# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:59:26 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: (2S)-2-amino-3-oxopropyl 4-{[(2S)-2-hydroxy-4-methylpentanoyl]amino}butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](O)C(=O)NCCCC(=O)OC[C@H](N)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
 2JF  2JF  '(2S)-2-amino-3-oxopropyl 4-{[(2S)-2-hydroxy-4-methylpentanoyl]amino}butanoate'  L-peptide  44  20  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2JF
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
 2JF  N    N  NH2   0  -0.777  80.0228  15.7304  -11.9732
 2JF  CA   C  CH1   0  -0.239  78.6210  15.5572  -12.3076
 2JF  CB   C  CH2   0  -0.177  78.2554  16.2510  -13.6096
 2JF  OG   O  O2    0  -0.456  78.3863  17.6649  -13.4767
 2JF  C8   C  C     0   0.593  79.4683  18.2777  -13.9476
 2JF  O18  O  O     0  -0.447  80.3865  17.7147  -14.4872
 2JF  C9   C  CH2   0  -0.581  79.3723  19.7742  -13.7898
 2JF  C10  C  CH2   0  -0.444  80.7203  20.4397  -13.5515
 2JF  C11  C  CH2   0  -0.302  81.3056  20.1736  -12.1677
 2JF  N12  N  NH1   0  -0.620  80.5109  20.7563  -11.1074
 2JF  C13  C  C     0   0.509  79.7093  20.0737  -10.2800
 2JF  O19  O  O     0  -0.492  79.5617  18.8588  -10.3047
 2JF  C14  C  CH1   0  -0.078  78.9976  20.9125   -9.2176
 2JF  O20  O  OH1   0  -0.655  77.7852  20.3057   -8.8636
 2JF  C15  C  CH2   0  -0.439  79.9402  21.1029   -8.0247
 2JF  C16  C  CH1   0  -0.229  79.3375  21.8673   -6.8444
 2JF  C21  C  CH3   0  -0.649  80.3397  21.9013   -5.6949
 2JF  C17  C  CH3   0  -0.662  78.9182  23.2836   -7.2235
 2JF  C    C  C1    0   0.162  78.2562  14.0887  -12.3456
 2JF  O    O  O     0  -0.370  77.7046  13.5270  -13.2575
 2JF  H1   H  HNH2  0   0.364  80.2123  15.4060  -11.0336
 2JF  H2   H  HNH2  0   0.354  80.6157  15.2031  -12.6021
 2JF  H4   H  HCH1  0   0.280  78.0334  16.0007  -11.4941
 2JF  H5   H  HCH2  0   0.259  77.2071  16.0737  -13.8466
 2JF  H6   H  HCH2  0   0.243  78.8593  15.8759  -14.4371
 2JF  H7   H  HCH2  0   0.263  78.6570  20.0346  -13.0090
 2JF  H8   H  HCH2  0   0.291  78.9425  20.1534  -14.7233
 2JF  H9   H  HCH2  0   0.242  81.4390  20.1108  -14.3039
 2JF  H10  H  HCH2  0   0.246  80.6081  21.5176  -13.6873
 2JF  H11  H  HCH2  0   0.247  81.4021  19.1043  -11.9812
 2JF  H12  H  HCH2  0   0.259  82.3106  20.5953  -12.1144
 2JF  H13  H  HNH1  0   0.401  80.5222  21.7620  -11.0326
 2JF  H14  H  HCH1  0   0.251  78.7452  21.8896   -9.6405
 2JF  H15  H  HOH1  0   0.438  77.9595  19.3657   -8.7301
 2JF  H16  H  HCH2  0   0.233  80.2726  20.1170   -7.6793
 2JF  H17  H  HCH2  0   0.226  80.8385  21.6282   -8.3669
 2JF  H18  H  HCH1  0   0.219  78.4508  21.3239   -6.5042
 2JF  H19  H  HCH3  0   0.225  79.9210  22.4018   -4.8203
 2JF  H20  H  HCH3  0   0.223  80.6356  20.8953   -5.3924
 2JF  H21  H  HCH3  0   0.212  81.2450  22.4408   -5.9832
 2JF  H22  H  HCH3  0   0.228  78.5367  23.8201   -6.3532
 2JF  H23  H  HCH3  0   0.213  79.7674  23.8511   -7.6126
