# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:42:17 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (3~{S})-3-[2-[(2~{R})-pyrrolidin-2-yl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@@H](c2ccccc12)c3c([nH]c4ccccc34)[C@H]5CCCN5
#
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
 F0N  F0N  (3~{S})-3-[2-[(2~{R})-pyrrolidin-2-yl]-1~{H}-indol-3-yl]-2,3-dihydroisoindol-1-one  ligand  43  24  .  2021-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F0N
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
 F0N  N1   N  NR15  0  -0.760  -2.1181   1.3566   0.5632
 F0N  C4   C  CR16  0  -0.300   4.0278  -1.5692   0.0509
 F0N  C5   C  CR16  0  -0.261   4.0216  -2.0006   1.3702
 F0N  C6   C  CR16  0  -0.244   2.8241  -2.0951   2.0801
 F0N  C7   C  CR16  0  -0.314   1.6089  -1.7634   1.4913
 F0N  C8   C  CR5   0   0.036  -0.3638   0.1795  -0.1519
 F0N  C10  C  CR56  0   0.327  -1.0358   2.1720   0.7308
 F0N  C13  C  CR16  0  -0.265   1.4379   3.3641   0.8663
 F0N  C15  C  CR56  0   0.062   0.1000   1.4620   0.2918
 F0N  C17  C  CH2   0  -0.442  -3.6420  -1.3063   0.8916
 F0N  N    N  NR15  0  -0.647   1.1846  -0.5505  -1.9242
 F0N  C    C  CR5   0   0.507   2.5214  -0.7423  -1.8893
 F0N  O    O  O     0  -0.475   3.3160  -0.5382  -2.7920
 F0N  C1   C  CR15  0  -0.247   0.4762  -0.9202  -0.7096
 F0N  C11  C  CR16  0  -0.307  -0.9582   3.4682   1.2360
 F0N  C12  C  CR16  0  -0.285   0.2924   4.0523   1.2969
 F0N  C14  C  CR16  0  -0.368   1.3541   2.0794   0.3655
 F0N  C16  C  CH1   0  -0.223  -2.7137  -0.9127  -0.2719
 F0N  C18  C  CH2   0  -0.475  -4.8286  -1.9741   0.1818
 F0N  C19  C  CH2   0  -0.324  -4.6614  -1.5760  -1.3066
 F0N  C2   C  CR56  0   0.146   1.6222  -1.3380   0.1760
 F0N  C3   C  CR56  0  -0.087   2.8114  -1.2432  -0.5257
 F0N  C9   C  CR5   0   0.350  -1.7231   0.1583   0.0308
 F0N  N2   N  NH1   0  -0.569  -3.6039  -0.5697  -1.3820
 F0N  H1   H  HNR5  0   0.406  -3.0626   1.6039   0.8088
 F0N  H3   H  HCR6  0   0.264   4.9513  -2.2627   1.8567
 F0N  H4   H  HCR6  0   0.266   2.8438  -2.4300   3.1091
 F0N  H5   H  HCR6  0   0.254   0.6853  -1.8329   2.0524
 F0N  H6   H  HCR6  0   0.248   2.4021   3.8516   0.9314
 F0N  H7   H  HCH2  0   0.250  -3.1464  -1.9570   1.6124
 F0N  H8   H  HCH2  0   0.226  -3.9733  -0.4163   1.4321
 F0N  H9   H  HNR5  0   0.400   0.7004  -0.2274  -2.7468
 F0N  H10  H  HCR5  0   0.293  -0.1561  -1.7926  -0.9073
 F0N  H11  H  HCR6  0   0.260  -1.8434   3.9962   1.5676
 F0N  H12  H  HCR6  0   0.251   0.3917   5.0578   1.6848
 F0N  H13  H  HCR6  0   0.238   2.2506   1.5664   0.0432
 F0N  H14  H  HCH1  0   0.258  -2.1593  -1.8067  -0.5738
 F0N  H15  H  HCH2  0   0.237  -4.8042  -3.0580   0.2981
 F0N  H16  H  HCH2  0   0.238  -5.7778  -1.6273   0.5898
 F0N  H17  H  HCH2  0   0.228  -4.3602  -2.4487  -1.8908
 F0N  H18  H  HCH2  0   0.242  -5.5769  -1.1890  -1.7525
