# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:54:07 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: ~{tert}-butyl ~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](O)C(=O)NCc2ccccc2
#
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
 8X8  8X8  '~{tert}-butyl ~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]carbamate'  ligand  57  28  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8X8
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
 8X8  C2   C  CT    0   0.192   1.0001  -4.3815   0.1192
 8X8  C3   C  CH3   0  -0.660   1.8601  -5.4190  -0.5929
 8X8  C4   C  CH3   0  -0.672  -0.4349  -4.4681  -0.3879
 8X8  C5   C  CH3   0  -0.669   1.0841  -4.5878   1.6272
 8X8  O1   O  O2    0  -0.504   1.6183  -3.1268  -0.2674
 8X8  C36  C  C     0   0.770   1.1300  -1.9441   0.1040
 8X8  O37  O  O     0  -0.507   0.1630  -1.7723   0.8172
 8X8  N38  N  NH1   0  -0.660   1.8896  -0.9505  -0.4116
 8X8  C40  C  CH1   0  -0.117   1.5066   0.4428  -0.3647
 8X8  C42  C  CH2   0  -0.414   2.7412   1.2890  -0.0527
 8X8  C45  C  CH1   0  -0.442   2.5615   2.8022  -0.0965
 8X8  C47  C  C     0   0.584   1.4514   3.3756   0.7762
 8X8  O48  O  O     0  -0.494   0.3256   2.9197   0.9285
 8X8  N49  N  NH1   0  -0.628   1.9155   4.5064   1.3282
 8X8  C51  C  CH2   0  -0.262   3.2459   4.8872   0.9022
 8X8  C54  C  CH2   0  -0.449   3.8022   3.5659   0.3736
 8X8  C57  C  CH1   0  -0.063   0.8165   0.8441  -1.6842
 8X8  O58  O  OH1   0  -0.669   1.6442   0.6138  -2.7868
 8X8  C66  C  C     0   0.523  -0.4794   0.0564  -1.8221
 8X8  O67  O  O     0  -0.498  -0.5449  -0.9065  -2.5765
 8X8  N68  N  NH1   0  -0.622  -1.4854   0.4709  -1.0510
 8X8  C70  C  CH2   0  -0.315  -2.7188  -0.2783  -0.9080
 8X8  C73  C  CR6   0   0.043  -3.4650   0.1681   0.3185
 8X8  C74  C  CR16  0  -0.290  -2.9280  -0.0559   1.5857
 8X8  C76  C  CR16  0  -0.302  -4.6908   0.8150   0.2090
 8X8  C78  C  CR16  0  -0.241  -5.3774   1.2274   1.3449
 8X8  C80  C  CR16  0  -0.263  -4.8381   0.9995   2.6028
 8X8  C82  C  CR16  0  -0.242  -3.6101   0.3579   2.7202
 8X8  H1   H  HCH3  0   0.237   1.8013  -5.3075  -1.6767
 8X8  H2   H  HCH3  0   0.237   2.9068  -5.3402  -0.2951
 8X8  H3   H  HCH3  0   0.230   1.5164  -6.4215  -0.3400
 8X8  H4   H  HCH3  0   0.250  -1.1104  -3.8115   0.1551
 8X8  H5   H  HCH3  0   0.234  -0.4895  -4.2193  -1.4492
 8X8  H6   H  HCH3  0   0.232  -0.7928  -5.4918  -0.2688
 8X8  H7   H  HCH3  0   0.233   0.7658  -5.6027   1.8678
 8X8  H8   H  HCH3  0   0.234   2.1100  -4.4714   1.9808
 8X8  H9   H  HCH3  0   0.244   0.4452  -3.9003   2.1768
 8X8  H10  H  HNH1  0   0.389   2.6313  -1.2048  -1.0461
 8X8  H11  H  HCH1  0   0.272   0.7928   0.5596   0.4472
 8X8  H12  H  HCH2  0   0.250   3.0963   1.0006   0.9403
 8X8  H13  H  HCH2  0   0.243   3.5438   1.0340  -0.7514
 8X8  H14  H  HCH1  0   0.287   2.3288   3.1165  -1.1223
 8X8  H15  H  HNH1  0   0.397   1.3160   5.1263   1.8510
 8X8  H16  H  HCH2  0   0.238   3.2040   5.6512   0.1210
 8X8  H17  H  HCH2  0   0.252   3.8256   5.2866   1.7333
 8X8  H18  H  HCH2  0   0.245   4.2853   3.0184   1.1863
 8X8  H19  H  HCH2  0   0.258   4.5376   3.7094  -0.4160
