# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:19:42 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 5-{2-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]ethyl}-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](CCn2c3CCNC(=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
 Y17  Y17  5-{2-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]ethyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one  ligand  44  23  .  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_Y17
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
 Y17  C01   C  CH3   0  -0.518   6.2933  -0.6759  -1.3290
 Y17  C03   C  C     0   0.532   4.9874   0.3671   0.4843
 Y17  C04   C  CH2   0  -0.584   3.5272   0.4337   0.8788
 Y17  C05   C  CH1   0  -0.292   2.8864  -0.7519   0.1588
 Y17  C06   C  CH2   0  -0.446   1.4361  -0.5547  -0.2461
 Y17  C07   C  CH2   0  -0.337   0.5235  -0.3942   0.9638
 Y17  C09   C  CR56  0   0.335  -1.7272  -1.2869   0.2974
 Y17  C10   C  CR16  0  -0.309  -1.5082  -2.6594   0.3562
 Y17  C11   C  CR16  0  -0.281  -2.5641  -3.4879   0.0187
 Y17  C12   C  CR16  0  -0.263  -3.8043  -2.9619  -0.3688
 Y17  C13   C  CR16  0  -0.376  -4.0161  -1.5967  -0.4297
 Y17  C14   C  CR56  0   0.093  -2.9657  -0.7379  -0.0971
 Y17  C15   C  CR5   0  -0.203  -2.7971   0.6818  -0.0500
 Y17  C16   C  CR5   0   0.385  -1.5097   0.9236   0.3636
 Y17  C17   C  CH2   0  -0.531  -0.9769   2.2925   0.5799
 Y17  C18   C  CH2   0  -0.284  -1.7833   3.2442  -0.2961
 Y17  C20   C  C     0   0.452  -3.7517   1.7590  -0.2632
 Y17  C22   C  CH2   0  -0.225   3.8180  -0.9713  -1.0367
 Y17  N02   N  NT    0  -0.452   5.0891  -0.4595  -0.5735
 Y17  N08   N  NR5   0  -0.591  -0.8667  -0.2471   0.5888
 Y17  N19   N  NH1   0  -0.650  -3.2111   3.0025  -0.1760
 Y17  O23   O  O     0  -0.501   5.9079   0.9714   1.0122
 Y17  H013  H  HCH3  0   0.240   6.2024  -0.2616  -2.3355
 Y17  H011  H  HCH3  0   0.253   7.1316  -0.1967  -0.8309
 Y17  H012  H  HCH3  0   0.243   6.5032  -1.7427  -1.4180
 Y17  H041  H  HCH2  0   0.278   3.4092   0.4189   1.9621
 Y17  H042  H  HCH2  0   0.268   3.1259   1.3884   0.5187
 Y17  H051  H  HCH1  0   0.264   2.9580  -1.6303   0.8087
 Y17  H062  H  HCH2  0   0.239   1.3496   0.3255  -0.8914
 Y17  H061  H  HCH2  0   0.254   1.1018  -1.4121  -0.8364
 Y17  H071  H  HCH2  0   0.273   0.6126  -1.2547   1.6290
 Y17  H072  H  HCH2  0   0.282   0.8074   0.4763   1.5556
 Y17  H101  H  HCR6  0   0.264  -0.5544  -3.0750   0.6553
 Y17  H111  H  HCR6  0   0.253  -2.4281  -4.5608   0.0546
 Y17  H121  H  HCR6  0   0.249  -4.6092  -3.6393  -0.6240
 Y17  H131  H  HCR6  0   0.245  -4.9757  -1.1992  -0.7307
 Y17  H172  H  HCH2  0   0.279  -1.0655   2.5615   1.6376
 Y17  H171  H  HCH2  0   0.270   0.0786   2.3786   0.3167
 Y17  H182  H  HCH2  0   0.266  -1.5875   4.2740  -0.0053
 Y17  H181  H  HCH2  0   0.240  -1.4584   3.1300  -1.3362