 F0N  H19  H  HNH1  0   0.339  -4.0146   0.3406  -1.2031
 F0N  H2   H  HCR6  0   0.263   4.9524  -1.4861  -0.5061

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
 F0N  C4   C5   aromatic  1.388  0.020  1.388
 F0N  C4   C3   aromatic  1.385  0.020  1.385
 F0N  C5   C6   aromatic  1.395  0.020  1.395
 F0N  O    C    double    1.220  0.020  1.220
 F0N  C3   C    single    1.481  0.020  1.481
 F0N  C3   C2   aromatic  1.384  0.020  1.384
 F0N  C    N    single    1.351  0.020  1.351
 F0N  C6   C7   aromatic  1.390  0.020  1.390
 F0N  C2   C7   aromatic  1.382  0.020  1.382
 F0N  C2   C1   single    1.507  0.020  1.507
 F0N  N    C1   single    1.454  0.020  1.454
 F0N  C1   C8   single    1.492  0.020  1.492
 F0N  C14  C13  aromatic  1.381  0.020  1.381
 F0N  C14  C15  aromatic  1.400  0.020  1.400
 F0N  C13  C12  aromatic  1.404  0.020  1.404
 F0N  C8   C15  aromatic  1.434  0.020  1.434
 F0N  C8   C9   aromatic  1.372  0.020  1.372
 F0N  C15  C10  aromatic  1.410  0.020  1.410
 F0N  C12  C11  aromatic  1.382  0.020  1.382
 F0N  C9   C16  single    1.490  0.020  1.490
 F0N  C9   N1   aromatic  1.369  0.020  1.369
 F0N  C10  C11  aromatic  1.393  0.020  1.393
 F0N  C10  N1   aromatic  1.365  0.020  1.365
 F0N  C16  N2   single    1.464  0.020  1.464
 F0N  C16  C17  single    1.540  0.020  1.540
 F0N  N2   C19  single    1.462  0.020  1.462
 F0N  C17  C18  single    1.535  0.020  1.535
 F0N  C19  C18  single    1.550  0.020  1.550
 F0N  N1   H1   single    0.860  0.020  1.020
 F0N  C4   H2   single    0.930  0.020  1.080
 F0N  C5   H3   single    0.930  0.020  1.080
 F0N  C6   H4   single    0.930  0.020  1.080
 F0N  C7   H5   single    0.930  0.020  1.080
 F0N  C13  H6   single    0.930  0.020  1.080
 F0N  C17  H7   single    0.970  0.020  1.090
 F0N  C17  H8   single    0.970  0.020  1.090
 F0N  N    H9   single    0.860  0.020  1.020
 F0N  C1   H10  single    0.970  0.020  1.090
 F0N  C11  H11  single    0.930  0.020  1.080
 F0N  C12  H12  single    0.930  0.020  1.080
 F0N  C14  H13  single    0.930  0.020  1.080
 F0N  C16  H14  single    0.970  0.020  1.090
 F0N  C18  H15  single    0.970  0.020  1.090
 F0N  C18  H16  single    0.970  0.020  1.090
 F0N  C19  H17  single    0.970  0.020  1.090
 F0N  C19  H18  single    0.970  0.020  1.090
 F0N  N2   H19  single    0.890  0.020  1.040

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
 F0N  H1   N1   C9   125.48  3.000
 F0N  H1   N1   C10  124.54  3.000
 F0N  C9   N1   C10  109.98  3.000
 F0N  H2   C4   C3   121.19  3.000
 F0N  H2   C4   C5   121.11  3.000
 F0N  C3   C4   C5   117.71  3.000
 F0N  H3   C5   C6   119.50  3.000
 F0N  H3   C5   C4   119.94  3.000
 F0N  C6   C5   C4   120.56  3.000
 F0N  H4   C6   C7   119.49  3.000
 F0N  H4   C6   C5   119.28  3.000
 F0N  C7   C6   C5   121.23  3.000
 F0N  H5   C7   C2   121.40  3.000
 F0N  H5   C7   C6   120.71  3.000
