# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 10:33:10 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,7-diyl)bis[2-(dimethylamino)acetamide]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CC(=O)Nc1ccc2C(=O)c3ccc(NC(=O)CN(C)C)cc3C(=O)c2c1
#
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
 5BD  5BD  N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,7-diyl)bis[2-(dimethylamino)acetamide]  ligand  54  30  .  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_5BD
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
 5BD  C1   C  CR16  0  -0.262  -2.5048  -2.9277   0.1208
 5BD  C2   C  CR16  0  -0.330  -3.6937  -2.2348   0.0741
 5BD  C3   C  CR6   0   0.421  -3.7082  -0.8386  -0.0394
 5BD  C5   C  CR16  0  -0.360   2.4374  -0.1493  -0.0964
 5BD  C6   C  CR6   0   0.421   3.6536  -0.8290  -0.0346
 5BD  C7   C  CR16  0  -0.330   3.6425  -2.2254   0.0775
 5BD  C8   C  CR16  0  -0.262   2.4553  -2.9214   0.1226
 5BD  C9   C  C     0   0.531  -5.2647   1.0900  -0.2545
 5BD  C11  C  CR66  0  -0.049  -1.2874  -2.2536   0.0592
 5BD  C12  C  CR66  0   0.004  -1.2991  -0.8618  -0.0520
 5BD  C13  C  CR6   0   0.312  -0.0282  -0.0947  -0.1159
 5BD  C14  C  CR6   0   0.328  -0.0247  -3.0155   0.1138
 5BD  O1   O  O     0  -0.442  -4.4424   1.9718  -0.3803
 5BD  N1   N  NH1   0  -0.751  -4.9519  -0.2261  -0.0713
 5BD  C4   C  CR16  0  -0.360  -2.4940  -0.1555  -0.1018
 5BD  O2   O  O     0  -0.368  -0.0296   1.1136  -0.2180
 5BD  O3   O  O     0  -0.386  -0.0233  -4.2291   0.2024
 5BD  C15  C  CR66  0  -0.049   1.2361  -2.2505   0.0608
 5BD  C16  C  CR66  0   0.005   1.2444  -0.8586  -0.0490
 5BD  N2   N  NH1   0  -0.751   4.8957  -0.2134  -0.0699
 5BD  C10  C  C     0   0.531   5.2018   1.1081  -0.2241
 5BD  O4   O  O     0  -0.441   4.3744   1.9902  -0.3075
 5BD  H1   H  HCR6  0   0.275  -2.5238  -4.0055   0.2057
 5BD  H2   H  HCR6  0   0.288  -4.6287  -2.7792   0.1254
 5BD  H5   H  HCR6  0   0.294   2.4091   0.9243  -0.1767
 5BD  H7   H  HCR6  0   0.288   4.5789  -2.7675   0.1298
 5BD  H8   H  HCR6  0   0.275   2.4772  -3.9992   0.2068
 5BD  C17  C  CH2   0  -0.409  -6.7648   1.3304  -0.3286
 5BD  H4   H  HCR6  0   0.294  -2.4688   0.9181  -0.1828
 5BD  HN2  H  HNH1  0   0.423   5.6824  -0.8427   0.0003
 5BD  C18  C  CH2   0  -0.409   6.6989   1.3559  -0.3236
 5BD  H81  H  HNH1  0   0.423  -5.7361  -0.8540   0.0315
 5BD  H9   H  HCH2  0   0.232  -7.2943   0.5926   0.2988
 5BD  N3   N  NT    0  -0.399  -7.1162   2.6880  -0.0180
 5BD  H10  H  HCH2  0   0.293  -7.0573   1.1111  -1.3615
 5BD  H11  H  HCH2  0   0.233   7.2434   0.6085   0.2787
 5BD  H12  H  HCH2  0   0.293   6.9716   1.1572  -1.3662
 5BD  N4   N  NT    0  -0.399   7.0516   2.7089   0.0055
 5BD  C19  C  CH3   0  -0.522  -8.4448   3.0152  -0.4915
 5BD  C20  C  CH3   0  -0.529  -6.9803   2.9767   1.3947
 5BD  H13  H  HCH3  0   0.239  -5.9569   2.8101   1.7310
 5BD  H14  H  HCH3  0   0.238  -7.2164   4.0250   1.5792
 5BD  H15  H  HCH3  0   0.197  -7.6469   2.3665   2.0233
 5BD  H16  H  HCH3  0   0.197  -9.2409   2.4334  -0.0024
 5BD  H17  H  HCH3  0   0.237  -8.6488   4.0710  -0.3099
 5BD  H18  H  HCH3  0   0.237  -8.5155   2.8422  -1.5661
