# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:07:08 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: 1-{3-oxo-3-[(2S)-2-(pyrrolidin-1-ylcarbonyl)pyrrolidin-1-yl]propyl}-3-phenylquinoxalin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCN1C(=O)C(=Nc2ccccc12)c3ccccc3)N4CCC[C@H]4C(=O)N5CCCC5
#
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
 X98  X98  1-{3-oxo-3-[(2S)-2-(pyrrolidin-1-ylcarbonyl)pyrrolidin-1-yl]propyl}-3-phenylquinoxalin-2(1H)-one  ligand  61  33  .  2021-08-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_X98
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
 X98  C    C  C     0   0.581  -1.8209   0.3629   0.1246
 X98  O    O  O     0  -0.506  -2.2316   0.2210   1.2706
 X98  C1   C  CH2   0  -0.609  -0.3921   0.0505  -0.2602
 X98  C2   C  CH2   0  -0.335   0.4522  -0.3113   0.9527
 X98  N3   N  NR6   0  -0.581   1.8263  -0.6161   0.5616
 X98  C4   C  CR6   0   0.535   2.7195   0.4242   0.5440
 X98  C5   C  CR6   0   0.032   4.1078   0.0624   0.1745
 X98  N6   N  N     0  -0.377   4.4608  -1.1386  -0.1103
 X98  C7   C  CR66  0   0.177   3.5309  -2.1419  -0.1217
 X98  C8   C  CR16  0  -0.317   3.9466  -3.4307  -0.4738
 X98  C9   C  CR16  0  -0.264   3.0434  -4.4682  -0.5273
 X98  C10  C  CR16  0  -0.249   1.7025  -4.2196  -0.2316
 X98  C11  C  CR16  0  -0.329   1.2696  -2.9569   0.1230
 X98  C12  C  CR66  0   0.411   2.1834  -1.8998   0.1924
 X98  O13  O  O     0  -0.458   2.3894   1.5609   0.8390
 X98  C14  C  CR6   0   0.075   5.1484   1.1092   0.1774
 X98  C15  C  CR16  0  -0.282   6.4118   0.7929   0.6802
 X98  C16  C  CR16  0  -0.243   7.4338   1.7289   0.6626
 X98  C17  C  CR16  0  -0.257   7.2126   2.9905   0.1252
 X98  C18  C  CR16  0  -0.243   5.9636   3.3080  -0.3918
 X98  C19  C  CR16  0  -0.275   4.9332   2.3796  -0.3593
 X98  N    N  NT    0  -0.464  -2.6075   0.8233  -0.8588
 X98  CA   C  CH1   0  -0.222  -3.9910   1.1520  -0.5999
 X98  C3   C  C     0   0.574  -4.8070  -0.1214  -0.3801
 X98  O1   O  O     0  -0.501  -4.4230  -1.2007  -0.8120
 X98  CB   C  CH2   0  -0.469  -4.4162   1.8706  -1.8890
 X98  CG   C  CH2   0  -0.480  -3.5747   1.1894  -2.9635
 X98  CD   C  CH2   0  -0.266  -2.2422   0.9330  -2.2670
 X98  N1   N  NR5   0  -0.475  -5.9697   0.0209   0.2680
 X98  CD1  C  CH2   0  -0.259  -6.8444  -1.1217   0.5165
 X98  CA1  C  CH2   0  -0.285  -6.5171   1.2663   0.8031
 X98  CB1  C  CH2   0  -0.474  -7.9655   0.9056   1.1091
 X98  CG1  C  CH2   0  -0.485  -7.8835  -0.5699   1.4856
 X98  H1   H  HCH2  0   0.285  -0.3863  -0.7661  -0.9896
 X98  H1A  H  HCH2  0   0.288   0.0449   0.9111  -0.7749
 X98  H2   H  HCH2  0   0.292   0.4818   0.5110   1.6616
 X98  H2A  H  HCH2  0   0.280   0.0451  -1.1671   1.4855
 X98  H8   H  HCR6  0   0.271   4.9930  -3.5838  -0.7038
 X98  H9   H  HCR6  0   0.266   3.3672  -5.4630  -0.8001
 X98  H10  H  HCR6  0   0.272   0.9804  -5.0234  -0.2797
 X98  H11  H  HCR6  0   0.282   0.2209  -2.8110   0.3361
 X98  H15  H  HCR6  0   0.256   6.5896  -0.1901   1.0968
