# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 01:28:02 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 5-{[(3R)-1-methyl-5-oxopyrrolidin-3-yl]methyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C[C@@H](Cn2c3CCNC(=O)c3c4ccccc24)CC1=O
#
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
 Y18  Y18  5-{[(3R)-1-methyl-5-oxopyrrolidin-3-yl]methyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one  ligand  41  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y18
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
 Y18  C02  C  C     0   0.452  -3.4699  -0.9109  -0.7285
 Y18  C04  C  CH2   0  -0.281  -2.5965  -2.9777   0.2979
 Y18  C05  C  CH2   0  -0.532  -1.1779  -2.4210   0.3438
 Y18  C06  C  CR5   0  -0.199  -2.3537  -0.2443  -0.0738
 Y18  C07  C  CR5   0   0.378  -1.2749  -0.9407   0.4114
 Y18  C10  C  CH1   0  -0.301   1.9523  -0.7762   0.3145
 Y18  C11  C  CH2   0  -0.229   3.3204  -1.1896   0.8639
 Y18  C14  C  C     0   0.533   3.7154   0.1055  -1.0458
 Y18  C15  C  CH2   0  -0.577   2.2879   0.3805  -0.6222
 Y18  C17  C  CR56  0   0.343  -0.8086   1.2119   0.7243
 Y18  C18  C  CR56  0   0.089  -2.0780   1.1463   0.1112
 Y18  C19  C  CR16  0  -0.374  -2.7662   2.3296  -0.1688
 Y18  C20  C  CR16  0  -0.263  -2.1812   3.5352   0.1715
 Y18  C21  C  CR16  0  -0.281  -0.9232   3.5813   0.7875
 Y18  C22  C  CR16  0  -0.310  -0.2206   2.4242   1.0731
 Y18  N03  N  NH1   0  -0.649  -3.4205  -2.2663  -0.6637
 Y18  N08  N  NR5   0  -0.591  -0.3435  -0.0795   0.8917
 Y18  N12  N  NT    0  -0.452   4.2307  -0.7958  -0.1881
 Y18  O01  O  O     0  -0.494  -4.3573  -0.3094  -1.3269
 Y18  O16  O  O     0  -0.498   4.3065   0.6276  -1.9774
 Y18  H1   H  HCH2  0   0.266  -2.5714  -4.0272   0.0117
 Y18  H2   H  HCH2  0   0.241  -3.0344  -2.9225   1.3004
 Y18  H3   H  HCH2  0   0.277  -0.6583  -2.8438   1.2050
 Y18  H4   H  HCH2  0   0.276  -0.6191  -2.7189  -0.5494
 Y18  H7   H  HCH1  0   0.278   1.5659  -1.6064  -0.2835
 Y18  H8   H  HCH2  0   0.239   3.5636  -0.6734   1.8011
 Y18  H9   H  HCH2  0   0.257   3.3845  -2.2622   1.0538
 Y18  H10  H  HCH3  0   0.255   6.1280  -0.7971  -1.0267
 Y18  H11  H  HCH3  0   0.240   6.1052  -0.8685   0.7415
 Y18  H12  H  HCH3  0   0.244   5.6800  -2.2994  -0.2069
 Y18  H13  H  HCH2  0   0.281   1.6227   0.4677  -1.4799
 Y18  H14  H  HCH2  0   0.273   2.2780   1.3431  -0.1001
 Y18  H15  H  HCR6  0   0.244  -3.7370   2.2991  -0.6442
 Y18  H16  H  HCR6  0   0.250  -2.7011   4.4610  -0.0381
 Y18  H17  H  HCR6  0   0.254  -0.4899   4.5393   1.0427
 Y18  H18  H  HCR6  0   0.264   0.7490   2.4767   1.5516
 Y18  H19  H  HNH1  0   0.395  -4.2232  -2.7575  -1.0270
