# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:00:16 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 6-(3-oxidanylpropyl)-2-(1,3,6-trimethyl-2-oxidanylidene-benzimidazol-5-yl)benzo[de]isoquinoline-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2cc(N3C(=O)c4cccc5c(CCCO)ccc(C3=O)c45)c(C)cc12
#
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
 7M8  7M8  6-(3-oxidanylpropyl)-2-(1,3,6-trimethyl-2-oxidanylidene-benzimidazol-5-yl)benzo[de]isoquinoline-1,3-dione  ligand  55  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7M8
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
 7M8  C1   C  CR16  0  -0.240   3.4929   2.8872   0.0572
 7M8  C2   C  CR16  0  -0.293   2.1091   2.7599   0.2333
 7M8  C3   C  CR66  0  -0.146   1.4998   1.5393   0.0576
 7M8  C4   C  C     0   0.305   2.2614   0.4080  -0.3051
 7M8  C8   C  CH2   0  -0.456   6.6438  -0.7184   0.2647
 7M8  C9   C  CH2   0  -0.140   8.1434  -0.5978   0.0769
 7M8  C10  C  CR66  0  -0.175   1.6343  -0.8431  -0.4754
 7M8  C11  C  CR16  0  -0.273   2.3823  -1.9344  -0.8481
 7M8  C12  C  CR16  0  -0.332   3.7605  -1.8120  -1.0564
 7M8  C13  C  CR6   0   0.542   0.1915  -0.9921  -0.2494
 7M8  C14  C  CR6   0   0.269  -1.9151   0.0245   0.3241
 7M8  C15  C  CR6   0   0.078  -2.3739  -0.2031   1.6219
 7M8  C16  C  CR16  0  -0.391  -3.7478  -0.3386   1.8367
 7M8  C17  C  CR56  0   0.363  -4.5993  -0.2467   0.7543
 7M8  C18  C  CR56  0   0.319  -4.1149  -0.0241  -0.5365
 7M8  C19  C  CR16  0  -0.326  -2.7656   0.1196  -0.7728
 7M8  C20  C  CR5   0   0.657  -6.3568  -0.1864  -0.6548
 7M8  C24  C  CR6   0   0.546   0.0454   1.4236   0.2500
 7M8  O3   O  O     0  -0.419  -0.6613   2.3663   0.5337
 7M8  N    N  NR6   0  -0.722  -0.5083   0.1582   0.0993
 7M8  O2   O  O     0  -0.420  -0.3904  -2.0506  -0.3495
 7M8  C6   C  CR6   0   0.131   4.4151  -0.6135  -0.8871
 7M8  C7   C  CH2   0  -0.554   5.9038  -0.5511  -1.0656
 7M8  O    O  OH1   0  -0.673   8.7771  -0.7841   1.3230
 7M8  C5   C  CR66  0   0.102   3.6602   0.5311  -0.4993
 7M8  C    C  CR16  0  -0.334   4.2487   1.8008  -0.3005
 7M8  N1   N  NR5   0  -0.587  -5.2029   0.0043  -1.3785
 7M8  C22  C  CH3   0  -0.535  -5.1472   0.2013  -2.8040
 7M8  O1   O  O     0  -0.500  -7.4950  -0.2143  -1.0870
 7M8  N2   N  NR5   0  -0.585  -5.9676  -0.3406   0.6575
 7M8  C23  C  CH3   0  -0.739  -1.4170  -0.2982   2.7749
 7M8  H1   H  HCR6  0   0.276   3.9635   3.8497   0.2027
 7M8  H2   H  HCR6  0   0.277   1.5226   3.6256   0.5094
 7M8  H3   H  HCH2  0   0.240   6.4015  -1.6961   0.6891
 7M8  H4   H  HCH2  0   0.238   6.3039   0.0329   0.9829
 7M8  H5   H  HCH2  0   0.193   8.4765  -1.3416  -0.6595
 7M8  H6   H  HCH2  0   0.193   8.3735   0.3890  -0.3467
 7M8  H7   H  HCR6  0   0.274   1.9081  -2.8971  -0.9849
 7M8  H8   H  HCR6  0   0.265   4.3216  -2.6877  -1.3567
 7M8  H9   H  HCR6  0   0.273  -4.1254  -0.5180   2.8353
