# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:11:14 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (6~{a}~{R},11~{b}~{S})-6~{a}-(1,4-dimethylpiperidin-4-yl)-7,11~{b}-dihydro-6~{H}-indolo[2,3-c]isoquinolin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(C)(CC1)[C@]23NC(=O)c4ccccc4[C@H]2c5ccccc5N3
#
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
 JJN  JJN  (6~{a}~{R},11~{b}~{S})-6~{a}-(1,4-dimethylpiperidin-4-yl)-7,11~{b}-dihydro-6~{H}-indolo[2,3-c]isoquinolin-5-one  ligand  51  26  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JJN
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
 JJN  C4   C  CR16  0  -0.350   0.5013   3.4944  -1.7953
 JJN  C5   C  CR56  0   0.376   0.2904   2.3487  -1.0428
 JJN  C6   C  CR56  0   0.085   1.2298   1.9233  -0.1070
 JJN  C8   C  C     0   0.342  -0.4131   0.2345  -0.4251
 JJN  C10  C  CR6   0   0.492   1.3284  -1.3469  -1.3864
 JJN  C13  C  CR66  0   0.213   1.7469  -0.3378   0.8521
 JJN  C15  C  CR16  0  -0.239   3.4666  -1.2221   2.2900
 JJN  C17  C  CR16  0  -0.276   3.1047  -2.1967   0.1273
 JJN  C20  C  CH2   0  -0.425  -2.3626   0.4535   1.1957
 JJN  C21  C  CH2   0  -0.281  -3.6893  -0.1139   1.6794
 JJN  C24  C  CH2   0  -0.443  -2.6423  -0.8761  -0.8817
 JJN  C1   C  CR16  0  -0.261   1.6806   4.2058  -1.5842
 JJN  C2   C  CR16  0  -0.277   2.6217   3.7864  -0.6526
 JJN  C3   C  CR16  0  -0.329   2.3939   2.6313   0.0976
 JJN  N7   N  NR15  0  -0.703  -0.7979   1.4960  -1.0426
 JJN  C9   C  C     0  -0.455   0.6903   0.6822   0.5663
 JJN  N11  N  NR16  0  -0.653   0.2037  -0.6095  -1.4520
 JJN  C12  C  CR66  0  -0.107   2.0786  -1.2875  -0.1084
 JJN  C14  C  CR16  0  -0.313   2.4448  -0.3135   2.0530
 JJN  C16  C  CR16  0  -0.258   3.7990  -2.1656   1.3257
 JJN  O18  O  O     0  -0.480   1.7050  -2.0361  -2.3260
 JJN  C19  C  CT    0  -0.081  -1.6362  -0.4838   0.2175
 JJN  N22  N  NT    0  -0.408  -4.5673  -0.4195   0.5682
 JJN  C23  C  CH2   0  -0.282  -3.9636  -1.3859  -0.3261
 JJN  C25  C  CH3   0  -0.680  -1.1656  -1.7413   0.9520
 JJN  H1   H  HCR6  0   0.257  -0.2226   3.8276  -2.5283
 JJN  H2   H  HCR6  0   0.265   4.0017  -1.1961   3.2302
 JJN  H3   H  HCR6  0   0.262   3.3531  -2.9317  -0.6264
 JJN  H4   H  HCH2  0   0.238  -2.5555   1.4118   0.7096
 JJN  H5   H  HCH2  0   0.234  -1.7428   0.6616   2.0717
 JJN  H6   H  HCH2  0   0.190  -3.5238  -0.9943   2.3262
 JJN  H7   H  HCH2  0   0.236  -4.1767   0.6346   2.3103
 JJN  H8   H  HCH2  0   0.227  -2.8669  -0.0128  -1.5156
 JJN  H9   H  HCH2  0   0.239  -2.2203  -1.6484  -1.5289
 JJN  H10  H  HCH3  0   0.230  -6.3235  -0.0954   1.6512
 JJN  H11  H  HCH3  0   0.230  -6.5243  -1.0304   0.1700
 JJN  H12  H  HCH3  0   0.189  -5.8266  -1.7945   1.6064
 JJN  H13  H  HCR6  0   0.253   1.8654   5.1007  -2.1649
 JJN  H14  H  HCR6  0   0.249   3.5337   4.3512  -0.5127
 JJN  H15  H  HCR6  0   0.248   3.1289   2.2961   0.8199
 JJN  H16  H  HNR5  0   0.380  -1.3563   1.4500  -1.8824
 JJN  H17  H  H     0   0.303   0.2210   0.9755   1.5109
 JJN  H18  H  HNR6  0   0.396  -0.3000  -0.6831  -2.3254
