# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 02:59:48 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 1,4-bis[(2-aminoethyl)amino]-5,8-dihydroxyanthracene-9,10-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNc1ccc(NCCN)c2C(=O)c3c(O)ccc(O)c3C(=O)c12
#
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
 3OK  3OK  1,4-bis[(2-aminoethyl)amino]-5,8-dihydroxyanthracene-9,10-dione  ligand  46  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3OK
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
 3OK  NAS  N  NH2   0  -0.800   5.7712   3.7333  -0.0661
 3OK  CAO  C  CH2   0  -0.318   5.0170   2.5032   0.0875
 3OK  CAQ  C  CH2   0  -0.273   3.5279   2.8092   0.0316
 3OK  NAU  N  NH1   0  -0.695   2.7723   1.5821   0.1330
 3OK  CAY  C  CR6   0   0.392   1.4333   1.4962   0.1050
 3OK  CAI  C  CR16  0  -0.324   0.6732   2.7028   0.0723
 3OK  CBE  C  CR66  0  -0.151   0.7179   0.2771   0.1100
 3OK  CAJ  C  CR16  0  -0.324  -0.6791   2.7023   0.0499
 3OK  CBA  C  CR6   0   0.437   1.4381  -0.9716   0.1415
 3OK  OAA  O  O     0  -0.553   2.6912  -1.0109   0.1703
 3OK  CBF  C  CR66  0  -0.151  -0.7227   0.2763   0.0793
 3OK  CBC  C  CR66  0  -0.191   0.7038  -2.2328   0.1410
 3OK  CAZ  C  CR6   0   0.392  -1.4386   1.4948   0.0492
 3OK  CBB  C  CR6   0   0.437  -1.4423  -0.9731   0.0815
 3OK  OAB  O  O     0  -0.555  -2.6960  -1.0132   0.0554
 3OK  CAW  C  CR6   0   0.342   1.4060  -3.4446   0.1699
 3OK  NAV  N  NH1   0  -0.695  -2.7775   1.5789   0.0165
 3OK  OAE  O  OH1   0  -0.633   2.7366  -3.5168   0.1987
 3OK  CAG  C  CR16  0  -0.327   0.6844  -4.6461   0.1691
 3OK  CAR  C  CH2   0  -0.272  -3.5340   2.8082   0.0690
 3OK  CAH  C  CR16  0  -0.327  -0.6877  -4.6467   0.1403
 3OK  CAP  C  CH2   0  -0.318  -5.0227   2.5008   0.0083
 3OK  CAX  C  CR6   0   0.342  -1.4096  -3.4458   0.1121
 3OK  NAT  N  NH2   0  -0.799  -5.7776   3.7348   0.1241
 3OK  OAF  O  OH1   0  -0.633  -2.7402  -3.5183   0.0858
 3OK  CBD  C  CR66  0  -0.191  -0.7078  -2.2335   0.1126
 3OK  H1   H  HNH2  0   0.355   6.7448   3.5629   0.1469
 3OK  H2   H  HNH2  0   0.345   5.7479   4.0308  -1.0334
 3OK  H4   H  HCH2  0   0.207   5.2550   1.7352  -0.6622
 3OK  H5   H  HCH2  0   0.236   5.2513   2.0723   1.0635
 3OK  H6   H  HCH2  0   0.238   3.2808   3.4942   0.8478
 3OK  H7   H  HCH2  0   0.234   3.2935   3.3274  -0.9057
 3OK  H8   H  HNH1  0   0.419   3.2686   0.7015   0.1330
 3OK  H9   H  HCR6  0   0.299   1.1852   3.6549   0.0683
 3OK  H10  H  HCR6  0   0.299  -1.1917   3.6539   0.0290
 3OK  H13  H  HNH1  0   0.417  -3.2726   0.6979   0.0412
 3OK  H14  H  HOH1  0   0.481   3.0617  -2.5814   0.1956
 3OK  H15  H  HCR6  0   0.280   1.2262  -5.5833   0.1918
 3OK  H16  H  HCH2  0   0.234  -3.3102   3.3582   0.9908
 3OK  H17  H  HCH2  0   0.239  -3.2774   3.4656  -0.7667