 8X8  H20  H  HCH1  0   0.258   0.5702   1.9095  -1.6447
 8X8  H21  H  HOH1  0   0.445   1.3716  -0.2301  -3.1737
 8X8  H22  H  HNH1  0   0.400  -1.3449   1.2807  -0.4651
 8X8  H23  H  HCH2  0   0.255  -3.3473  -0.1545  -1.7932
 8X8  H24  H  HCH2  0   0.259  -2.4737  -1.3403  -0.8322
 8X8  H25  H  HCR6  0   0.271  -1.9751  -0.5635   1.6794
 8X8  H26  H  HCR6  0   0.254  -5.1135   0.9984  -0.7718
 8X8  H27  H  HCR6  0   0.256  -6.3311   1.7293   1.2442
 8X8  H28  H  HCR6  0   0.257  -5.3713   1.3172   3.4895
 8X8  H29  H  HCR6  0   0.256  -3.1856   0.1760   3.6991

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
 8X8  O48  C47  double    1.224  0.020  1.224
 8X8  C47  N49  single    1.341  0.020  1.341
 8X8  C47  C45  single    1.524  0.020  1.524
 8X8  N49  C51  single    1.448  0.020  1.448
 8X8  C42  C45  single    1.524  0.020  1.524
 8X8  C42  C40  single    1.529  0.020  1.529
 8X8  C45  C54  single    1.531  0.020  1.531
 8X8  O67  C66  double    1.225  0.020  1.225
 8X8  C57  C40  single    1.542  0.020  1.542
 8X8  C57  C66  single    1.523  0.020  1.523
 8X8  C57  O58  single    1.398  0.020  1.398
 8X8  C40  N38  single    1.446  0.020  1.446
 8X8  N38  C36  single    1.353  0.020  1.353
 8X8  C51  C54  single    1.528  0.020  1.528
 8X8  C66  N68  single    1.334  0.020  1.334
 8X8  C3   C2   single    1.524  0.020  1.524
 8X8  O1   C36  single    1.332  0.020  1.332
 8X8  O1   C2   single    1.451  0.020  1.451
 8X8  C36  O37  double    1.214  0.020  1.214
 8X8  N68  C70  single    1.450  0.020  1.450
 8X8  C2   C4   single    1.524  0.020  1.524
 8X8  C2   C5   single    1.524  0.020  1.524
 8X8  C70  C73  single    1.504  0.020  1.504
 8X8  C73  C76  aromatic  1.390  0.020  1.390
 8X8  C73  C74  aromatic  1.394  0.020  1.394
 8X8  C76  C78  aromatic  1.390  0.020  1.390
 8X8  C74  C82  aromatic  1.387  0.020  1.387
 8X8  C78  C80  aromatic  1.387  0.020  1.387
 8X8  C82  C80  aromatic  1.390  0.020  1.390
 8X8  C3   H1   single    0.970  0.020  1.090
 8X8  C3   H2   single    0.970  0.020  1.090
 8X8  C3   H3   single    0.970  0.020  1.090
 8X8  C4   H4   single    0.970  0.020  1.090
 8X8  C4   H5   single    0.970  0.020  1.090
 8X8  C4   H6   single    0.970  0.020  1.090
 8X8  C5   H7   single    0.970  0.020  1.090
 8X8  C5   H8   single    0.970  0.020  1.090
 8X8  C5   H9   single    0.970  0.020  1.090
 8X8  N38  H10  single    0.860  0.020  1.020
 8X8  C40  H11  single    0.970  0.020  1.090
 8X8  C42  H12  single    0.970  0.020  1.090
 8X8  C42  H13  single    0.970  0.020  1.090
 8X8  C45  H14  single    0.970  0.020  1.090
 8X8  N49  H15  single    0.860  0.020  1.020
 8X8  C51  H16  single    0.970  0.020  1.090
 8X8  C51  H17  single    0.970  0.020  1.090
 8X8  C54  H18  single    0.970  0.020  1.090
 8X8  C54  H19  single    0.970  0.020  1.090
 8X8  C57  H20  single    0.970  0.020  1.090
 8X8  O58  H21  single    0.850  0.020  0.980
 8X8  N68  H22  single    0.860  0.020  1.020
 8X8  C70  H23  single    0.970  0.020  1.090
 8X8  C70  H24  single    0.970  0.020  1.090
 8X8  C74  H25  single    0.930  0.020  1.080
 8X8  C76  H26  single    0.930  0.020  1.080
