# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:52:54 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-(2-{[(5-methyl-1,3,4-thiadiazol-2-yl)methyl]amino}ethyl)-1H-benzo[de]isoquinoline-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(CNCCN2C(=O)c3cccc4cccc(C2=O)c34)nn1
#
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
 NF1  NF1  2-(2-{[(5-methyl-1,3,4-thiadiazol-2-yl)methyl]amino}ethyl)-1H-benzo[de]isoquinoline-1,3(2H)-dione  ligand  41  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NF1
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
 NF1  OAN  O  O     0  -0.431   1.0144  -2.1454   0.1972
 NF1  CAM  C  CR6   0   0.563   1.7419  -1.1746   0.2303
 NF1  CAE  C  CR66  0  -0.143   3.1949  -1.2734   0.0127
 NF1  CAD  C  C     0   0.298   3.9884  -0.1101   0.0126
 NF1  CAF  C  CR16  0  -0.291   3.7756  -2.5040  -0.1910
 NF1  CAA  C  CR16  0  -0.249   5.1601  -2.6113  -0.3968
 NF1  CAB  C  CR16  0  -0.300   5.9481  -1.4899  -0.4033
 NF1  CAC  C  CR66  0   0.117   5.3822  -0.2118  -0.2030
 NF1  CAG  C  CR16  0  -0.300   6.1577   0.9680  -0.2102
 NF1  CAH  C  CR16  0  -0.249   5.5704   2.1908  -0.0141
 NF1  CAI  C  CR16  0  -0.291   4.1867   2.2860   0.2038
 NF1  CAJ  C  CR66  0  -0.142   3.4042   1.1545   0.2201
 NF1  CAK  C  CR6   0   0.564   1.9559   1.2662   0.4610
 NF1  OAO  O  O     0  -0.432   1.4084   2.3350   0.6372
 NF1  NAL  N  NR6   0  -0.613   1.2233   0.0874   0.4876
 NF1  CAP  C  CH2   0  -0.336  -0.2104   0.1905   0.7507
 NF1  CAQ  C  CH2   0  -0.264  -1.0149   0.4272  -0.5211
 NF1  NAR  N  NH1   0  -0.612  -2.4146   0.5583  -0.1694
 NF1  CAS  C  CH2   0  -0.317  -3.2999   0.6356  -1.3082
 NF1  CAT  C  CR5   0   0.068  -4.7094   0.4494  -0.8591
 NF1  SAX  S  S2    0   0.200  -5.0705  -0.5152   0.5242
 NF1  NAU  N  N     0  -0.266  -5.7568   0.9272  -1.4382
 NF1  NAV  N  N     0  -0.259  -6.9127   0.5566  -0.8414
 NF1  CAW  C  CR5   0   0.069  -6.7368  -0.1987   0.1938
 NF1  CAY  C  CH3   0  -0.722  -7.8392  -0.7404   1.0289
 NF1  H1   H  HCR6  0   0.276   3.1650  -3.3968  -0.1900
 NF1  H2   H  HCR6  0   0.275   5.6003  -3.5866  -0.5517
 NF1  H3   H  HCR6  0   0.276   7.0160  -1.5735  -0.5616
 NF1  H4   H  HCR6  0   0.276   7.2257   0.8942  -0.3729
 NF1  H5   H  HCR6  0   0.275   6.1707   3.0899  -0.0251
 NF1  H6   H  HCR6  0   0.275   3.7382   3.2572   0.3624
 NF1  H7   H  HCH2  0   0.272  -0.5411  -0.7260   1.2318
 NF1  H8   H  HCH2  0   0.268  -0.3670   1.0045   1.4560
 NF1  H9   H  HCH2  0   0.219  -0.6215   1.3014  -1.0571
 NF1  H10  H  HCH2  0   0.240  -0.9061  -0.4316  -1.1873
 NF1  H11  H  HNH1  0   0.360  -2.5386   1.3822   0.4078
 NF1  H13  H  HCH2  0   0.249  -3.2317   1.5645  -1.8885