 7M8  H10  H  HCR6  0   0.278  -2.3726   0.2988  -1.7654
 7M8  H11  H  HCH3  0   0.269  -7.8878  -0.5669   1.3905
 7M8  H12  H  HCH3  0   0.256  -6.6612  -1.5073   2.2485
 7M8  H13  H  HCH3  0   0.256  -6.7715   0.2456   2.4947
 7M8  H14  H  HCH2  0   0.255   6.1996   0.3871  -1.5414
 7M8  H15  H  HCH2  0   0.268   6.2108  -1.3460  -1.7485
 7M8  H16  H  HOH1  0   0.454   9.7261  -0.7071   1.1905
 7M8  H17  H  HCR6  0   0.266   5.3145   1.9280  -0.4311
 7M8  H18  H  HCH3  0   0.269  -6.1474   0.1035  -3.2148
 7M8  H19  H  HCH3  0   0.256  -4.7640   1.1927  -3.0439
 7M8  H20  H  HCH3  0   0.256  -4.5053  -0.5474  -3.2675
 7M8  H21  H  HCH3  0   0.250  -0.9009   0.6476   2.9500
 7M8  H22  H  HCH3  0   0.258  -1.9435  -0.5546   3.6925
 7M8  H23  H  HCH3  0   0.248  -0.6546  -1.0612   2.6118
 7M8  C21  C  CH3   0  -0.536  -6.8675  -0.5546   1.7617

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
 7M8  O1   C20  double    1.218  0.020  1.218
 7M8  C22  N1   single    1.440  0.020  1.440
 7M8  C20  N1   single    1.375  0.020  1.375
 7M8  C20  N2   single    1.377  0.020  1.377
 7M8  N1   C18  single    1.376  0.020  1.376
 7M8  N2   C21  single    1.440  0.020  1.440
 7M8  N2   C17  single    1.375  0.020  1.375
 7M8  C18  C17  aromatic  1.397  0.020  1.397
 7M8  C18  C19  aromatic  1.377  0.020  1.377
 7M8  C17  C16  aromatic  1.380  0.020  1.380
 7M8  C19  C14  aromatic  1.391  0.020  1.391
 7M8  O3   C24  double    1.212  0.020  1.212
 7M8  C16  C15  aromatic  1.397  0.020  1.397
 7M8  C14  C15  aromatic  1.395  0.020  1.395
 7M8  C14  N    single    1.431  0.020  1.431
 7M8  C24  N    single    1.389  0.020  1.389
 7M8  C24  C3   single    1.472  0.020  1.472
 7M8  C2   C3   aromatic  1.375  0.020  1.375
 7M8  C2   C1   aromatic  1.401  0.020  1.401
 7M8  C15  C23  single    1.501  0.020  1.501
 7M8  N    C13  single    1.391  0.020  1.391
 7M8  C3   C4   aromatic  1.411  0.020  1.411
 7M8  C1   C    aromatic  1.371  0.020  1.371
 7M8  C4   C5   aromatic  1.418  0.020  1.418
 7M8  C4   C10  aromatic  1.410  0.020  1.410
 7M8  C    C5   aromatic  1.413  0.020  1.413
 7M8  C13  C10  single    1.468  0.020  1.468
 7M8  C13  O2   double    1.212  0.020  1.212
 7M8  C5   C6   aromatic  1.425  0.020  1.425
 7M8  C10  C11  aromatic  1.375  0.020  1.375
 7M8  C11  C12  aromatic  1.399  0.020  1.399
 7M8  C6   C12  aromatic  1.376  0.020  1.376
 7M8  C6   C7   single    1.501  0.020  1.501
 7M8  C7   C8   single    1.531  0.020  1.531
 7M8  C8   C9   single    1.516  0.020  1.516
 7M8  C9   O    single    1.410  0.020  1.410
 7M8  C1   H1   single    0.930  0.020  1.080
 7M8  C2   H2   single    0.930  0.020  1.080
 7M8  C8   H3   single    0.970  0.020  1.090
 7M8  C8   H4   single    0.970  0.020  1.090
 7M8  C9   H5   single    0.970  0.020  1.090
 7M8  C9   H6   single    0.970  0.020  1.090
 7M8  C11  H7   single    0.930  0.020  1.080
 7M8  C12  H8   single    0.930  0.020  1.080