 Y17  H221  H  HCH2  0   0.252   3.8989  -2.0244  -1.3117
 Y17  H222  H  HCH2  0   0.234   3.4796  -0.4223  -1.9242
 Y17  H191  H  HNH1  0   0.395  -3.8222   3.7685  -0.4161
 Y17  O21   O  O     0  -0.495  -4.9488   1.5709  -0.4601

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
 Y17  C01  N02   single    1.438  0.020  1.438
 Y17  N02  C22   single    1.446  0.020  1.446
 Y17  N02  C03   single    1.346  0.020  1.346
 Y17  C22  C05   single    1.531  0.020  1.531
 Y17  O23  C03   double    1.221  0.020  1.221
 Y17  C03  C04   single    1.514  0.020  1.514
 Y17  C04  C05   single    1.528  0.020  1.528
 Y17  C05  C06   single    1.519  0.020  1.519
 Y17  C06  C07   single    1.524  0.020  1.524
 Y17  C07  N08   single    1.447  0.020  1.447
 Y17  C10  C11   aromatic  1.384  0.020  1.384
 Y17  C10  C09   aromatic  1.391  0.020  1.391
 Y17  N08  C09   aromatic  1.381  0.020  1.381
 Y17  N08  C16   aromatic  1.355  0.020  1.355
 Y17  C11  C12   aromatic  1.402  0.020  1.402
 Y17  C09  C14   aromatic  1.411  0.020  1.411
 Y17  C16  C17   single    1.485  0.020  1.485
 Y17  C16  C15   aromatic  1.374  0.020  1.374
 Y17  C17  C18   single    1.524  0.020  1.524
 Y17  C12  C13   aromatic  1.383  0.020  1.383
 Y17  C14  C15   aromatic  1.430  0.020  1.430
 Y17  C14  C13   aromatic  1.397  0.020  1.397
 Y17  C15  C20   single    1.455  0.020  1.455
 Y17  C18  N19   single    1.453  0.020  1.453
 Y17  C20  N19   single    1.359  0.020  1.359
 Y17  C20  O21   double    1.228  0.020  1.228
 Y17  C01  H013  single    0.970  0.020  1.090
 Y17  C01  H011  single    0.970  0.020  1.090
 Y17  C01  H012  single    0.970  0.020  1.090
 Y17  C04  H041  single    0.970  0.020  1.090
 Y17  C04  H042  single    0.970  0.020  1.090
 Y17  C05  H051  single    0.970  0.020  1.090
 Y17  C06  H062  single    0.970  0.020  1.090
 Y17  C06  H061  single    0.970  0.020  1.090
 Y17  C07  H071  single    0.970  0.020  1.090
 Y17  C07  H072  single    0.970  0.020  1.090
 Y17  C10  H101  single    0.930  0.020  1.080
 Y17  C11  H111  single    0.930  0.020  1.080
 Y17  C12  H121  single    0.930  0.020  1.080
 Y17  C13  H131  single    0.930  0.020  1.080
 Y17  C17  H172  single    0.970  0.020  1.090
 Y17  C17  H171  single    0.970  0.020  1.090
 Y17  C18  H182  single    0.970  0.020  1.090
 Y17  C18  H181  single    0.970  0.020  1.090
 Y17  C22  H221  single    0.970  0.020  1.090
 Y17  C22  H222  single    0.970  0.020  1.090
 Y17  N19  H191  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
 Y17  H012  C01  H011  108.68  3.000
 Y17  H012  C01  H013  108.17  3.000
 Y17  H011  C01  H013  108.62  3.000
 Y17  H012  C01  N02   110.56  3.000
 Y17  H011  C01  N02   109.81  3.000
 Y17  H013  C01  N02   110.94  3.000
 Y17  O23   C03  N02   125.91  3.000
 Y17  O23   C03  C04   126.34  3.000
 Y17  N02   C03  C04   107.74  3.000
 Y17  H042  C04  H041  107.38  3.000
 Y17  H042  C04  C05   111.56  3.000