 NF1  H14  H  HCH2  0   0.273  -3.0519  -0.1797  -1.9949
 NF1  H15  H  HCH3  0   0.269  -7.7272  -0.4427   2.0711
 NF1  H16  H  HCH3  0   0.268  -8.7932  -0.3696   0.6613
 NF1  H17  H  HCH3  0   0.269  -7.8543  -1.8298   0.9969

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
 NF1  CAY  CAW  single    1.485  0.020  1.485
 NF1  SAX  CAW  aromatic  1.728  0.020  1.728
 NF1  SAX  CAT  aromatic  1.725  0.020  1.725
 NF1  CAW  NAV  aromatic  1.293  0.020  1.293
 NF1  CAT  CAS  single    1.491  0.020  1.491
 NF1  CAT  NAU  aromatic  1.289  0.020  1.289
 NF1  NAV  NAU  aromatic  1.353  0.020  1.353
 NF1  NAR  CAS  single    1.445  0.020  1.445
 NF1  NAR  CAQ  single    1.449  0.020  1.449
 NF1  OAO  CAK  double    1.214  0.020  1.214
 NF1  CAP  CAQ  single    1.523  0.020  1.523
 NF1  CAP  NAL  single    1.461  0.020  1.461
 NF1  CAK  NAL  single    1.388  0.020  1.388
 NF1  CAK  CAJ  single    1.472  0.020  1.472
 NF1  NAL  CAM  single    1.389  0.020  1.389
 NF1  CAI  CAJ  aromatic  1.376  0.020  1.376
 NF1  CAI  CAH  aromatic  1.404  0.020  1.404
 NF1  CAJ  CAD  aromatic  1.408  0.020  1.408
 NF1  CAM  OAN  double    1.214  0.020  1.214
 NF1  CAM  CAE  single    1.472  0.020  1.472
 NF1  CAH  CAG  aromatic  1.371  0.020  1.371
 NF1  CAD  CAE  aromatic  1.408  0.020  1.408
 NF1  CAD  CAC  aromatic  1.414  0.020  1.414
 NF1  CAE  CAF  aromatic  1.376  0.020  1.376
 NF1  CAG  CAC  aromatic  1.412  0.020  1.412
 NF1  CAC  CAB  aromatic  1.412  0.020  1.412
 NF1  CAF  CAA  aromatic  1.404  0.020  1.404
 NF1  CAB  CAA  aromatic  1.371  0.020  1.371
 NF1  CAF  H1   single    0.930  0.020  1.080
 NF1  CAA  H2   single    0.930  0.020  1.080
 NF1  CAB  H3   single    0.930  0.020  1.080
 NF1  CAG  H4   single    0.930  0.020  1.080
 NF1  CAH  H5   single    0.930  0.020  1.080
 NF1  CAI  H6   single    0.930  0.020  1.080
 NF1  CAP  H7   single    0.970  0.020  1.090
 NF1  CAP  H8   single    0.970  0.020  1.090
 NF1  CAQ  H9   single    0.970  0.020  1.090
 NF1  CAQ  H10  single    0.970  0.020  1.090
 NF1  NAR  H11  single    0.890  0.020  1.040
 NF1  CAS  H13  single    0.970  0.020  1.090
 NF1  CAS  H14  single    0.970  0.020  1.090
 NF1  CAY  H15  single    0.970  0.020  1.090
 NF1  CAY  H16  single    0.970  0.020  1.090
 NF1  CAY  H17  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
 NF1  NAL  CAM  CAE  117.19  3.000
 NF1  CAE  CAM  OAN  122.27  3.000
 NF1  NAL  CAM  OAN  120.55  3.000
 NF1  CAF  CAE  CAD  120.07  3.000
 NF1  CAF  CAE  CAM  119.89  3.000
 NF1  CAD  CAE  CAM  120.04  3.000
 NF1  CAJ  CAD  CAC  119.73  3.000
 NF1  CAC  CAD  CAE  119.74  3.000
 NF1  CAJ  CAD  CAE  120.53  3.000
 NF1  H1   CAF  CAA  119.59  3.000
