  C3   122.29  3.000
 AP  H4   C4   C5   120.21  3.000
 AP  H4   C4   C3A  118.48  3.000
 AP  C5   C4   C3A  121.32  3.000
 AP  H5   C5   C5A  118.63  3.000
 AP  H5   C5   C4   120.57  3.000
 AP  C5A  C5   C4   120.81  3.000
 AP  C12  C5A  C6   119.12  3.000
 AP  C12  C5A  C5   119.03  3.000
 AP  C6   C5A  C5   121.85  3.000
 AP  H6   C6   C7   120.01  3.000
 AP  H6   C6   C5A  119.24  3.000
 AP  C7   C6   C5A  120.75  3.000
 AP  H7   C7   C8   119.80  3.000
 AP  H7   C7   C6   119.62  3.000
 AP  C8   C7   C6   120.58  3.000
 AP  H8   C8   C8A  119.42  3.000
 AP  H8   C8   C7   120.10  3.000
 AP  C8A  C8   C7   120.48  3.000
 AP  C12  C8A  C9   118.49  3.000
 AP  C12  C8A  C8   119.44  3.000
 AP  C9   C8A  C8   122.07  3.000
 AP  H9   C9   C10  120.03  3.000
 AP  H9   C9   C8A  118.74  3.000
 AP  C10  C9   C8A  121.23  3.000
 AP  H10  C10  C1A  120.03  3.000
 AP  H10  C10  C9   118.27  3.000
 AP  C1A  C10  C9   121.69  3.000
 AP  C11  C1A  C10  118.35  3.000
 AP  C11  C1A  C1   119.43  3.000
 AP  C10  C1A  C1   122.22  3.000
 AP  C12  C11  C1A  119.98  3.000
 AP  C12  C11  C3A  119.28  3.000
 AP  C1A  C11  C3A  120.74  3.000
 AP  C11  C12  C8A  120.25  3.000
 AP  C11  C12  C5A  120.13  3.000
 AP  C8A  C12  C5A  119.63  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
 AP  CONST_01  C3A  C3   C2   C1     0.00  0.0  0
 AP  CONST_02  C9   C10  C1A  C1   180.00  0.0  0
 AP  CONST_03  C3A  C11  C1A  C1     0.00  0.0  0
 AP  CONST_04  C12  C11  C1A  C1   180.00  0.0  0
 AP  CONST_05  C10  C1A  C1   C2   180.00  0.0  0
 AP  CONST_06  C11  C1A  C1   C2     0.00  0.0  0
 AP  CONST_07  C4   C3A  C3   C2   180.00  0.0  0
 AP  CONST_08  C11  C3A  C3   C2     0.00  0.0  0
 AP  CONST_09  C1A  C1   C2   C3     0.00  0.0  0
 AP  CONST_10  C5   C4   C3A  C3   180.00  0.0  0
 AP  CONST_11  C1A  C11  C3A  C3     0.00  0.0  0
 AP  CONST_12  C12  C11  C3A  C3   180.00  0.0  0
 AP  CONST_13  C5A  C5   C4   C3A    0.00  0.0  0
 AP  CONST_14  C10  C1A  C11  C3A  180.00  0.0  0
 AP  CONST_15  C5A  C12  C11  C3A    0.00  0.0  0
 AP  CONST_16  C8A  C12  C11  C3A  180.00  0.0  0
 AP  CONST_17  C1A  C11  C3A  C4   180.00  0.0  0
 AP  CONST_18  C12  C11  C3A  C4     0.00  0.0  0
 AP  CONST_19  C6   C5A  C5   C4   180.00  0.0  0
 AP  CONST_20  C12  C5A  C5   C4     0.00  0.0  0
 AP  CONST_21  C11  C3A  C4   C5     0.00  0.0  0
 AP  CONST_22  C7   C6   C5A  C5   180.00  0.0  0