 JJN  H19  H  HCR6  0   0.261   2.1862   0.4193   2.8081
 JJN  H20  H  HCR6  0   0.263   4.5939  -2.8762   1.5088
 JJN  H22  H  HCH2  0   0.238  -4.6466  -1.5622  -1.1613
 JJN  H23  H  HCH2  0   0.192  -3.8240  -2.3658   0.1633
 JJN  H24  H  HCH3  0   0.242  -0.4779  -1.5080   1.7654
 JJN  H25  H  HCH3  0   0.250  -2.0066  -2.2719   1.3949
 JJN  H26  H  HCH3  0   0.237  -0.6689  -2.4431   0.2808
 JJN  C26  C  CH3   0  -0.516  -5.8649  -0.8606   1.0228

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
 JJN  C1   C2   aromatic  1.389  0.020  1.389
 JJN  C1   C4   aromatic  1.393  0.020  1.393
 JJN  C2   C3   aromatic  1.396  0.020  1.396
 JJN  C4   C5   aromatic  1.387  0.020  1.387
 JJN  C3   C6   aromatic  1.378  0.020  1.378
 JJN  C5   C6   aromatic  1.393  0.020  1.393
 JJN  C5   N7   single    1.383  0.020  1.383
 JJN  C6   C9   single    1.512  0.020  1.512
 JJN  N7   C8   single    1.456  0.020  1.456
 JJN  C9   C8   single    1.549  0.020  1.549
 JJN  C9   C13  single    1.496  0.020  1.496
 JJN  C8   N11  single    1.465  0.020  1.465
 JJN  C8   C19  single    1.557  0.020  1.557
 JJN  N11  C10  single    1.347  0.020  1.347
 JJN  C10  O18  double    1.225  0.020  1.225
 JJN  C10  C12  single    1.483  0.020  1.483
 JJN  C13  C12  aromatic  1.391  0.020  1.391
 JJN  C13  C14  aromatic  1.389  0.020  1.389
 JJN  C25  C19  single    1.530  0.020  1.530
 JJN  C12  C17  aromatic  1.391  0.020  1.391
 JJN  C24  C19  single    1.541  0.020  1.541
 JJN  C24  C23  single    1.521  0.020  1.521
 JJN  C19  C20  single    1.537  0.020  1.537
 JJN  C14  C15  aromatic  1.388  0.020  1.388
 JJN  C17  C16  aromatic  1.385  0.020  1.385
 JJN  C15  C16  aromatic  1.389  0.020  1.389
 JJN  C23  N22  single    1.448  0.020  1.448
 JJN  C20  C21  single    1.522  0.020  1.522
 JJN  N22  C21  single    1.449  0.020  1.449
 JJN  N22  C26  single    1.444  0.020  1.444
 JJN  C4   H1   single    0.930  0.020  1.080
 JJN  C15  H2   single    0.930  0.020  1.080
 JJN  C17  H3   single    0.930  0.020  1.080
 JJN  C20  H4   single    0.970  0.020  1.090
 JJN  C20  H5   single    0.970  0.020  1.090
 JJN  C21  H6   single    0.970  0.020  1.090
 JJN  C21  H7   single    0.970  0.020  1.090
 JJN  C24  H8   single    0.970  0.020  1.090
 JJN  C24  H9   single    0.970  0.020  1.090
 JJN  C26  H10  single    0.970  0.020  1.090
 JJN  C26  H11  single    0.970  0.020  1.090
 JJN  C26  H12  single    0.970  0.020  1.090
 JJN  C1   H13  single    0.930  0.020  1.080
 JJN  C2   H14  single    0.930  0.020  1.080
 JJN  C3   H15  single    0.930  0.020  1.080
 JJN  N7   H16  single    0.890  0.020  1.040
 JJN  C9   H17  single    0.970  0.020  1.090
 JJN  N11  H18  single    0.860  0.020  1.020
 JJN  C14  H19  single    0.930  0.020  1.080
 JJN  C16  H20  single    0.930  0.020  1.080
 JJN  C23  H22  single    0.970  0.020  1.090
 JJN  C23  H23  single    0.970  0.020  1.090
 JJN  C25  H24  single    0.970  0.020  1.090
 JJN  C25  H25  single    0.970  0.020  1.090
 JJN  C25  H26  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
