# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 17:39:58 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: benzyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CC2)NC(=O)OCc3ccccc3
#
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
 XTP  XTP  'benzyl [(2S)-3-cyclopropyl-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]carbamate'  ligand  58  29  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XTP
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
 XTP  C10   C  C     0   0.566  -11.1962  15.1873   4.5552
 XTP  C15   C  CH2   0  -0.467  -16.4596  12.8931   0.0435
 XTP  C17   C  CH2   0  -0.490  -18.4484  13.9047  -1.3214
 XTP  C20   C  C     0   0.761  -15.0136  16.2941   0.3779
 XTP  C22   C  CH2   0  -0.222  -14.2821  18.4349  -0.2761
 XTP  C24   C  CR16  0  -0.293  -11.9814  19.1930   0.3174
 XTP  C26   C  CR16  0  -0.262  -10.0014  18.0593  -0.4443
 XTP  C28   C  CR16  0  -0.291  -12.1838  17.2090  -1.0133
 XTP  C02   C  C     0   0.553  -14.1708  13.4888   0.8250
 XTP  C04   C  CH1   0  -0.134  -12.5858  12.3102   2.3142
 XTP  C05   C  CH2   0  -0.422  -11.9791  13.0048   3.5324
 XTP  C06   C  CH1   0  -0.418  -11.7766  14.4968   3.3297
 XTP  C07   C  CH2   0  -0.467  -10.8073  14.8919   2.2160
 XTP  C08   C  CH2   0  -0.259  -10.2570  16.2406   2.6783
 XTP  C12   C  CH2   0  -0.128  -12.7707  10.8105   2.5277
 XTP  C14   C  CH1   0  -0.193  -15.6177  13.9813   0.7144
 XTP  C16   C  CH1   0  -0.234  -17.9174  13.2542  -0.0792
 XTP  C18   C  CH2   0  -0.487  -18.7893  12.4776  -1.0159
 XTP  C23   C  CR6   0   0.046  -12.7876  18.2514  -0.3171
 XTP  C25   C  CR16  0  -0.242  -10.5986  19.1041   0.2492
 XTP  C27   C  CR16  0  -0.237  -10.7989  17.1110  -1.0687
 XTP  N03   N  NH1   0  -0.632  -13.8727  12.8883   1.9863
 XTP  N09   N  NH1   0  -0.630  -10.3353  16.1229   4.1192
 XTP  N19   N  NH1   0  -0.654  -15.6716  15.2003  -0.0485
 XTP  O01   O  O     0  -0.484  -13.3946  13.6105  -0.1096
 XTP  O11   O  O     0  -0.488  -11.4710  14.9477   5.7196
 XTP  O13   O  OH1   0  -0.663  -11.5139  10.2272   2.7691
 XTP  O21   O  O2    0  -0.485  -15.0089  17.2497  -0.5612
 XTP  O29   O  O     0  -0.497  -14.5066  16.4129   1.4733
 XTP  H151  H  HCH2  0   0.261  -16.3569  11.9816   0.6376
 XTP  H152  H  HCH2  0   0.246  -16.0442  12.6696  -0.9448
 XTP  H172  H  HCH2  0   0.243  -17.7578  14.0894  -2.1362
 XTP  H171  H  HCH2  0   0.250  -19.2222  14.6544  -1.2185
 XTP  H221  H  HCH2  0   0.271  -14.5888  19.1366  -1.0531
 XTP  H222  H  HCH2  0   0.251  -14.5864  18.8612   0.6826
 XTP  H261  H  HCR6  0   0.253   -8.9229  17.9816  -0.4914
 XTP  H281  H  HCR6  0   0.251  -12.7838  16.4618  -1.5173
 XTP  H041  H  HCH1  0   0.262  -11.9383  12.4579   1.4482
 XTP  H052  H  HCH2  0   0.233  -12.6275  12.8367   4.3981
 XTP  H051  H  HCH2  0   0.244  -11.0195  12.5363   3.7616
 XTP  H061  H  HCH1  0   0.280  -12.7461  14.9760   3.1432
 XTP  H071  H  HCH2  0   0.254  -11.2769  14.9527   1.2366
 XTP  H072  H  HCH2  0   0.240   -9.9962  14.1610   2.1539
 XTP  H082  H  HCH2  0   0.244   -9.2321  16.4141   2.3517
 XTP  H081  H  HCH2  0   0.238  -10.8679  17.0707   2.3115
 XTP  H121  H  HCH2  0   0.193  -13.4626  10.6546   3.3674
 XTP  H141  H  HCH1  0   0.272  -16.0267  14.1641   1.7133
 XTP  H161  H  HCH1  0   0.254  -18.3827  13.5612   0.8528
 XTP  H181  H  HCH2  0   0.250  -19.7990  12.2448  -0.7034