 AP  CONST_23  C8A  C12  C5A  C5   180.00  0.0  0
 AP  CONST_24  C11  C12  C5A  C5     0.00  0.0  0
 AP  CONST_25  C8   C7   C6   C5A    0.00  0.0  0
 AP  CONST_26  C8   C8A  C12  C5A    0.00  0.0  0
 AP  CONST_27  C9   C8A  C12  C5A  180.00  0.0  0
 AP  CONST_28  C1A  C11  C12  C5A  180.00  0.0  0
 AP  CONST_29  C8A  C12  C5A  C6     0.00  0.0  0
 AP  CONST_30  C11  C12  C5A  C6   180.00  0.0  0
 AP  CONST_31  C8A  C8   C7   C6     0.00  0.0  0
 AP  CONST_32  C12  C5A  C6   C7     0.00  0.0  0
 AP  CONST_33  C9   C8A  C8   C7   180.00  0.0  0
 AP  CONST_34  C12  C8A  C8   C7     0.00  0.0  0
 AP  CONST_35  C10  C9   C8A  C8   180.00  0.0  0
 AP  CONST_36  C11  C12  C8A  C8   180.00  0.0  0
 AP  CONST_37  C1A  C10  C9   C8A    0.00  0.0  0
 AP  CONST_38  C1A  C11  C12  C8A    0.00  0.0  0
 AP  CONST_39  C11  C12  C8A  C9     0.00  0.0  0
 AP  CONST_40  C11  C1A  C10  C9     0.00  0.0  0
 AP  CONST_41  C12  C8A  C9   C10    0.00  0.0  0
 AP  CONST_42  C12  C11  C1A  C10    0.00  0.0  0
 AP  CONST_43  C3   C2   C1   N1   180.00  0.0  0
 AP  CONST_44  C10  C1A  C1   N1     0.00  0.0  0
 AP  CONST_45  C11  C1A  C1   N1   180.00  0.0  0
 AP  CONST_46  H3   C3   C2   C1   180.00  0.0  0
 AP  CONST_47  H10  C10  C1A  C1     0.00  0.0  0
 AP  CONST_48  H4   C4   C3A  C3     0.00  0.0  0
 AP  CONST_49  H2   C2   C3   C3A  180.00  0.0  0
 AP  CONST_50  H5   C5   C4   C3A  180.00  0.0  0
 AP  CONST_51  H6   C6   C5A  C5     0.00  0.0  0
 AP  CONST_52  H7   C7   C6   C5A  180.00  0.0  0
 AP  CONST_53  H8   C8   C7   C6   180.00  0.0  0
 AP  CONST_54  H9   C9   C8A  C8     0.00  0.0  0

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
 AP  plan-1  N1   0.020
 AP  plan-1  C1   0.020
 AP  plan-1  C2   0.020
 AP  plan-1  C3   0.020
 AP  plan-1  C3A  0.020
 AP  plan-1  C4   0.020
 AP  plan-1  C5   0.020
 AP  plan-1  C5A  0.020
 AP  plan-1  C6   0.020
 AP  plan-1  C7   0.020
 AP  plan-1  C8   0.020
 AP  plan-1  C8A  0.020
 AP  plan-1  C9   0.020
 AP  plan-1  C10  0.020
 AP  plan-1  C1A  0.020
 AP  plan-1  C11  0.020
 AP  plan-1  C12  0.020
 AP  plan-1  H2   0.020
 AP  plan-1  H3   0.020
 AP  plan-1  H4   0.020
 AP  plan-1  H5   0.020
 AP  plan-1  H6   0.020
 AP  plan-1  H7   0.020
 AP  plan-1  H8   0.020
 AP  plan-1  H9   0.020
 AP  plan-1  H10  0.020
 AP  plan-2  N1   0.020
 AP  plan-2  C1   0.020
 AP  plan-2  HN1  0.020
 AP  plan-2  HN2  0.020

