# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:33:13 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (3S)-3-[(2R)-2-amino-5-cyclopropyl-5-oxopentyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC(=O)C1CC1)C[C@@H]2CCNC2=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
 2UA  2UA  (3S)-3-[(2R)-2-amino-5-cyclopropyl-5-oxopentyl]pyrrolidin-2-one  peptide  36  16  .  2022-07-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_2UA
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
 2UA  C1   C  CH1   0  -0.401  -4.7045   0.5222   0.1040
 2UA  C2   C  CH2   0  -0.459  -5.8501   0.5248  -0.8796
 2UA  C3   C  CH2   0  -0.461  -5.9728  -0.2552   0.3724
 2UA  C4   C  C     0   0.440  -3.4764  -0.2347  -0.2396
 2UA  C5   C  CH2   0  -0.587  -2.1928   0.3316   0.3066
 2UA  C6   C  CH2   0  -0.414  -0.9395  -0.4444  -0.0563
 2UA  C7   C  CH1   0  -0.099   0.3419   0.2101   0.4710
 2UA  C8   C  CH2   0  -0.412   1.5647  -0.5805   0.0076
 2UA  C9   C  CH1   0  -0.401   2.8752   0.1333   0.2911
 2UA  C10  C  CH2   0  -0.466   3.0882   1.4300  -0.4910
 2UA  C11  C  CH2   0  -0.259   4.6084   1.5342  -0.6255
 2UA  N1   N  NH1   0  -0.630   5.0133   0.1444  -0.5915
 2UA  C12  C  C     0   0.563   4.1028  -0.6895  -0.0622
 2UA  O1   O  O     0  -0.500   4.2468  -1.8896   0.1157
 2UA  O2   O  O     0  -0.426  -3.5126  -1.2465  -0.9094
 2UA  N    N  NH2   0  -0.791   0.3937   0.3805   1.9169
 2UA  H1   H  HCH1  0   0.273  -4.5558   1.4237   0.6861
 2UA  H2   H  HCH2  0   0.264  -6.4061   1.4481  -0.9725
 2UA  H3   H  HCH2  0   0.258  -5.7028  -0.0145  -1.8064
 2UA  H4   H  HCH2  0   0.258  -5.9089  -1.3340   0.3136
 2UA  H5   H  HCH2  0   0.265  -6.6110   0.1235   1.1594
 2UA  H6   H  HCH2  0   0.269  -2.1192   1.3717  -0.0353
 2UA  H7   H  HCH2  0   0.221  -1.0086  -1.4681   0.3260
 2UA  H8   H  HCH1  0   0.227   0.4022   1.2147   0.0361
 2UA  H9   H  HCH2  0   0.226   1.5629  -1.5618   0.4925
 2UA  H10  H  HCH2  0   0.226   1.4826  -0.7644  -1.0687
 2UA  H11  H  HCH1  0   0.276   2.9383   0.3395   1.3667
 2UA  H12  H  HCH2  0   0.240   2.6379   1.3357  -1.4831
 2UA  H13  H  HCH2  0   0.253   2.6552   2.3054  -0.0101
 2UA  H14  H  HCH2  0   0.248   4.9176   2.0104  -1.5557
 2UA  H15  H  HCH2  0   0.233   5.0521   2.0950   0.2024
 2UA  H16  H  HNH1  0   0.394   5.9540  -0.1527  -0.7996
 2UA  H17  H  HNH2  0   0.350  -0.3143   1.0364   2.2206
 2UA  H18  H  HCH2  0   0.263  -2.3195   0.4060   1.3930
 2UA  H19  H  HCH2  0   0.224  -0.8662  -0.5271  -1.1440
 2UA  H20  H  HNH2  0   0.335   0.1748  -0.4984   2.3734

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
 2UA  C1   C2   single  1.510  0.020  1.510
 2UA  C1   C3   single  1.512  0.020  1.512
 2UA  C1   C4   single  1.483  0.020  1.483
 2UA  C1   H1   single  0.970  0.020  1.090
 2UA  C2   C3   single  1.480  0.020  1.480
 2UA  C2   H2   single  0.970  0.020  1.090
 2UA  C2   H3   single  0.970  0.020  1.090
 2UA  C3   H4   single  0.970  0.020  1.090
 2UA  C3   H5   single  0.970  0.020  1.090
 2UA  C4   C5   single  1.506  0.020  1.506
 2UA  C4   O2   double  1.214  0.020  1.214
 2UA  C5   C6   single  1.518  0.020  1.518
 2UA  C5   H6   single  0.970  0.020  1.090
 2UA  C5   H18  single  0.970  0.020  1.090
 2UA  C6   C7   single  1.532  0.020  1.532
 2UA  C6   H7   single  0.970  0.020  1.090
 2UA  C6   H19  single  0.970  0.020  1.090
 2UA  C7   C8   single  1.528  0.020  1.528
 2UA  C7   N    single  1.457  0.020  1.457
 2UA  C7   H8   single  0.970  0.020  1.090
 2UA  C8   C9   single  1.519  0.020  1.519
 2UA  C8   H9   single  0.970  0.020  1.090
 2UA  C8   H10  single  0.970  0.020  1.090
 2UA  C9   C10  single  1.529  0.020  1.529
 2UA  C9   C12  single  1.519  0.020  1.519
 2UA  C9   H11  single  0.970  0.020  1.090
 2UA  C10  C11  single  1.530  0.020  1.530
 2UA  C10  H12  single  0.970  0.020  1.090
 2UA  C10  H13  single  0.970  0.020  1.090
 2UA  C11  N1   single  1.448  0.020  1.448