 Y18  C09  C  CH2   0  -0.343   0.9538  -0.4542   1.4146
 Y18  C13  C  CH3   0  -0.517   5.6070  -1.2117  -0.1678
 Y18  H5   H  HCH2  0   0.283   0.8298  -1.3121   2.0784
 Y18  H6   H  HCH2  0   0.280   1.3223   0.3623   2.0358

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
 Y18  C13  N12  single    1.438  0.020  1.438
 Y18  O16  C14  double    1.221  0.020  1.221
 Y18  N12  C14  single    1.347  0.020  1.347
 Y18  N12  C11  single    1.446  0.020  1.446
 Y18  C14  C15  single    1.514  0.020  1.514
 Y18  C11  C10  single    1.531  0.020  1.531
 Y18  C10  C15  single    1.526  0.020  1.526
 Y18  C10  C09  single    1.520  0.020  1.520
 Y18  C09  N08  single    1.448  0.020  1.448
 Y18  N08  C17  aromatic  1.383  0.020  1.383
 Y18  N08  C07  aromatic  1.356  0.020  1.356
 Y18  C22  C17  aromatic  1.392  0.020  1.392
 Y18  C22  C21  aromatic  1.384  0.020  1.384
 Y18  C17  C18  aromatic  1.411  0.020  1.411
 Y18  C05  C07  single    1.485  0.020  1.485
 Y18  C05  C04  single    1.525  0.020  1.525
 Y18  C07  C06  aromatic  1.373  0.020  1.373
 Y18  C21  C20  aromatic  1.402  0.020  1.402
 Y18  C04  N03  single    1.453  0.020  1.453
 Y18  C18  C06  aromatic  1.430  0.020  1.430
 Y18  C18  C19  aromatic  1.397  0.020  1.397
 Y18  C06  C02  single    1.456  0.020  1.456
 Y18  C20  C19  aromatic  1.383  0.020  1.383
 Y18  N03  C02  single    1.358  0.020  1.358
 Y18  C02  O01  double    1.228  0.020  1.228
 Y18  C04  H1   single    0.970  0.020  1.090
 Y18  C04  H2   single    0.970  0.020  1.090
 Y18  C05  H3   single    0.970  0.020  1.090
 Y18  C05  H4   single    0.970  0.020  1.090
 Y18  C09  H5   single    0.970  0.020  1.090
 Y18  C09  H6   single    0.970  0.020  1.090
 Y18  C10  H7   single    0.970  0.020  1.090
 Y18  C11  H8   single    0.970  0.020  1.090
 Y18  C11  H9   single    0.970  0.020  1.090
 Y18  C13  H10  single    0.970  0.020  1.090
 Y18  C13  H11  single    0.970  0.020  1.090
 Y18  C13  H12  single    0.970  0.020  1.090
 Y18  C15  H13  single    0.970  0.020  1.090
 Y18  C15  H14  single    0.970  0.020  1.090
 Y18  C19  H15  single    0.930  0.020  1.080
 Y18  C20  H16  single    0.930  0.020  1.080
 Y18  C21  H17  single    0.930  0.020  1.080
 Y18  C22  H18  single    0.930  0.020  1.080
 Y18  N03  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
 Y18  O01  C02  N03  122.59  3.000
 Y18  O01  C02  C06  123.31  3.000
 Y18  N03  C02  C06  114.06  3.000
 Y18  H2   C04  H1   107.37  3.000
 Y18  H2   C04  N03  110.75  3.000
 Y18  H1   C04  N03  108.14  3.000
 Y18  H2   C04  C05  109.03  3.000
 Y18  H1   C04  C05  109.79  3.000
 Y18  N03  C04  C05  111.65  3.000
 Y18  H4   C05  H3   107.18  3.000
 Y18  H4   C05  C07  109.98  3.000
