# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:44:00 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: ethyl (2Z,4S)-4-[(N-acetyl-L-phenylalanyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)\C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(C)=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
 5F2  5F2  'ethyl (2Z,4S)-4-[(N-acetyl-L-phenylalanyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate'  ligand  59  30  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5F2
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
 5F2  N1   N  NR15  0  -0.618  -4.6667   1.9533   0.5012
 5F2  C2   C  CH1   0  -0.200   2.2817   1.0552  -0.1697
 5F2  C3   C  CH2   0  -0.555   3.0267  -0.1991  -0.6748
 5F2  C4   C  CR6   0   0.156   4.4744   0.0986  -0.9456
 5F2  C5   C  CR16  0  -0.310   5.4614  -0.2504  -0.0285
 5F2  C6   C  CR16  0  -0.243   6.7949   0.0567  -0.2670
 5F2  C7   C  CR16  0  -0.271   7.1596   0.7217  -1.4300
 5F2  C8   C  CR16  0  -0.241   6.1829   1.0729  -2.3537
 5F2  C9   C  CR16  0  -0.306   4.8521   0.7621  -2.1113
 5F2  C19  C  CH3   0  -0.689  -5.2510  -4.8967   1.3847
 5F2  C20  C  C     0   0.531   3.1306   1.1422   2.1356
 5F2  C22  C  CH3   0  -0.778   3.7682   2.0475   3.1605
 5F2  O3   O  O     0  -0.455  -1.8911  -2.4551   1.2301
 5F2  C16  C  C     0   0.579  -2.5258  -2.7884   0.2594
 5F2  O2   O  O2    0  -0.461  -3.5952  -3.5702   0.3086
 5F2  C18  C  CH2   0  -0.179  -4.0650  -3.9877   1.5982
 5F2  C14  C  C1    0  -0.161  -1.6488  -1.3022  -1.5425
 5F2  C10  C  CH1   0  -0.142  -1.3133  -0.0946  -0.7182
 5F2  C11  C  CH2   0  -0.432  -2.0539   1.1349  -1.2631
 5F2  C12  C  CR15  0  -0.405  -3.5821   1.0196  -1.3168
 5F2  C26  C  CH2   0  -0.465  -4.2298   2.3412  -1.7412
 5F2  C25  C  CH2   0  -0.261  -4.5100   3.0596  -0.4179
 5F2  C13  C  CR5   0   0.546  -4.1733   0.7821   0.0668
 5F2  O1   O  O     0  -0.483  -4.1832  -0.2724   0.6831
 5F2  N    N  NH1   0  -0.653   0.1251   0.1145  -0.7788
 5F2  C17  C  C     0   0.576   0.7992   0.8096   0.1553
 5F2  O4   O  O     0  -0.476   0.2747   1.2530   1.1608
 5F2  N2   N  NH1   0  -0.620   2.9433   1.7031   0.9274
 5F2  O21  O  O     0  -0.500   2.8004  -0.0059   2.3945
 5F2  H1   H  HNR5  0   0.396  -5.0286   2.0675   1.4354
 5F2  H2   H  HCH1  0   0.304   2.2865   1.7831  -0.9874
 5F2  H3   H  HCH2  0   0.272   2.9336  -1.0066   0.0499
 5F2  H4   H  HCH2  0   0.259   2.5585  -0.5413  -1.5993
 5F2  H5   H  HCR6  0   0.245   5.1826  -0.7689   0.8809
 5F2  H6   H  HCR6  0   0.253   7.5494  -0.2243   0.4569
 5F2  H7   H  HCR6  0   0.254   8.1982   0.9607  -1.6189
 5F2  H8   H  HCR6  0   0.253   6.4590   1.5867  -3.2658