 F0N  C2   C7   C6   117.89  3.000
 F0N  C9   C8   C1   126.61  3.000
 F0N  C9   C8   C15  107.04  3.000
 F0N  C1   C8   C15  126.35  3.000
 F0N  C11  C10  C15  122.46  3.000
 F0N  C11  C10  N1   130.11  3.000
 F0N  C15  C10  N1   107.43  3.000
 F0N  H6   C13  C14  119.65  3.000
 F0N  H6   C13  C12  119.18  3.000
 F0N  C14  C13  C12  121.17  3.000
 F0N  C14  C15  C10  118.90  3.000
 F0N  C10  C15  C8   106.63  3.000
 F0N  C14  C15  C8   134.46  3.000
 F0N  H8   C17  H7   107.27  3.000
 F0N  H8   C17  C18  110.40  3.000
 F0N  H7   C17  C18  113.41  3.000
 F0N  H8   C17  C16  110.39  3.000
 F0N  H7   C17  C16  112.21  3.000
 F0N  C18  C17  C16  103.17  3.000
 F0N  H9   N    C1   121.96  3.000
 F0N  H9   N    C    122.82  3.000
 F0N  C1   N    C    115.12  3.000
 F0N  C3   C    O    127.61  3.000
 F0N  C3   C    N    105.39  3.000
 F0N  O    C    N    127.00  3.000
 F0N  H10  C1   C2   108.91  3.000
 F0N  H10  C1   N    109.45  3.000
 F0N  C2   C1   N    101.00  3.000
 F0N  H10  C1   C8   109.24  3.000
 F0N  N    C1   C8   113.53  3.000
 F0N  C2   C1   C8   114.38  3.000
 F0N  H11  C11  C12  121.36  3.000
 F0N  H11  C11  C10  121.28  3.000
 F0N  C12  C11  C10  117.37  3.000
 F0N  H12  C12  C11  119.45  3.000
 F0N  H12  C12  C13  119.37  3.000
 F0N  C11  C12  C13  121.18  3.000
 F0N  H13  C14  C15  121.17  3.000
 F0N  H13  C14  C13  119.91  3.000
 F0N  C15  C14  C13  118.92  3.000
 F0N  H14  C16  N2   106.88  3.000
 F0N  H14  C16  C9   107.85  3.000
 F0N  N2   C16  C9   112.95  3.000
 F0N  H14  C16  C17  107.76  3.000
 F0N  N2   C16  C17  105.45  3.000
 F0N  C9   C16  C17  115.54  3.000
 F0N  H16  C18  H15  107.21  3.000
 F0N  H16  C18  C19  111.82  3.000
 F0N  H15  C18  C19  110.81  3.000
 F0N  H16  C18  C17  111.20  3.000
 F0N  H15  C18  C17  111.46  3.000
 F0N  C19  C18  C17  104.41  3.000
 F0N  H18  C19  H17  107.25  3.000
 F0N  H18  C19  N2   110.02  3.000
 F0N  H17  C19  N2   108.84  3.000
 F0N  H18  C19  C18  113.19  3.000
 F0N  H17  C19  C18  109.76  3.000
 F0N  N2   C19  C18  107.72  3.000
 F0N  C3   C2   C1   109.66  3.000
 F0N  C1   C2   C7   129.56  3.000
 F0N  C3   C2   C7   120.78  3.000
 F0N  C2   C3   C    108.76  3.000
 F0N  C2   C3   C4   121.83  3.000
 F0N  C    C3   C4   129.40  3.000
 F0N  C16  C9   C8   130.00  3.000
 F0N  C16  C9   N1   121.08  3.000
 F0N  C8   C9   N1   108.91  3.000
 F0N  H19  N2   C19  108.40  3.000
 F0N  H19  N2   C16  108.83  3.000
 F0N  C19  N2   C16  103.86  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
 F0N  CONST_01  C15  C8   C9   N1     0.00   0.0  0
 F0N  CONST_02  C14  C15  C10  N1   180.00   0.0  0
 F0N  CONST_03  C8   C15  C10  N1     0.00   0.0  0
 F0N  CONST_04  C12  C11  C10  N1   180.00   0.0  0
 F0N  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 F0N  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 F0N  CONST_07  C2   C3   C4   C5     0.00   0.0  0
