# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:05:37 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 1-[(3R,4R)-4-(1H-indol-3-yl)-2,5-dioxopyrrolidin-3-yl]pyrrolo[3,2,1-ij]quinolinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)[C@H]([C@@H]1c2c[nH]c3ccccc23)C4=C[n+]5cccc6cccc4c56
#
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
 M97  M97  1-[(3R,4R)-4-(1H-indol-3-yl)-2,5-dioxopyrrolidin-3-yl]pyrrolo[3,2,1-ij]quinolinium  ligand  44  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M97
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
 M97  C1   C  CR15  0  -0.556  -1.2387  -1.6524  -0.1760
 M97  N1   N  NR15  0  -0.688  -4.2393   0.1578   0.9455
 M97  O1   O  O     0  -0.397  -2.5788  -3.5965  -0.8195
 M97  C2   C  CR5   0   0.132   0.8925  -0.6020   0.7287
 M97  N2   N  NR15  0  -0.690  -0.5197  -3.8435   0.1534
 M97  O2   O  O     0  -0.394   1.5027  -3.4885   1.1800
 M97  C3   C  CR15  0  -0.041   1.0319   0.4560   1.5537
 M97  N3   N  N     1  -0.556   2.0099   1.3242   1.0240
 M97  C4   C  CR5   0   0.065  -2.3583  -0.7284   0.1324
 M97  C5   C  CR15  0  -0.063  -3.5203  -0.9908   0.8037
 M97  C6   C  CR15  0  -0.571  -0.1111  -1.6795   0.8776
 M97  C7   C  CR5   0   0.603  -1.5887  -3.1221  -0.3301
 M97  C8   C  CR5   0   0.593   0.4429  -3.0894   0.7740
 M97  C9   C  CR56  0   0.357  -3.5626   1.1962   0.3741
 M97  C10  C  CR56  0   0.043  -2.3622   0.6749  -0.1535
 M97  C11  C  CR16  0  -0.362  -1.4712   1.5380  -0.8027
 M97  C12  C  CR16  0  -0.265  -1.7943   2.8759  -0.9062
 M97  C13  C  CR16  0  -0.284  -2.9942   3.3752  -0.3711
 M97  C14  C  CR16  0  -0.302  -3.8929   2.5470   0.2726
 M97  C15  C  CR66  0   0.126   3.4399   1.3835  -0.9202
 M97  C16  C  CR16  0  -0.112   3.9440   2.6133  -0.4547
 M97  C17  C  CR16  0  -0.372   3.4601   3.1443   0.7281
 M97  C18  C  CR16  0   0.102   2.4828   2.4852   1.4686
 M97  C19  C  C     0   0.404   2.4698   0.7875  -0.1338
 M97  C20  C  CR56  0   0.117   1.8210  -0.4188  -0.3824
 M97  C21  C  CR16  0  -0.393   2.1827  -1.0921  -1.5276
 M97  C22  C  CR16  0  -0.220   3.1690  -0.5277  -2.3715
 M97  C23  C  CR16  0  -0.315   3.7880   0.6698  -2.0934
 M97  H1   H  HCR5  0   0.328  -0.8068  -1.3687  -1.1459
 M97  HN2  H  HNR5  0   0.433  -0.4515  -4.8497   0.0586
 M97  H3   H  HCR5  0   0.338   0.5275   0.7058   2.4728
 M97  H5   H  HCR5  0   0.288  -3.8991  -1.9224   1.1930
 M97  H6   H  HCR5  0   0.358  -0.5682  -1.6089   1.8711
 M97  H11  H  HCR6  0   0.232  -0.5441   1.1682  -1.2259
 M97  H12  H  HCR6  0   0.249  -1.1151   3.5537  -1.4064
 M97  H13  H  HCR6  0   0.252  -3.2187   4.4297  -0.4660
 M97  H14  H  HCR6  0   0.262  -4.8166   2.9328   0.6844
 M97  H16  H  HCR6  0   0.320   4.7020   3.1430  -1.0161
 M97  H17  H  HCR6  0   0.322   3.8320   4.0861   1.1014
 M97  H18  H  HCR6  0   0.361   2.0837   2.8720   2.3947
 M97  H21  H  HCR6  0   0.288   1.7377  -2.0389  -1.8050
 M97  H22  H  HCR6  0   0.297   3.4435  -1.0646  -3.2685
 M97  H23  H  HCR6  0   0.298   4.5369   1.0685  -2.7642
 M97  HN1  H  HNR5  0   0.413  -5.1362   0.2194   1.3980

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
