# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:04:37 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-({2-[(6-chloro-1,2,3,4-tetrahydroacridin-9-yl)amino]ethyl}amino)-5-hydroxynaphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc2C(=O)C(=CC(=O)c12)NCCNc3c4CCCCc4nc5cc(Cl)ccc35
#
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
 TJH  TJH  2-({2-[(6-chloro-1,2,3,4-tetrahydroacridin-9-yl)amino]ethyl}amino)-5-hydroxynaphthalene-1,4-dione  ligand  54  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TJH
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
 TJH  OAB  O   O     0  -0.362   3.6361   0.6066   2.3576
 TJH  CBB  C   CR6   0   0.310   4.0557   0.2440   1.2810
 TJH  CBE  C   CR66  0  -0.014   5.4934   0.0691   1.0028
 TJH  CAH  C   CR16  0  -0.301   6.4113   0.3388   2.0021
 TJH  CAE  C   CR16  0  -0.228   7.7695   0.1776   1.7384
 TJH  CAF  C   CR16  0  -0.329   8.2032  -0.2468   0.5009
 TJH  CAV  C   CR6   0   0.383   7.2808  -0.5248  -0.5169
 TJH  OAC  O   OH1   0  -0.626   7.7446  -0.9326  -1.6934
 TJH  CBF  C   CR66  0  -0.217   5.9108  -0.3638  -0.2646
 TJH  CBA  C   CR6   0   0.461   4.9253  -0.6453  -1.3255
 TJH  OAA  O   O     0  -0.505   5.3179  -1.0291  -2.4394
 TJH  CAJ  C   CR16  0  -0.523   3.5340  -0.4699  -1.0503
 TJH  CAX  C   CR6   0   0.353   3.0850  -0.0437   0.1685
 TJH  NAS  N   NH1   0  -0.656   1.8113   0.1536   0.4838
 TJH  CAN  C   CH2   0  -0.275   0.7208  -0.0428  -0.4389
 TJH  CAO  C   CH2   0  -0.357  -0.5866   0.4187   0.1836
 TJH  NAT  N   NH1   0  -0.682  -1.6800   0.2682  -0.7632
 TJH  CAZ  C   CR6   0   0.364  -2.9206  -0.1946  -0.3452
 TJH  CAY  C   CR6   0  -0.010  -3.0873  -1.5039   0.0793
 TJH  CAQ  C   CH2   0  -0.502  -1.9298  -2.4735   0.0484
 TJH  CAM  C   CH2   0  -0.439  -2.2382  -3.8632   0.5986
 TJH  CAL  C   CH2   0  -0.449  -3.6309  -4.3249   0.2118
 TJH  CAP  C   CH2   0  -0.510  -4.6501  -3.3646   0.8030
 TJH  CAW  C   CR6   0   0.175  -4.4010  -1.9384   0.3940
 TJH  NAR  N   N     0  -0.485  -5.4639  -1.1717   0.3216
 TJH  CBC  C   CR66  0   0.164  -5.3156   0.1102  -0.0626
 TJH  CBD  C   CR66  0   0.066  -4.0593   0.6628  -0.4015
 TJH  CAI  C   CR16  0  -0.343  -3.9957   2.0299  -0.7536
 TJH  CAG  C   CR16  0  -0.214  -5.1206   2.8066  -0.7984
 TJH  CAU  C   CR6   0  -0.054  -6.3650   2.2307  -0.4856
 TJH  CL   CL  CL    0  -0.124  -7.7807   3.2262  -0.5606
 TJH  CAK  C   CR16  0  -0.258  -6.4739   0.9199  -0.1214
 TJH  H1   H   HCR6  0   0.273   6.0814   0.6736   2.9756
 TJH  H2   H   HCR6  0   0.277   8.4950   0.3885   2.5124
 TJH  H3   H   HCR6  0   0.282   9.2598  -0.3695   0.2992
 TJH  H4   H   HOH1  0   0.478   6.9565  -1.0768  -2.2757
 TJH  H5   H   HCR6  0   0.284   2.8432  -0.6864  -1.8549