 3OK  H18  H  HCR6  0   0.280  -1.2292  -5.5843   0.1396
 3OK  H19  H  HCH2  0   0.236  -5.2497   2.0450  -0.9581
 3OK  H20  H  HCH2  0   0.206  -5.2677   1.7530   0.7759
 3OK  H21  H  HNH2  0   0.356  -6.7497   3.5585  -0.0913
 3OK  H22  H  HNH2  0   0.345  -5.7618   4.0565   1.0838
 3OK  H24  H  HOH1  0   0.480  -3.0648  -2.5829   0.0675

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
 3OK  NAT  CAP  single    1.451  0.020  1.451
 3OK  CAP  CAR  single    1.521  0.020  1.521
 3OK  CAR  NAV  single    1.444  0.020  1.444
 3OK  NAV  CAZ  single    1.342  0.020  1.342
 3OK  CAJ  CAZ  aromatic  1.426  0.020  1.426
 3OK  CAJ  CAI  aromatic  1.353  0.020  1.353
 3OK  CAZ  CBF  aromatic  1.414  0.020  1.414
 3OK  CAI  CAY  aromatic  1.426  0.020  1.426
 3OK  NAS  CAO  single    1.451  0.020  1.451
 3OK  OAB  CBB  double    1.255  0.020  1.255
 3OK  CAO  CAQ  single    1.521  0.020  1.521
 3OK  CBF  CBB  single    1.442  0.020  1.442
 3OK  CBF  CBE  aromatic  1.441  0.020  1.441
 3OK  CAY  CBE  aromatic  1.414  0.020  1.414
 3OK  CAY  NAU  single    1.342  0.020  1.342
 3OK  CBB  CBD  single    1.459  0.020  1.459
 3OK  CBE  CBA  single    1.442  0.020  1.442
 3OK  NAU  CAQ  single    1.445  0.020  1.445
 3OK  OAF  CAX  single    1.333  0.020  1.333
 3OK  CBD  CAX  aromatic  1.401  0.020  1.401
 3OK  CBD  CBC  aromatic  1.412  0.020  1.412
 3OK  CBA  CBC  single    1.459  0.020  1.459
 3OK  CBA  OAA  double    1.254  0.020  1.254
 3OK  CAX  CAH  aromatic  1.401  0.020  1.401
 3OK  CBC  CAW  aromatic  1.401  0.020  1.401
 3OK  CAH  CAG  aromatic  1.372  0.020  1.372
 3OK  CAW  CAG  aromatic  1.402  0.020  1.402
 3OK  CAW  OAE  single    1.333  0.020  1.333
 3OK  NAS  H1   single    0.890  0.020  1.040
 3OK  NAS  H2   single    0.890  0.020  1.040
 3OK  CAO  H4   single    0.970  0.020  1.090
 3OK  CAO  H5   single    0.970  0.020  1.090
 3OK  CAQ  H6   single    0.970  0.020  1.090
 3OK  CAQ  H7   single    0.970  0.020  1.090
 3OK  NAU  H8   single    0.860  0.020  1.020
 3OK  CAI  H9   single    0.930  0.020  1.080
 3OK  CAJ  H10  single    0.930  0.020  1.080
 3OK  NAV  H13  single    0.860  0.020  1.020
 3OK  OAE  H14  single    0.850  0.020  0.980
 3OK  CAG  H15  single    0.930  0.020  1.080
 3OK  CAR  H16  single    0.970  0.020  1.090
 3OK  CAR  H17  single    0.970  0.020  1.090
 3OK  CAH  H18  single    0.930  0.020  1.080
 3OK  CAP  H19  single    0.970  0.020  1.090
 3OK  CAP  H20  single    0.970  0.020  1.090
 3OK  NAT  H21  single    0.890  0.020  1.040
 3OK  NAT  H22  single    0.890  0.020  1.040
 3OK  OAF  H24  single    0.850  0.020  0.980

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
 3OK  H2   NAS  H1   105.85  3.000
 3OK  H2   NAS  CAO  109.78  3.000
 3OK  H1   NAS  CAO  109.59  3.000
 3OK  H5   CAO  H4   106.70  3.000
 3OK  H5   CAO  CAQ  108.79  3.000