 8X8  C78  H27  single    0.930  0.020  1.080
 8X8  C80  H28  single    0.930  0.020  1.080
 8X8  C82  H29  single    0.930  0.020  1.080

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
 8X8  O1   C2   C5   110.92  3.000
 8X8  C5   C2   C4   111.92  3.000
 8X8  O1   C2   C4   111.19  3.000
 8X8  C5   C2   C3   109.82  3.000
 8X8  C4   C2   C3   109.70  3.000
 8X8  O1   C2   C3   102.93  3.000
 8X8  H3   C3   H2   107.80  3.000
 8X8  H3   C3   H1   107.92  3.000
 8X8  H2   C3   H1   108.39  3.000
 8X8  H3   C3   C2   109.87  3.000
 8X8  H2   C3   C2   111.38  3.000
 8X8  H1   C3   C2   111.35  3.000
 8X8  H6   C4   H5   107.68  3.000
 8X8  H6   C4   H4   107.96  3.000
 8X8  H5   C4   H4   108.48  3.000
 8X8  H6   C4   C2   109.01  3.000
 8X8  H5   C4   C2   110.95  3.000
 8X8  H4   C4   C2   112.60  3.000
 8X8  H9   C5   H8   108.72  3.000
 8X8  H9   C5   H7   107.78  3.000
 8X8  H8   C5   H7   107.59  3.000
 8X8  H9   C5   C2   112.46  3.000
 8X8  H8   C5   C2   110.97  3.000
 8X8  H7   C5   C2   109.16  3.000
 8X8  C36  O1   C2   122.49  3.000
 8X8  N38  C36  O37  124.56  3.000
 8X8  O37  C36  O1   125.55  3.000
 8X8  N38  C36  O1   109.88  3.000
 8X8  H10  N38  C40  117.27  3.000
 8X8  H10  N38  C36  117.87  3.000
 8X8  C40  N38  C36  123.14  3.000
 8X8  H11  C40  C57  108.49  3.000
 8X8  H11  C40  C42  108.56  3.000
 8X8  C57  C40  C42  113.07  3.000
 8X8  H11  C40  N38  107.56  3.000
 8X8  C57  C40  N38  109.97  3.000
 8X8  C42  C40  N38  109.03  3.000
 8X8  H13  C42  H12  106.27  3.000
 8X8  H13  C42  C45  107.42  3.000
 8X8  H12  C42  C45  109.04  3.000
 8X8  H13  C42  C40  109.45  3.000
 8X8  H12  C42  C40  107.55  3.000
 8X8  C45  C42  C40  116.64  3.000
 8X8  H14  C45  C54  108.41  3.000
 8X8  H14  C45  C47  105.84  3.000
 8X8  C54  C45  C47  103.11  3.000
 8X8  H14  C45  C42  109.64  3.000
 8X8  C54  C45  C42  113.01  3.000
 8X8  C47  C45  C42  116.29  3.000
 8X8  N49  C47  O48  125.52  3.000
 8X8  N49  C47  C45  107.51  3.000
 8X8  O48  C47  C45  126.94  3.000
 8X8  H15  N49  C51  122.48  3.000
 8X8  H15  N49  C47  121.73  3.000
 8X8  C51  N49  C47  114.75  3.000
 8X8  H17  C51  H16  108.02  3.000
 8X8  H17  C51  C54  112.78  3.000
 8X8  H16  C51  C54  111.78  3.000
 8X8  H17  C51  N49  111.16  3.000
 8X8  H16  C51  N49  111.02  3.000
 8X8  C54  C51  N49  102.06  3.000
 8X8  H19  C54  H18  107.87  3.000
 8X8  H19  C54  C51  112.52  3.000
 8X8  H18  C54  C51  109.69  3.000
 8X8  H19  C54  C45  112.99  3.000
 8X8  H18  C54  C45  109.68  3.000
 8X8  C51  C54  C45  104.04  3.000
 8X8  H20  C57  C66  108.39  3.000
 8X8  H20  C57  O58  108.80  3.000
 8X8  C66  C57  O58  110.32  3.000
 8X8  H20  C57  C40  108.86  3.000
 8X8  O58  C57  C40  111.53  3.000
 8X8  C66  C57  C40  108.89  3.000
 8X8  H21  O58  C57  107.00  3.000
 8X8  N68  C66  O67  124.06  3.000
 8X8  N68  C66  C57  115.39  3.000
 8X8  O67  C66  C57  120.53  3.000
 8X8  H22  N68  C70  118.40  3.000
 8X8  H22  N68  C66  118.69  3.000
 8X8  C70  N68  C66  122.55  3.000
 8X8  H24  C70  H23  107.18  3.000
 8X8  H24  C70  C73  110.08  3.000
 8X8  H23  C70  C73  109.98  3.000
 8X8  H24  C70  N68  108.56  3.000