 TJH  H6   H   HNH1  0   0.411   1.6083   0.4628   1.4235
 TJH  H7   H   HCH2  0   0.256   0.9133   0.5247  -1.3553
 TJH  H8   H   HCH2  0   0.254   0.6482  -1.0972  -0.7247
 TJH  H9   H   HCH2  0   0.267  -0.8006  -0.1504   1.0881
 TJH  H10  H   HCH2  0   0.269  -0.4943   1.4642   0.4956
 TJH  H11  H   HNH1  0   0.386  -1.7406   1.0662  -1.3764
 TJH  H12  H   HCH2  0   0.247  -1.5989  -2.5530  -0.9934
 TJH  H13  H   HCH2  0   0.251  -1.0718  -2.0826   0.5965
 TJH  H14  H   HCH2  0   0.241  -1.4774  -4.5601   0.2425
 TJH  H15  H   HCH2  0   0.225  -2.1633  -3.8527   1.6907
 TJH  H16  H   HCH2  0   0.226  -3.7317  -4.3571  -0.8777
 TJH  H17  H   HCH2  0   0.241  -3.8188  -5.3363   0.5763
 TJH  H18  H   HCH2  0   0.252  -5.6691  -3.6315   0.5203
 TJH  H19  H   HCH2  0   0.251  -4.6065  -3.4246   1.8964
 TJH  H20  H   HCR6  0   0.257  -3.0479   2.5001  -0.9805
 TJH  H21  H   HCR6  0   0.283  -5.0527   3.8529  -1.0651
 TJH  H22  H   HCR6  0   0.279  -7.4288   0.4778   0.1297

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
 TJH  OAC  CAV  single    1.329  0.020  1.329
 TJH  OAA  CBA  double    1.242  0.020  1.242
 TJH  CL   CAU  single    1.732  0.020  1.732
 TJH  CAV  CAF  aromatic  1.401  0.020  1.401
 TJH  CAV  CBF  aromatic  1.402  0.020  1.402
 TJH  CBA  CBF  single    1.475  0.020  1.475
 TJH  CBA  CAJ  single    1.429  0.020  1.429
 TJH  CAG  CAU  aromatic  1.406  0.020  1.406
 TJH  CAG  CAI  aromatic  1.368  0.020  1.368
 TJH  CAF  CAE  aromatic  1.378  0.020  1.378
 TJH  CBF  CBE  aromatic  1.403  0.020  1.403
 TJH  CAJ  CAX  double    1.367  0.020  1.367
 TJH  CAU  CAK  aromatic  1.365  0.020  1.365
 TJH  CAI  CBD  aromatic  1.413  0.020  1.413
 TJH  CAO  CAN  single    1.520  0.020  1.520
 TJH  CAO  NAT  single    1.454  0.020  1.454
 TJH  CAE  CAH  aromatic  1.393  0.020  1.393
 TJH  CAN  NAS  single    1.442  0.020  1.442
 TJH  CBE  CAH  aromatic  1.383  0.020  1.383
 TJH  CBE  CBB  single    1.475  0.020  1.475
 TJH  CAX  NAS  single    1.327  0.020  1.327
 TJH  CAX  CBB  single    1.504  0.020  1.504
 TJH  CAK  CBC  aromatic  1.414  0.020  1.414
 TJH  CBD  CBC  aromatic  1.414  0.020  1.414
 TJH  CBD  CAZ  aromatic  1.427  0.020  1.427
 TJH  CBB  OAB  double    1.211  0.020  1.211
 TJH  CBC  NAR  aromatic  1.346  0.020  1.346
 TJH  NAT  CAZ  single    1.388  0.020  1.388
 TJH  CAZ  CAY  aromatic  1.386  0.020  1.386
 TJH  NAR  CAW  aromatic  1.313  0.020  1.313
 TJH  CAY  CAW  aromatic  1.419  0.020  1.419
 TJH  CAY  CAQ  single    1.510  0.020  1.510
 TJH  CAW  CAP  single    1.504  0.020  1.504
 TJH  CAQ  CAM  single    1.526  0.020  1.526
 TJH  CAP  CAL  single    1.520  0.020  1.520
 TJH  CAM  CAL  single    1.517  0.020  1.517