 F0N  CONST_08  C2   C7   C6   C5     0.00   0.0  0
 F0N  CONST_09  C3   C4   C5   C6     0.00   0.0  0
 F0N  CONST_10  C3   C2   C7   C6     0.00   0.0  0
 F0N  CONST_11  C13  C14  C15  C8   180.00   0.0  0
 F0N  CONST_12  C11  C10  C15  C8   180.00   0.0  0
 F0N  CONST_13  C10  N1   C9   C8     0.00   0.0  0
 F0N  CONST_14  C13  C14  C15  C10    0.00   0.0  0
 F0N  CONST_15  C9   C8   C15  C10    0.00   0.0  0
 F0N  CONST_16  C13  C12  C11  C10    0.00   0.0  0
 F0N  CONST_17  C12  C13  C14  C15    0.00   0.0  0
 F0N  CONST_18  C12  C11  C10  C15    0.00   0.0  0
 F0N  CONST_19  C9   N1   C10  C15    0.00   0.0  0
 F0N  CONST_20  C14  C13  C12  C11    0.00   0.0  0
 F0N  CONST_21  C14  C15  C10  C11    0.00   0.0  0
 F0N  CONST_22  C9   N1   C10  C11  180.00   0.0  0
 F0N  CONST_23  C9   C8   C15  C14  180.00   0.0  0
 F0N  CONST_24  C1   C8   C9   N1   180.00   0.0  0
 F0N  CONST_25  C1   C8   C15  C10  180.00   0.0  0
 F0N  CONST_26  C16  C9   N1   C10  180.00   0.0  0
 F0N  CONST_27  C16  C9   C8   C15  180.00   0.0  0
 F0N  CONST_28  C14  C15  C8   C1     0.00   0.0  0
 F0N  CONST_29  C16  C9   C8   C1     0.00   0.0  0
 F0N  CONST_30  C3   C    N    C1     0.00   0.0  0
 F0N  CONST_31  C1   N    C    O    180.00   0.0  0
 F0N  CONST_32  H11  C11  C10  N1     0.00   0.0  0
 F0N  CONST_33  H4   C6   C5   C4   180.00   0.0  0
 F0N  CONST_34  H5   C7   C6   C5   180.00   0.0  0
 F0N  CONST_35  H2   C4   C5   C6   180.00   0.0  0
 F0N  CONST_36  H3   C5   C6   C7   180.00   0.0  0
 F0N  CONST_37  H13  C14  C15  C8     0.00   0.0  0
 F0N  CONST_38  H1   N1   C9   C8   180.00   0.0  0
 F0N  CONST_39  H12  C12  C11  C10  180.00   0.0  0
 F0N  CONST_40  H6   C13  C14  C15  180.00   0.0  0
 F0N  CONST_41  H9   N    C    C3   180.00   0.0  0
 F0N  Var_01    N2   C19  C18  C17   -9.32  30.0  1
 F0N  Var_02    C18  C19  N2   C16   30.61  30.0  1
 F0N  Var_03    C19  C18  C17  C16  -14.46  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
 F0N  chir_01  C1   C2  N   C8   positiv
 F0N  chir_02  C16  N2  C9  C17  negativ

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
 F0N  plan-1  N1   0.020
 F0N  plan-1  C8   0.020
 F0N  plan-1  C10  0.020
 F0N  plan-1  C13  0.020
 F0N  plan-1  C15  0.020
 F0N  plan-1  C1   0.020
 F0N  plan-1  C11  0.020
 F0N  plan-1  C12  0.020
 F0N  plan-1  C14  0.020
 F0N  plan-1  C16  0.020
 F0N  plan-1  C9   0.020
 F0N  plan-1  H1   0.020
 F0N  plan-1  H6   0.020
 F0N  plan-1  H11  0.020
 F0N  plan-1  H12  0.020
 F0N  plan-1  H13  0.020
 F0N  plan-2  C4   0.020
 F0N  plan-2  C5   0.020
 F0N  plan-2  C6   0.020
 F0N  plan-2  C7   0.020
 F0N  plan-2  N    0.020
 F0N  plan-2  C    0.020
 F0N  plan-2  O    0.020
 F0N  plan-2  C1   0.020
 F0N  plan-2  C2   0.020
 F0N  plan-2  C3   0.020
 F0N  plan-2  H3   0.020
 F0N  plan-2  H4   0.020
 F0N  plan-2  H5   0.020
 F0N  plan-2  H9   0.020
 F0N  plan-2  H2   0.020