 2JF  H24  H  HCH3  0   0.229  78.1322  23.3002   -7.9796
 2JF  H25  H  H     0   0.205  78.5802  13.5350  -11.4433

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
 2JF  C10  C9   single  1.522  0.020  1.522
 2JF  C10  C11  single  1.526  0.020  1.526
 2JF  C9   C8   single  1.508  0.020  1.508
 2JF  O18  C8   double  1.205  0.020  1.205
 2JF  C8   OG   single  1.330  0.020  1.330
 2JF  OG   CB   single  1.426  0.020  1.426
 2JF  CB   CA   single  1.521  0.033  1.521
 2JF  C11  N12  single  1.448  0.020  1.448
 2JF  O    C    double  1.231  0.020  1.231
 2JF  CA   C    single  1.525  0.021  1.525
 2JF  CA   N    single  1.458  0.019  1.458
 2JF  N12  C13  single  1.339  0.020  1.339
 2JF  O19  C13  double  1.224  0.020  1.224
 2JF  C13  C14  single  1.529  0.020  1.529
 2JF  C14  O20  single  1.401  0.020  1.401
 2JF  C14  C15  single  1.532  0.020  1.532
 2JF  C15  C16  single  1.530  0.020  1.530
 2JF  C17  C16  single  1.525  0.020  1.525
 2JF  C16  C21  single  1.525  0.020  1.525
 2JF  N    H1   single  0.890  0.020  1.040
 2JF  N    H2   single  0.890  0.020  1.040
 2JF  CA   H4   single  0.970  0.020  1.090
 2JF  CB   H5   single  0.970  0.020  1.090
 2JF  CB   H6   single  0.970  0.020  1.090
 2JF  C9   H7   single  0.970  0.020  1.090
 2JF  C9   H8   single  0.970  0.020  1.090
 2JF  C10  H9   single  0.970  0.020  1.090
 2JF  C10  H10  single  0.970  0.020  1.090
 2JF  C11  H11  single  0.970  0.020  1.090
 2JF  C11  H12  single  0.970  0.020  1.090
 2JF  N12  H13  single  0.860  0.020  1.020
 2JF  C14  H14  single  0.970  0.020  1.090
 2JF  O20  H15  single  0.850  0.020  0.980
 2JF  C15  H16  single  0.970  0.020  1.090
 2JF  C15  H17  single  0.970  0.020  1.090
 2JF  C16  H18  single  0.970  0.020  1.090
 2JF  C21  H19  single  0.970  0.020  1.090
 2JF  C21  H20  single  0.970  0.020  1.090
 2JF  C21  H21  single  0.970  0.020  1.090
 2JF  C17  H22  single  0.970  0.020  1.090
 2JF  C17  H23  single  0.970  0.020  1.090
 2JF  C17  H24  single  0.970  0.020  1.090
 2JF  C    H25  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
 2JF  H2   N    H1   107.47  3.000
 2JF  H2   N    CA   111.12  3.000
 2JF  H1   N    CA   110.89  3.000
 2JF  H4   CA   C    106.36  3.000
 2JF  H4   CA   CB   108.77  3.000
 2JF  C    CA   CB   110.50  1.500
 2JF  H4   CA   N    107.35  3.000
 2JF  C    CA   N    111.00  2.800
 2JF  CB   CA   N    110.40  1.500
 2JF  H6   CB   H5   108.17  3.000
 2JF  H6   CB   OG   111.14  3.000
 2JF  H5   CB   OG   105.66  3.000
 2JF  H6   CB   CA   111.08  3.000
 2JF  H5   CB   CA   110.09  3.000
 2JF  OG   CB   CA   110.52  3.000
 2JF  C8   OG   CB   119.91  3.000
 2JF  C9   C8   O18  124.00  3.000
 2JF  O18  C8   OG   124.30  3.000
 2JF  C9   C8   OG   111.63  3.000
 2JF  H8   C9   H7   105.68  3.000
 2JF  H8   C9   C10  109.24  3.000
 2JF  H7   C9   C10  111.37  3.000
 2JF  H8   C9   C8   106.22  3.000
 2JF  H7   C9   C8   110.71  3.000
 2JF  C10  C9   C8   113.20  3.000
 2JF  H10  C10  H9   106.22  3.000