 TJH  CAH  H1   single    0.930  0.020  1.080
 TJH  CAE  H2   single    0.930  0.020  1.080
 TJH  CAF  H3   single    0.930  0.020  1.080
 TJH  OAC  H4   single    0.850  0.020  0.980
 TJH  CAJ  H5   single    0.930  0.020  1.080
 TJH  NAS  H6   single    0.860  0.020  1.020
 TJH  CAN  H7   single    0.970  0.020  1.090
 TJH  CAN  H8   single    0.970  0.020  1.090
 TJH  CAO  H9   single    0.970  0.020  1.090
 TJH  CAO  H10  single    0.970  0.020  1.090
 TJH  NAT  H11  single    0.890  0.020  1.040
 TJH  CAQ  H12  single    0.970  0.020  1.090
 TJH  CAQ  H13  single    0.970  0.020  1.090
 TJH  CAM  H14  single    0.970  0.020  1.090
 TJH  CAM  H15  single    0.970  0.020  1.090
 TJH  CAL  H16  single    0.970  0.020  1.090
 TJH  CAL  H17  single    0.970  0.020  1.090
 TJH  CAP  H18  single    0.970  0.020  1.090
 TJH  CAP  H19  single    0.970  0.020  1.090
 TJH  CAI  H20  single    0.930  0.020  1.080
 TJH  CAG  H21  single    0.930  0.020  1.080
 TJH  CAK  H22  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
 TJH  CAX  CBB  CBE  117.83  3.000
 TJH  CAX  CBB  OAB  119.42  3.000
 TJH  CBE  CBB  OAB  122.75  3.000
 TJH  CBF  CBE  CAH  121.02  3.000
 TJH  CAH  CBE  CBB  119.17  3.000
 TJH  CBF  CBE  CBB  119.81  3.000
 TJH  H1   CAH  CAE  120.26  3.000
 TJH  H1   CAH  CBE  120.56  3.000
 TJH  CAE  CAH  CBE  119.19  3.000
 TJH  H2   CAE  CAF  119.44  3.000
 TJH  H2   CAE  CAH  119.74  3.000
 TJH  CAF  CAE  CAH  120.83  3.000
 TJH  H3   CAF  CAV  118.98  3.000
 TJH  H3   CAF  CAE  120.62  3.000
 TJH  CAV  CAF  CAE  120.40  3.000
 TJH  CBF  CAV  OAC  122.38  3.000
 TJH  CBF  CAV  CAF  119.31  3.000
 TJH  OAC  CAV  CAF  118.31  3.000
 TJH  H4   OAC  CAV  106.71  3.000
 TJH  CBA  CBF  CAV  120.09  3.000
 TJH  CBA  CBF  CBE  120.66  3.000
 TJH  CAV  CBF  CBE  119.25  3.000
 TJH  CAJ  CBA  OAA  121.23  3.000
 TJH  CAJ  CBA  CBF  119.24  3.000
 TJH  OAA  CBA  CBF  119.53  3.000
 TJH  H5   CAJ  CAX  121.04  3.000
 TJH  H5   CAJ  CBA  116.98  3.000
 TJH  CAX  CAJ  CBA  121.99  3.000
 TJH  NAS  CAX  CAJ  124.99  3.000
 TJH  NAS  CAX  CBB  114.53  3.000
 TJH  CAJ  CAX  CBB  120.47  3.000
 TJH  H6   NAS  CAN  119.02  3.000
 TJH  H6   NAS  CAX  117.36  3.000
 TJH  CAN  NAS  CAX  123.62  3.000
 TJH  H8   CAN  H7   107.00  3.000
 TJH  H8   CAN  CAO  110.02  3.000
 TJH  H7   CAN  CAO  109.67  3.000
 TJH  H8   CAN  NAS  110.39  3.000
 TJH  H7   CAN  NAS  109.39  3.000
 TJH  CAO  CAN  NAS  110.31  3.000
 TJH  H10  CAO  H9   106.18  3.000
 TJH  H10  CAO  NAT  110.35  3.000
 TJH  H9   CAO  NAT  109.80  3.000
 TJH  H10  CAO  CAN  109.52  3.000
 TJH  H9   CAO  CAN  110.50  3.000
 TJH  NAT  CAO  CAN  110.41  3.000
 TJH  H11  NAT  CAZ  113.15  3.000
 TJH  H11  NAT  CAO  111.06  3.000
 TJH  CAZ  NAT  CAO  120.68  3.000