 NF1  H1   CAF  CAE  119.99  3.000
 NF1  CAA  CAF  CAE  120.42  3.000
 NF1  H2   CAA  CAB  120.22  3.000
 NF1  H2   CAA  CAF  119.44  3.000
 NF1  CAB  CAA  CAF  120.34  3.000
 NF1  H3   CAB  CAC  119.07  3.000
 NF1  H3   CAB  CAA  120.29  3.000
 NF1  CAC  CAB  CAA  120.63  3.000
 NF1  CAG  CAC  CAB  122.38  3.000
 NF1  CAB  CAC  CAD  118.80  3.000
 NF1  CAG  CAC  CAD  118.82  3.000
 NF1  H4   CAG  CAH  120.33  3.000
 NF1  H4   CAG  CAC  119.05  3.000
 NF1  CAH  CAG  CAC  120.62  3.000
 NF1  H5   CAH  CAI  119.50  3.000
 NF1  H5   CAH  CAG  120.16  3.000
 NF1  CAI  CAH  CAG  120.33  3.000
 NF1  H6   CAI  CAJ  120.06  3.000
 NF1  H6   CAI  CAH  119.50  3.000
 NF1  CAJ  CAI  CAH  120.44  3.000
 NF1  CAK  CAJ  CAI  119.94  3.000
 NF1  CAI  CAJ  CAD  120.05  3.000
 NF1  CAK  CAJ  CAD  120.01  3.000
 NF1  NAL  CAK  OAO  120.46  3.000
 NF1  NAL  CAK  CAJ  117.25  3.000
 NF1  OAO  CAK  CAJ  122.29  3.000
 NF1  CAP  NAL  CAK  117.48  3.000
 NF1  CAK  NAL  CAM  124.83  3.000
 NF1  CAP  NAL  CAM  117.64  3.000
 NF1  H8   CAP  H7   107.46  3.000
 NF1  H8   CAP  CAQ  110.42  3.000
 NF1  H7   CAP  CAQ  109.88  3.000
 NF1  H8   CAP  NAL  108.09  3.000
 NF1  H7   CAP  NAL  108.59  3.000
 NF1  CAQ  CAP  NAL  112.26  3.000
 NF1  H10  CAQ  H9   107.01  3.000
 NF1  H10  CAQ  NAR  108.38  3.000
 NF1  H9   CAQ  NAR  113.10  3.000
 NF1  H10  CAQ  CAP  109.54  3.000
 NF1  H9   CAQ  CAP  110.00  3.000
 NF1  NAR  CAQ  CAP  108.75  3.000
 NF1  H11  NAR  CAS  109.29  3.000
 NF1  H11  NAR  CAQ  109.27  3.000
 NF1  CAS  NAR  CAQ  113.92  3.000
 NF1  H14  CAS  H13  106.54  3.000
 NF1  H14  CAS  CAT  108.07  3.000
 NF1  H13  CAS  CAT  108.89  3.000
 NF1  H14  CAS  NAR  108.41  3.000
 NF1  H13  CAS  NAR  115.10  3.000
 NF1  CAT  CAS  NAR  109.59  3.000
 NF1  NAU  CAT  SAX  113.43  3.000
 NF1  NAU  CAT  CAS  125.92  3.000
 NF1  SAX  CAT  CAS  120.62  3.000
 NF1  CAW  SAX  CAT   86.91  3.000
 NF1  NAV  NAU  CAT  113.25  3.000
 NF1  CAW  NAV  NAU  113.38  3.000
 NF1  CAY  CAW  NAV  124.20  3.000
 NF1  NAV  CAW  SAX  113.03  3.000
 NF1  CAY  CAW  SAX  122.78  3.000
 NF1  H17  CAY  H16  108.58  3.000
 NF1  H17  CAY  H15  107.61  3.000
 NF1  H16  CAY  H15  108.68  3.000
 NF1  H17  CAY  CAW  111.00  3.000
 NF1  H16  CAY  CAW  109.67  3.000
 NF1  H15  CAY  CAW  111.22  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
 NF1  CONST_01  CAI  CAJ  CAD  CAE   180.00   0.0  0
 NF1  CONST_02  CAG  CAC  CAD  CAE   180.00   0.0  0
 NF1  CONST_03  CAB  CAC  CAD  CAE     0.00   0.0  0
 NF1  CONST_04  CAB  CAA  CAF  CAE     0.00   0.0  0
 NF1  CONST_05  CAH  CAI  CAJ  CAD     0.00   0.0  0
 NF1  CONST_06  CAA  CAF  CAE  CAD     0.00   0.0  0
 NF1  CONST_07  CAH  CAG  CAC  CAD     0.00   0.0  0