 Y18  H3   C05  C07  112.42  3.000
 Y18  H4   C05  C04  110.55  3.000
 Y18  H3   C05  C04  108.98  3.000
 Y18  C07  C05  C04  107.74  3.000
 Y18  C18  C06  C07  107.23  3.000
 Y18  C18  C06  C02  130.65  3.000
 Y18  C07  C06  C02  121.96  3.000
 Y18  N08  C07  C06  110.04  3.000
 Y18  C06  C07  C05  122.75  3.000
 Y18  N08  C07  C05  127.17  3.000
 Y18  H7   C10  C15  108.51  3.000
 Y18  H7   C10  C11  107.87  3.000
 Y18  C15  C10  C11  103.20  3.000
 Y18  H7   C10  C09  108.93  3.000
 Y18  C15  C10  C09  115.35  3.000
 Y18  C11  C10  C09  112.61  3.000
 Y18  H9   C11  H8   107.50  3.000
 Y18  H9   C11  N12  110.94  3.000
 Y18  H8   C11  N12  110.72  3.000
 Y18  H9   C11  C10  112.35  3.000
 Y18  H8   C11  C10  112.18  3.000
 Y18  N12  C11  C10  103.18  3.000
 Y18  O16  C14  N12  125.95  3.000
 Y18  N12  C14  C15  107.71  3.000
 Y18  O16  C14  C15  126.32  3.000
 Y18  H14  C15  H13  107.44  3.000
 Y18  H14  C15  C14  107.55  3.000
 Y18  H13  C15  C14  111.72  3.000
 Y18  H14  C15  C10  111.82  3.000
 Y18  H13  C15  C10  114.20  3.000
 Y18  C14  C15  C10  103.97  3.000
 Y18  N08  C17  C22  129.87  3.000
 Y18  C22  C17  C18  121.96  3.000
 Y18  N08  C17  C18  108.17  3.000
 Y18  C19  C18  C17  119.39  3.000
 Y18  C19  C18  C06  134.66  3.000
 Y18  C17  C18  C06  105.95  3.000
 Y18  H15  C19  C20  120.84  3.000
 Y18  H15  C19  C18  120.42  3.000
 Y18  C20  C19  C18  118.73  3.000
 Y18  H16  C20  C21  119.22  3.000
 Y18  H16  C20  C19  119.67  3.000
 Y18  C21  C20  C19  121.11  3.000
 Y18  H17  C21  C22  119.24  3.000
 Y18  H17  C21  C20  119.49  3.000
 Y18  C22  C21  C20  121.27  3.000
 Y18  H18  C22  C21  120.37  3.000
 Y18  H18  C22  C17  122.10  3.000
 Y18  C21  C22  C17  117.53  3.000
 Y18  H19  N03  C04  116.83  3.000
 Y18  H19  N03  C02  116.10  3.000
 Y18  C04  N03  C02  122.76  3.000
 Y18  C17  N08  C09  125.93  3.000
 Y18  C17  N08  C07  108.61  3.000
 Y18  C09  N08  C07  125.36  3.000
 Y18  C14  N12  C13  124.67  3.000
 Y18  C14  N12  C11  113.88  3.000
 Y18  C13  N12  C11  120.91  3.000
 Y18  H6   C09  H5   106.29  3.000
 Y18  H6   C09  N08  108.35  3.000
 Y18  H5   C09  N08  108.73  3.000
 Y18  H6   C09  C10  110.42  3.000
 Y18  H5   C09  C10  110.37  3.000
 Y18  N08  C09  C10  112.46  3.000
 Y18  H12  C13  H11  108.22  3.000
 Y18  H12  C13  H10  108.66  3.000
 Y18  H11  C13  H10  108.63  3.000
 Y18  H12  C13  N12  110.61  3.000
 Y18  H11  C13  N12  110.95  3.000
 Y18  H10  C13  N12  109.72  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
 Y18  CONST_01  C17  N08  C07  C06     0.00   0.0  0
 Y18  CONST_02  N08  C17  C18  C06     0.00   0.0  0
 Y18  CONST_03  C22  C17  C18  C06   180.00   0.0  0
