# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 17:47:04 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-{[(2S,3S)-3-(benzylcarbamoyl)oxiran-2-yl]carbonyl}-L-isoleucyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NC(=O)[C@H]1O[C@@H]1C(=O)NCc2ccccc2)C(=O)N3CCC[C@H]3C(O)=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
 78A  78A  N-{[(2S,3S)-3-(benzylcarbamoyl)oxiran-2-yl]carbonyl}-L-isoleucyl-L-proline  ligand  59  31  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_78A
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
 78A  N3    N  NH1    0  -0.632   3.7834  -0.2577  -2.0299
 78A  C10   C  CH2    0  -0.398   4.9859   0.5327  -1.8483
 78A  C11   C  CR6    0   0.124   4.8946   1.4369  -0.6441
 78A  C16   C  CR16   0  -0.295   4.1598   2.6184  -0.7096
 78A  C15   C  CR16   0  -0.243   4.0323   3.4348   0.4052
 78A  C14   C  CR16   0  -0.266   4.6431   3.0790   1.6017
 78A  C13   C  CR16   0  -0.243   5.3818   1.9059   1.6745
 78A  C12   C  CR16   0  -0.292   5.5039   1.0887   0.5573
 78A  C2    C  CH1    0  -0.147   2.1717  -1.9537  -1.5657
 78A  O1    O  O2     0  -0.444   2.0325  -3.3283  -1.3181
 78A  C3    C  CH1    0  -0.149   1.4493  -2.4567  -0.3888
 78A  C4    C  C      0   0.568  -0.0523  -2.3841  -0.4064
 78A  O4    O  O      0  -0.483  -0.7060  -2.7905  -1.3512
 78A  N1    N  NH1    0  -0.642  -0.5765  -1.8276   0.6927
 78A  C5    C  CH1    0  -0.192  -1.9693  -1.4671   0.7720
 78A  C6    C  C      0   0.572  -2.2494  -0.3095  -0.1991
 78A  O5    O  O      0  -0.504  -1.3260   0.3356  -0.6786
 78A  C17   C  CH1    0  -0.269  -2.3558  -1.1311   2.2249
 78A  C19   C  CH2    0  -0.444  -1.7167   0.1709   2.7189
 78A  C18   C  CH3    0  -0.661  -2.0672  -2.3240   3.1330
 78A  C20   C  CH3    0  -0.668  -2.1142   0.5347   4.1437
 78A  N2    N  NT     0  -0.469  -3.5262  -0.0479  -0.4966
 78A  C7    C  CH1    0  -0.140  -3.8461   1.0832  -1.3597
 78A  C8    C  C      0   0.406  -3.3736   2.4409  -0.8025
 78A  O6    O  OC    -1  -0.618  -3.1138   3.3086  -1.6597
 78A  C23   C  CH2    0  -0.493  -5.3785   1.0339  -1.4505
 78A  C22   C  CH2    0  -0.459  -5.7237  -0.4202  -1.1520
 78A  C21   C  CH2    0  -0.288  -4.7096  -0.7839  -0.0783
 78A  O7    O  O      0  -0.592  -3.3612   2.5744   0.4337
 78A  C9    C  C      0   0.575   3.5501  -1.3883  -1.3530
 78A  O2    O  O      0  -0.480   4.3515  -1.9261  -0.6078
 78A  HN3   H  HNH1   0   0.411   3.0441   0.1394  -2.5877
 78A  H101  H  HCH2   0   0.270   5.8408  -0.1362  -1.7593
 78A  H102  H  HCH2   0   0.278   5.1260   1.1181  -2.7567
 78A  H16   H  HCR6   0   0.253   3.6851   2.9058  -1.6409
 78A  H15   H  HCR6   0   0.256   3.4586   4.3505   0.3400
 78A  H14   H  HCR6   0   0.256   4.5458   3.7156   2.4717
 78A  H13   H  HCR6   0   0.255   5.8623   1.6236   2.6027