 NF1  CONST_08  CAA  CAB  CAC  CAD     0.00   0.0  0
 NF1  CONST_09  CAJ  CAD  CAE  CAF   180.00   0.0  0
 NF1  CONST_10  CAC  CAD  CAE  CAF     0.00   0.0  0
 NF1  CONST_11  CAC  CAB  CAA  CAF     0.00   0.0  0
 NF1  CONST_12  CAG  CAC  CAB  CAA   180.00   0.0  0
 NF1  CONST_13  CAJ  CAD  CAC  CAB   180.00   0.0  0
 NF1  CONST_14  CAH  CAG  CAC  CAB   180.00   0.0  0
 NF1  CONST_15  CAI  CAJ  CAD  CAC     0.00   0.0  0
 NF1  CONST_16  CAI  CAH  CAG  CAC     0.00   0.0  0
 NF1  CONST_17  CAJ  CAI  CAH  CAG     0.00   0.0  0
 NF1  CONST_18  CAJ  CAD  CAC  CAG     0.00   0.0  0
 NF1  CONST_19  NAV  CAW  SAX  CAT     0.00   0.0  0
 NF1  CONST_20  CAW  NAV  NAU  CAT     0.00   0.0  0
 NF1  CONST_21  NAU  NAV  CAW  SAX     0.00   0.0  0
 NF1  CONST_22  NAV  NAU  CAT  SAX     0.00   0.0  0
 NF1  CONST_23  CAW  SAX  CAT  NAU     0.00   0.0  0
 NF1  CONST_24  CAK  NAL  CAM  CAE     0.00   0.0  0
 NF1  CONST_25  CAW  SAX  CAT  CAS   180.00   0.0  0
 NF1  CONST_26  NAV  NAU  CAT  CAS   180.00   0.0  0
 NF1  CONST_27  CAY  CAW  SAX  CAT   180.00   0.0  0
 NF1  CONST_28  CAY  CAW  NAV  NAU   180.00   0.0  0
 NF1  CONST_29  CAK  NAL  CAM  OAN   180.00   0.0  0
 NF1  CONST_30  CAP  NAL  CAM  CAE   180.00   0.0  0
 NF1  CONST_31  H1   CAF  CAE  CAM     0.00   0.0  0
 NF1  CONST_32  H2   CAA  CAF  CAE   180.00   0.0  0
 NF1  CONST_33  H6   CAI  CAJ  CAD   180.00   0.0  0
 NF1  CONST_34  H4   CAG  CAC  CAD   180.00   0.0  0
 NF1  CONST_35  H3   CAB  CAC  CAD   180.00   0.0  0
 NF1  CONST_36  H5   CAH  CAG  CAC   180.00   0.0  0
 NF1  CONST_37  CAP  NAL  CAM  OAN     0.00   0.0  0
 NF1  Var_01    CAQ  CAP  NAL  CAM   -90.56  30.0  2
 NF1  Var_02    SAX  CAT  CAS  NAR   -29.63  30.0  1
 NF1  Var_03    H15  CAY  CAW  SAX    56.91  30.0  2
 NF1  Var_04    NAR  CAQ  CAP  NAL  -178.25  30.0  3
 NF1  Var_05    CAT  CAS  NAR  CAQ   166.94  30.0  3
 NF1  Var_06    CAS  NAR  CAQ  CAP  -173.37  30.0  2

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
 NF1  plan-1  CAS  0.020
 NF1  plan-1  CAT  0.020
 NF1  plan-1  SAX  0.020
 NF1  plan-1  NAU  0.020
 NF1  plan-1  NAV  0.020
 NF1  plan-1  CAW  0.020
 NF1  plan-1  CAY  0.020
 NF1  plan-2  OAN  0.020
 NF1  plan-2  CAM  0.020
 NF1  plan-2  CAE  0.020
 NF1  plan-2  CAD  0.020
 NF1  plan-2  CAF  0.020
 NF1  plan-2  CAA  0.020
 NF1  plan-2  CAB  0.020
 NF1  plan-2  CAC  0.020
 NF1  plan-2  CAG  0.020
 NF1  plan-2  CAH  0.020
 NF1  plan-2  CAI  0.020
 NF1  plan-2  CAJ  0.020
 NF1  plan-2  CAK  0.020
 NF1  plan-2  OAO  0.020
 NF1  plan-2  NAL  0.020
 NF1  plan-2  CAP  0.020
 NF1  plan-2  H1   0.020
 NF1  plan-2  H2   0.020
 NF1  plan-2  H3   0.020
 NF1  plan-2  H4   0.020
 NF1  plan-2  H5   0.020
 NF1  plan-2  H6   0.020