 X98  H16  H  HCR6  0   0.260   8.4034   1.4720   1.0687
 X98  H17  H  HCR6  0   0.261   8.0103   3.7214   0.1068
 X98  H18  H  HCR6  0   0.260   5.7876   4.2843  -0.8243
 X98  H19  H  HCR6  0   0.256   3.9732   2.6444  -0.7774
 X98  HA   H  HCH1  0   0.289  -4.0672   1.8108   0.2675
 X98  HB2  H  HCH2  0   0.262  -5.4872   1.8040  -2.0790
 X98  HB3  H  HCH2  0   0.261  -4.1593   2.9283  -1.8091
 X98  HG2  H  HCH2  0   0.248  -4.0322   0.2456  -3.2616
 X98  HG3  H  HCH2  0   0.259  -3.4571   1.8001  -3.8571
 X98  HD2  H  HCH2  0   0.246  -1.5439   1.7608  -2.4188
 X98  HD3  H  HCH2  0   0.255  -1.7635   0.0213  -2.6261
 X98  HD   H  HCH2  0   0.237  -7.3061  -1.4585  -0.4159
 X98  HDA  H  HCH2  0   0.247  -6.2849  -1.9603   0.9314
 X98  HA1  H  HCH2  0   0.246  -5.9855   1.5661   1.7110
 X98  HAA  H  HCH2  0   0.258  -6.4454   2.0840   0.0853
 X98  HB   H  HCH2  0   0.254  -8.3858   1.5311   1.8953
 X98  HBA  H  HCH2  0   0.241  -8.5786   1.0331   0.2144
 X98  HG   H  HCH2  0   0.253  -8.8379  -1.0881   1.4026
 X98  HGA  H  HCH2  0   0.240  -7.5344  -0.6795   2.5147

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
 X98  C    O    double    1.226  0.020  1.226
 X98  C    C1   single    1.512  0.020  1.512
 X98  C1   C2   single    1.521  0.020  1.521
 X98  C2   N3   single    1.461  0.020  1.461
 X98  N3   C4   single    1.371  0.020  1.371
 X98  N3   C12  single    1.383  0.020  1.383
 X98  C4   C5   single    1.481  0.020  1.481
 X98  C4   O13  double    1.220  0.020  1.220
 X98  C5   N6   double    1.284  0.020  1.284
 X98  C5   C14  single    1.476  0.020  1.476
 X98  N6   C7   single    1.368  0.020  1.368
 X98  C7   C8   aromatic  1.399  0.020  1.399
 X98  C7   C12  aromatic  1.405  0.020  1.405
 X98  C8   C9   aromatic  1.377  0.020  1.377
 X98  C9   C10  aromatic  1.395  0.020  1.395
 X98  C10  C11  aromatic  1.381  0.020  1.381
 X98  C11  C12  aromatic  1.399  0.020  1.399
 X98  C14  C15  aromatic  1.396  0.020  1.396
 X98  C14  C19  aromatic  1.396  0.020  1.396
 X98  C15  C16  aromatic  1.386  0.020  1.386
 X98  C16  C17  aromatic  1.389  0.020  1.389
 X98  C17  C18  aromatic  1.389  0.020  1.389
 X98  C18  C19  aromatic  1.387  0.020  1.387
 X98  C1   H1   single    0.970  0.020  1.090
 X98  C1   H1A  single    0.970  0.020  1.090
 X98  C2   H2   single    0.970  0.020  1.090
 X98  C2   H2A  single    0.970  0.020  1.090
 X98  C8   H8   single    0.930  0.020  1.080
 X98  C9   H9   single    0.930  0.020  1.080
 X98  C10  H10  single    0.930  0.020  1.080
 X98  C11  H11  single    0.930  0.020  1.080
 X98  C15  H15  single    0.930  0.020  1.080
 X98  C16  H16  single    0.930  0.020  1.080
 X98  C17  H17  single    0.930  0.020  1.080
 X98  C18  H18  single    0.930  0.020  1.080
 X98  C19  H19  single    0.930  0.020  1.080
 X98  N    CA   single    1.445  0.020  1.445
 X98  N    CD   single    1.459  0.020  1.459
 X98  CA   C3   single    1.528  0.020  1.528
 X98  CA   CB   single    1.536  0.020  1.536
 X98  CA   HA   single    0.970  0.020  1.090
