# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:49:37 2022
#   Inital geometry file: a 151 line input string
#   Ligand name: N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](CO)C[C@@H]3CCNC3=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
 XV4  XV4  N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide  ligand  64  32  .  2022-03-29  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XV4
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
 XV4  C10   C  C     0   0.567  16.3930  11.8854  -7.4263
 XV4  C15   C  CH2   0  -0.439  10.2167  15.4623  -6.6259
 XV4  C17   C  CH3   0  -0.649   7.8687  16.0874  -7.1761
 XV4  C20   C  C     0   0.497  11.6133  13.0527  -4.1724
 XV4  C21   C  CR5   0   0.257  11.3038  12.8045  -2.7546
 XV4  C22   C  CR15  0  -0.410  10.4101  13.3842  -1.8895
 XV4  C24   C  CR6   0   0.314   9.9368  12.8598   0.6120
 XV4  C26   C  CH3   0  -0.433   8.3247  13.9933   1.9243
 XV4  C28   C  CR16  0  -0.260  11.3370  11.0601   1.4356
 XV4  C02   C  C     0   0.566  12.6457  15.0569  -6.1796
 XV4  C04   C  CH1   0  -0.128  14.6182  15.3526  -7.6373
 XV4  C05   C  CH2   0  -0.427  15.4993  14.1733  -8.0457
 XV4  C06   C  CH1   0  -0.413  15.5306  13.0660  -7.0053
 XV4  C07   C  CH2   0  -0.468  16.1052  13.4526  -5.6423
 XV4  C08   C  CH2   0  -0.258  16.6997  12.1472  -5.1118
 XV4  C12   C  CH2   0  -0.129  14.5735  16.4426  -8.7031
 XV4  C14   C  CH1   0  -0.212  11.2409  14.4448  -6.1209
 XV4  C18   C  CH3   0  -0.662   8.5754  13.6913  -7.4065
 XV4  C23   C  CR56  0  -0.026  10.5641  12.7202  -0.6428
 XV4  C27   C  CR16  0  -0.421  10.3289  12.0246   1.6410
 XV4  C29   C  CR16  0  -0.332  11.9732  10.8973   0.2277
 XV4  C30   C  CR56  0   0.368  11.5671  11.7446  -0.8104
 XV4  N03   N  NH1   0  -0.637  13.2697  14.9031  -7.3591
 XV4  N09   N  NH1   0  -0.631  17.0367  11.4450  -6.3316
 XV4  N19   N  NH1   0  -0.658  10.9340  14.0457  -4.7727
 XV4  N31   N  NR15  0  -0.724  11.9928  11.8213  -2.0962
 XV4  O01   O  O     0  -0.482  13.1181  15.6533  -5.2261
 XV4  O11   O  O     0  -0.487  16.4741  11.4130  -8.5483
 XV4  O13   O  OH1   0  -0.663  15.8771  16.9354  -8.8985
 XV4  O25   O  O2    0  -0.458   8.9944  13.8122   0.6928
 XV4  O32   O  O     0  -0.487  12.4403  12.3646  -4.7601
 XV4  H152  H  HCH2  0   0.246  10.4934  15.7345  -7.6486
 XV4  H151  H  HCH2  0   0.245  10.2984  16.3760  -6.0278
 XV4  H172  H  HCH3  0   0.226   7.9766  17.0146  -6.6107
 XV4  H173  H  HCH3  0   0.215   8.1180  16.3024  -8.2178
 XV4  H171  H  HCH3  0   0.228   6.8180  15.7966  -7.1398
 XV4  H221  H  HCR5  0   0.262   9.7184  14.1817  -2.1119
 XV4  H262  H  HCH3  0   0.258   7.6168  14.8049   1.7755
 XV4  H263  H  HCH3  0   0.228   7.7763  13.0964   2.2241
 XV4  H261  H  HCH3  0   0.228   9.0142  14.2685   2.7266
 XV4  H281  H  HCR6  0   0.254  11.6140  10.4275   2.2691
 XV4  H041  H  HCH1  0   0.261  15.0004  15.7946  -6.7151
 XV4  H051  H  HCH2  0   0.234  15.1406  13.7697  -8.9984
 XV4  H052  H  HCH2  0   0.245  16.5139  14.5374  -8.2222
 XV4  H061  H  HCH1  0   0.276  14.5172  12.6660  -6.8711