 78A  H12   H  HCR6   0   0.250   6.0759   0.1713   0.6209
 78A  H2    H  HCH1   0   0.291   1.5942  -1.5644  -2.4023
 78A  H3    H  HCH1   0   0.292   1.9396  -2.4019   0.5817
 78A  HN1   H  HNH1   0   0.405   0.0549  -1.4307   1.3712
 78A  H5    H  HCH1   0   0.278  -2.5536  -2.3406   0.4675
 78A  H17   H  HCH1   0   0.253  -3.4388  -0.9789   2.2307
 78A  H191  H  HCH2   0   0.259  -2.0164   0.9844   2.0546
 78A  H192  H  HCH2   0   0.208  -0.6239   0.1103   2.6641
 78A  H181  H  HCH3   0   0.221  -0.9969  -2.4871   3.2716
 78A  H182  H  HCH3   0   0.241  -2.5051  -2.1776   4.1197
 78A  H183  H  HCH3   0   0.234  -2.4914  -3.2411   2.7208
 78A  H201  H  HCH3   0   0.233  -1.7258   1.5177   4.4108
 78A  H202  H  HCH3   0   0.218  -3.1999   0.5683   4.2549
 78A  H203  H  HCH3   0   0.224  -1.7284  -0.1767   4.8740
 78A  H7    H  HCH1   0   0.227  -3.4064   0.9195  -2.3484
 78A  H231  H  HCH2   0   0.250  -5.7414   1.3743  -2.4191
 78A  H232  H  HCH2   0   0.234  -5.8208   1.6764  -0.6849
 78A  H221  H  HCH2   0   0.236  -5.5740  -1.0453  -2.0350
 78A  H222  H  HCH2   0   0.247  -6.7503  -0.5593  -0.8139
 78A  H211  H  HCH2   0   0.253  -4.5256  -1.8568  -0.0224
 78A  H212  H  HCH2   0   0.236  -5.0566  -0.4491   0.9042

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
 78A  N3   C10   single    1.450  0.020  1.450
 78A  N3   C9    single    1.338  0.020  1.338
 78A  N3   HN3   single    0.860  0.020  1.020
 78A  C10  C11   single    1.509  0.020  1.509
 78A  C10  H101  single    0.970  0.020  1.090
 78A  C10  H102  single    0.970  0.020  1.090
 78A  C11  C16   aromatic  1.393  0.020  1.393
 78A  C11  C12   aromatic  1.391  0.020  1.391
 78A  C16  C15   aromatic  1.388  0.020  1.388
 78A  C16  H16   single    0.930  0.020  1.080
 78A  C15  C14   aromatic  1.390  0.020  1.390
 78A  C15  H15   single    0.930  0.020  1.080
 78A  C14  C13   aromatic  1.388  0.020  1.388
 78A  C14  H14   single    0.930  0.020  1.080
 78A  C13  C12   aromatic  1.390  0.020  1.390
 78A  C13  H13   single    0.930  0.020  1.080
 78A  C12  H12   single    0.930  0.020  1.080
 78A  C2   O1    single    1.404  0.020  1.404
 78A  C2   C3    single    1.470  0.020  1.470
 78A  C2   C9    single    1.505  0.020  1.505
 78A  C2   H2    single    0.970  0.020  1.090
 78A  O1   C3    single    1.401  0.020  1.401
 78A  C3   C4    single    1.503  0.020  1.503
 78A  C3   H3    single    0.970  0.020  1.090
 78A  C4   O4    double    1.219  0.020  1.219
 78A  C4   N1    single    1.339  0.020  1.339
 78A  N1   C5    single    1.441  0.020  1.441
 78A  N1   HN1   single    0.860  0.020  1.020
 78A  C5   C6    single    1.537  0.020  1.537
 78A  C5   C17   single    1.540  0.020  1.540
 78A  C5   H5    single    0.970  0.020  1.090
 78A  C6   O5    double    1.224  0.020  1.224
 78A  C6   N2    single    1.337  0.020  1.337