 Y17  H041  C04  C05   114.36  3.000
 Y17  H042  C04  C03   107.79  3.000
 Y17  H041  C04  C03   111.28  3.000
 Y17  C05   C04  C03   104.33  3.000
 Y17  H051  C05  C22   107.98  3.000
 Y17  H051  C05  C06   108.96  3.000
 Y17  C22   C05  C06   113.04  3.000
 Y17  H051  C05  C04   108.38  3.000
 Y17  C06   C05  C04   115.17  3.000
 Y17  C22   C05  C04   102.94  3.000
 Y17  H061  C06  H062  106.74  3.000
 Y17  H061  C06  C07   109.16  3.000
 Y17  H062  C06  C07   109.63  3.000
 Y17  H061  C06  C05   109.52  3.000
 Y17  H062  C06  C05   109.69  3.000
 Y17  C07   C06  C05   111.96  3.000
 Y17  H072  C07  H071  106.11  3.000
 Y17  H072  C07  N08   108.04  3.000
 Y17  H071  C07  N08   108.45  3.000
 Y17  H072  C07  C06   111.04  3.000
 Y17  H071  C07  C06   110.61  3.000
 Y17  N08   C07  C06   112.34  3.000
 Y17  N08   C09  C14   108.24  3.000
 Y17  C14   C09  C10   122.27  3.000
 Y17  N08   C09  C10   129.49  3.000
 Y17  H101  C10  C11   120.65  3.000
 Y17  H101  C10  C09   121.94  3.000
 Y17  C11   C10  C09   117.40  3.000
 Y17  H111  C11  C12   119.50  3.000
 Y17  H111  C11  C10   119.31  3.000
 Y17  C12   C11  C10   121.19  3.000
 Y17  H121  C12  C13   119.57  3.000
 Y17  H121  C12  C11   119.23  3.000
 Y17  C13   C12  C11   121.21  3.000
 Y17  H131  C13  C14   120.50  3.000
 Y17  H131  C13  C12   120.73  3.000
 Y17  C14   C13  C12   118.76  3.000
 Y17  C15   C14  C13   134.96  3.000
 Y17  C13   C14  C09   119.17  3.000
 Y17  C15   C14  C09   105.87  3.000
 Y17  C20   C15  C16   121.91  3.000
 Y17  C20   C15  C14   130.74  3.000
 Y17  C16   C15  C14   107.16  3.000
 Y17  N08   C16  C17   127.04  3.000
 Y17  C17   C16  C15   122.85  3.000
 Y17  N08   C16  C15   110.04  3.000
 Y17  H171  C17  H172  106.97  3.000
 Y17  H171  C17  C18   108.90  3.000
 Y17  H172  C17  C18   111.03  3.000
 Y17  H171  C17  C16   112.62  3.000
 Y17  H172  C17  C16   109.77  3.000
 Y17  C18   C17  C16   107.58  3.000
 Y17  H181  C18  H182  107.41  3.000
 Y17  H181  C18  N19   110.64  3.000
 Y17  H182  C18  N19   108.20  3.000
 Y17  H181  C18  C17   108.88  3.000
 Y17  H182  C18  C17   110.01  3.000
 Y17  N19   C18  C17   111.62  3.000
 Y17  O21   C20  N19   122.58  3.000
 Y17  O21   C20  C15   123.36  3.000
 Y17  N19   C20  C15   114.02  3.000
 Y17  H222  C22  H221  107.57  3.000
 Y17  H222  C22  N02   110.67  3.000
 Y17  H221  C22  N02   110.92  3.000
 Y17  H222  C22  C05   111.85  3.000
 Y17  H221  C22  C05   112.33  3.000
 Y17  N02   C22  C05   103.53  3.000
 Y17  C22   N02  C03   113.74  3.000
 Y17  C03   N02  C01   124.64  3.000
 Y17  C22   N02  C01   120.96  3.000
 Y17  C16   N08  C09   108.66  3.000
 Y17  C16   N08  C07   125.93  3.000
 Y17  C09   N08  C07   125.22  3.000
 Y17  H191  N19  C20   116.02  3.000
 Y17  H191  N19  C18   116.69  3.000
 Y17  C20   N19  C18   122.54  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
 Y17  CONST_01  C12   C11  C10  C09     0.00   0.0  0