 M97  C1   C6   single    1.544  0.020  1.544
 M97  C1   H1   single    0.970  0.020  1.090
 M97  N1   C9   aromatic  1.365  0.020  1.365
 M97  N1   HN1  single    0.860  0.020  1.020
 M97  O1   C7   double    1.202  0.020  1.202
 M97  C2   C20  single    1.460  0.020  1.460
 M97  C2   C3   double    1.349  0.020  1.349
 M97  N2   C7   single    1.377  0.020  1.377
 M97  N2   C8   single    1.371  0.020  1.371
 M97  N2   HN2  single    0.860  0.020  1.020
 M97  C3   N3   single    1.411  0.020  1.411
 M97  C3   H3   single    0.930  0.020  1.080
 M97  N3   C18  aromatic  1.330  0.020  1.330
 M97  C4   C1   single    1.484  0.020  1.484
 M97  C4   C10  aromatic  1.432  0.020  1.432
 M97  C5   N1   aromatic  1.363  0.020  1.363
 M97  C5   C4   aromatic  1.367  0.020  1.367
 M97  C5   H5   single    0.930  0.020  1.080
 M97  C6   C2   single    1.480  0.020  1.480
 M97  C6   H6   single    0.970  0.020  1.090
 M97  C7   C1   single    1.519  0.020  1.519
 M97  C8   O2   double    1.203  0.020  1.203
 M97  C8   C6   single    1.518  0.020  1.518
 M97  C9   C10  aromatic  1.411  0.020  1.411
 M97  C9   C14  aromatic  1.394  0.020  1.394
 M97  C10  C11  aromatic  1.400  0.020  1.400
 M97  C11  C12  aromatic  1.380  0.020  1.380
 M97  C11  H11  single    0.930  0.020  1.080
 M97  C12  H12  single    0.930  0.020  1.080
 M97  C13  C12  aromatic  1.406  0.020  1.406
 M97  C13  H13  single    0.930  0.020  1.080
 M97  C14  C13  aromatic  1.381  0.020  1.381
 M97  C14  H14  single    0.930  0.020  1.080
 M97  C15  C16  aromatic  1.408  0.020  1.408
 M97  C16  C17  aromatic  1.384  0.020  1.384
 M97  C16  H16  single    0.930  0.020  1.080
 M97  C17  H17  single    0.930  0.020  1.080
 M97  C18  C17  aromatic  1.392  0.020  1.392
 M97  C18  H18  single    0.930  0.020  1.080
 M97  C19  N3   aromatic  1.356  0.020  1.356
 M97  C19  C15  aromatic  1.384  0.020  1.384
 M97  C20  C19  aromatic  1.392  0.020  1.392
 M97  C21  C20  aromatic  1.377  0.020  1.377
 M97  C21  C22  aromatic  1.415  0.020  1.415
 M97  C21  H21  single    0.930  0.020  1.080
 M97  C22  C23  aromatic  1.376  0.020  1.376
 M97  C22  H22  single    0.930  0.020  1.080
 M97  C23  C15  aromatic  1.417  0.020  1.417
 M97  C23  H23  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
 M97  H1   C1   C7   104.53  3.000
 M97  C7   C1   C6   102.75  3.000
 M97  H1   C1   C6   108.66  3.000
 M97  C7   C1   C4   116.73  3.000
 M97  H1   C1   C4   108.61  3.000
 M97  C6   C1   C4   114.85  3.000
 M97  HN1  N1   C9   125.70  3.000
 M97  HN1  N1   C5   124.66  3.000
 M97  C9   N1   C5   109.64  3.000
 M97  C20  C2   C6   126.82  3.000
 M97  C6   C2   C3   125.42  3.000
 M97  C20  C2   C3   107.54  3.000
 M97  HN2  N2   C8   122.77  3.000
 M97  HN2  N2   C7   122.67  3.000
 M97  C8   N2   C7   114.56  3.000
 M97  H3   C3   N3   120.13  3.000
 M97  H3   C3   C2   130.92  3.000
 M97  N3   C3   C2   108.95  3.000
 M97  C19  N3   C18  120.67  3.000
 M97  C19  N3   C3   108.18  3.000
 M97  C18  N3   C3   131.15  3.000
 M97  C10  C4   C5   106.49  3.000
 M97  C5   C4   C1   128.58  3.000
 M97  C10  C4   C1   124.80  3.000