 5F2  H9   H  HCR6  0   0.247   4.0972   1.0355  -2.8404
 5F2  H10  H  HCH3  0   0.239  -5.6321  -5.2203   2.3528
 5F2  H11  H  HCH3  0   0.236  -6.0596  -4.3874   0.8607
 5F2  H12  H  HCH3  0   0.236  -4.9763  -5.7873   0.8194
 5F2  H13  H  HCH3  0   0.269   2.9864   2.5434   3.7385
 5F2  H14  H  HCH3  0   0.260   4.3711   1.4623   3.8512
 5F2  H15  H  HCH3  0   0.251   4.3911   2.8210   2.7140
 5F2  H16  H  HCH2  0   0.234  -4.3451  -3.1091   2.1831
 5F2  H17  H  HCH2  0   0.234  -3.2684  -4.5077   2.1338
 5F2  H18  H  H     0   0.280  -2.4599  -3.1861  -1.8896
 5F2  H20  H  H     0   0.278  -1.4666  -1.1911  -2.6092
 5F2  H22  H  HCH1  0   0.280  -1.5761  -0.2564   0.3225
 5F2  H23  H  HCH2  0   0.255  -1.7663   2.0005  -0.6593
 5F2  H24  H  HCH2  0   0.247  -1.6996   1.3337  -2.2792
 5F2  H25  H  HCR5  0   0.278  -3.8635   0.1980  -1.9784
 5F2  H26  H  HCH2  0   0.254  -3.5993   2.9305  -2.4062
 5F2  H27  H  HCH2  0   0.258  -5.1701   2.1459  -2.2582
 5F2  H28  H  HCH2  0   0.254  -5.4132   3.6678  -0.4577
 5F2  H29  H  HCH2  0   0.237  -3.6837   3.7111  -0.1187
 5F2  H30  H  HNH1  0   0.405   0.5868  -0.1075  -1.6467
 5F2  H31  H  HNH1  0   0.404   3.2324   2.6565   0.7913
 5F2  C15  C  C1    0  -0.353  -2.2011  -2.4439  -1.1431

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
 5F2  O3   C16  double    1.207  0.020  1.207
 5F2  C16  O2   single    1.326  0.020  1.326
 5F2  C16  C15  single    1.480  0.020  1.480
 5F2  C18  O2   single    1.435  0.020  1.435
 5F2  C18  C19  single    1.509  0.020  1.509
 5F2  C15  C14  double    1.330  0.020  1.330
 5F2  C14  C10  single    1.500  0.020  1.500
 5F2  C11  C10  single    1.535  0.020  1.535
 5F2  C11  C12  single    1.534  0.020  1.534
 5F2  C10  N    single    1.455  0.020  1.455
 5F2  O1   C13  double    1.221  0.020  1.221
 5F2  C13  C12  single    1.523  0.020  1.523
 5F2  C13  N1   single    1.343  0.020  1.343
 5F2  C12  C26  single    1.532  0.020  1.532
 5F2  N    C17  single    1.345  0.020  1.345
 5F2  N1   C25  single    1.447  0.020  1.447
 5F2  O4   C17  double    1.218  0.020  1.218
 5F2  C25  C26  single    1.532  0.020  1.532
 5F2  C17  C2   single    1.537  0.020  1.537
 5F2  C3   C2   single    1.544  0.020  1.544
 5F2  C3   C4   single    1.503  0.020  1.503
 5F2  C2   N2   single    1.436  0.020  1.436
 5F2  C4   C5   aromatic  1.392  0.020  1.392
 5F2  C4   C9   aromatic  1.393  0.020  1.393
 5F2  C5   C6   aromatic  1.389  0.020  1.389
 5F2  O21  C20  double    1.222  0.020  1.222
 5F2  N2   C20  single    1.345  0.020  1.345
 5F2  C9   C8   aromatic  1.388  0.020  1.388
 5F2  C20  C22  single    1.509  0.020  1.509
 5F2  C6   C7   aromatic  1.388  0.020  1.388