 5BD  C21  C  CH3   0  -0.528   6.9466   2.9686   1.4266
 5BD  C22  C  CH3   0  -0.522   8.3680   3.0513  -0.4907
 5BD  H19  H  HCH3  0   0.198   7.6300   2.3485   2.0268
 5BD  H20  H  HCH3  0   0.238   7.1824   4.0140   1.6271
 5BD  H21  H  HCH3  0   0.239   5.9317   2.7902   1.7821
 5BD  H22  H  HCH3  0   0.237   8.4168   2.8957  -1.5692
 5BD  H23  H  HCH3  0   0.237   8.5701   4.1053  -0.2964
 5BD  H24  H  HCH3  0   0.196   9.1774   2.4664  -0.0279

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
 5BD  C1   C2   aromatic  1.377  0.020  1.377
 5BD  C1   C11  aromatic  1.393  0.020  1.393
 5BD  C1   H1   single    0.930  0.020  1.080
 5BD  C2   C3   aromatic  1.401  0.020  1.401
 5BD  C2   H2   single    0.930  0.020  1.080
 5BD  C3   N1   single    1.387  0.020  1.387
 5BD  C3   C4   aromatic  1.395  0.020  1.395
 5BD  C5   C6   aromatic  1.395  0.020  1.395
 5BD  C5   C16  aromatic  1.389  0.020  1.389
 5BD  C5   H5   single    0.930  0.020  1.080
 5BD  C6   C7   aromatic  1.401  0.020  1.401
 5BD  C6   N2   single    1.387  0.020  1.387
 5BD  C7   C8   aromatic  1.377  0.020  1.377
 5BD  C7   H7   single    0.930  0.020  1.080
 5BD  C8   C15  aromatic  1.393  0.020  1.393
 5BD  C8   H8   single    0.930  0.020  1.080
 5BD  C9   O1   double    1.212  0.020  1.212
 5BD  C9   N1   single    1.365  0.020  1.365
 5BD  C9   C17  single    1.521  0.020  1.521
 5BD  C11  C12  aromatic  1.396  0.020  1.396
 5BD  C11  C14  single    1.476  0.020  1.476
 5BD  C12  C13  single    1.486  0.020  1.486
 5BD  C12  C4   aromatic  1.389  0.020  1.389
 5BD  C13  O2   double    1.213  0.020  1.213
 5BD  C13  C16  single    1.486  0.020  1.486
 5BD  C14  O3   double    1.217  0.020  1.217
 5BD  C14  C15  single    1.476  0.020  1.476
 5BD  N1   H81  single    0.860  0.020  1.020
 5BD  C4   H4   single    0.930  0.020  1.080
 5BD  C15  C16  aromatic  1.396  0.020  1.396
 5BD  N2   C10  single    1.365  0.020  1.365
 5BD  N2   HN2  single    0.860  0.020  1.020
 5BD  C10  O4   double    1.212  0.020  1.212
 5BD  C10  C18  single    1.521  0.020  1.521
 5BD  C17  H9   single    0.970  0.020  1.090
 5BD  C17  N3   single    1.436  0.020  1.436
 5BD  C17  H10  single    0.970  0.020  1.090
 5BD  C18  H11  single    0.970  0.020  1.090
 5BD  C18  H12  single    0.970  0.020  1.090
 5BD  C18  N4   single    1.436  0.020  1.436
 5BD  N3   C19  single    1.448  0.020  1.448
 5BD  N3   C20  single    1.448  0.020  1.448
 5BD  N4   C21  single    1.448  0.020  1.448
 5BD  N4   C22  single    1.448  0.020  1.448
 5BD  C19  H16  single    0.970  0.020  1.090
 5BD  C19  H17  single    0.970  0.020  1.090
 5BD  C19  H18  single    0.970  0.020  1.090
 5BD  C20  H13  single    0.970  0.020  1.090
 5BD  C20  H14  single    0.970  0.020  1.090
 5BD  C20  H15  single    0.970  0.020  1.090
 5BD  C21  H19  single    0.970  0.020  1.090
 5BD  C21  H20  single    0.970  0.020  1.090
 5BD  C21  H21  single    0.970  0.020  1.090
 5BD  C22  H22  single    0.970  0.020  1.090
 5BD  C22  H23  single    0.970  0.020  1.090
 5BD  C22  H24  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
 5BD  H1   C1   C11  120.08  3.000
 5BD  H1   C1   C2   119.28  3.000
 5BD  C11  C1   C2   120.64  3.000