 XTP  H182  H  HCH2  0   0.243  -18.3231  11.7079  -1.6195
 XTP  H251  H  HCR6  0   0.255   -9.9877  19.8452   0.7486
 XTP  H271  H  HCR6  0   0.254  -10.3436  16.2895  -1.6071
 XTP  H031  H  HNH1  0   0.400  -14.5720  12.8843   2.7144
 XTP  H091  H  HNH1  0   0.392   -9.9163  16.7949   4.7434
 XTP  H191  H  HNH1  0   0.405  -15.9389  15.1468  -1.0191
 XTP  H1    H  HCH2  0   0.208  -13.2500  10.3905   1.6339
 XTP  H2    H  HOH1  0   0.456  -11.6440   9.2957   2.9674
 XTP  H241  H  HCR6  0   0.251  -12.4394  20.0045   0.8718

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
 XTP  C18  C17   single    1.499  0.020  1.499
 XTP  C18  C16   single    1.497  0.020  1.497
 XTP  C27  C28   aromatic  1.389  0.020  1.389
 XTP  C27  C26   aromatic  1.388  0.020  1.388
 XTP  C28  C23   aromatic  1.391  0.020  1.391
 XTP  O21  C22   single    1.419  0.020  1.419
 XTP  O21  C20   single    1.340  0.020  1.340
 XTP  C15  C16   single    1.507  0.020  1.507
 XTP  C15  C14   single    1.531  0.020  1.531
 XTP  N19  C20   single    1.346  0.020  1.346
 XTP  N19  C14   single    1.439  0.020  1.439
 XTP  C17  C16   single    1.499  0.020  1.499
 XTP  C26  C25   aromatic  1.389  0.020  1.389
 XTP  O01  C02   double    1.221  0.020  1.221
 XTP  C23  C22   single    1.506  0.020  1.506
 XTP  C23  C24   aromatic  1.392  0.020  1.392
 XTP  C20  O29   double    1.213  0.020  1.213
 XTP  C25  C24   aromatic  1.387  0.020  1.387
 XTP  C14  C02   single    1.532  0.020  1.532
 XTP  C02  N03   single    1.341  0.020  1.341
 XTP  N03  C04   single    1.448  0.020  1.448
 XTP  C07  C08   single    1.528  0.020  1.528
 XTP  C07  C06   single    1.528  0.020  1.528
 XTP  C04  C12   single    1.526  0.020  1.526
 XTP  C04  C05   single    1.528  0.020  1.528
 XTP  C08  N09   single    1.448  0.020  1.448
 XTP  C12  O13   single    1.406  0.020  1.406
 XTP  C06  C05   single    1.519  0.020  1.519
 XTP  C06  C10   single    1.522  0.020  1.522
 XTP  N09  C10   single    1.344  0.020  1.344
 XTP  C10  O11   double    1.220  0.020  1.220
 XTP  C15  H151  single    0.970  0.020  1.090
 XTP  C15  H152  single    0.970  0.020  1.090
 XTP  C17  H172  single    0.970  0.020  1.090
 XTP  C17  H171  single    0.970  0.020  1.090
 XTP  C22  H221  single    0.970  0.020  1.090
 XTP  C22  H222  single    0.970  0.020  1.090
 XTP  C24  H241  single    0.930  0.020  1.080
 XTP  C26  H261  single    0.930  0.020  1.080
 XTP  C28  H281  single    0.930  0.020  1.080
 XTP  C04  H041  single    0.970  0.020  1.090
 XTP  C05  H052  single    0.970  0.020  1.090
 XTP  C05  H051  single    0.970  0.020  1.090
 XTP  C06  H061  single    0.970  0.020  1.090
 XTP  C07  H071  single    0.970  0.020  1.090
 XTP  C07  H072  single    0.970  0.020  1.090
 XTP  C08  H082  single    0.970  0.020  1.090
 XTP  C08  H081  single    0.970  0.020  1.090
 XTP  C12  H121  single    0.970  0.020  1.090
 XTP  C14  H141  single    0.970  0.020  1.090
 XTP  C16  H161  single    0.970  0.020  1.090
 XTP  C18  H181  single    0.970  0.020  1.090
 XTP  C18  H182  single    0.970  0.020  1.090
 XTP  C25  H251  single    0.930  0.020  1.080
 XTP  C27  H271  single    0.930  0.020  1.080
 XTP  N03  H031  single    0.860  0.020  1.020
 XTP  N09  H091  single    0.860  0.020  1.020
 XTP  N19  H191  single    0.860  0.020  1.020
 XTP  C12  H1    single    0.970  0.020  1.090