 X98  C3   O1   double    1.224  0.020  1.224
 X98  CB   CG   single    1.525  0.020  1.525
 X98  CB   HB2  single    0.970  0.020  1.090
 X98  CB   HB3  single    0.970  0.020  1.090
 X98  CG   CD   single    1.525  0.020  1.525
 X98  CG   HG2  single    0.970  0.020  1.090
 X98  CG   HG3  single    0.970  0.020  1.090
 X98  CD   HD2  single    0.970  0.020  1.090
 X98  CD   HD3  single    0.970  0.020  1.090
 X98  N1   CD1  single    1.460  0.020  1.460
 X98  N1   CA1  single    1.462  0.020  1.462
 X98  CD1  CG1  single    1.524  0.020  1.524
 X98  CA1  CB1  single    1.524  0.020  1.524
 X98  CB1  CG1  single    1.525  0.020  1.525
 X98  CD1  HD   single    0.970  0.020  1.090
 X98  CD1  HDA  single    0.970  0.020  1.090
 X98  CA1  HA1  single    0.970  0.020  1.090
 X98  CA1  HAA  single    0.970  0.020  1.090
 X98  CB1  HB   single    0.970  0.020  1.090
 X98  CB1  HBA  single    0.970  0.020  1.090
 X98  CG1  HG   single    0.970  0.020  1.090
 X98  CG1  HGA  single    0.970  0.020  1.090
 X98  C    N    single    1.341  0.020  1.341
 X98  C3   N1   single    1.339  0.020  1.339

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
 X98  N    C    C1   116.01  3.000
 X98  N    C    O    121.94  3.000
 X98  C1   C    O    122.05  3.000
 X98  H1A  C1   H1   105.74  3.000
 X98  H1A  C1   C2   109.91  3.000
 X98  H1   C1   C2   110.53  3.000
 X98  H1A  C1   C    109.55  3.000
 X98  H1   C1   C    109.18  3.000
 X98  C2   C1   C    111.75  3.000
 X98  H2A  C2   H2   106.64  3.000
 X98  H2A  C2   N3   108.61  3.000
 X98  H2   C2   N3   107.88  3.000
 X98  H2A  C2   C1   111.72  3.000
 X98  H2   C2   C1   110.82  3.000
 X98  N3   C2   C1   110.99  3.000
 X98  C12  N3   C4   122.19  3.000
 X98  C12  N3   C2   120.54  3.000
 X98  C4   N3   C2   117.25  3.000
 X98  O13  C4   C5   122.79  3.000
 X98  O13  C4   N3   121.84  3.000
 X98  C5   C4   N3   115.36  3.000
 X98  C14  C5   N6   118.04  3.000
 X98  C14  C5   C4   119.14  3.000
 X98  N6   C5   C4   122.79  3.000
 X98  C7   N6   C5   120.07  3.000
 X98  C12  C7   C8   120.00  3.000
 X98  C12  C7   N6   121.59  3.000
 X98  C8   C7   N6   118.41  3.000
 X98  H8   C8   C9   121.30  3.000
 X98  H8   C8   C7   118.10  3.000
 X98  C9   C8   C7   120.61  3.000
 X98  H9   C9   C10  120.34  3.000
 X98  H9   C9   C8   120.45  3.000
 X98  C10  C9   C8   119.20  3.000
 X98  H10  C10  C11  118.79  3.000
 X98  H10  C10  C9   119.98  3.000
 X98  C11  C10  C9   121.23  3.000
 X98  H11  C11  C12  121.49  3.000
 X98  H11  C11  C10  118.58  3.000
 X98  C12  C11  C10  119.92  3.000
 X98  C11  C12  C7   119.03  3.000
 X98  C11  C12  N3   123.10  3.000
 X98  C7   C12  N3   117.87  3.000
 X98  C19  C14  C15  118.96  3.000
 X98  C19  C14  C5   122.41  3.000
 X98  C15  C14  C5   118.56  3.000
 X98  H15  C15  C16  119.81  3.000
 X98  H15  C15  C14  119.54  3.000
 X98  C16  C15  C14  120.65  3.000
 X98  H16  C16  C17  120.24  3.000
 X98  H16  C16  C15  119.71  3.000
 X98  C17  C16  C15  120.05  3.000