 78A  C17  C19   single    1.532  0.020  1.532
 78A  C17  C18   single    1.527  0.020  1.527
 78A  C17  H17   single    0.970  0.020  1.090
 78A  C19  C20   single    1.523  0.020  1.523
 78A  C19  H191  single    0.970  0.020  1.090
 78A  C19  H192  single    0.970  0.020  1.090
 78A  C18  H181  single    0.970  0.020  1.090
 78A  C18  H182  single    0.970  0.020  1.090
 78A  C18  H183  single    0.970  0.020  1.090
 78A  C20  H201  single    0.970  0.020  1.090
 78A  C20  H202  single    0.970  0.020  1.090
 78A  C20  H203  single    0.970  0.020  1.090
 78A  N2   C7    single    1.458  0.020  1.458
 78A  N2   C21   single    1.455  0.020  1.455
 78A  C7   C8    single    1.542  0.020  1.542
 78A  C7   C23   single    1.536  0.020  1.536
 78A  C7   H7    single    0.970  0.020  1.090
 78A  C8   O6    deloc     1.247  0.020  1.247
 78A  C8   O7    deloc     1.243  0.020  1.243
 78A  C23  C22   single    1.524  0.020  1.524
 78A  C23  H231  single    0.970  0.020  1.090
 78A  C23  H232  single    0.970  0.020  1.090
 78A  C22  C21   single    1.521  0.020  1.521
 78A  C22  H221  single    0.970  0.020  1.090
 78A  C22  H222  single    0.970  0.020  1.090
 78A  C21  H211  single    0.970  0.020  1.090
 78A  C21  H212  single    0.970  0.020  1.090
 78A  C9   O2    double    1.219  0.020  1.219

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
 78A  HN3   N3   C9    119.02  3.000
 78A  HN3   N3   C10   117.57  3.000
 78A  C9    N3   C10   122.79  3.000
 78A  H102  C10  H101  107.28  3.000
 78A  H102  C10  C11   110.56  3.000
 78A  H101  C10  C11   110.51  3.000
 78A  H102  C10  N3    107.16  3.000
 78A  H101  C10  N3    109.04  3.000
 78A  C11   C10  N3    112.12  3.000
 78A  C12   C11  C16   118.94  3.000
 78A  C12   C11  C10   120.85  3.000
 78A  C16   C11  C10   120.18  3.000
 78A  H16   C16  C15   119.60  3.000
 78A  H16   C16  C11   119.75  3.000
 78A  C15   C16  C11   120.65  3.000
 78A  H15   C15  C14   120.08  3.000
 78A  H15   C15  C16   119.87  3.000
 78A  C14   C15  C16   120.04  3.000
 78A  H14   C14  C13   120.18  3.000
 78A  H14   C14  C15   120.13  3.000
 78A  C13   C14  C15   119.69  3.000
 78A  H13   C13  C12   119.80  3.000
 78A  H13   C13  C14   120.09  3.000
 78A  C12   C13  C14   120.11  3.000
 78A  H12   C12  C13   119.83  3.000
 78A  H12   C12  C11   119.60  3.000
 78A  C13   C12  C11   120.57  3.000
 78A  H2    C2   C9    117.40  3.000
 78A  H2    C2   C3    118.49  3.000
 78A  C9    C2   C3    117.75  3.000
 78A  H2    C2   O1    115.67  3.000
 78A  C9    C2   O1    115.71  3.000
 78A  C3    C2   O1     58.32  3.000
 78A  C3    O1   C2     63.20  3.000
 78A  H3    C3   C4    117.24  3.000
 78A  H3    C3   O1    115.79  3.000
 78A  C4    C3   O1    115.98  3.000
 78A  H3    C3   C2    118.37  3.000
 78A  C4    C3   C2    117.71  3.000