 XTP  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
 XTP  O11   C10  N09   126.19  3.000
 XTP  O11   C10  C06   126.41  3.000
 XTP  N09   C10  C06   107.39  3.000
 XTP  H152  C15  H151  106.54  3.000
 XTP  H152  C15  C16   110.02  3.000
 XTP  H151  C15  C16   109.58  3.000
 XTP  H152  C15  C14   109.40  3.000
 XTP  H151  C15  C14   107.64  3.000
 XTP  C16   C15  C14   113.41  3.000
 XTP  H171  C17  H172  114.14  3.000
 XTP  H171  C17  C18   118.52  3.000
 XTP  H172  C17  C18   117.41  3.000
 XTP  H171  C17  C16   118.36  3.000
 XTP  H172  C17  C16   118.10  3.000
 XTP  C18   C17  C16    59.91  3.000
 XTP  O29   C20  O21   124.18  3.000
 XTP  O29   C20  N19   124.76  3.000
 XTP  O21   C20  N19   111.05  3.000
 XTP  H222  C22  H221  107.20  3.000
 XTP  H222  C22  O21   111.08  3.000
 XTP  H221  C22  O21   104.48  3.000
 XTP  H222  C22  C23   110.35  3.000
 XTP  H221  C22  C23   109.74  3.000
 XTP  O21   C22  C23   113.64  3.000
 XTP  H241  C24  C25   119.61  3.000
 XTP  H241  C24  C23   119.64  3.000
 XTP  C25   C24  C23   120.75  3.000
 XTP  H261  C26  C27   120.27  3.000
 XTP  H261  C26  C25   120.28  3.000
 XTP  C27   C26  C25   119.45  3.000
 XTP  H281  C28  C27   119.01  3.000
 XTP  H281  C28  C23   120.63  3.000
 XTP  C27   C28  C23   120.35  3.000
 XTP  O01   C02  N03   124.49  3.000
 XTP  N03   C02  C14   114.60  3.000
 XTP  O01   C02  C14   120.86  3.000
 XTP  H041  C04  N03   107.07  3.000
 XTP  H041  C04  C12   108.41  3.000
 XTP  N03   C04  C12   108.44  3.000
 XTP  H041  C04  C05   109.61  3.000
 XTP  C12   C04  C05   112.54  3.000
 XTP  N03   C04  C05   110.60  3.000
 XTP  H051  C05  H052  106.78  3.000
 XTP  H051  C05  C06   109.40  3.000
 XTP  H052  C05  C06   109.59  3.000
 XTP  H051  C05  C04   108.74  3.000
 XTP  H052  C05  C04   109.00  3.000
 XTP  C06   C05  C04   113.14  3.000
 XTP  H061  C06  C07   108.88  3.000
 XTP  H061  C06  C05   109.50  3.000
 XTP  C07   C06  C05   115.82  3.000
 XTP  H061  C06  C10   106.00  3.000
 XTP  C05   C06  C10   112.89  3.000
 XTP  C07   C06  C10   103.16  3.000
 XTP  H072  C07  H071  107.84  3.000
 XTP  H072  C07  C08   109.88  3.000
 XTP  H071  C07  C08   112.23  3.000
 XTP  H072  C07  C06   109.82  3.000
 XTP  H071  C07  C06   113.37  3.000
 XTP  C08   C07  C06   103.66  3.000
 XTP  H081  C08  H082  107.70  3.000
 XTP  H081  C08  N09   111.42  3.000
 XTP  H082  C08  N09   111.23  3.000
 XTP  H081  C08  C07   111.54  3.000
 XTP  H082  C08  C07   112.86  3.000
 XTP  N09   C08  C07   102.11  3.000
 XTP  H1    C12  H121  107.04  3.000
 XTP  H1    C12  O13   111.80  3.000
 XTP  H121  C12  O13   111.87  3.000
 XTP  H1    C12  C04   108.36  3.000
 XTP  H121  C12  C04   108.81  3.000
 XTP  O13   C12  C04   108.86  3.000
 XTP  H141  C14  N19   109.17  3.000
 XTP  H141  C14  C02   109.91  3.000
 XTP  N19   C14  C02   110.23  3.000
 XTP  H141  C14  C15   108.25  3.000
 XTP  C02   C14  C15   108.81  3.000
 XTP  N19   C14  C15   110.44  3.000
 XTP  H161  C16  C18   115.73  3.000
 XTP  H161  C16  C17   115.89  3.000
 XTP  C18   C16  C17    60.03  3.000
 XTP  H161  C16  C15   114.35  3.000
 XTP  C17   C16  C15   120.93  3.000
 XTP  C18   C16  C15   119.35  3.000
 XTP  H182  C18  H181  114.17  3.000
 XTP  H182  C18  C16   117.81  3.000
 XTP  H181  C18  C16   118.31  3.000
 XTP  H182  C18  C17   117.72  3.000
 XTP  H181  C18  C17   118.42  3.000