 5BD  H2   C2   C3   119.72  3.000
 5BD  H2   C2   C1   119.40  3.000
 5BD  C3   C2   C1   120.88  3.000
 5BD  C4   C3   N1   124.30  3.000
 5BD  C4   C3   C2   118.87  3.000
 5BD  N1   C3   C2   116.83  3.000
 5BD  H5   C5   C16  119.29  3.000
 5BD  H5   C5   C6   120.80  3.000
 5BD  C16  C5   C6   119.91  3.000
 5BD  N2   C6   C7   116.85  3.000
 5BD  N2   C6   C5   124.31  3.000
 5BD  C7   C6   C5   118.84  3.000
 5BD  H7   C7   C8   119.39  3.000
 5BD  H7   C7   C6   119.72  3.000
 5BD  C8   C7   C6   120.88  3.000
 5BD  H8   C8   C15  120.08  3.000
 5BD  H8   C8   C7   119.27  3.000
 5BD  C15  C8   C7   120.65  3.000
 5BD  C17  C9   N1   112.63  3.000
 5BD  C17  C9   O1   123.30  3.000
 5BD  N1   C9   O1   124.04  3.000
 5BD  C14  C11  C12  121.65  3.000
 5BD  C14  C11  C1   119.75  3.000
 5BD  C12  C11  C1   118.59  3.000
 5BD  C4   C12  C13  118.15  3.000
 5BD  C4   C12  C11  121.13  3.000
 5BD  C13  C12  C11  120.72  3.000
 5BD  C16  C13  O2   121.14  3.000
 5BD  C16  C13  C12  117.72  3.000
 5BD  O2   C13  C12  121.14  3.000
 5BD  C15  C14  O3   121.24  3.000
 5BD  C15  C14  C11  117.52  3.000
 5BD  O3   C14  C11  121.24  3.000
 5BD  H81  N1   C9   115.80  3.000
 5BD  H81  N1   C3   114.80  3.000
 5BD  C9   N1   C3   129.38  3.000
 5BD  H4   C4   C12  119.31  3.000
 5BD  H4   C4   C3   120.80  3.000
 5BD  C12  C4   C3   119.89  3.000
 5BD  C16  C15  C14  121.65  3.000
 5BD  C16  C15  C8   118.58  3.000
 5BD  C14  C15  C8   119.77  3.000
 5BD  C15  C16  C13  120.73  3.000
 5BD  C15  C16  C5   121.13  3.000
 5BD  C13  C16  C5   118.14  3.000
 5BD  HN2  N2   C10  115.88  3.000
 5BD  HN2  N2   C6   114.79  3.000
 5BD  C10  N2   C6   129.30  3.000
 5BD  C18  C10  O4   123.29  3.000
 5BD  C18  C10  N2   112.69  3.000
 5BD  O4   C10  N2   123.99  3.000
 5BD  H10  C17  N3   109.13  3.000
 5BD  H10  C17  H9   105.90  3.000
 5BD  N3   C17  H9   113.05  3.000
 5BD  H10  C17  C9   106.12  3.000
 5BD  N3   C17  C9   112.34  3.000
 5BD  H9   C17  C9   109.87  3.000
 5BD  N4   C18  H12  109.13  3.000
 5BD  N4   C18  H11  113.06  3.000
 5BD  H12  C18  H11  105.88  3.000
 5BD  N4   C18  C10  112.34  3.000
 5BD  H12  C18  C10  106.12  3.000
 5BD  H11  C18  C10  109.85  3.000
 5BD  C20  N3   C19  111.10  3.000
 5BD  C20  N3   C17  112.11  3.000
 5BD  C19  N3   C17  111.55  3.000
 5BD  C22  N4   C21  111.09  3.000
 5BD  C22  N4   C18  111.56  3.000
 5BD  C21  N4   C18  112.08  3.000
 5BD  H18  C19  H17  107.79  3.000
 5BD  H18  C19  H16  107.88  3.000
 5BD  H17  C19  H16  107.61  3.000
 5BD  H18  C19  N3   110.23  3.000
 5BD  H17  C19  N3   109.63  3.000
 5BD  H16  C19  N3   113.51  3.000
 5BD  H15  C20  H14  107.77  3.000
 5BD  H15  C20  H13  107.91  3.000
 5BD  H14  C20  H13  107.34  3.000
 5BD  H15  C20  N3   112.94  3.000
 5BD  H14  C20  N3   109.66  3.000
 5BD  H13  C20  N3   111.01  3.000
 5BD  H21  C21  H20  107.36  3.000
 5BD  H21  C21  H19  107.94  3.000
 5BD  H20  C21  H19  107.79  3.000
 5BD  H21  C21  N4   110.99  3.000
 5BD  H20  C21  N4   109.67  3.000
 5BD  H19  C21  N4   112.89  3.000
 5BD  H24  C22  H23  107.60  3.000
 5BD  H24  C22  H22  107.89  3.000
 5BD  H23  C22  H22  107.80  3.000
 5BD  H24  C22  N4   113.50  3.000