 2JF  H10  C10  C11  108.92  3.000
 2JF  H9   C10  C11  108.67  3.000
 2JF  H10  C10  C9   108.73  3.000
 2JF  H9   C10  C9   110.10  3.000
 2JF  C11  C10  C9   113.92  3.000
 2JF  H12  C11  H11  106.82  3.000
 2JF  H12  C11  N12  108.32  3.000
 2JF  H11  C11  N12  108.56  3.000
 2JF  H12  C11  C10  109.28  3.000
 2JF  H11  C11  C10  111.12  3.000
 2JF  N12  C11  C10  112.55  3.000
 2JF  H13  N12  C13  117.98  3.000
 2JF  H13  N12  C11  116.71  3.000
 2JF  C13  N12  C11  125.18  3.000
 2JF  C14  C13  O19  120.15  3.000
 2JF  C14  C13  N12  115.36  3.000
 2JF  O19  C13  N12  124.44  3.000
 2JF  H14  C14  C15  109.38  3.000
 2JF  H14  C14  O20  106.54  3.000
 2JF  C15  C14  O20  112.92  3.000
 2JF  H14  C14  C13  109.19  3.000
 2JF  C15  C14  C13  108.83  3.000
 2JF  O20  C14  C13  109.92  3.000
 2JF  H15  O20  C14  107.48  3.000
 2JF  H17  C15  H16  106.33  3.000
 2JF  H17  C15  C16  108.93  3.000
 2JF  H16  C15  C16  109.01  3.000
 2JF  H17  C15  C14  108.72  3.000
 2JF  H16  C15  C14  108.67  3.000
 2JF  C16  C15  C14  114.86  3.000
 2JF  H18  C16  C17  108.40  3.000
 2JF  H18  C16  C21  108.01  3.000
 2JF  C17  C16  C21  110.32  3.000
 2JF  H18  C16  C15  108.12  3.000
 2JF  C21  C16  C15  109.49  3.000
 2JF  C17  C16  C15  112.37  3.000
 2JF  H21  C21  H20  107.68  3.000
 2JF  H21  C21  H19  107.63  3.000
 2JF  H20  C21  H19  107.74  3.000
 2JF  H21  C21  C16  110.89  3.000
 2JF  H20  C21  C16  111.49  3.000
 2JF  H19  C21  C16  111.23  3.000
 2JF  H24  C17  H23  107.77  3.000
 2JF  H24  C17  H22  107.06  3.000
 2JF  H23  C17  H22  107.47  3.000
 2JF  H24  C17  C16  112.62  3.000
 2JF  H23  C17  C16  110.92  3.000
 2JF  H22  C17  C16  110.76  3.000
 2JF  H25  C    O    121.18  3.000
 2JF  H25  C    CA   113.22  3.000
 2JF  O    C    CA   120.80  1.700

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
 2JF  CONST_01  O19  C13  N12  C11     0.00   0.0  0
 2JF  CONST_02  C14  C13  N12  C11   180.00   0.0  0
 2JF  CONST_03  H13  N12  C13  O19   180.00   0.0  0
 2JF  Var_01    C9   C8   OG   CB    176.25  30.0  1
 2JF  Var_02    C10  C9   C8   OG    147.61  30.0  1
 2JF  Var_03    C11  C10  C9   C8    -71.81  30.0  1
 2JF  Var_04    N12  C11  C10  C9    -65.43  30.0  3
 2JF  Var_05    C13  N12  C11  C10   105.26  30.0  3
 2JF  Var_06    C17  C16  C15  C14   -60.96  30.0  3
 2JF  Var_07    H5   CB   OG   C8   -140.77  30.0  3
 2JF  Var_08    H22  C17  C16  C15  -177.30  30.0  3
 2JF  Var_09    H19  C21  C16  C15  -177.43  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
 2JF  chir_01  CA   CB   C    N    negativ
 2JF  chir_02  C14  C13  O20  C15  negativ

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
 2JF  plan-1  C11  0.020
 2JF  plan-1  N12  0.020
 2JF  plan-1  C13  0.020
 2JF  plan-1  O19  0.020
 2JF  plan-1  C14  0.020
 2JF  plan-1  H13  0.020
 2JF  plan-2  OG   0.020
 2JF  plan-2  C8   0.020
 2JF  plan-2  O18  0.020
 2JF  plan-2  C9   0.020
 2JF  plan-3  CA   0.020
 2JF  plan-3  C    0.020
 2JF  plan-3  O    0.020
 2JF  plan-3  H25  0.020