 XTP  C16   C18  C17    60.07  3.000
 XTP  C28   C23  C24   118.91  3.000
 XTP  C24   C23  C22   118.66  3.000
 XTP  C28   C23  C22   122.37  3.000
 XTP  H251  C25  C26   120.18  3.000
 XTP  H251  C25  C24   119.73  3.000
 XTP  C26   C25  C24   120.09  3.000
 XTP  H271  C27  C28   119.51  3.000
 XTP  H271  C27  C26   120.05  3.000
 XTP  C28   C27  C26   120.44  3.000
 XTP  H031  N03  C04   116.78  3.000
 XTP  H031  N03  C02   118.19  3.000
 XTP  C04   N03  C02   124.91  3.000
 XTP  H091  N09  C08   122.64  3.000
 XTP  H091  N09  C10   121.96  3.000
 XTP  C08   N09  C10   114.46  3.000
 XTP  H191  N19  C14   118.39  3.000
 XTP  H191  N19  C20   118.54  3.000
 XTP  C14   N19  C20   120.14  3.000
 XTP  H2    O13  C12   108.44  3.000
 XTP  C22   O21  C20   117.16  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
 XTP  CONST_01  C27   C28  C23  C24     0.00   0.0  0
 XTP  CONST_02  C27   C26  C25  C24     0.00   0.0  0
 XTP  CONST_03  C23   C28  C27  C26     0.00   0.0  0
 XTP  CONST_04  C23   C24  C25  C26     0.00   0.0  0
 XTP  CONST_05  C25   C26  C27  C28     0.00   0.0  0
 XTP  CONST_06  C25   C24  C23  C28     0.00   0.0  0
 XTP  CONST_07  C08   N09  C10  C06     0.00   0.0  0
 XTP  CONST_08  C27   C28  C23  C22   180.00   0.0  0
 XTP  CONST_09  C25   C24  C23  C22   180.00   0.0  0
 XTP  CONST_10  O11   C10  N09  C08   180.00   0.0  0
 XTP  CONST_11  H281  C28  C23  C24   180.00   0.0  0
 XTP  CONST_12  H261  C26  C25  C24   180.00   0.0  0
 XTP  CONST_13  H241  C24  C25  C26   180.00   0.0  0
 XTP  CONST_14  H271  C27  C28  C23   180.00   0.0  0
 XTP  CONST_15  H251  C25  C24  C23   180.00   0.0  0
 XTP  CONST_16  H091  N09  C10  C06   180.00   0.0  0
 XTP  CONST_17  O01   C02  N03  C04     0.00   0.0  0
 XTP  CONST_18  C14   C02  N03  C04   180.00   0.0  0
 XTP  CONST_19  H031  N03  C02  C14     0.00   0.0  0
 XTP  Var_01    C07   C08  N09  C10   -20.50  30.0  1
 XTP  Var_02    N09   C08  C07  C06    29.12  30.0  1
 XTP  Var_03    C17   C18  C16  C15  -110.89  30.0  1
 XTP  Var_04    H172  C17  C18  C16   108.23  30.0  1
 XTP  Var_05    C14   C15  C16  C17    93.29  30.0  1
 XTP  Var_06    O21   C22  C23  C24  -161.07  30.0  2
 XTP  Var_07    C23   C22  O21  C20    72.34  30.0  3
 XTP  Var_08    N19   C20  O21  C22  -176.49  30.0  3
 XTP  Var_09    O21   C20  N19  C14   170.18  30.0  2

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
 XTP  chir_01  C04  N03  C12  C05  positiv
 XTP  chir_02  C06  C10  C05  C07  positiv
 XTP  chir_03  C14  N19  C15  C02  negativ
 XTP  chir_04  C16  C18  C15  C17  both

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
 XTP  plan-1  C02   0.020
 XTP  plan-1  C04   0.020
 XTP  plan-1  C14   0.020
 XTP  plan-1  N03   0.020
 XTP  plan-1  O01   0.020
 XTP  plan-1  H031  0.020
 XTP  plan-2  C22   0.020
 XTP  plan-2  C24   0.020
 XTP  plan-2  C26   0.020
 XTP  plan-2  C28   0.020
 XTP  plan-2  C23   0.020
 XTP  plan-2  C25   0.020
 XTP  plan-2  C27   0.020
 XTP  plan-2  H261  0.020
 XTP  plan-2  H281  0.020
 XTP  plan-2  H251  0.020
 XTP  plan-2  H271  0.020
 XTP  plan-2  H241  0.020
 XTP  plan-3  C10   0.020
 XTP  plan-3  C06   0.020
 XTP  plan-3  C08   0.020
 XTP  plan-3  N09   0.020
 XTP  plan-3  O11   0.020
 XTP  plan-3  H091  0.020
 XTP  plan-4  C20   0.020
 XTP  plan-4  N19   0.020
 XTP  plan-4  O21   0.020
 XTP  plan-4  O29   0.020