 XV4  H071  H  HCH2  0   0.243  16.8954  14.1963  -5.7742
 XV4  H072  H  HCH2  0   0.254  15.3642  13.8710  -4.9644
 XV4  H082  H  HCH2  0   0.248  17.5823  12.3073  -4.4931
 XV4  H081  H  HCH2  0   0.232  15.9716  11.5850  -4.5188
 XV4  H121  H  HCH2  0   0.207  13.8876  17.2304  -8.3663
 XV4  H141  H  HCH1  0   0.276  11.2164  13.5608  -6.7639
 XV4  H161  H  HCH1  0   0.224   8.4562  14.7994  -5.5842
 XV4  H181  H  HCH3  0   0.232   7.5205  13.4165  -7.4508
 XV4  H182  H  HCH3  0   0.216   8.9313  13.8041  -8.4336
 XV4  H183  H  HCH3  0   0.231   9.1081  12.8518  -6.9579
 XV4  H271  H  HCR6  0   0.273   9.8752  12.0916   2.6203
 XV4  H291  H  HCR6  0   0.258  12.7449  10.1528   0.0855
 XV4  H031  H  HNH1  0   0.400  12.8095  14.3621  -8.0766
 XV4  H091  H  HNH1  0   0.393  17.5797  10.5953  -6.3376
 XV4  H191  H  HNH1  0   0.413  10.3769  14.6706  -4.2116
 XV4  H311  H  HNR5  0   0.408  12.7081  11.2490  -2.5166
 XV4  H1    H  HCH2  0   0.192  14.1532  16.0215  -9.6273
 XV4  H2    H  HOH1  0   0.456  15.8497  17.5855  -9.6061
 XV4  C16   C  CH1   0  -0.235   8.7625  14.9833  -6.6197

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
 XV4  O13  C12   single    1.407  0.020  1.407
 XV4  C12  C04   single    1.525  0.020  1.525
 XV4  C05  C04   single    1.528  0.020  1.528
 XV4  C05  C06   single    1.520  0.020  1.520
 XV4  C18  C16   single    1.524  0.020  1.524
 XV4  C04  N03   single    1.448  0.020  1.448
 XV4  N03  C02   single    1.343  0.020  1.343
 XV4  O11  C10   double    1.220  0.020  1.220
 XV4  C10  C06   single    1.521  0.020  1.521
 XV4  C10  N09   single    1.344  0.020  1.344
 XV4  C16  C15   single    1.531  0.020  1.531
 XV4  C16  C17   single    1.526  0.020  1.526
 XV4  C06  C07   single    1.529  0.020  1.529
 XV4  C15  C14   single    1.529  0.020  1.529
 XV4  C02  C14   single    1.534  0.020  1.534
 XV4  C02  O01   double    1.220  0.020  1.220
 XV4  C14  N19   single    1.439  0.020  1.439
 XV4  C07  C08   single    1.529  0.020  1.529
 XV4  N09  C08   single    1.447  0.020  1.447
 XV4  O32  C20   double    1.226  0.020  1.226
 XV4  N19  C20   single    1.345  0.020  1.345
 XV4  C20  C21   single    1.472  0.020  1.472
 XV4  C21  N31   aromatic  1.369  0.020  1.369
 XV4  C21  C22   aromatic  1.372  0.020  1.372
 XV4  N31  C30   aromatic  1.357  0.020  1.357
 XV4  C22  C23   aromatic  1.421  0.020  1.421
 XV4  C30  C23   aromatic  1.409  0.020  1.409
 XV4  C30  C29   aromatic  1.400  0.020  1.400
 XV4  C23  C24   aromatic  1.410  0.020  1.410
 XV4  C29  C28   aromatic  1.375  0.020  1.375
 XV4  C24  O25   single    1.342  0.020  1.342
 XV4  C24  C27   aromatic  1.382  0.020  1.382
 XV4  O25  C26   single    1.413  0.020  1.413
 XV4  C28  C27   aromatic  1.410  0.020  1.410
 XV4  C15  H152  single    0.970  0.020  1.090
 XV4  C15  H151  single    0.970  0.020  1.090
 XV4  C17  H172  single    0.970  0.020  1.090
 XV4  C17  H173  single    0.970  0.020  1.090
 XV4  C17  H171  single    0.970  0.020  1.090
 XV4  C22  H221  single    0.930  0.020  1.080