 7M8  C16  H9   single    0.930  0.020  1.080
 7M8  C19  H10  single    0.930  0.020  1.080
 7M8  C21  H11  single    0.970  0.020  1.090
 7M8  C21  H12  single    0.970  0.020  1.090
 7M8  C21  H13  single    0.970  0.020  1.090
 7M8  C7   H14  single    0.970  0.020  1.090
 7M8  C7   H15  single    0.970  0.020  1.090
 7M8  O    H16  single    0.850  0.020  0.980
 7M8  C    H17  single    0.930  0.020  1.080
 7M8  C22  H18  single    0.970  0.020  1.090
 7M8  C22  H19  single    0.970  0.020  1.090
 7M8  C22  H20  single    0.970  0.020  1.090
 7M8  C23  H21  single    0.970  0.020  1.090
 7M8  C23  H22  single    0.970  0.020  1.090
 7M8  C23  H23  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
 7M8  H1   C1   C    120.04  3.000
 7M8  H1   C1   C2   119.60  3.000
 7M8  C    C1   C2   120.36  3.000
 7M8  H2   C2   C3   120.18  3.000
 7M8  H2   C2   C1   119.68  3.000
 7M8  C3   C2   C1   120.15  3.000
 7M8  C24  C3   C4   120.26  3.000
 7M8  C4   C3   C2   120.34  3.000
 7M8  C24  C3   C2   119.40  3.000
 7M8  C5   C4   C10  119.96  3.000
 7M8  C10  C4   C3   120.16  3.000
 7M8  C5   C4   C3   119.87  3.000
 7M8  H4   C8   H3   106.89  3.000
 7M8  H4   C8   C7   110.20  3.000
 7M8  H3   C8   C7   109.14  3.000
 7M8  H4   C8   C9   109.53  3.000
 7M8  H3   C8   C9   109.79  3.000
 7M8  C7   C8   C9   111.20  3.000
 7M8  H6   C9   H5   106.64  3.000
 7M8  H6   C9   O    111.43  3.000
 7M8  H5   C9   O    111.51  3.000
 7M8  H6   C9   C8   109.06  3.000
 7M8  H5   C9   C8   109.22  3.000
 7M8  O    C9   C8   108.93  3.000
 7M8  C13  C10  C11  119.74  3.000
 7M8  C11  C10  C4   119.69  3.000
 7M8  C13  C10  C4   120.57  3.000
 7M8  H7   C11  C12  119.39  3.000
 7M8  H7   C11  C10  120.15  3.000
 7M8  C12  C11  C10  120.46  3.000
 7M8  H8   C12  C6   119.48  3.000
 7M8  H8   C12  C11  118.75  3.000
 7M8  C6   C12  C11  121.76  3.000
 7M8  O2   C13  N    120.09  3.000
 7M8  O2   C13  C10  123.22  3.000
 7M8  N    C13  C10  116.69  3.000
 7M8  N    C14  C19  118.08  3.000
 7M8  N    C14  C15  118.99  3.000
 7M8  C19  C14  C15  122.92  3.000
 7M8  C23  C15  C16  120.17  3.000
 7M8  C23  C15  C14  121.00  3.000
 7M8  C16  C15  C14  118.83  3.000
 7M8  H9   C16  C17  121.28  3.000
 7M8  H9   C16  C15  120.06  3.000
 7M8  C17  C16  C15  118.66  3.000
 7M8  N2   C17  C18  106.92  3.000
 7M8  C18  C17  C16  121.43  3.000
 7M8  N2   C17  C16  131.65  3.000
 7M8  N1   C18  C19  131.87  3.000
 7M8  C19  C18  C17  121.00  3.000
 7M8  N1   C18  C17  107.13  3.000
 7M8  H10  C19  C18  122.02  3.000
 7M8  H10  C19  C14  120.82  3.000
 7M8  C18  C19  C14  117.16  3.000
 7M8  N2   C20  O1   126.84  3.000
 7M8  N2   C20  N1   106.25  3.000
 7M8  O1   C20  N1   126.91  3.000
 7M8  N    C24  O3   120.10  3.000
 7M8  N    C24  C3   116.82  3.000
 7M8  O3   C24  C3   123.07  3.000
 7M8  C24  N    C14  117.37  3.000
 7M8  C24  N    C13  125.45  3.000
 7M8  C14  N    C13  117.18  3.000