 5BD  H23  C22  N4   109.63  3.000
 5BD  H22  C22  N4   110.23  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
 5BD  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 5BD  CONST_02  C4   C12  C11  C1      0.00   0.0  0
 5BD  CONST_03  C12  C11  C1   C2      0.00   0.0  0
 5BD  CONST_04  C12  C4   C3   C2      0.00   0.0  0
 5BD  CONST_05  C11  C1   C2   C3      0.00   0.0  0
 5BD  CONST_06  C11  C12  C4   C3      0.00   0.0  0
 5BD  CONST_07  C8   C7   C6   C5      0.00   0.0  0
 5BD  CONST_08  C8   C15  C16  C5      0.00   0.0  0
 5BD  CONST_09  C15  C16  C5   C6      0.00   0.0  0
 5BD  CONST_10  C15  C8   C7   C6      0.00   0.0  0
 5BD  CONST_11  C16  C5   C6   C7      0.00   0.0  0
 5BD  CONST_12  C16  C15  C8   C7      0.00   0.0  0
 5BD  CONST_13  N1   C3   C2   C1    180.00   0.0  0
 5BD  CONST_14  N2   C6   C7   C8    180.00   0.0  0
 5BD  CONST_15  N1   C3   C4   C12   180.00   0.0  0
 5BD  CONST_16  N2   C6   C5   C16   180.00   0.0  0
 5BD  CONST_17  H4   C4   C3   C2    180.00   0.0  0
 5BD  CONST_18  H1   C1   C2   C3    180.00   0.0  0
 5BD  CONST_19  H7   C7   C6   C5    180.00   0.0  0
 5BD  CONST_20  H8   C8   C7   C6    180.00   0.0  0
 5BD  CONST_21  H5   C5   C6   C7    180.00   0.0  0
 5BD  CONST_22  H2   C2   C1   C11   180.00   0.0  0
 5BD  CONST_23  C9   N1   C3   C2    180.00   0.0  0
 5BD  CONST_24  C10  N2   C6   C5      0.00   0.0  0
 5BD  CONST_25  C10  N2   C6   C7    180.00   0.0  0
 5BD  CONST_26  C4   C3   N1   C9      0.00   0.0  0
 5BD  CONST_27  H81  N1   C3   C2      0.00   0.0  0
 5BD  CONST_28  HN2  N2   C6   C5    180.00   0.0  0
 5BD  CONST_29  O1   C9   N1   C3      0.00   0.0  0
 5BD  CONST_30  C17  C9   N1   C3    180.00   0.0  0
 5BD  CONST_31  O4   C10  N2   C6      0.00   0.0  0
 5BD  CONST_32  C18  C10  N2   C6    180.00   0.0  0
 5BD  Var_01    C19  N3   C17  C9    161.74  30.0  3
 5BD  Var_02    N3   C17  C9   O1    -23.71  30.0  3
 5BD  Var_03    N4   C18  C10  N2   -158.56  30.0  3
 5BD  Var_04    C21  N4   C18  C10    73.09  30.0  3
 5BD  Var_05    H16  C19  N3   C17    64.06  30.0  3
 5BD  Var_06    H13  C20  N3   C17    59.24  30.0  3
 5BD  Var_07    H19  C21  N4   C18    62.11  30.0  3
 5BD  Var_08    H22  C22  N4   C18    56.87  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
 5BD  plan-1  C1   0.020
 5BD  plan-1  C2   0.020
 5BD  plan-1  C3   0.020
 5BD  plan-1  C5   0.020
 5BD  plan-1  C6   0.020
 5BD  plan-1  C7   0.020
 5BD  plan-1  C8   0.020
 5BD  plan-1  C11  0.020
 5BD  plan-1  C12  0.020
 5BD  plan-1  C13  0.020
 5BD  plan-1  C14  0.020
 5BD  plan-1  N1   0.020
 5BD  plan-1  C4   0.020
 5BD  plan-1  O2   0.020
 5BD  plan-1  O3   0.020
 5BD  plan-1  C15  0.020
 5BD  plan-1  C16  0.020
 5BD  plan-1  N2   0.020
 5BD  plan-1  H1   0.020
 5BD  plan-1  H2   0.020
 5BD  plan-1  H5   0.020
 5BD  plan-1  H7   0.020
 5BD  plan-1  H8   0.020
 5BD  plan-1  H4   0.020
 5BD  plan-2  C3   0.020
 5BD  plan-2  C9   0.020
 5BD  plan-2  O1   0.020
 5BD  plan-2  N1   0.020
 5BD  plan-2  C17  0.020
 5BD  plan-2  H81  0.020
 5BD  plan-3  C6   0.020
 5BD  plan-3  N2   0.020
 5BD  plan-3  C10  0.020
 5BD  plan-3  O4   0.020
 5BD  plan-3  HN2  0.020
 5BD  plan-3  C18  0.020