 Y18  CONST_04  C20  C19  C18  C06   180.00   0.0  0
 Y18  CONST_05  C22  C17  N08  C07   180.00   0.0  0
 Y18  CONST_06  C18  C17  N08  C07     0.00   0.0  0
 Y18  CONST_07  C17  C18  C06  C07     0.00   0.0  0
 Y18  CONST_08  C19  C18  C06  C07   180.00   0.0  0
 Y18  CONST_09  C20  C21  C22  C17     0.00   0.0  0
 Y18  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 Y18  CONST_11  C21  C22  C17  C18     0.00   0.0  0
 Y18  CONST_12  N08  C07  C06  C18     0.00   0.0  0
 Y18  CONST_13  C21  C20  C19  C18     0.00   0.0  0
 Y18  CONST_14  N08  C17  C18  C19   180.00   0.0  0
 Y18  CONST_15  C22  C17  C18  C19     0.00   0.0  0
 Y18  CONST_16  C22  C21  C20  C19     0.00   0.0  0
 Y18  CONST_17  N08  C17  C22  C21   180.00   0.0  0
 Y18  CONST_19  C15  C14  N12  C11     0.00   0.0  0
 Y18  CONST_20  C09  N08  C07  C05     0.00   0.0  0
 Y18  CONST_21  C09  N08  C07  C06   180.00   0.0  0
 Y18  CONST_22  C22  C17  N08  C09     0.00   0.0  0
 Y18  CONST_23  C18  C17  N08  C09   180.00   0.0  0
 Y18  CONST_25  O16  C14  N12  C11   180.00   0.0  0
 Y18  CONST_26  C15  C14  N12  C13   180.00   0.0  0
 Y18  CONST_27  H15  C19  C18  C06     0.00   0.0  0
 Y18  CONST_28  H17  C21  C22  C17   180.00   0.0  0
 Y18  CONST_29  H18  C22  C17  C18   180.00   0.0  0
 Y18  CONST_30  H16  C20  C19  C18   180.00   0.0  0
 Y18  CONST_31  H19  N03  C02  C06   180.00   0.0  0
 Y18  CONST_32  O16  C14  N12  C13     0.00   0.0  0
 Y18  Var_01    C05  C04  N03  C02   -47.42  30.0  1
 Y18  Var_02    N08  C07  C05  C04   156.75  30.0  1
 Y18  Var_03    N03  C04  C05  C07    46.67  30.0  1
 Y18  Var_04    N03  C02  C06  C07     7.71  30.0  1
 Y18  Var_05    C14  N12  C11  C10    18.69  30.0  1
 Y18  Var_06    N12  C14  C15  C10   -16.22  30.0  1
 Y18  Var_07    C10  C09  N08  C07    77.68  30.0  2
 Y18  Var_08    H10  C13  N12  C11  -178.71  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
 Y18  chir_01  C10  C11  C15  C09  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
 Y18  plan-1  C02  0.020
 Y18  plan-1  C04  0.020
 Y18  plan-1  C06  0.020
 Y18  plan-1  N03  0.020
 Y18  plan-1  O01  0.020
 Y18  plan-1  H19  0.020
 Y18  plan-2  C02  0.020
 Y18  plan-2  C05  0.020
 Y18  plan-2  C06  0.020
 Y18  plan-2  C07  0.020
 Y18  plan-2  C17  0.020
 Y18  plan-2  C18  0.020
 Y18  plan-2  C19  0.020
 Y18  plan-2  C20  0.020
 Y18  plan-2  C21  0.020
 Y18  plan-2  C22  0.020
 Y18  plan-2  N08  0.020
 Y18  plan-2  H15  0.020
 Y18  plan-2  H16  0.020
 Y18  plan-2  H17  0.020
 Y18  plan-2  H18  0.020
 Y18  plan-2  C09  0.020
 Y18  plan-3  C11  0.020
 Y18  plan-3  C14  0.020
 Y18  plan-3  C15  0.020
 Y18  plan-3  N12  0.020
 Y18  plan-3  O16  0.020
 Y18  plan-3  C13  0.020