 7M8  C5   C6   C7   121.64  3.000
 7M8  C7   C6   C12  119.57  3.000
 7M8  C5   C6   C12  118.76  3.000
 7M8  H15  C7   H14  106.06  3.000
 7M8  H15  C7   C6   108.85  3.000
 7M8  H14  C7   C6   110.86  3.000
 7M8  H15  C7   C8   109.14  3.000
 7M8  H14  C7   C8   109.95  3.000
 7M8  C6   C7   C8   111.81  3.000
 7M8  H16  O    C9   108.14  3.000
 7M8  C    C5   C6   122.64  3.000
 7M8  C6   C5   C4   119.36  3.000
 7M8  C    C5   C4   118.01  3.000
 7M8  H17  C    C5   119.94  3.000
 7M8  H17  C    C1   118.79  3.000
 7M8  C5   C    C1   121.27  3.000
 7M8  C22  N1   C20  124.91  3.000
 7M8  C20  N1   C18  109.79  3.000
 7M8  C22  N1   C18  125.30  3.000
 7M8  H20  C22  H19  108.92  3.000
 7M8  H20  C22  H18  108.65  3.000
 7M8  H19  C22  H18  108.82  3.000
 7M8  H20  C22  N1   110.48  3.000
 7M8  H19  C22  N1   110.86  3.000
 7M8  H18  C22  N1   109.06  3.000
 7M8  C21  N2   C20  124.78  3.000
 7M8  C21  N2   C17  125.30  3.000
 7M8  C20  N2   C17  109.91  3.000
 7M8  H23  C23  H22  107.42  3.000
 7M8  H23  C23  H21  107.43  3.000
 7M8  H22  C23  H21  107.31  3.000
 7M8  H23  C23  C15  112.02  3.000
 7M8  H22  C23  C15  110.73  3.000
 7M8  H21  C23  C15  111.70  3.000
 7M8  H13  C21  H12  108.96  3.000
 7M8  H13  C21  H11  108.73  3.000
 7M8  H12  C21  H11  108.71  3.000
 7M8  H13  C21  N2   110.59  3.000
 7M8  H12  C21  N2   110.74  3.000
 7M8  H11  C21  N2   109.06  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
 7M8  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 7M8  CONST_02  C4   C5   C    C1      0.00   0.0  0
 7M8  CONST_03  C6   C5   C    C1    180.00   0.0  0
 7M8  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 7M8  CONST_05  C10  C4   C3   C2    180.00   0.0  0
 7M8  CONST_06  C5   C    C1   C2      0.00   0.0  0
 7M8  CONST_07  C    C1   C2   C3      0.00   0.0  0
 7M8  CONST_08  C    C5   C4   C3      0.00   0.0  0
 7M8  CONST_09  C6   C5   C4   C3    180.00   0.0  0
 7M8  CONST_10  C11  C10  C4   C3    180.00   0.0  0
 7M8  CONST_11  C12  C6   C5   C4      0.00   0.0  0
 7M8  CONST_12  C12  C11  C10  C4      0.00   0.0  0
 7M8  CONST_13  C    C5   C4   C10   180.00   0.0  0
 7M8  CONST_14  C6   C5   C4   C10     0.00   0.0  0
 7M8  CONST_15  C6   C12  C11  C10     0.00   0.0  0
 7M8  CONST_16  C5   C4   C10  C11     0.00   0.0  0
 7M8  CONST_17  C5   C6   C12  C11     0.00   0.0  0
 7M8  CONST_18  C    C5   C6   C12   180.00   0.0  0
 7M8  CONST_19  C17  C18  C19  C14     0.00   0.0  0
 7M8  CONST_20  C17  C16  C15  C14     0.00   0.0  0
 7M8  CONST_21  C18  C17  C16  C15     0.00   0.0  0
 7M8  CONST_22  C18  C19  C14  C15     0.00   0.0  0
 7M8  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 7M8  CONST_24  C19  C14  C15  C16     0.00   0.0  0
 7M8  CONST_25  N    C14  C15  C16   180.00   0.0  0
 7M8  CONST_26  N    C14  C19  C18   180.00   0.0  0
 7M8  CONST_27  C14  N    C13  C10   180.00   0.0  0