 XV4  C26  H262  single    0.970  0.020  1.090
 XV4  C26  H263  single    0.970  0.020  1.090
 XV4  C26  H261  single    0.970  0.020  1.090
 XV4  C28  H281  single    0.930  0.020  1.080
 XV4  C04  H041  single    0.970  0.020  1.090
 XV4  C05  H051  single    0.970  0.020  1.090
 XV4  C05  H052  single    0.970  0.020  1.090
 XV4  C06  H061  single    0.970  0.020  1.090
 XV4  C07  H071  single    0.970  0.020  1.090
 XV4  C07  H072  single    0.970  0.020  1.090
 XV4  C08  H082  single    0.970  0.020  1.090
 XV4  C08  H081  single    0.970  0.020  1.090
 XV4  C12  H121  single    0.970  0.020  1.090
 XV4  C14  H141  single    0.970  0.020  1.090
 XV4  C16  H161  single    0.970  0.020  1.090
 XV4  C18  H181  single    0.970  0.020  1.090
 XV4  C18  H182  single    0.970  0.020  1.090
 XV4  C18  H183  single    0.970  0.020  1.090
 XV4  C27  H271  single    0.930  0.020  1.080
 XV4  C29  H291  single    0.930  0.020  1.080
 XV4  N03  H031  single    0.860  0.020  1.020
 XV4  N09  H091  single    0.860  0.020  1.020
 XV4  N19  H191  single    0.860  0.020  1.020
 XV4  N31  H311  single    0.860  0.020  1.020
 XV4  C12  H1    single    0.970  0.020  1.090
 XV4  O13  H2    single    0.850  0.020  0.980

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
 XV4  O11   C10  N09   126.17  3.000
 XV4  N09   C10  C06   107.48  3.000
 XV4  O11   C10  C06   126.34  3.000
 XV4  H151  C15  H152  106.50  3.000
 XV4  H151  C15  C16   109.25  3.000
 XV4  H152  C15  C16   108.78  3.000
 XV4  H151  C15  C14   108.95  3.000
 XV4  H152  C15  C14   107.75  3.000
 XV4  C16   C15  C14   115.25  3.000
 XV4  H171  C17  H173  107.70  3.000
 XV4  H171  C17  H172  107.73  3.000
 XV4  H173  C17  H172  107.71  3.000
 XV4  H171  C17  C16   111.05  3.000
 XV4  H173  C17  C16   110.88  3.000
 XV4  H172  C17  C16   111.59  3.000
 XV4  O32   C20  N19   122.78  3.000
 XV4  N19   C20  C21   116.63  3.000
 XV4  O32   C20  C21   120.59  3.000
 XV4  N31   C21  C22   109.14  3.000
 XV4  C22   C21  C20   132.28  3.000
 XV4  N31   C21  C20   118.58  3.000
 XV4  H221  C22  C23   126.57  3.000
 XV4  H221  C22  C21   126.86  3.000
 XV4  C23   C22  C21   106.57  3.000
 XV4  O25   C24  C27   125.67  3.000
 XV4  C27   C24  C23   118.46  3.000
 XV4  O25   C24  C23   115.87  3.000
 XV4  H261  C26  H263  108.77  3.000
 XV4  H261  C26  H262  108.85  3.000
 XV4  H263  C26  H262  108.87  3.000
 XV4  H261  C26  O25   111.89  3.000
 XV4  H263  C26  O25   111.81  3.000
 XV4  H262  C26  O25   106.56  3.000
 XV4  H281  C28  C29   119.27  3.000
 XV4  H281  C28  C27   118.07  3.000
 XV4  C29   C28  C27   122.66  3.000
 XV4  O01   C02  N03   124.23  3.000
 XV4  O01   C02  C14   121.33  3.000
 XV4  N03   C02  C14   114.42  3.000
 XV4  H041  C04  N03   106.82  3.000
 XV4  H041  C04  C12   108.13  3.000
 XV4  N03   C04  C12   109.19  3.000
 XV4  H041  C04  C05   109.66  3.000
 XV4  N03   C04  C05   110.41  3.000
 XV4  C12   C04  C05   112.45  3.000
 XV4  H052  C05  H051  106.66  3.000
 XV4  H052  C05  C06   109.53  3.000
 XV4  H051  C05  C06   109.51  3.000
 XV4  H052  C05  C04   108.75  3.000