 X98  H17  C17  C18  120.16  3.000
 X98  H17  C17  C16  120.17  3.000
 X98  C18  C17  C16  119.67  3.000
 X98  H18  C18  C19  119.49  3.000
 X98  H18  C18  C17  120.09  3.000
 X98  C19  C18  C17  120.42  3.000
 X98  H19  C19  C18  119.14  3.000
 X98  H19  C19  C14  120.60  3.000
 X98  C18  C19  C14  120.23  3.000
 X98  CD   N    CA   113.29  3.000
 X98  CD   N    C    125.94  3.000
 X98  CA   N    C    120.55  3.000
 X98  HA   CA   CB   111.41  3.000
 X98  HA   CA   C3   110.56  3.000
 X98  CB   CA   C3   111.27  3.000
 X98  HA   CA   N    110.26  3.000
 X98  CB   CA   N    102.77  3.000
 X98  C3   CA   N    110.33  3.000
 X98  N1   C3   O1   122.47  3.000
 X98  N1   C3   CA   116.41  3.000
 X98  O1   C3   CA   121.08  3.000
 X98  HB3  CB   HB2  107.67  3.000
 X98  HB3  CB   CG   110.76  3.000
 X98  HB2  CB   CG   113.08  3.000
 X98  HB3  CB   CA   109.08  3.000
 X98  HB2  CB   CA   112.94  3.000
 X98  CG   CB   CA   103.27  3.000
 X98  HG3  CG   HG2  107.84  3.000
 X98  HG3  CG   CD   112.00  3.000
 X98  HG2  CG   CD   110.23  3.000
 X98  HG3  CG   CB   112.79  3.000
 X98  HG2  CG   CB   110.35  3.000
 X98  CD   CG   CB   103.62  3.000
 X98  HD3  CD   HD2  107.87  3.000
 X98  HD3  CD   CG   111.94  3.000
 X98  HD2  CD   CG   111.54  3.000
 X98  HD3  CD   N    111.40  3.000
 X98  HD2  CD   N    110.53  3.000
 X98  CG   CD   N    103.57  3.000
 X98  CA1  N1   CD1  112.34  3.000
 X98  CA1  N1   C3   126.37  3.000
 X98  CD1  N1   C3   121.30  3.000
 X98  HDA  CD1  HD   107.72  3.000
 X98  HDA  CD1  CG1  112.73  3.000
 X98  HD   CD1  CG1  111.46  3.000
 X98  HDA  CD1  N1   111.05  3.000
 X98  HD   CD1  N1   110.42  3.000
 X98  CG1  CD1  N1   103.49  3.000
 X98  HAA  CA1  HA1  107.99  3.000
 X98  HAA  CA1  CB1  111.85  3.000
 X98  HA1  CA1  CB1  111.10  3.000
 X98  HAA  CA1  N1   111.92  3.000
 X98  HA1  CA1  N1   110.81  3.000
 X98  CB1  CA1  N1   103.16  3.000
 X98  HBA  CB1  HB   107.92  3.000
 X98  HBA  CB1  CG1  110.21  3.000
 X98  HB   CB1  CG1  113.47  3.000
 X98  HBA  CB1  CA1  109.96  3.000
 X98  HB   CB1  CA1  112.08  3.000
 X98  CG1  CB1  CA1  103.15  3.000
 X98  HGA  CG1  HG   107.71  3.000
 X98  HGA  CG1  CB1  110.30  3.000
 X98  HG   CG1  CB1  113.23  3.000
 X98  HGA  CG1  CD1  110.17  3.000
 X98  HG   CG1  CD1  112.12  3.000
 X98  CB1  CG1  CD1  103.29  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
 X98  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 X98  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 X98  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 X98  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 X98  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 X98  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 X98  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 X98  CONST_08  C17  C18  C19  C14    0.00   0.0  0
 X98  CONST_09  C18  C19  C14  C15    0.00   0.0  0
 X98  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 X98  CONST_11  C19  C14  C15  C16    0.00   0.0  0