 TJH  CBD  CAZ  CAY  118.93  3.000
 TJH  CAY  CAZ  NAT  120.95  3.000
 TJH  CBD  CAZ  NAT  120.07  3.000
 TJH  CAW  CAY  CAQ  121.16  3.000
 TJH  CAQ  CAY  CAZ  120.52  3.000
 TJH  CAW  CAY  CAZ  117.93  3.000
 TJH  H13  CAQ  H12  105.44  3.000
 TJH  H13  CAQ  CAM  107.71  3.000
 TJH  H12  CAQ  CAM  109.73  3.000
 TJH  H13  CAQ  CAY  111.26  3.000
 TJH  H12  CAQ  CAY  107.30  3.000
 TJH  CAM  CAQ  CAY  114.99  3.000
 TJH  H15  CAM  H14  106.49  3.000
 TJH  H15  CAM  CAL  108.66  3.000
 TJH  H14  CAM  CAL  111.24  3.000
 TJH  H15  CAM  CAQ  109.70  3.000
 TJH  H14  CAM  CAQ  108.84  3.000
 TJH  CAL  CAM  CAQ  111.75  3.000
 TJH  H17  CAL  H16  106.82  3.000
 TJH  H17  CAL  CAP  109.89  3.000
 TJH  H16  CAL  CAP  110.12  3.000
 TJH  H17  CAL  CAM  110.78  3.000
 TJH  H16  CAL  CAM  110.31  3.000
 TJH  CAP  CAL  CAM  108.91  3.000
 TJH  H19  CAP  H18  106.40  3.000
 TJH  H19  CAP  CAW  108.46  3.000
 TJH  H18  CAP  CAW  108.44  3.000
 TJH  H19  CAP  CAL  109.07  3.000
 TJH  H18  CAP  CAL  111.78  3.000
 TJH  CAW  CAP  CAL  112.47  3.000
 TJH  NAR  CAW  CAP  115.77  3.000
 TJH  CAP  CAW  CAY  120.26  3.000
 TJH  NAR  CAW  CAY  123.95  3.000
 TJH  CBC  NAR  CAW  118.87  3.000
 TJH  CAK  CBC  CBD  119.60  3.000
 TJH  CBD  CBC  NAR  122.58  3.000
 TJH  CAK  CBC  NAR  117.82  3.000
 TJH  CAI  CBD  CBC  118.55  3.000
 TJH  CBC  CBD  CAZ  117.71  3.000
 TJH  CAI  CBD  CAZ  123.73  3.000
 TJH  H20  CAI  CAG  117.82  3.000
 TJH  H20  CAI  CBD  120.80  3.000
 TJH  CAG  CAI  CBD  121.36  3.000
 TJH  H21  CAG  CAU  120.43  3.000
 TJH  H21  CAG  CAI  120.37  3.000
 TJH  CAU  CAG  CAI  119.20  3.000
 TJH  CAK  CAU  CL   119.89  3.000
 TJH  CAK  CAU  CAG  121.55  3.000
 TJH  CL   CAU  CAG  118.56  3.000
 TJH  H22  CAK  CAU  121.66  3.000
 TJH  H22  CAK  CBC  118.64  3.000
 TJH  CAU  CAK  CBC  119.71  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
 TJH  CONST_01  CAF  CAV  CBF  CBE     0.00   0.0  0
 TJH  CONST_02  CAF  CAE  CAH  CBE     0.00   0.0  0
 TJH  CONST_03  CAV  CAF  CAE  CAH     0.00   0.0  0
 TJH  CONST_04  CAV  CBF  CBE  CAH     0.00   0.0  0
 TJH  CONST_05  CBF  CAV  CAF  CAE     0.00   0.0  0
 TJH  CONST_06  CBF  CBE  CAH  CAE     0.00   0.0  0
 TJH  CONST_07  CAG  CAI  CBD  CAZ   180.00   0.0  0
 TJH  CONST_08  CAK  CBC  CBD  CAZ   180.00   0.0  0
 TJH  CONST_09  NAR  CBC  CBD  CAZ     0.00   0.0  0
 TJH  CONST_10  NAR  CAW  CAY  CAZ     0.00   0.0  0
 TJH  CONST_11  CAI  CBD  CAZ  CAY   180.00   0.0  0
 TJH  CONST_12  CBC  CBD  CAZ  CAY     0.00   0.0  0
 TJH  CONST_13  CBC  NAR  CAW  CAY     0.00   0.0  0
 TJH  CONST_14  CAK  CBC  NAR  CAW   180.00   0.0  0
 TJH  CONST_15  CBD  CBC  NAR  CAW     0.00   0.0  0
 TJH  CONST_16  CBD  CAZ  CAY  CAW     0.00   0.0  0