 M97  H5   C5   C4   129.91  3.000
 M97  H5   C5   N1   120.35  3.000
 M97  C4   C5   N1   109.74  3.000
 M97  H6   C6   C8   105.89  3.000
 M97  C8   C6   C2   114.95  3.000
 M97  H6   C6   C2   109.10  3.000
 M97  C8   C6   C1   103.67  3.000
 M97  H6   C6   C1   108.24  3.000
 M97  C2   C6   C1   114.45  3.000
 M97  N2   C7   O1   125.14  3.000
 M97  N2   C7   C1   107.00  3.000
 M97  O1   C7   C1   127.81  3.000
 M97  C6   C8   O2   127.33  3.000
 M97  C6   C8   N2   106.58  3.000
 M97  O2   C8   N2   126.07  3.000
 M97  C14  C9   C10  122.15  3.000
 M97  C14  C9   N1   130.55  3.000
 M97  C10  C9   N1   107.29  3.000
 M97  C11  C10  C9   119.14  3.000
 M97  C11  C10  C4   134.02  3.000
 M97  C9   C10  C4   106.84  3.000
 M97  H11  C11  C12  120.10  3.000
 M97  H11  C11  C10  120.99  3.000
 M97  C12  C11  C10  118.91  3.000
 M97  H12  C12  C13  119.30  3.000
 M97  C13  C12  C11  121.04  3.000
 M97  H12  C12  C11  119.66  3.000
 M97  H13  C13  C14  119.35  3.000
 M97  C14  C13  C12  121.32  3.000
 M97  H13  C13  C12  119.33  3.000
 M97  H14  C14  C13  121.25  3.000
 M97  H14  C14  C9   121.31  3.000
 M97  C13  C14  C9   117.43  3.000
 M97  C23  C15  C19  115.21  3.000
 M97  C23  C15  C16  128.74  3.000
 M97  C19  C15  C16  116.05  3.000
 M97  H16  C16  C17  120.05  3.000
 M97  H16  C16  C15  120.45  3.000
 M97  C17  C16  C15  119.50  3.000
 M97  H17  C17  C18  118.11  3.000
 M97  C18  C17  C16  121.23  3.000
 M97  H17  C17  C16  120.66  3.000
 M97  H18  C18  C17  123.09  3.000
 M97  H18  C18  N3   117.89  3.000
 M97  C17  C18  N3   119.02  3.000
 M97  C20  C19  C15  126.76  3.000
 M97  C20  C19  N3   109.71  3.000
 M97  C15  C19  N3   123.53  3.000
 M97  C21  C20  C19  116.74  3.000
 M97  C21  C20  C2   137.64  3.000
 M97  C19  C20  C2   105.62  3.000
 M97  H21  C21  C22  118.85  3.000
 M97  H21  C21  C20  122.20  3.000
 M97  C22  C21  C20  118.94  3.000
 M97  H22  C22  C23  119.05  3.000
 M97  H22  C22  C21  118.27  3.000
 M97  C23  C22  C21  122.67  3.000
 M97  H23  C23  C22  120.45  3.000
 M97  H23  C23  C15  119.87  3.000
 M97  C22  C23  C15  119.68  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
 M97  CONST_01  C4   C10  C9   N1     0.00   0.0  0
 M97  CONST_02  C11  C10  C9   N1   180.00   0.0  0
 M97  CONST_03  C13  C14  C9   N1   180.00   0.0  0
 M97  CONST_04  C10  C4   C5   N1     0.00   0.0  0
 M97  CONST_05  C16  C17  C18  N3     0.00   0.0  0
 M97  CONST_06  C16  C15  C19  N3     0.00   0.0  0
 M97  CONST_07  C23  C15  C19  N3   180.00   0.0  0
 M97  CONST_08  C21  C20  C19  N3   180.00   0.0  0
 M97  CONST_09  C14  C9   C10  C4   180.00   0.0  0
 M97  CONST_10  C12  C11  C10  C4   180.00   0.0  0
 M97  CONST_11  C9   N1   C5   C4     0.00   0.0  0
 M97  CONST_12  C10  C9   N1   C5     0.00   0.0  0
 M97  CONST_13  C14  C9   N1   C5   180.00   0.0  0
 M97  CONST_14  C9   C10  C4   C5     0.00   0.0  0
 M97  CONST_15  C11  C10  C4   C5   180.00   0.0  0
 M97  CONST_16  C12  C11  C10  C9     0.00   0.0  0
 M97  CONST_17  C12  C13  C14  C9     0.00   0.0  0
 M97  CONST_18  C13  C14  C9   C10    0.00   0.0  0
 M97  CONST_19  C13  C12  C11  C10    0.00   0.0  0