 3OK  H4   CAO  CAQ  109.11  3.000
 3OK  H5   CAO  NAS  108.51  3.000
 3OK  H4   CAO  NAS  114.05  3.000
 3OK  CAQ  CAO  NAS  109.53  3.000
 3OK  H7   CAQ  H6   107.08  3.000
 3OK  H7   CAQ  NAU  110.46  3.000
 3OK  H6   CAQ  NAU  111.19  3.000
 3OK  H7   CAQ  CAO  109.62  3.000
 3OK  H6   CAQ  CAO  108.64  3.000
 3OK  NAU  CAQ  CAO  109.79  3.000
 3OK  H8   NAU  CAY  115.73  3.000
 3OK  H8   NAU  CAQ  118.89  3.000
 3OK  CAY  NAU  CAQ  125.08  3.000
 3OK  CBE  CAY  CAI  117.38  3.000
 3OK  CBE  CAY  NAU  124.06  3.000
 3OK  CAI  CAY  NAU  118.56  3.000
 3OK  H9   CAI  CAJ  118.28  3.000
 3OK  H9   CAI  CAY  119.51  3.000
 3OK  CAJ  CAI  CAY  122.20  3.000
 3OK  CBF  CBE  CBA  119.96  3.000
 3OK  CBA  CBE  CAY  119.62  3.000
 3OK  CBF  CBE  CAY  120.43  3.000
 3OK  H10  CAJ  CAZ  119.52  3.000
 3OK  H10  CAJ  CAI  118.30  3.000
 3OK  CAZ  CAJ  CAI  122.18  3.000
 3OK  CBC  CBA  OAA  118.41  3.000
 3OK  OAA  CBA  CBE  121.79  3.000
 3OK  CBC  CBA  CBE  119.81  3.000
 3OK  CBB  CBF  CAZ  119.62  3.000
 3OK  CBB  CBF  CBE  119.96  3.000
 3OK  CAZ  CBF  CBE  120.41  3.000
 3OK  CBD  CBC  CAW  120.07  3.000
 3OK  CAW  CBC  CBA  119.70  3.000
 3OK  CBD  CBC  CBA  120.23  3.000
 3OK  NAV  CAZ  CBF  124.04  3.000
 3OK  CBF  CAZ  CAJ  117.39  3.000
 3OK  NAV  CAZ  CAJ  118.57  3.000
 3OK  CBD  CBB  OAB  118.42  3.000
 3OK  CBD  CBB  CBF  119.82  3.000
 3OK  OAB  CBB  CBF  121.76  3.000
 3OK  CAG  CAW  OAE  117.88  3.000
 3OK  OAE  CAW  CBC  123.20  3.000
 3OK  CAG  CAW  CBC  118.92  3.000
 3OK  H13  NAV  CAR  118.97  3.000
 3OK  H13  NAV  CAZ  115.69  3.000
 3OK  CAR  NAV  CAZ  125.10  3.000
 3OK  H14  OAE  CAW  106.05  3.000
 3OK  H15  CAG  CAH  120.02  3.000
 3OK  H15  CAG  CAW  118.97  3.000
 3OK  CAH  CAG  CAW  121.01  3.000
 3OK  H17  CAR  H16  107.04  3.000
 3OK  H17  CAR  CAP  108.69  3.000
 3OK  H16  CAR  CAP  109.55  3.000
 3OK  H17  CAR  NAV  111.15  3.000
 3OK  H16  CAR  NAV  110.52  3.000
 3OK  CAP  CAR  NAV  109.82  3.000
 3OK  H18  CAH  CAX  118.98  3.000
 3OK  H18  CAH  CAG  120.03  3.000
 3OK  CAX  CAH  CAG  121.00  3.000
 3OK  H20  CAP  H19  106.72  3.000
 3OK  H20  CAP  NAT  114.00  3.000
 3OK  H19  CAP  NAT  108.50  3.000
 3OK  H20  CAP  CAR  109.13  3.000
 3OK  H19  CAP  CAR  108.84  3.000
 3OK  NAT  CAP  CAR  109.51  3.000
 3OK  CBD  CAX  OAF  123.18  3.000
 3OK  CBD  CAX  CAH  118.92  3.000
 3OK  OAF  CAX  CAH  117.90  3.000
 3OK  H22  NAT  H21  105.81  3.000
 3OK  H22  NAT  CAP  109.74  3.000
 3OK  H21  NAT  CAP  109.56  3.000
 3OK  H24  OAF  CAX  106.03  3.000
 3OK  CAX  CBD  CBB  119.69  3.000
 3OK  CAX  CBD  CBC  120.09  3.000
 3OK  CBB  CBD  CBC  120.22  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
 3OK  CONST_01  CAZ  CAJ  CAI  CAY     0.00   0.0  0
 3OK  CONST_02  CAZ  CBF  CBE  CAY     0.00   0.0  0
 3OK  CONST_03  CBF  CAZ  CAJ  CAI     0.00   0.0  0