 5F2  C8   C7   aromatic  1.389  0.020  1.389
 5F2  N1   H1   single    0.860  0.020  1.020
 5F2  C2   H2   single    0.970  0.020  1.090
 5F2  C3   H3   single    0.970  0.020  1.090
 5F2  C3   H4   single    0.970  0.020  1.090
 5F2  C5   H5   single    0.930  0.020  1.080
 5F2  C6   H6   single    0.930  0.020  1.080
 5F2  C7   H7   single    0.930  0.020  1.080
 5F2  C8   H8   single    0.930  0.020  1.080
 5F2  C9   H9   single    0.930  0.020  1.080
 5F2  C19  H10  single    0.970  0.020  1.090
 5F2  C19  H11  single    0.970  0.020  1.090
 5F2  C19  H12  single    0.970  0.020  1.090
 5F2  C22  H13  single    0.970  0.020  1.090
 5F2  C22  H14  single    0.970  0.020  1.090
 5F2  C22  H15  single    0.970  0.020  1.090
 5F2  C18  H16  single    0.970  0.020  1.090
 5F2  C18  H17  single    0.970  0.020  1.090
 5F2  C15  H18  single    0.930  0.020  1.080
 5F2  C14  H20  single    0.930  0.020  1.080
 5F2  C10  H22  single    0.970  0.020  1.090
 5F2  C11  H23  single    0.970  0.020  1.090
 5F2  C11  H24  single    0.970  0.020  1.090
 5F2  C12  H25  single    0.970  0.020  1.090
 5F2  C26  H26  single    0.970  0.020  1.090
 5F2  C26  H27  single    0.970  0.020  1.090
 5F2  C25  H28  single    0.970  0.020  1.090
 5F2  C25  H29  single    0.970  0.020  1.090
 5F2  N    H30  single    0.860  0.020  1.020
 5F2  N2   H31  single    0.860  0.020  1.020

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
 5F2  H1   N1   C13  122.02  3.000
 5F2  H1   N1   C25  122.74  3.000
 5F2  C13  N1   C25  114.93  3.000
 5F2  H2   C2   N2   105.59  3.000
 5F2  H2   C2   C17  105.56  3.000
 5F2  N2   C2   C17  110.78  3.000
 5F2  H2   C2   C3   107.09  3.000
 5F2  N2   C2   C3   113.22  3.000
 5F2  C17  C2   C3   113.87  3.000
 5F2  H4   C3   H3   107.13  3.000
 5F2  H4   C3   C4   108.82  3.000
 5F2  H3   C3   C4   110.44  3.000
 5F2  H4   C3   C2   108.96  3.000
 5F2  H3   C3   C2   110.09  3.000
 5F2  C4   C3   C2   111.28  3.000
 5F2  C9   C4   C5   118.58  3.000
 5F2  C9   C4   C3   120.42  3.000
 5F2  C5   C4   C3   120.98  3.000
 5F2  H5   C5   C6   119.80  3.000
 5F2  H5   C5   C4   119.38  3.000
 5F2  C6   C5   C4   120.81  3.000
 5F2  H6   C6   C7   120.09  3.000
 5F2  H6   C6   C5   119.79  3.000
 5F2  C7   C6   C5   120.12  3.000
 5F2  H7   C7   C8   120.17  3.000
 5F2  H7   C7   C6   120.27  3.000
 5F2  C8   C7   C6   119.56  3.000
 5F2  H8   C8   C9   119.86  3.000
 5F2  H8   C8   C7   120.05  3.000
 5F2  C9   C8   C7   120.08  3.000
 5F2  H9   C9   C8   119.57  3.000
 5F2  H9   C9   C4   119.58  3.000
 5F2  C8   C9   C4   120.84  3.000
 5F2  H12  C19  H11  108.63  3.000
 5F2  H12  C19  H10  107.83  3.000
 5F2  H11  C19  H10  107.85  3.000
 5F2  H12  C19  C18  111.55  3.000