 JJN  H1   C4   C1   120.75  3.000
 JJN  H1   C4   C5   121.33  3.000
 JJN  C1   C4   C5   117.92  3.000
 JJN  N7   C5   C6   110.04  3.000
 JJN  N7   C5   C4   128.99  3.000
 JJN  C6   C5   C4   120.96  3.000
 JJN  C9   C6   C3   131.10  3.000
 JJN  C9   C6   C5   108.02  3.000
 JJN  C3   C6   C5   120.85  3.000
 JJN  C19  C8   N11  110.74  3.000
 JJN  C19  C8   C9   115.38  3.000
 JJN  N11  C8   C9   108.36  3.000
 JJN  C19  C8   N7   111.53  3.000
 JJN  N11  C8   N7   108.24  3.000
 JJN  C9   C8   N7   102.07  3.000
 JJN  O18  C10  C12  121.88  3.000
 JJN  C12  C10  N11  116.27  3.000
 JJN  O18  C10  N11  121.85  3.000
 JJN  C14  C13  C12  119.28  3.000
 JJN  C14  C13  C9   120.54  3.000
 JJN  C12  C13  C9   120.13  3.000
 JJN  H2   C15  C16  120.06  3.000
 JJN  H2   C15  C14  119.79  3.000
 JJN  C16  C15  C14  120.15  3.000
 JJN  H3   C17  C16  120.20  3.000
 JJN  H3   C17  C12  119.70  3.000
 JJN  C16  C17  C12  120.11  3.000
 JJN  H5   C20  H4   106.86  3.000
 JJN  H5   C20  C19  110.99  3.000
 JJN  H4   C20  C19  109.60  3.000
 JJN  H5   C20  C21  108.09  3.000
 JJN  H4   C20  C21  108.34  3.000
 JJN  C19  C20  C21  112.76  3.000
 JJN  H7   C21  H6   105.93  3.000
 JJN  H7   C21  N22  108.47  3.000
 JJN  H6   C21  N22  111.82  3.000
 JJN  H7   C21  C20  108.47  3.000
 JJN  H6   C21  C20  110.64  3.000
 JJN  N22  C21  C20  111.30  3.000
 JJN  H9   C24  H8   107.08  3.000
 JJN  H9   C24  C23  108.36  3.000
 JJN  H8   C24  C23  107.32  3.000
 JJN  H9   C24  C19  110.51  3.000
 JJN  H8   C24  C19  110.27  3.000
 JJN  C23  C24  C19  113.07  3.000
 JJN  H13  C1   C2   119.58  3.000
 JJN  H13  C1   C4   119.02  3.000
 JJN  C2   C1   C4   121.39  3.000
 JJN  H14  C2   C3   120.00  3.000
 JJN  H14  C2   C1   120.02  3.000
 JJN  C3   C2   C1   119.98  3.000
 JJN  H15  C3   C2   120.23  3.000
 JJN  H15  C3   C6   120.88  3.000
 JJN  C2   C3   C6   118.90  3.000
 JJN  H16  N7   C8   117.35  3.000
 JJN  H16  N7   C5   117.61  3.000
 JJN  C8   N7   C5   109.04  3.000
 JJN  H17  C9   C13  108.69  3.000
 JJN  H17  C9   C8   108.92  3.000
 JJN  C13  C9   C8   115.35  3.000
 JJN  H17  C9   C6   108.50  3.000
 JJN  C13  C9   C6   113.13  3.000
 JJN  C8   C9   C6   101.92  3.000
 JJN  H18  N11  C10  114.73  3.000
 JJN  H18  N11  C8   115.96  3.000
 JJN  C10  N11  C8   129.26  3.000
 JJN  C17  C12  C13  120.34  3.000
 JJN  C17  C12  C10  119.54  3.000
 JJN  C13  C12  C10  120.12  3.000
 JJN  H19  C14  C15  119.97  3.000
 JJN  H19  C14  C13  119.62  3.000
 JJN  C15  C14  C13  120.41  3.000
 JJN  H20  C16  C17  119.99  3.000
 JJN  H20  C16  C15  120.29  3.000
 JJN  C17  C16  C15  119.72  3.000
 JJN  C25  C19  C24  109.50  3.000
 JJN  C24  C19  C20  107.50  3.000
 JJN  C25  C19  C20  109.93  3.000
 JJN  C20  C19  C8   110.64  3.000
 JJN  C24  C19  C8   109.63  3.000
 JJN  C25  C19  C8   109.60  3.000
 JJN  C23  N22  C26  111.42  3.000
 JJN  C26  N22  C21  111.56  3.000
 JJN  C23  N22  C21  111.20  3.000
 JJN  H23  C23  H22  105.93  3.000
 JJN  H23  C23  N22  111.79  3.000
 JJN  H22  C23  N22  108.60  3.000
 JJN  H23  C23  C24  110.45  3.000