 78A  O1    C3   C2     58.48  3.000
 78A  N1    C4   O4    124.40  3.000
 78A  N1    C4   C3    113.68  3.000
 78A  O4    C4   C3    121.92  3.000
 78A  HN1   N1   C5    118.03  3.000
 78A  HN1   N1   C4    118.09  3.000
 78A  C5    N1   C4    121.85  3.000
 78A  H5    C5   C17   107.61  3.000
 78A  H5    C5   C6    109.16  3.000
 78A  C17   C5   C6    112.70  3.000
 78A  H5    C5   N1    107.52  3.000
 78A  C17   C5   N1    110.42  3.000
 78A  C6    C5   N1    109.26  3.000
 78A  N2    C6   O5    122.01  3.000
 78A  N2    C6   C5    117.53  3.000
 78A  O5    C6   C5    120.46  3.000
 78A  H17   C17  C18   107.02  3.000
 78A  H17   C17  C19   107.04  3.000
 78A  C18   C17  C19   113.16  3.000
 78A  H17   C17  C5    106.49  3.000
 78A  C18   C17  C5    110.07  3.000
 78A  C19   C17  C5    112.63  3.000
 78A  H192  C19  H191  106.53  3.000
 78A  H192  C19  C20   108.68  3.000
 78A  H191  C19  C20   108.63  3.000
 78A  H192  C19  C17   110.66  3.000
 78A  H191  C19  C17   108.80  3.000
 78A  C20   C19  C17   113.31  3.000
 78A  H183  C18  H182  107.38  3.000
 78A  H183  C18  H181  107.67  3.000
 78A  H182  C18  H181  107.41  3.000
 78A  H183  C18  C17   111.01  3.000
 78A  H182  C18  C17   110.96  3.000
 78A  H181  C18  C17   112.19  3.000
 78A  H203  C20  H202  107.68  3.000
 78A  H203  C20  H201  107.35  3.000
 78A  H202  C20  H201  107.55  3.000
 78A  H203  C20  C19   112.24  3.000
 78A  H202  C20  C19   111.23  3.000
 78A  H201  C20  C19   110.58  3.000
 78A  C21   N2   C7    112.59  3.000
 78A  C21   N2   C6    127.86  3.000
 78A  C7    N2   C6    119.54  3.000
 78A  H7    C7   C23   110.04  3.000
 78A  H7    C7   C8    109.58  3.000
 78A  C23   C7   C8    110.82  3.000
 78A  H7    C7   N2    109.30  3.000
 78A  C23   C7   N2    103.24  3.000
 78A  C8    C7   N2    113.70  3.000
 78A  O7    C8   O6    127.34  3.000
 78A  O7    C8   C7    117.19  3.000
 78A  O6    C8   C7    115.35  3.000
 78A  H232  C23  H231  107.72  3.000
 78A  H232  C23  C22   109.39  3.000
 78A  H231  C23  C22   113.39  3.000
 78A  H232  C23  C7    110.09  3.000
 78A  H231  C23  C7    112.03  3.000
 78A  C22   C23  C7    104.19  3.000
 78A  H222  C22  H221  107.88  3.000
 78A  H222  C22  C21   112.25  3.000
 78A  H221  C22  C21   110.02  3.000
 78A  H222  C22  C23   113.33  3.000
 78A  H221  C22  C23   110.89  3.000
 78A  C21   C22  C23   102.44  3.000
 78A  H212  C21  H211  107.97  3.000
 78A  H212  C21  C22   110.44  3.000
 78A  H211  C21  C22   112.59  3.000
 78A  H212  C21  N2    111.17  3.000
 78A  H211  C21  N2    112.05  3.000
 78A  C22   C21  N2    102.61  3.000
 78A  O2    C9   C2    121.51  3.000
 78A  O2    C9   N3    124.56  3.000
 78A  C2    C9   N3    113.93  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