 XV4  H051  C05  C04   109.15  3.000
 XV4  C06   C05  C04   113.03  3.000
 XV4  H061  C06  C07   109.28  3.000
 XV4  H061  C06  C05   109.27  3.000
 XV4  C07   C06  C05   115.72  3.000
 XV4  H061  C06  C10   105.92  3.000
 XV4  C07   C06  C10   103.29  3.000
 XV4  C05   C06  C10   112.80  3.000
 XV4  H072  C07  H071  107.82  3.000
 XV4  H072  C07  C08   112.14  3.000
 XV4  H071  C07  C08   109.97  3.000
 XV4  H072  C07  C06   113.38  3.000
 XV4  H071  C07  C06   109.64  3.000
 XV4  C08   C07  C06   103.86  3.000
 XV4  H081  C08  H082  107.86  3.000
 XV4  H081  C08  N09   111.25  3.000
 XV4  H082  C08  N09   111.17  3.000
 XV4  H081  C08  C07   111.58  3.000
 XV4  H082  C08  C07   112.73  3.000
 XV4  N09   C08  C07   102.25  3.000
 XV4  H1    C12  H121  107.09  3.000
 XV4  H1    C12  O13   111.82  3.000
 XV4  H121  C12  O13   111.72  3.000
 XV4  H1    C12  C04   108.97  3.000
 XV4  H121  C12  C04   108.48  3.000
 XV4  O13   C12  C04   108.68  3.000
 XV4  H141  C14  N19   108.78  3.000
 XV4  H141  C14  C02   108.70  3.000
 XV4  N19   C14  C02   109.99  3.000
 XV4  H141  C14  C15   109.19  3.000
 XV4  N19   C14  C15   110.55  3.000
 XV4  C02   C14  C15   109.59  3.000
 XV4  H183  C18  H182  107.87  3.000
 XV4  H183  C18  H181  107.16  3.000
 XV4  H182  C18  H181  107.62  3.000
 XV4  H183  C18  C16   112.34  3.000
 XV4  H182  C18  C16   110.96  3.000
 XV4  H181  C18  C16   110.68  3.000
 XV4  C30   C23  C24   119.42  3.000
 XV4  C24   C23  C22   133.34  3.000
 XV4  C30   C23  C22   107.24  3.000
 XV4  H271  C27  C28   118.31  3.000
 XV4  H271  C27  C24   121.19  3.000
 XV4  C28   C27  C24   120.51  3.000
 XV4  H291  C29  C30   121.73  3.000
 XV4  H291  C29  C28   121.81  3.000
 XV4  C30   C29  C28   116.46  3.000
 XV4  N31   C30  C29   130.24  3.000
 XV4  C29   C30  C23   122.49  3.000
 XV4  N31   C30  C23   107.27  3.000
 XV4  H031  N03  C04   117.01  3.000
 XV4  H031  N03  C02   118.28  3.000
 XV4  C04   N03  C02   124.45  3.000
 XV4  H091  N09  C08   122.63  3.000
 XV4  H091  N09  C10   121.95  3.000
 XV4  C08   N09  C10   114.58  3.000
 XV4  H191  N19  C14   117.87  3.000
 XV4  H191  N19  C20   119.25  3.000
 XV4  C14   N19  C20   121.02  3.000
 XV4  H311  N31  C30   125.86  3.000
 XV4  H311  N31  C21   124.35  3.000
 XV4  C30   N31  C21   109.79  3.000
 XV4  H2    O13  C12   108.22  3.000
 XV4  C26   O25  C24   118.43  3.000
 XV4  H161  C16  C18   108.14  3.000
 XV4  H161  C16  C17   107.60  3.000
 XV4  C18   C16  C17   110.69  3.000
 XV4  H161  C16  C15   108.78  3.000
 XV4  C17   C16  C15   109.18  3.000
 XV4  C18   C16  C15   112.32  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
 XV4  CONST_01  C23   C30  N31  C21     0.00   0.0  0
 XV4  CONST_02  C29   C30  N31  C21   180.00   0.0  0
 XV4  CONST_03  C30   C23  C22  C21     0.00   0.0  0
 XV4  CONST_04  C24   C23  C22  C21   180.00   0.0  0
 XV4  CONST_05  C30   N31  C21  C22     0.00   0.0  0
 XV4  CONST_06  N31   C30  C23  C22     0.00   0.0  0
 XV4  CONST_07  C29   C30  C23  C22   180.00   0.0  0
 XV4  CONST_08  C27   C24  C23  C22   180.00   0.0  0