 X98  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 X98  CONST_13  C16  C15  C14  C5   180.00   0.0  0
 X98  CONST_14  C18  C19  C14  C5   180.00   0.0  0
 X98  CONST_15  C12  N3   C4   C5     0.00   0.0  0
 X98  CONST_16  CD1  N1   C3   CA   180.00   0.0  0
 X98  CONST_17  CA1  N1   C3   CA     0.00   0.0  0
 X98  CONST_18  C5   C4   N3   C2   180.00   0.0  0
 X98  CONST_19  O13  C4   N3   C12  180.00   0.0  0
 X98  CONST_20  H11  C11  C12  N3     0.00   0.0  0
 X98  CONST_21  H15  C15  C14  C5     0.00   0.0  0
 X98  CONST_22  H19  C19  C14  C5     0.00   0.0  0
 X98  CONST_23  H8   C8   C7   N6     0.00   0.0  0
 X98  CONST_24  H9   C9   C8   C7   180.00   0.0  0
 X98  CONST_25  H10  C10  C9   C8   180.00   0.0  0
 X98  CONST_26  H16  C16  C15  C14  180.00   0.0  0
 X98  CONST_27  H18  C18  C19  C14  180.00   0.0  0
 X98  CONST_28  H17  C17  C16  C15  180.00   0.0  0
 X98  CONST_29  CA   N    C    O      0.00   0.0  0
 X98  CONST_30  CD   N    C    O    180.00   0.0  0
 X98  CONST_31  CA   N    C    C1   180.00   0.0  0
 X98  CONST_32  CD   N    C    C1     0.00   0.0  0
 X98  CONST_33  CD1  N1   C3   O1     0.00   0.0  0
 X98  CONST_34  CA1  N1   C3   O1   180.00   0.0  0
 X98  CONST_35  O13  C4   N3   C2     0.00   0.0  0
 X98  Var_01    C15  C14  C5   C4   139.21  30.0  2
 X98  Var_02    CB   CG   CD   N     27.28  30.0  1
 X98  Var_03    CG   CD   N    CA    -7.38  30.0  1
 X98  Var_04    CD   CG   CB   CA   -36.77  30.0  1
 X98  Var_05    CB1  CG1  CD1  N1    29.89  30.0  1
 X98  Var_06    CG1  CB1  CA1  N1    31.79  30.0  1
 X98  Var_07    CB1  CA1  N1   CD1  -13.60  30.0  1
 X98  Var_08    CA1  CB1  CG1  CD1  -38.44  30.0  1
 X98  Var_09    CG1  CD1  N1   CA1  -10.27  30.0  1
 X98  Var_10    C4   N3   C2   C1    90.47  30.0  3
 X98  Var_11    N3   C2   C1   C    179.72  30.0  3
 X98  Var_12    N    C    C1   C2   173.52  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
 X98  chir_01  CA  N  C3  CB  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
 X98  plan-1  C5   0.020
 X98  plan-1  C14  0.020
 X98  plan-1  C15  0.020
 X98  plan-1  C16  0.020
 X98  plan-1  C17  0.020
 X98  plan-1  C18  0.020
 X98  plan-1  C19  0.020
 X98  plan-1  H15  0.020
 X98  plan-1  H16  0.020
 X98  plan-1  H17  0.020
 X98  plan-1  H18  0.020
 X98  plan-1  H19  0.020
 X98  plan-2  C2   0.020
 X98  plan-2  N3   0.020
 X98  plan-2  C4   0.020
 X98  plan-2  C5   0.020
 X98  plan-2  N6   0.020
 X98  plan-2  C7   0.020
 X98  plan-2  C8   0.020
 X98  plan-2  C9   0.020
 X98  plan-2  C10  0.020
 X98  plan-2  C11  0.020
 X98  plan-2  C12  0.020
 X98  plan-2  O13  0.020
 X98  plan-2  C14  0.020
 X98  plan-2  H8   0.020
 X98  plan-2  H9   0.020
 X98  plan-2  H10  0.020
 X98  plan-2  H11  0.020
 X98  plan-3  C    0.020
 X98  plan-3  O    0.020
 X98  plan-3  C1   0.020
 X98  plan-3  N    0.020
 X98  plan-3  CA   0.020
 X98  plan-3  CD   0.020
 X98  plan-4  CA   0.020
 X98  plan-4  C3   0.020
 X98  plan-4  O1   0.020
 X98  plan-4  N1   0.020
 X98  plan-4  CD1  0.020
 X98  plan-4  CA1  0.020