 7M8  CONST_28  C24  N    C13  C10     0.00   0.0  0
 7M8  CONST_29  N1   C20  N2   C17     0.00   0.0  0
 7M8  CONST_30  C20  N1   C18  C17     0.00   0.0  0
 7M8  CONST_31  N2   C20  N1   C18     0.00   0.0  0
 7M8  CONST_32  C20  N2   C17  C18     0.00   0.0  0
 7M8  CONST_33  N2   C17  C18  N1      0.00   0.0  0
 7M8  CONST_34  C7   C6   C5   C4    180.00   0.0  0
 7M8  CONST_35  C7   C6   C12  C11   180.00   0.0  0
 7M8  CONST_36  C23  C15  C16  C17   180.00   0.0  0
 7M8  CONST_37  C23  C15  C14  C19   180.00   0.0  0
 7M8  CONST_38  C23  C15  C14  N       0.00   0.0  0
 7M8  CONST_39  C    C5   C6   C7      0.00   0.0  0
 7M8  CONST_40  O2   C13  N    C14     0.00   0.0  0
 7M8  CONST_41  O1   C20  N2   C17   180.00   0.0  0
 7M8  CONST_42  C22  N1   C18  C17   180.00   0.0  0
 7M8  CONST_43  O1   C20  N1   C18   180.00   0.0  0
 7M8  CONST_44  C21  N2   C17  C18   180.00   0.0  0
 7M8  CONST_45  N1   C20  N2   C21   180.00   0.0  0
 7M8  CONST_46  O2   C13  N    C24   180.00   0.0  0
 7M8  CONST_47  N2   C20  N1   C22   180.00   0.0  0
 7M8  CONST_48  H17  C    C1   C2    180.00   0.0  0
 7M8  CONST_49  H1   C1   C2   C3    180.00   0.0  0
 7M8  CONST_50  H2   C2   C3   C4    180.00   0.0  0
 7M8  CONST_51  H7   C11  C10  C4    180.00   0.0  0
 7M8  CONST_52  H8   C12  C11  C10   180.00   0.0  0
 7M8  CONST_53  H9   C16  C15  C14   180.00   0.0  0
 7M8  CONST_54  H10  C19  C14  C15   180.00   0.0  0
 7M8  CONST_55  O1   C20  N2   C21     0.00   0.0  0
 7M8  CONST_56  O1   C20  N1   C22     0.00   0.0  0
 7M8  Var_01    C19  C14  N    C13   -86.45  30.0  3
 7M8  Var_02    C5   C6   C7   C8     83.65  30.0  3
 7M8  Var_03    H21  C23  C15  C14    64.89  30.0  2
 7M8  Var_04    H11  C21  N2   C17   178.97  30.0  3
 7M8  Var_05    H18  C22  N1   C18   175.87  30.0  3
 7M8  Var_06    C6   C7   C8   C9   -177.73  30.0  1
 7M8  Var_07    O    C9   C8   C7   -178.90  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
 7M8  plan-1  C14  0.020
 7M8  plan-1  C15  0.020
 7M8  plan-1  C16  0.020
 7M8  plan-1  C17  0.020
 7M8  plan-1  C18  0.020
 7M8  plan-1  C19  0.020
 7M8  plan-1  C20  0.020
 7M8  plan-1  N    0.020
 7M8  plan-1  N1   0.020
 7M8  plan-1  C22  0.020
 7M8  plan-1  O1   0.020
 7M8  plan-1  N2   0.020
 7M8  plan-1  C23  0.020
 7M8  plan-1  H9   0.020
 7M8  plan-1  H10  0.020
 7M8  plan-1  C21  0.020
 7M8  plan-2  C1   0.020
 7M8  plan-2  C2   0.020
 7M8  plan-2  C3   0.020
 7M8  plan-2  C4   0.020
 7M8  plan-2  C10  0.020
 7M8  plan-2  C11  0.020
 7M8  plan-2  C12  0.020
 7M8  plan-2  C13  0.020
 7M8  plan-2  C14  0.020
 7M8  plan-2  C24  0.020
 7M8  plan-2  O3   0.020
 7M8  plan-2  N    0.020
 7M8  plan-2  O2   0.020
 7M8  plan-2  C6   0.020
 7M8  plan-2  C7   0.020
 7M8  plan-2  C5   0.020
 7M8  plan-2  C    0.020
 7M8  plan-2  H1   0.020
 7M8  plan-2  H2   0.020
 7M8  plan-2  H7   0.020
 7M8  plan-2  H8   0.020
 7M8  plan-2  H17  0.020