 XV4  CONST_09  N31   C30  C23  C24   180.00   0.0  0
 XV4  CONST_10  C29   C30  C23  C24     0.00   0.0  0
 XV4  CONST_11  C29   C28  C27  C24     0.00   0.0  0
 XV4  CONST_12  N31   C30  C29  C28   180.00   0.0  0
 XV4  CONST_13  C23   C30  C29  C28     0.00   0.0  0
 XV4  CONST_14  C23   C24  C27  C28     0.00   0.0  0
 XV4  CONST_15  N31   C21  C22  C23     0.00   0.0  0
 XV4  CONST_16  C30   C23  C24  C27     0.00   0.0  0
 XV4  CONST_17  C30   C29  C28  C27     0.00   0.0  0
 XV4  CONST_18  C08   N09  C10  C06     0.00   0.0  0
 XV4  CONST_19  C30   N31  C21  C20   180.00   0.0  0
 XV4  CONST_20  C23   C22  C21  C20   180.00   0.0  0
 XV4  CONST_21  O25   C24  C23  C22     0.00   0.0  0
 XV4  CONST_22  O25   C24  C27  C28   180.00   0.0  0
 XV4  CONST_23  O25   C24  C23  C30   180.00   0.0  0
 XV4  CONST_24  O11   C10  N09  C08   180.00   0.0  0
 XV4  CONST_25  H311  N31  C21  C22   180.00   0.0  0
 XV4  CONST_26  H221  C22  C23  C24     0.00   0.0  0
 XV4  CONST_27  H281  C28  C27  C24   180.00   0.0  0
 XV4  CONST_28  H291  C29  C30  C23   180.00   0.0  0
 XV4  CONST_29  H271  C27  C24  C23   180.00   0.0  0
 XV4  CONST_30  H091  N09  C10  C06   180.00   0.0  0
 XV4  CONST_31  C14   N19  C20  C21   180.00   0.0  0
 XV4  CONST_32  H191  N19  C20  C21     0.00   0.0  0
 XV4  CONST_33  C14   C02  N03  C04   180.00   0.0  0
 XV4  CONST_34  O01   C02  N03  C04     0.00   0.0  0
 XV4  CONST_35  O32   C20  N19  C14     0.00   0.0  0
 XV4  CONST_36  H031  N03  C02  C14     0.00   0.0  0
 XV4  Var_01    C07   C08  N09  C10   -19.70  30.0  1
 XV4  Var_02    N09   C08  C07  C06    28.04  30.0  1
 XV4  Var_03    O32   C20  C21  C22  -177.61  30.0  2
 XV4  Var_04    C23   C24  O25  C26   179.61  30.0  1
 XV4  Var_05    H262  C26  O25  C24   179.72  30.0  3
 XV4  Var_06    C14   C15  C16  C17  -178.73  30.0  3
 XV4  Var_07    H181  C18  C16  C15  -175.57  30.0  3
 XV4  Var_08    H172  C17  C16  C15   -56.98  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
 XV4  chir_01  C04  C12  C05  N03  positiv
 XV4  chir_02  C06  C07  C10  C05  positiv
 XV4  chir_03  C14  N19  C15  C02  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
 XV4  plan-1  C20   0.020
 XV4  plan-1  C21   0.020
 XV4  plan-1  C22   0.020
 XV4  plan-1  C24   0.020
 XV4  plan-1  C28   0.020
 XV4  plan-1  C23   0.020
 XV4  plan-1  C27   0.020
 XV4  plan-1  C29   0.020
 XV4  plan-1  C30   0.020
 XV4  plan-1  N31   0.020
 XV4  plan-1  O25   0.020
 XV4  plan-1  H221  0.020
 XV4  plan-1  H281  0.020
 XV4  plan-1  H271  0.020
 XV4  plan-1  H291  0.020
 XV4  plan-1  H311  0.020
 XV4  plan-2  C02   0.020
 XV4  plan-2  C04   0.020
 XV4  plan-2  C14   0.020
 XV4  plan-2  N03   0.020
 XV4  plan-2  O01   0.020
 XV4  plan-2  H031  0.020
 XV4  plan-3  C20   0.020
 XV4  plan-3  C21   0.020
 XV4  plan-3  C14   0.020
 XV4  plan-3  N19   0.020
 XV4  plan-3  O32   0.020
 XV4  plan-3  H191  0.020
 XV4  plan-4  C10   0.020
 XV4  plan-4  C06   0.020
 XV4  plan-4  C08   0.020
 XV4  plan-4  N09   0.020
 XV4  plan-4  O11   0.020
 XV4  plan-4  H091  0.020