 5F2  H11  C19  C18  111.69  3.000
 5F2  H10  C19  C18  109.15  3.000
 5F2  O21  C20  N2   122.97  3.000
 5F2  N2   C20  C22  114.76  3.000
 5F2  O21  C20  C22  122.27  3.000
 5F2  H15  C22  H14  108.99  3.000
 5F2  H15  C22  H13  107.71  3.000
 5F2  H14  C22  H13  107.77  3.000
 5F2  H15  C22  C20  112.92  3.000
 5F2  H14  C22  C20  110.05  3.000
 5F2  H13  C22  C20  109.25  3.000
 5F2  C15  C16  O2   110.45  3.000
 5F2  C15  C16  O3   125.63  3.000
 5F2  O2   C16  O3   123.87  3.000
 5F2  C18  O2   C16  117.98  3.000
 5F2  H17  C18  H16  107.91  3.000
 5F2  H17  C18  O2   109.92  3.000
 5F2  H16  C18  O2   109.35  3.000
 5F2  H17  C18  C19  110.85  3.000
 5F2  H16  C18  C19  111.02  3.000
 5F2  O2   C18  C19  107.78  3.000
 5F2  H20  C14  C10  114.78  3.000
 5F2  H20  C14  C15  116.86  3.000
 5F2  C10  C14  C15  128.24  3.000
 5F2  H22  C10  N    107.50  3.000
 5F2  H22  C10  C11  110.05  3.000
 5F2  N    C10  C11  110.30  3.000
 5F2  H22  C10  C14  110.66  3.000
 5F2  N    C10  C14  108.29  3.000
 5F2  C11  C10  C14  109.98  3.000
 5F2  H24  C11  H23  106.48  3.000
 5F2  H24  C11  C12  107.69  3.000
 5F2  H23  C11  C12  109.92  3.000
 5F2  H24  C11  C10  108.60  3.000
 5F2  H23  C11  C10  108.12  3.000
 5F2  C12  C11  C10  115.65  3.000
 5F2  H25  C12  C13  109.46  3.000
 5F2  H25  C12  C26  111.87  3.000
 5F2  C13  C12  C26  102.83  3.000
 5F2  H25  C12  C11  109.55  3.000
 5F2  C26  C12  C11  111.48  3.000
 5F2  C13  C12  C11  111.51  3.000
 5F2  H27  C26  H26  107.85  3.000
 5F2  H27  C26  C25  109.62  3.000
 5F2  H26  C26  C25  112.30  3.000
 5F2  H27  C26  C12  109.96  3.000
 5F2  H26  C26  C12  113.02  3.000
 5F2  C25  C26  C12  104.05  3.000
 5F2  H29  C25  H28  107.68  3.000
 5F2  H29  C25  C26  112.18  3.000
 5F2  H28  C25  C26  112.46  3.000
 5F2  H29  C25  N1   111.31  3.000
 5F2  H28  C25  N1   111.11  3.000
 5F2  C26  C25  N1   102.12  3.000
 5F2  O1   C13  C12  126.59  3.000
 5F2  C12  C13  N1   107.48  3.000
 5F2  O1   C13  N1   125.92  3.000
 5F2  H30  N    C17  118.82  3.000
 5F2  H30  N    C10  117.21  3.000
 5F2  C17  N    C10  122.73  3.000
 5F2  O4   C17  N    123.07  3.000
 5F2  O4   C17  C2   122.12  3.000
 5F2  N    C17  C2   114.76  3.000
 5F2  H31  N2   C20  118.49  3.000
 5F2  H31  N2   C2   117.18  3.000
 5F2  C20  N2   C2   124.22  3.000
 5F2  H18  C15  C14  118.70  3.000
 5F2  H18  C15  C16  116.15  3.000
 5F2  C14  C15  C16  125.14  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
 5F2  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 5F2  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 5F2  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 5F2  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 5F2  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 5F2  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 5F2  CONST_07  C25  N1   C13  C12     0.00   0.0  0
