# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 25 19:59:45 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](CCC(O)=O)NC(=O)OC(C)(C)C)C(=O)N[C@@H](CC(F)F)C(=O)C(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
 2ZF  2ZF  N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide  peptide  66  35  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2ZF
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
 2ZF  O1    O  O      0  -0.519   4.7000  -0.5108   1.4835
 2ZF  C     C  C      0   0.760   4.7201  -0.6102   0.2728
 2ZF  O2    O  O2     0  -0.506   5.7385  -1.0763  -0.4507
 2ZF  CT    C  CT     0   0.193   7.0156  -1.4431   0.1347
 2ZF  C1    C  CH3    0  -0.671   6.8662  -2.6039   1.1111
 2ZF  C2    C  CH3    0  -0.659   7.8302  -1.8886  -1.0742
 2ZF  C3    C  CH3    0  -0.673   7.6772  -0.2365   0.7899
 2ZF  N     N  NH1    0  -0.647   3.7012  -0.2647  -0.5413
 2ZF  CA    C  CH1    0  -0.232   2.4550   0.2767  -0.0666
 2ZF  C4    C  C      0   0.573   1.3019  -0.5827  -0.5749
 2ZF  O     O  O      0  -0.492   1.3240  -1.0927  -1.6849
 2ZF  CB    C  CH2    0  -0.395   2.2380   1.7260  -0.5234
 2ZF  CG    C  CH2    0  -0.590   3.2945   2.6738   0.0162
 2ZF  CD    C  C      0   0.416   3.1088   4.1516  -0.3758
 2ZF  OE1   O  O      0  -0.606   2.1311   4.4464  -1.0903
 2ZF  OE2   O  OC    -1  -0.630   3.9702   4.9418   0.0634
 2ZF  N1    N  NH1    0  -0.636   0.2627  -0.6689   0.2690
 2ZF  CA1   C  CH1    0  -0.206  -0.9643  -1.3759  -0.0244
 2ZF  C5    C  C      0   0.559  -2.1154  -0.5512   0.5400
 2ZF  O3    O  O      0  -0.483  -2.1036  -0.1836   1.7051
 2ZF  CB1   C  CH2    0  -0.402  -0.9578  -2.7725   0.6056
 2ZF  CG1   C  CH1    0  -0.257  -2.2233  -3.6034   0.3896
 2ZF  CD1   C  CH3    0  -0.653  -2.4966  -3.8791  -1.0858
 2ZF  CD2   C  CH3    0  -0.649  -2.0996  -4.9144   1.1608
 2ZF  N2    N  NH1    0  -0.626  -3.1044  -0.2842  -0.3250
 2ZF  CA2   C  CH1    0  -0.226  -4.3394   0.3691   0.0267
 2ZF  C6    C  C      0   0.255  -5.5261  -0.5417  -0.2719
 2ZF  O4    O  O      0  -0.366  -5.3904  -1.5469  -0.9223
 2ZF  CB2   C  CH2    0  -0.567  -4.5104   1.6878  -0.7386
 2ZF  CG2   C  CH1    0   0.552  -3.3954   2.6620  -0.4674
 2ZF  F1    F  F      0  -0.346  -3.6112   3.8143  -1.1675
 2ZF  F2    F  F      0  -0.346  -3.3704   3.0132   0.8514
 2ZF  CD3   C  C      0   0.358  -6.9050  -0.1199   0.3078
 2ZF  OE11  O  OC    -1  -0.571  -7.8867  -0.6844  -0.1876
 2ZF  OE21  O  O      0  -0.569  -6.8542   0.7285   1.2138
 2ZF  H11   H  HCH3   0   0.234   6.3303  -3.4363   0.6523
 2ZF  H12   H  HCH3   0   0.233   7.8566  -2.9636   1.3923
 2ZF  H13   H  HCH3   0   0.246   6.3473  -2.3140   2.0213
 2ZF  H21   H  HCH3   0   0.237   7.9252  -1.0876  -1.8090
 2ZF  H22   H  HCH3   0   0.230   8.8341  -2.1732  -0.7602
 2ZF  H23   H  HCH3   0   0.237   7.3763  -2.7519  -1.5638
 2ZF  H31   H  HCH3   0   0.245   7.1625   0.0749   1.6959
 2ZF  H32   H  HCH3   0   0.235   8.7016  -0.4925   1.0618
 2ZF  H33   H  HCH3   0   0.235   7.7184   0.6096   0.1019
 2ZF  H     H  HNH1   0   0.393   3.8144  -0.3789  -1.5366
 2ZF  HA    H  HCH1   0   0.270   2.4803   0.2513   1.0243
 2ZF  HB2   H  HCH2   0   0.224   2.2204   1.7580  -1.6161
 2ZF  HB3   H  HCH2   0   0.227   1.2474   2.0460  -0.1911
 2ZF  HG2   H  HCH2   0   0.225   3.3252   2.6080   1.1095
 2ZF  HG3   H  HCH2   0   0.228   4.2877   2.3575  -0.3174