 3OK  CONST_04  CBF  CBE  CAY  CAI     0.00   0.0  0
 3OK  CONST_05  CAJ  CAZ  CBF  CBE     0.00   0.0  0
 3OK  CONST_06  CAJ  CAI  CAY  CBE     0.00   0.0  0
 3OK  CONST_07  CAH  CAX  CBD  CBC     0.00   0.0  0
 3OK  CONST_08  CAH  CAG  CAW  CBC     0.00   0.0  0
 3OK  CONST_09  CAX  CBD  CBC  CAW     0.00   0.0  0
 3OK  CONST_10  CAX  CAH  CAG  CAW     0.00   0.0  0
 3OK  CONST_11  CBD  CAX  CAH  CAG     0.00   0.0  0
 3OK  CONST_12  CBD  CBC  CAW  CAG     0.00   0.0  0
 3OK  CONST_13  CAJ  CAI  CAY  NAU   180.00   0.0  0
 3OK  CONST_14  CBF  CBE  CAY  NAU   180.00   0.0  0
 3OK  CONST_15  CBA  CBE  CAY  NAU     0.00   0.0  0
 3OK  CONST_16  NAV  CAZ  CAJ  CAI   180.00   0.0  0
 3OK  CONST_17  NAV  CAZ  CBF  CBE   180.00   0.0  0
 3OK  CONST_18  OAE  CAW  CBC  CBA     0.00   0.0  0
 3OK  CONST_19  OAF  CAX  CBD  CBC   180.00   0.0  0
 3OK  CONST_20  NAV  CAZ  CBF  CBB     0.00   0.0  0
 3OK  CONST_21  OAF  CAX  CBD  CBB     0.00   0.0  0
 3OK  CONST_22  CBD  CBC  CAW  OAE   180.00   0.0  0
 3OK  CONST_23  CAH  CAG  CAW  OAE   180.00   0.0  0
 3OK  CONST_24  OAF  CAX  CAH  CAG   180.00   0.0  0
 3OK  CONST_25  H10  CAJ  CAI  CAY   180.00   0.0  0
 3OK  CONST_26  H9   CAI  CAY  CBE   180.00   0.0  0
 3OK  CONST_27  H15  CAG  CAW  CBC   180.00   0.0  0
 3OK  CONST_28  H18  CAH  CAG  CAW   180.00   0.0  0
 3OK  CONST_29  CAI  CAY  NAU  CAQ     0.00   0.0  0
 3OK  CONST_30  CBE  CAY  NAU  CAQ   180.00   0.0  0
 3OK  CONST_31  CAR  NAV  CAZ  CAJ     0.00   0.0  0
 3OK  CONST_32  CAR  NAV  CAZ  CBF   180.00   0.0  0
 3OK  CONST_33  H8   NAU  CAY  CAI   180.00   0.0  0
 3OK  CONST_34  H13  NAV  CAZ  CAJ   180.00   0.0  0
 3OK  Var_01    CAY  NAU  CAQ  CAO  -179.40  30.0  2
 3OK  Var_02    CAP  CAR  NAV  CAZ   179.99  30.0  1
 3OK  Var_03    NAU  CAQ  CAO  NAS   177.83  30.0  3
 3OK  Var_04    NAT  CAP  CAR  NAV   177.37  30.0  2
 3OK  Var_05    H1   NAS  CAO  CAQ   169.17  30.0  3
 3OK  Var_06    H21  NAT  CAP  CAR   169.27  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
 3OK  plan-1  NAU  0.020
 3OK  plan-1  CAY  0.020
 3OK  plan-1  CAI  0.020
 3OK  plan-1  CBE  0.020
 3OK  plan-1  CAJ  0.020
 3OK  plan-1  CBA  0.020
 3OK  plan-1  OAA  0.020
 3OK  plan-1  CBF  0.020
 3OK  plan-1  CBC  0.020
 3OK  plan-1  CAZ  0.020
 3OK  plan-1  CBB  0.020
 3OK  plan-1  OAB  0.020
 3OK  plan-1  CAW  0.020
 3OK  plan-1  NAV  0.020
 3OK  plan-1  OAE  0.020
 3OK  plan-1  CAG  0.020
 3OK  plan-1  CAH  0.020
 3OK  plan-1  CAX  0.020
 3OK  plan-1  OAF  0.020
 3OK  plan-1  CBD  0.020
 3OK  plan-1  H9   0.020
 3OK  plan-1  H10  0.020
 3OK  plan-1  H15  0.020
 3OK  plan-1  H18  0.020
 3OK  plan-2  CAQ  0.020
 3OK  plan-2  NAU  0.020
 3OK  plan-2  CAY  0.020
 3OK  plan-2  H8   0.020
 3OK  plan-3  CAZ  0.020
 3OK  plan-3  NAV  0.020
 3OK  plan-3  CAR  0.020
 3OK  plan-3  H13  0.020