 M97  CONST_20  C14  C9   C10  C11    0.00   0.0  0
 M97  CONST_21  C14  C13  C12  C11    0.00   0.0  0
 M97  CONST_22  C18  C17  C16  C15    0.00   0.0  0
 M97  CONST_23  C18  N3   C19  C15    0.00   0.0  0
 M97  CONST_24  C21  C20  C19  C15    0.00   0.0  0
 M97  CONST_25  C21  C22  C23  C15    0.00   0.0  0
 M97  CONST_26  C20  C19  C15  C16  180.00   0.0  0
 M97  CONST_27  C22  C23  C15  C16  180.00   0.0  0
 M97  CONST_28  C19  C15  C16  C17    0.00   0.0  0
 M97  CONST_29  C23  C15  C16  C17  180.00   0.0  0
 M97  CONST_30  C19  N3   C18  C17    0.00   0.0  0
 M97  CONST_31  C20  C19  N3   C18  180.00   0.0  0
 M97  CONST_32  C22  C23  C15  C19    0.00   0.0  0
 M97  CONST_33  C22  C21  C20  C19    0.00   0.0  0
 M97  CONST_34  C23  C15  C19  C20    0.00   0.0  0
 M97  CONST_35  C23  C22  C21  C20    0.00   0.0  0
 M97  CONST_36  C9   C10  C4   C1   180.00   0.0  0
 M97  CONST_37  C11  C10  C4   C1     0.00   0.0  0
 M97  CONST_38  N1   C5   C4   C1   180.00   0.0  0
 M97  CONST_39  C8   N2   C7   C1     0.00   0.0  0
 M97  CONST_40  C8   N2   C7   O1   180.00   0.0  0
 M97  CONST_41  H5   C5   C4   C1     0.00   0.0  0
 M97  CONST_42  H14  C14  C9   N1     0.00   0.0  0
 M97  CONST_43  H21  C21  C20  C2     0.00   0.0  0
 M97  CONST_44  H18  C18  N3   C3     0.00   0.0  0
 M97  CONST_45  H17  C17  C18  N3   180.00   0.0  0
 M97  CONST_46  H11  C11  C10  C4     0.00   0.0  0
 M97  CONST_47  HN1  N1   C5   C4   180.00   0.0  0
 M97  CONST_48  H13  C13  C14  C9   180.00   0.0  0
 M97  CONST_49  H12  C12  C11  C10  180.00   0.0  0
 M97  CONST_50  H22  C22  C23  C15  180.00   0.0  0
 M97  CONST_51  H23  C23  C15  C16    0.00   0.0  0
 M97  CONST_52  H16  C16  C17  C18  180.00   0.0  0
 M97  CONST_53  HN2  N2   C7   C1   180.00   0.0  0
 M97  Var_01    C7   N2   C8   C6     7.50  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 M97  chir_01  C1  C6  C4  C7  positiv
 M97  chir_02  C6  C1  C2  C8  positiv

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
 M97  plan-1  C1   0.020
 M97  plan-1  N1   0.020
 M97  plan-1  C4   0.020
 M97  plan-1  C5   0.020
 M97  plan-1  C9   0.020
 M97  plan-1  C10  0.020
 M97  plan-1  C11  0.020
 M97  plan-1  C12  0.020
 M97  plan-1  C13  0.020
 M97  plan-1  C14  0.020
 M97  plan-1  H5   0.020
 M97  plan-1  H11  0.020
 M97  plan-1  H12  0.020
 M97  plan-1  H13  0.020
 M97  plan-1  H14  0.020
 M97  plan-1  HN1  0.020
 M97  plan-2  C2   0.020
 M97  plan-2  C3   0.020
 M97  plan-2  N3   0.020
 M97  plan-2  C6   0.020
 M97  plan-2  C15  0.020
 M97  plan-2  C16  0.020
 M97  plan-2  C17  0.020
 M97  plan-2  C18  0.020
 M97  plan-2  C19  0.020
 M97  plan-2  C20  0.020
 M97  plan-2  C21  0.020
 M97  plan-2  C22  0.020
 M97  plan-2  C23  0.020
 M97  plan-2  H3   0.020
 M97  plan-2  H16  0.020
 M97  plan-2  H17  0.020
 M97  plan-2  H18  0.020
 M97  plan-2  H21  0.020
 M97  plan-2  H22  0.020
 M97  plan-2  H23  0.020
 M97  plan-3  C1   0.020
 M97  plan-3  O1   0.020
 M97  plan-3  N2   0.020
 M97  plan-3  C7   0.020
 M97  plan-3  C8   0.020
 M97  plan-3  HN2  0.020
 M97  plan-4  N2   0.020
 M97  plan-4  O2   0.020
 M97  plan-4  C6   0.020
 M97  plan-4  C8   0.020