 2ZF  H1    H  HNH1   0   0.403   0.3587  -0.2897   1.1988
 2ZF  HA1   H  HCH1   0   0.274  -1.0453  -1.4571  -1.1090
 2ZF  HB21  H  HCH2   0   0.239  -0.0984  -3.3128   0.1969
 2ZF  HB31  H  HCH2   0   0.234  -0.7740  -2.6618   1.6784
 2ZF  HG    H  HCH1   0   0.228  -3.0805  -3.0573   0.7998
 2ZF  HD11  H  HCH3   0   0.231  -3.3504  -4.5486  -1.2000
 2ZF  HD12  H  HCH3   0   0.221  -2.7288  -2.9750  -1.6489
 2ZF  HD13  H  HCH3   0   0.216  -1.6354  -4.3560  -1.5593
 2ZF  HD21  H  HCH3   0   0.227  -1.9282  -4.7382   2.2241
 2ZF  HD22  H  HCH3   0   0.228  -3.0047  -5.5158   1.0646
 2ZF  HD23  H  HCH3   0   0.215  -1.2650  -5.5107   0.7842
 2ZF  H14   H  HNH1   0   0.405  -3.0318  -0.6517  -1.2609
 2ZF  HA2   H  HCH1   0   0.295  -4.3297   0.5716   1.0971
 2ZF  HB22  H  HCH2   0   0.272  -4.5291   1.4897  -1.8136
 2ZF  HB1   H  HCH2   0   0.283  -5.4616   2.1476  -0.4671
 2ZF  HG1   H  HCH1   0   0.187  -2.4071   2.2881  -0.7360

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
 2ZF  O1   C     double  1.215  0.020  1.215
 2ZF  C    O2    single  1.333  0.020  1.333
 2ZF  O2   CT    single  1.452  0.020  1.452
 2ZF  CT   C1    single  1.524  0.020  1.524
 2ZF  CT   C2    single  1.524  0.020  1.524
 2ZF  CT   C3    single  1.524  0.020  1.524
 2ZF  C1   H11   single  0.970  0.020  1.090
 2ZF  C1   H12   single  0.970  0.020  1.090
 2ZF  C1   H13   single  0.970  0.020  1.090
 2ZF  C2   H21   single  0.970  0.020  1.090
 2ZF  C2   H22   single  0.970  0.020  1.090
 2ZF  C2   H23   single  0.970  0.020  1.090
 2ZF  C3   H31   single  0.970  0.020  1.090
 2ZF  C3   H32   single  0.970  0.020  1.090
 2ZF  C3   H33   single  0.970  0.020  1.090
 2ZF  N    CA    single  1.458  0.019  1.458
 2ZF  N    H     single  0.860  0.020  0.860
 2ZF  CA   C4    single  1.525  0.020  1.525
 2ZF  CA   CB    single  1.521  0.033  1.521
 2ZF  CA   HA    single  0.970  0.020  0.970
 2ZF  C4   O     double  1.222  0.020  1.222
 2ZF  CB   CG    single  1.518  0.020  1.518
 2ZF  CB   HB2   single  0.970  0.020  1.090
 2ZF  CB   HB3   single  0.970  0.020  1.090
 2ZF  CG   CD    single  1.540  0.020  1.540
 2ZF  CG   HG2   single  0.970  0.020  1.090
 2ZF  CG   HG3   single  0.970  0.020  1.090
 2ZF  CD   OE1   deloc   1.246  0.020  1.246
 2ZF  CD   OE2   deloc   1.249  0.020  1.249
 2ZF  N1   CA1   single  1.446  0.020  1.446
 2ZF  N1   H1    single  0.860  0.020  1.020
 2ZF  CA1  C5    single  1.524  0.020  1.524
 2ZF  CA1  CB1   single  1.532  0.020  1.532
 2ZF  CA1  HA1   single  0.970  0.020  1.090
 2ZF  C5   O3    double  1.222  0.020  1.222
 2ZF  CB1  CG1   single  1.529  0.020  1.529
 2ZF  CB1  HB21  single  0.970  0.020  1.090
 2ZF  CB1  HB31  single  0.970  0.020  1.090
 2ZF  CG1  CD1   single  1.526  0.020  1.526
 2ZF  CG1  CD2   single  1.526  0.020  1.526
 2ZF  CG1  HG    single  0.970  0.020  1.090
 2ZF  CD1  HD11  single  0.970  0.020  1.090
 2ZF  CD1  HD12  single  0.970  0.020  1.090
 2ZF  CD1  HD13  single  0.970  0.020  1.090
 2ZF  CD2  HD21  single  0.970  0.020  1.090
 2ZF  CD2  HD22  single  0.970  0.020  1.090
 2ZF  CD2  HD23  single  0.970  0.020  1.090
 2ZF  N2   CA2   single  1.441  0.020  1.441
 2ZF  N2   H14   single  0.860  0.020  1.020
 2ZF  CA2  C6    single  1.525  0.020  1.525
 2ZF  CA2  CB2   single  1.534  0.020  1.534
 2ZF  CA2  HA2   single  0.970  0.020  1.090