 8X8  H23  C70  N68  110.53  3.000
 8X8  C73  C70  N68  110.44  3.000
 8X8  C76  C73  C74  119.07  3.000
 8X8  C74  C73  C70  120.17  3.000
 8X8  C76  C73  C70  120.76  3.000
 8X8  H25  C74  C82  120.09  3.000
 8X8  H25  C74  C73  119.50  3.000
 8X8  C82  C74  C73  120.40  3.000
 8X8  H26  C76  C78  119.79  3.000
 8X8  H26  C76  C73  119.61  3.000
 8X8  C78  C76  C73  120.61  3.000
 8X8  H27  C78  C80  120.20  3.000
 8X8  H27  C78  C76  119.79  3.000
 8X8  C80  C78  C76  120.01  3.000
 8X8  H28  C80  C82  120.09  3.000
 8X8  H28  C80  C78  120.20  3.000
 8X8  C82  C80  C78  119.71  3.000
 8X8  H29  C82  C80  120.02  3.000
 8X8  H29  C82  C74  119.79  3.000
 8X8  C80  C82  C74  120.19  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
 8X8  CONST_01  C80  C78  C76  C73     0.00   0.0  0
 8X8  CONST_02  C80  C82  C74  C73     0.00   0.0  0
 8X8  CONST_03  C78  C76  C73  C74     0.00   0.0  0
 8X8  CONST_04  C78  C80  C82  C74     0.00   0.0  0
 8X8  CONST_05  C82  C74  C73  C76     0.00   0.0  0
 8X8  CONST_06  C82  C80  C78  C76     0.00   0.0  0
 8X8  CONST_07  C51  N49  C47  C45     0.00   0.0  0
 8X8  CONST_08  C78  C76  C73  C70   180.00   0.0  0
 8X8  CONST_09  C82  C74  C73  C70   180.00   0.0  0
 8X8  CONST_10  C51  N49  C47  O48   180.00   0.0  0
 8X8  CONST_11  H27  C78  C76  C73   180.00   0.0  0
 8X8  CONST_12  H29  C82  C74  C73   180.00   0.0  0
 8X8  CONST_13  H26  C76  C73  C74   180.00   0.0  0
 8X8  CONST_14  H28  C80  C82  C74   180.00   0.0  0
 8X8  CONST_15  H25  C74  C73  C76   180.00   0.0  0
 8X8  CONST_16  H15  N49  C47  C45   180.00   0.0  0
 8X8  CONST_17  C70  N68  C66  C57   180.00   0.0  0
 8X8  CONST_18  C70  N68  C66  O67     0.00   0.0  0
 8X8  CONST_19  H22  N68  C66  C57     0.00   0.0  0
 8X8  Var_01    N49  C51  C54  C45    28.19  30.0  1
 8X8  Var_02    C54  C51  N49  C47   -20.31  30.0  1
 8X8  Var_03    C76  C73  C70  N68   113.66  30.0  2
 8X8  Var_04    C73  C70  N68  C66   161.84  30.0  3
 8X8  Var_05    N38  C36  O1   C2   -179.12  30.0  3
 8X8  Var_06    C40  N38  C36  O1    170.11  30.0  2
 8X8  Var_07    H4   C4   C2   C3    174.63  30.0  3
 8X8  Var_08    H7   C5   C2   C3    -57.54  30.0  3
 8X8  Var_09    H1   C3   C2   C4     55.38  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
 8X8  chir_01  C40  C42  C57  N38  negativ
 8X8  chir_02  C45  C47  C42  C54  positiv
 8X8  chir_03  C57  O58  C40  C66  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
 8X8  plan-1  C70  0.020
 8X8  plan-1  C73  0.020
 8X8  plan-1  C74  0.020
 8X8  plan-1  C76  0.020
 8X8  plan-1  C78  0.020
 8X8  plan-1  C80  0.020
 8X8  plan-1  C82  0.020
 8X8  plan-1  H25  0.020
 8X8  plan-1  H26  0.020
 8X8  plan-1  H27  0.020
 8X8  plan-1  H28  0.020
 8X8  plan-1  H29  0.020
 8X8  plan-2  C57  0.020
 8X8  plan-2  C66  0.020
 8X8  plan-2  O67  0.020
 8X8  plan-2  N68  0.020
 8X8  plan-2  C70  0.020
 8X8  plan-2  H22  0.020
 8X8  plan-3  C45  0.020
 8X8  plan-3  C47  0.020
 8X8  plan-3  O48  0.020
 8X8  plan-3  N49  0.020
 8X8  plan-3  C51  0.020
 8X8  plan-3  H15  0.020
 8X8  plan-4  O1   0.020
 8X8  plan-4  C36  0.020
 8X8  plan-4  O37  0.020
 8X8  plan-4  N38  0.020