 5F2  CONST_08  C6   C5   C4   C3    180.00   0.0  0
 5F2  CONST_09  C8   C9   C4   C3    180.00   0.0  0
 5F2  CONST_10  O1   C13  N1   C25   180.00   0.0  0
 5F2  CONST_11  H6   C6   C5   C4    180.00   0.0  0
 5F2  CONST_12  H8   C8   C9   C4    180.00   0.0  0
 5F2  CONST_13  H9   C9   C4   C5    180.00   0.0  0
 5F2  CONST_14  H7   C7   C6   C5    180.00   0.0  0
 5F2  CONST_15  H5   C5   C6   C7    180.00   0.0  0
 5F2  CONST_16  H1   N1   C13  C12   180.00   0.0  0
 5F2  CONST_17  C10  N    C17  C2    180.00   0.0  0
 5F2  CONST_18  O21  C20  N2   C2      0.00   0.0  0
 5F2  CONST_19  C22  C20  N2   C2    180.00   0.0  0
 5F2  CONST_20  O4   C17  N    C10     0.00   0.0  0
 5F2  CONST_21  H30  N    C17  C2      0.00   0.0  0
 5F2  CONST_22  H31  N2   C20  C22     0.00   0.0  0
 5F2  Var_01    C12  C26  C25  N1    -27.54  30.0  1
 5F2  Var_02    C13  N1   C25  C26    17.78  30.0  1
 5F2  Var_03    C5   C4   C3   C2    100.35  30.0  2
 5F2  Var_04    C10  C14  C15  C16    -4.21   0.0  2
 5F2  Var_05    C14  C15  C16  O3    -34.27  30.0  2
 5F2  Var_06    C15  C16  O2   C18  -179.13  30.0  1
 5F2  Var_07    H16  C18  O2   C16    61.06  30.0  1
 5F2  Var_08    H10  C19  C18  O2   -179.48  30.0  3
 5F2  Var_09    H13  C22  C20  N2     93.24  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
 5F2  chir_01  C2   C17  C3   N2   positiv
 5F2  chir_02  C10  N    C14  C11  positiv
 5F2  chir_03  C12  C26  C13  C11  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
 5F2  plan-1  C3   0.020
 5F2  plan-1  C4   0.020
 5F2  plan-1  C5   0.020
 5F2  plan-1  C6   0.020
 5F2  plan-1  C7   0.020
 5F2  plan-1  C8   0.020
 5F2  plan-1  C9   0.020
 5F2  plan-1  H5   0.020
 5F2  plan-1  H6   0.020
 5F2  plan-1  H7   0.020
 5F2  plan-1  H8   0.020
 5F2  plan-1  H9   0.020
 5F2  plan-2  C2   0.020
 5F2  plan-2  C10  0.020
 5F2  plan-2  N    0.020
 5F2  plan-2  C17  0.020
 5F2  plan-2  O4   0.020
 5F2  plan-2  H30  0.020
 5F2  plan-3  C2   0.020
 5F2  plan-3  C20  0.020
 5F2  plan-3  C22  0.020
 5F2  plan-3  N2   0.020
 5F2  plan-3  O21  0.020
 5F2  plan-3  H31  0.020
 5F2  plan-4  N1   0.020
 5F2  plan-4  C12  0.020
 5F2  plan-4  C25  0.020
 5F2  plan-4  C13  0.020
 5F2  plan-4  O1   0.020
 5F2  plan-4  H1   0.020
 5F2  plan-5  O3   0.020
 5F2  plan-5  C16  0.020
 5F2  plan-5  O2   0.020
 5F2  plan-5  C15  0.020
 5F2  plan-6  C16  0.020
 5F2  plan-6  C14  0.020
 5F2  plan-6  C10  0.020
 5F2  plan-6  H18  0.020
 5F2  plan-6  H20  0.020
 5F2  plan-6  C15  0.020