 TJH  CONST_17  CAU  CAK  CBC  NAR   180.00   0.0  0
 TJH  CONST_18  CAI  CBD  CBC  NAR   180.00   0.0  0
 TJH  CONST_19  CAG  CAU  CAK  CBC     0.00   0.0  0
 TJH  CONST_20  CAG  CAI  CBD  CBC     0.00   0.0  0
 TJH  CONST_21  CAU  CAG  CAI  CBD     0.00   0.0  0
 TJH  CONST_22  CAU  CAK  CBC  CBD     0.00   0.0  0
 TJH  CONST_23  CAK  CAU  CAG  CAI     0.00   0.0  0
 TJH  CONST_24  CAK  CBC  CBD  CAI     0.00   0.0  0
 TJH  CONST_25  OAC  CAV  CBF  CBE   180.00   0.0  0
 TJH  CONST_26  OAC  CAV  CAF  CAE   180.00   0.0  0
 TJH  CONST_27  CBA  CBF  CAV  OAC     0.00   0.0  0
 TJH  CONST_28  CAI  CBD  CAZ  NAT     0.00   0.0  0
 TJH  CONST_29  CBC  CBD  CAZ  NAT   180.00   0.0  0
 TJH  CONST_30  CAW  CAY  CAZ  NAT   180.00   0.0  0
 TJH  CONST_31  CAQ  CAY  CAZ  NAT     0.00   0.0  0
 TJH  CONST_32  CL   CAU  CAK  CBC   180.00   0.0  0
 TJH  CONST_33  CL   CAU  CAG  CAI   180.00   0.0  0
 TJH  CONST_34  H1   CAH  CBE  CBB     0.00   0.0  0
 TJH  CONST_35  H2   CAE  CAH  CBE   180.00   0.0  0
 TJH  CONST_36  H3   CAF  CAE  CAH   180.00   0.0  0
 TJH  CONST_37  H20  CAI  CBD  CAZ     0.00   0.0  0
 TJH  CONST_38  H22  CAK  CBC  NAR     0.00   0.0  0
 TJH  CONST_39  H21  CAG  CAI  CBD   180.00   0.0  0
 TJH  Var_01    CAM  CAQ  CAY  CAZ   177.53  30.0  1
 TJH  Var_02    CAL  CAP  CAW  CAY   -27.80  30.0  1
 TJH  Var_03    CAL  CAM  CAQ  CAY    38.43  30.0  1
 TJH  Var_04    CAP  CAL  CAM  CAQ   -61.47  30.0  1
 TJH  Var_05    CAW  CAP  CAL  CAM    55.52  30.0  1
 TJH  Var_06    CAN  NAS  CAX  CBB   179.05  30.0  2
 TJH  Var_07    CAO  CAN  NAS  CAX  -173.57  30.0  1
 TJH  Var_08    CAZ  NAT  CAO  CAN   139.49  30.0  3
 TJH  Var_09    NAT  CAO  CAN  NAS   177.87  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
 TJH  plan-1  OAB  0.020
 TJH  plan-1  CBB  0.020
 TJH  plan-1  CBE  0.020
 TJH  plan-1  CAH  0.020
 TJH  plan-1  CAE  0.020
 TJH  plan-1  CAF  0.020
 TJH  plan-1  CAV  0.020
 TJH  plan-1  OAC  0.020
 TJH  plan-1  CBF  0.020
 TJH  plan-1  CBA  0.020
 TJH  plan-1  OAA  0.020
 TJH  plan-1  CAJ  0.020
 TJH  plan-1  CAX  0.020
 TJH  plan-1  NAS  0.020
 TJH  plan-1  H1   0.020
 TJH  plan-1  H2   0.020
 TJH  plan-1  H3   0.020
 TJH  plan-1  H5   0.020
 TJH  plan-2  NAT  0.020
 TJH  plan-2  CAZ  0.020
 TJH  plan-2  CAY  0.020
 TJH  plan-2  CAQ  0.020
 TJH  plan-2  CAP  0.020
 TJH  plan-2  CAW  0.020
 TJH  plan-2  NAR  0.020
 TJH  plan-2  CBC  0.020
 TJH  plan-2  CBD  0.020
 TJH  plan-2  CAI  0.020
 TJH  plan-2  CAG  0.020
 TJH  plan-2  CAU  0.020
 TJH  plan-2  CL   0.020
 TJH  plan-2  CAK  0.020
 TJH  plan-2  H20  0.020
 TJH  plan-2  H21  0.020
 TJH  plan-2  H22  0.020
 TJH  plan-3  CAO  0.020
 TJH  plan-3  NAT  0.020
 TJH  plan-3  CAZ  0.020
 TJH  plan-3  H11  0.020