 Y17  CONST_02  C15   C16  N08  C09     0.00   0.0  0
 Y17  CONST_03  C16   C15  C14  C09     0.00   0.0  0
 Y17  CONST_04  C12   C13  C14  C09     0.00   0.0  0
 Y17  CONST_05  C13   C12  C11  C10     0.00   0.0  0
 Y17  CONST_06  C16   N08  C09  C10   180.00   0.0  0
 Y17  CONST_07  C15   C14  C09  C10   180.00   0.0  0
 Y17  CONST_08  C13   C14  C09  C10     0.00   0.0  0
 Y17  CONST_09  N08   C09  C10  C11   180.00   0.0  0
 Y17  CONST_10  C14   C09  C10  C11     0.00   0.0  0
 Y17  CONST_11  C14   C13  C12  C11     0.00   0.0  0
 Y17  CONST_12  C15   C14  C13  C12   180.00   0.0  0
 Y17  CONST_13  N08   C09  C14  C13   180.00   0.0  0
 Y17  CONST_14  C16   C15  C14  C13   180.00   0.0  0
 Y17  CONST_15  C16   N08  C09  C14     0.00   0.0  0
 Y17  CONST_16  N08   C16  C15  C14     0.00   0.0  0
 Y17  CONST_17  N08   C09  C14  C15     0.00   0.0  0
 Y17  CONST_18  C22   N02  C03  C04     0.00   0.0  0
 Y17  CONST_20  C10   C09  N08  C07     0.00   0.0  0
 Y17  CONST_21  C14   C09  N08  C07   180.00   0.0  0
 Y17  CONST_22  C17   C16  N08  C07     0.00   0.0  0
 Y17  CONST_23  C15   C16  N08  C07   180.00   0.0  0
 Y17  CONST_24  C04   C03  N02  C01   180.00   0.0  0
 Y17  CONST_26  O23   C03  N02  C22   180.00   0.0  0
 Y17  CONST_27  H111  C11  C10  C09   180.00   0.0  0
 Y17  CONST_28  H131  C13  C14  C09   180.00   0.0  0
 Y17  CONST_29  H121  C12  C11  C10   180.00   0.0  0
 Y17  CONST_30  H101  C10  C11  C12   180.00   0.0  0
 Y17  CONST_31  H191  N19  C20  C15   180.00   0.0  0
 Y17  CONST_32  O23   C03  N02  C01     0.00   0.0  0
 Y17  Var_01    C05   C22  N02  C03   -19.03  30.0  1
 Y17  Var_02    N02   C03  C04  C05    15.24  30.0  1
 Y17  Var_03    N19   C20  C15  C14  -178.00  30.0  1
 Y17  Var_04    C18   C17  C16  C15   -25.50  30.0  1
 Y17  Var_05    N19   C18  C17  C16    46.92  30.0  1
 Y17  Var_06    C20   N19  C18  C17   -48.21  30.0  1
 Y17  Var_07    N08   C07  C06  C05  -178.21  30.0  3
 Y17  Var_08    C09   N08  C07  C06    82.94  30.0  2
 Y17  Var_09    H013  C01  N02  C03  -111.51  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
 Y17  chir_01  C05  C22  C04  C06  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
 Y17  plan-1  C01   0.020
 Y17  plan-1  C03   0.020
 Y17  plan-1  C04   0.020
 Y17  plan-1  C22   0.020
 Y17  plan-1  N02   0.020
 Y17  plan-1  O23   0.020
 Y17  plan-2  C07   0.020
 Y17  plan-2  C09   0.020
 Y17  plan-2  C10   0.020
 Y17  plan-2  C11   0.020
 Y17  plan-2  C12   0.020
 Y17  plan-2  C13   0.020
 Y17  plan-2  C14   0.020
 Y17  plan-2  C15   0.020
 Y17  plan-2  C16   0.020
 Y17  plan-2  C17   0.020
 Y17  plan-2  C20   0.020
 Y17  plan-2  N08   0.020
 Y17  plan-2  H101  0.020
 Y17  plan-2  H111  0.020
 Y17  plan-2  H121  0.020
 Y17  plan-2  H131  0.020
 Y17  plan-3  C15   0.020
 Y17  plan-3  C18   0.020
 Y17  plan-3  C20   0.020
 Y17  plan-3  N19   0.020
 Y17  plan-3  H191  0.020
 Y17  plan-3  O21   0.020