 78A  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 78A  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 78A  CONST_03  C13   C12  C11  C16     0.00   0.0  0
 78A  CONST_04  C13   C14  C15  C16     0.00   0.0  0
 78A  CONST_05  C12   C11  C16  C15     0.00   0.0  0
 78A  CONST_06  C12   C13  C14  C15     0.00   0.0  0
 78A  CONST_07  C15   C16  C11  C10   180.00   0.0  0
 78A  CONST_08  C13   C12  C11  C10   180.00   0.0  0
 78A  CONST_09  H15   C15  C16  C11   180.00   0.0  0
 78A  CONST_10  H13   C13  C12  C11   180.00   0.0  0
 78A  CONST_11  H12   C12  C11  C16   180.00   0.0  0
 78A  CONST_12  H14   C14  C15  C16   180.00   0.0  0
 78A  CONST_13  H16   C16  C15  C14   180.00   0.0  0
 78A  CONST_14  C7    N2   C6   C5    180.00   0.0  0
 78A  CONST_15  C21   N2   C6   C5      0.00   0.0  0
 78A  CONST_16  C7    N2   C6   O5      0.00   0.0  0
 78A  CONST_17  C21   N2   C6   O5    180.00   0.0  0
 78A  CONST_18  C2    C9   N3   C10   180.00   0.0  0
 78A  CONST_19  C5    N1   C4   C3    180.00   0.0  0
 78A  CONST_20  HN3   N3   C9   C2      0.00   0.0  0
 78A  CONST_21  HN1   N1   C4   C3      0.00   0.0  0
 78A  CONST_22  O2    C9   N3   C10     0.00   0.0  0
 78A  CONST_23  C5    N1   C4   O4      0.00   0.0  0
 78A  Var_01    C23   C22  C21  N2    -36.08  30.0  1
 78A  Var_02    C22   C21  N2   C7     22.34  30.0  1
 78A  Var_03    C21   C22  C23  C7     37.41  30.0  1
 78A  Var_04    C4    C3   O1   C2    107.94  30.0  1
 78A  Var_05    C16   C11  C10  N3    -77.73  30.0  2
 78A  Var_06    O1    C2   C9   N3    156.97  30.0  1
 78A  Var_07    O4    C4   C3   C2     49.41  30.0  3
 78A  Var_08    C9    N3   C10  C11   -81.74  30.0  1
 78A  Var_09    H201  C20  C19  C17  -173.77  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
 78A  chir_03  C5   N1  C6   C17  positiv
 78A  chir_04  C17  C5  C19  C18  positiv
 78A  chir_05  C7   N2  C23  C8   negativ
 78A  chir_06  C2   O1  C3   C9   both
 78A  chir_07  C3   O1  C2   C4   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
 78A  plan-1  C3   0.020
 78A  plan-1  C4   0.020
 78A  plan-1  O4   0.020
 78A  plan-1  N1   0.020
 78A  plan-1  C5   0.020
 78A  plan-1  HN1  0.020
 78A  plan-2  C10  0.020
 78A  plan-2  C11  0.020
 78A  plan-2  C16  0.020
 78A  plan-2  C15  0.020
 78A  plan-2  C14  0.020
 78A  plan-2  C13  0.020
 78A  plan-2  C12  0.020
 78A  plan-2  H16  0.020
 78A  plan-2  H15  0.020
 78A  plan-2  H14  0.020
 78A  plan-2  H13  0.020
 78A  plan-2  H12  0.020
 78A  plan-3  N3   0.020
 78A  plan-3  C10  0.020
 78A  plan-3  C2   0.020
 78A  plan-3  C9   0.020
 78A  plan-3  O2   0.020
 78A  plan-3  HN3  0.020
 78A  plan-4  C5   0.020
 78A  plan-4  C6   0.020
 78A  plan-4  O5   0.020
 78A  plan-4  N2   0.020
 78A  plan-4  C7   0.020
 78A  plan-4  C21  0.020
 78A  plan-5  C7   0.020
 78A  plan-5  C8   0.020
 78A  plan-5  O6   0.020
 78A  plan-5  O7   0.020