 2UA  C11  H14  single  0.970  0.020  1.090
 2UA  C11  H15  single  0.970  0.020  1.090
 2UA  N1   C12  single  1.343  0.020  1.343
 2UA  N1   H16  single  0.860  0.020  1.020
 2UA  C12  O1   double  1.222  0.020  1.222
 2UA  N    H17  single  0.890  0.020  1.040
 2UA  N    H20  single  0.890  0.020  1.040

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
 2UA  H1   C1   C4   115.82  3.000
 2UA  H1   C1   C3   116.60  3.000
 2UA  C4   C1   C3   118.26  3.000
 2UA  H1   C1   C2   116.92  3.000
 2UA  C4   C1   C2   118.57  3.000
 2UA  C3   C1   C2    58.67  3.000
 2UA  H3   C2   H2   114.94  3.000
 2UA  H3   C2   C3   118.22  3.000
 2UA  H2   C2   C3   118.68  3.000
 2UA  H3   C2   C1   116.98  3.000
 2UA  H2   C2   C1   116.58  3.000
 2UA  C3   C2   C1    60.73  3.000
 2UA  H5   C3   H4   115.04  3.000
 2UA  H5   C3   C2   118.67  3.000
 2UA  H4   C3   C2   118.33  3.000
 2UA  H5   C3   C1   116.37  3.000
 2UA  H4   C3   C1   116.97  3.000
 2UA  C2   C3   C1    60.61  3.000
 2UA  O2   C4   C5   122.63  3.000
 2UA  O2   C4   C1   121.90  3.000
 2UA  C5   C4   C1   115.47  3.000
 2UA  H18  C5   H6   104.61  3.000
 2UA  H18  C5   C6   111.53  3.000
 2UA  H6   C5   C6   110.77  3.000
 2UA  H18  C5   C4   106.65  3.000
 2UA  H6   C5   C4   107.50  3.000
 2UA  C6   C5   C4   115.14  3.000
 2UA  H19  C6   H7   106.31  3.000
 2UA  H19  C6   C7   108.57  3.000
 2UA  H7   C6   C7   109.39  3.000
 2UA  H19  C6   C5   109.38  3.000
 2UA  H7   C6   C5   110.02  3.000
 2UA  C7   C6   C5   112.94  3.000
 2UA  H8   C7   N    106.53  3.000
 2UA  H8   C7   C8   108.05  3.000
 2UA  N    C7   C8   109.45  3.000
 2UA  H8   C7   C6   107.51  3.000
 2UA  N    C7   C6   114.90  3.000
 2UA  C8   C7   C6   110.11  3.000
 2UA  H10  C8   H9   106.54  3.000
 2UA  H10  C8   C9   109.09  3.000
 2UA  H9   C8   C9   109.88  3.000
 2UA  H10  C8   C7   108.96  3.000
 2UA  H9   C8   C7   109.16  3.000
 2UA  C9   C8   C7   112.99  3.000
 2UA  H11  C9   C12  106.45  3.000
 2UA  H11  C9   C10  109.51  3.000
 2UA  C12  C9   C10  103.16  3.000
 2UA  H11  C9   C8   108.72  3.000
 2UA  C12  C9   C8   113.53  3.000
 2UA  C10  C9   C8   115.04  3.000
 2UA  H13  C10  H12  107.84  3.000
 2UA  H13  C10  C11  112.30  3.000
 2UA  H12  C10  C11  109.59  3.000
 2UA  H13  C10  C9   113.61  3.000
 2UA  H12  C10  C9   109.48  3.000
 2UA  C11  C10  C9   103.96  3.000
 2UA  H15  C11  H14  107.87  3.000
 2UA  H15  C11  N1   111.16  3.000
 2UA  H14  C11  N1   111.11  3.000
 2UA  H15  C11  C10  111.80  3.000
 2UA  H14  C11  C10  112.75  3.000
 2UA  N1   C11  C10  102.15  3.000
 2UA  H16  N1   C12  122.06  3.000
 2UA  H16  N1   C11  122.61  3.000
 2UA  C12  N1   C11  114.55  3.000
 2UA  O1   C12  N1   125.96  3.000
 2UA  O1   C12  C9   126.39  3.000
 2UA  N1   C12  C9   107.64  3.000
 2UA  H20  N    H17  106.00  3.000
 2UA  H20  N    C7   109.74  3.000
 2UA  H17  N    C7   110.41  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
 2UA  CONST_01  C11  N1   C12  C9      0.00   0.0  0
 2UA  CONST_02  O1   C12  N1   C11   180.00   0.0  0
 2UA  CONST_03  H16  N1   C12  C9    180.00   0.0  0
 2UA  Var_01    N1   C11  C10  C9     28.00  30.0  1
 2UA  Var_02    C12  N1   C11  C10   -19.55  30.0  1
 2UA  Var_03    C4   C1   C3   C2   -107.97  30.0  1
 2UA  Var_04    H4   C3   C2   C1   -106.72  30.0  1
 2UA  Var_05    C5   C4   C1   C2    148.62  30.0  3
 2UA  Var_06    C6   C5   C4   C1   -179.66  30.0  3
 2UA  Var_07    C7   C6   C5   C4    177.38  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
 2UA  chir_02  C7  C6  C8   N    positiv
 2UA  chir_03  C9  C8  C10  C12  positiv
 2UA  chir_04  C1  C2  C3   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
 2UA  plan-1  C1   0.020
 2UA  plan-1  C4   0.020
 2UA  plan-1  C5   0.020
 2UA  plan-1  O2   0.020
 2UA  plan-2  C9   0.020
 2UA  plan-2  C11  0.020
 2UA  plan-2  N1   0.020
 2UA  plan-2  C12  0.020
 2UA  plan-2  O1   0.020
 2UA  plan-2  H16  0.020