 JJN  H22  C23  C24  108.52  3.000
 JJN  N22  C23  C24  111.34  3.000
 JJN  H26  C25  H25  106.78  3.000
 JJN  H26  C25  H24  108.03  3.000
 JJN  H25  C25  H24  106.74  3.000
 JJN  H26  C25  C19  111.93  3.000
 JJN  H25  C25  C19  110.99  3.000
 JJN  H24  C25  C19  112.09  3.000
 JJN  H12  C26  H11  107.64  3.000
 JJN  H12  C26  H10  107.69  3.000
 JJN  H11  C26  H10  107.77  3.000
 JJN  H12  C26  N22  113.23  3.000
 JJN  H11  C26  N22  110.15  3.000
 JJN  H10  C26  N22  110.17  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
 JJN  CONST_01  C3   C2   C1   C4     0.00   0.0  0
 JJN  CONST_02  C3   C6   C5   C4     0.00   0.0  0
 JJN  CONST_03  C2   C1   C4   C5     0.00   0.0  0
 JJN  CONST_04  C2   C3   C6   C5     0.00   0.0  0
 JJN  CONST_05  C1   C2   C3   C6     0.00   0.0  0
 JJN  CONST_06  C1   C4   C5   C6     0.00   0.0  0
 JJN  CONST_07  C16  C17  C12  C13    0.00   0.0  0
 JJN  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 JJN  CONST_09  C12  C13  C14  C15    0.00   0.0  0
 JJN  CONST_10  C12  C17  C16  C15    0.00   0.0  0
 JJN  CONST_11  C14  C13  C12  C17    0.00   0.0  0
 JJN  CONST_12  C14  C15  C16  C17    0.00   0.0  0
 JJN  CONST_13  C12  C10  N11  C8     0.00   0.0  0
 JJN  CONST_14  O18  C10  N11  C8   180.00   0.0  0
 JJN  CONST_15  H14  C2   C1   C4   180.00   0.0  0
 JJN  CONST_16  H13  C1   C4   C5   180.00   0.0  0
 JJN  CONST_17  H15  C3   C6   C5   180.00   0.0  0
 JJN  CONST_18  H1   C4   C5   C6   180.00   0.0  0
 JJN  CONST_19  H3   C17  C12  C10    0.00   0.0  0
 JJN  CONST_20  H2   C15  C14  C13  180.00   0.0  0
 JJN  CONST_21  H19  C14  C13  C9     0.00   0.0  0
 JJN  CONST_22  H20  C16  C17  C12  180.00   0.0  0
 JJN  CONST_23  H18  N11  C10  C12  180.00   0.0  0
 JJN  Var_01    C8   N7   C5   C4   162.38  30.0  1
 JJN  Var_02    N11  C10  C12  C13  -10.94  30.0  1
 JJN  Var_03    C23  N22  C21  C20   59.40  30.0  1
 JJN  Var_04    C24  C23  N22  C21  -58.90  30.0  1
 JJN  Var_05    N22  C23  C24  C19   55.87  30.0  1
 JJN  Var_06    N22  C21  C20  C19  -56.77  30.0  1
 JJN  Var_07    H10  C26  N22  C21   58.07  30.0  3

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
 JJN  chir_01  C8   C9  N11  C19  negativ
 JJN  chir_02  C9   C6  C8   C13  negativ
 JJN  chir_03  C19  C8  C24  C20  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
 JJN  plan-1  C8   0.020
 JJN  plan-1  C10  0.020
 JJN  plan-1  N11  0.020
 JJN  plan-1  C12  0.020
 JJN  plan-1  O18  0.020
 JJN  plan-1  H18  0.020
 JJN  plan-2  C10  0.020
 JJN  plan-2  C13  0.020
 JJN  plan-2  C15  0.020
 JJN  plan-2  C17  0.020
 JJN  plan-2  C9   0.020
 JJN  plan-2  C12  0.020
 JJN  plan-2  C14  0.020
 JJN  plan-2  C16  0.020
 JJN  plan-2  H2   0.020
 JJN  plan-2  H3   0.020
 JJN  plan-2  H19  0.020
 JJN  plan-2  H20  0.020
 JJN  plan-3  C4   0.020
 JJN  plan-3  C5   0.020
 JJN  plan-3  C6   0.020
 JJN  plan-3  C1   0.020
 JJN  plan-3  C2   0.020
 JJN  plan-3  C3   0.020
 JJN  plan-3  N7   0.020
 JJN  plan-3  C9   0.020
 JJN  plan-3  H1   0.020
 JJN  plan-3  H13  0.020
 JJN  plan-3  H14  0.020
 JJN  plan-3  H15  0.020