 2ZF  C6   O4    double  1.205  0.020  1.205
 2ZF  C6   CD3   single  1.554  0.020  1.554
 2ZF  CB2  CG2   single  1.505  0.020  1.505
 2ZF  CB2  HB22  single  0.970  0.020  1.090
 2ZF  CB2  HB1   single  0.970  0.020  1.090
 2ZF  CG2  F1    single  1.366  0.020  1.366
 2ZF  CG2  F2    single  1.365  0.020  1.365
 2ZF  CG2  HG1   single  0.970  0.020  1.090
 2ZF  CD3  OE11  deloc   1.236  0.020  1.236
 2ZF  CD3  OE21  deloc   1.242  0.020  1.242
 2ZF  C    N     single  1.349  0.020  1.349
 2ZF  C4   N1    single  1.341  0.020  1.341
 2ZF  C5   N2    single  1.341  0.020  1.341

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
 2ZF  N     C    O2    109.81  3.000
 2ZF  N     C    O1    124.60  3.000
 2ZF  O2    C    O1    125.59  3.000
 2ZF  CT    O2   C     122.77  3.000
 2ZF  C3    CT   C2    109.90  3.000
 2ZF  C3    CT   C1    111.72  3.000
 2ZF  C2    CT   C1    109.75  3.000
 2ZF  C3    CT   O2    110.80  3.000
 2ZF  C2    CT   O2    102.95  3.000
 2ZF  C1    CT   O2    111.37  3.000
 2ZF  H13   C1   H12   107.79  3.000
 2ZF  H13   C1   H11   108.73  3.000
 2ZF  H12   C1   H11   107.63  3.000
 2ZF  H13   C1   CT    112.34  3.000
 2ZF  H12   C1   CT    109.10  3.000
 2ZF  H11   C1   CT    111.09  3.000
 2ZF  H23   C2   H22   107.81  3.000
 2ZF  H23   C2   H21   108.35  3.000
 2ZF  H22   C2   H21   107.79  3.000
 2ZF  H23   C2   CT    111.39  3.000
 2ZF  H22   C2   CT    109.88  3.000
 2ZF  H21   C2   CT    111.47  3.000
 2ZF  H33   C3   H32   107.68  3.000
 2ZF  H33   C3   H31   108.73  3.000
 2ZF  H32   C3   H31   107.71  3.000
 2ZF  H33   C3   CT    111.05  3.000
 2ZF  H32   C3   CT    109.21  3.000
 2ZF  H31   C3   CT    112.30  3.000
 2ZF  H     N    CA    114.00  3.000
 2ZF  H     N    C     118.80  3.000
 2ZF  CA    N    C     111.00  2.800
 2ZF  HA    CA   CB    109.00  3.000
 2ZF  HA    CA   C4    109.72  3.000
 2ZF  CB    CA   C4    109.02  3.000
 2ZF  HA    CA   N     110.00  3.000
 2ZF  CB    CA   N     110.40  1.500
 2ZF  C4    CA   N     109.43  3.000
 2ZF  N1    C4   O     123.96  3.000
 2ZF  N1    C4   CA    114.35  3.000
 2ZF  O     C4   CA    121.62  3.000
 2ZF  HB3   CB   HB2   106.30  3.000
 2ZF  HB3   CB   CG    109.87  3.000
 2ZF  HB2   CB   CG    110.37  3.000
 2ZF  HB3   CB   CA    108.31  3.000
 2ZF  HB2   CB   CA    109.11  3.000
 2ZF  CG    CB   CA    112.66  3.000
 2ZF  HG3   CG   HG2   105.15  3.000
 2ZF  HG3   CG   CD    108.00  3.000
 2ZF  HG2   CG   CD    108.36  3.000
 2ZF  HG3   CG   CB    110.04  3.000
 2ZF  HG2   CG   CB    109.67  3.000
 2ZF  CD    CG   CB    115.13  3.000
 2ZF  OE2   CD   OE1   126.38  3.000
 2ZF  OE2   CD   CG    115.75  3.000
 2ZF  OE1   CD   CG    117.87  3.000
 2ZF  H1    N1   CA1   116.84  3.000
 2ZF  H1    N1   C4    118.81  3.000
 2ZF  CA1   N1   C4    124.13  3.000
 2ZF  HA1   CA1  CB1   109.96  3.000
 2ZF  HA1   CA1  C5    110.64  3.000
 2ZF  CB1   CA1  C5    110.13  3.000
 2ZF  HA1   CA1  N1    107.53  3.000
 2ZF  CB1   CA1  N1    111.01  3.000
 2ZF  C5    CA1  N1    107.52  3.000
 2ZF  N2    C5   O3    124.22  3.000
 2ZF  N2    C5   CA1   115.20  3.000
 2ZF  O3    C5   CA1   120.57  3.000
 2ZF  HB31  CB1  HB21  106.51  3.000
 2ZF  HB31  CB1  CG1   109.42  3.000
 2ZF  HB21  CB1  CG1   109.20  3.000
 2ZF  HB31  CB1  CA1   108.16  3.000
 2ZF  HB21  CB1  CA1   107.44  3.000
 2ZF  CG1   CB1  CA1   115.70  3.000
 2ZF  HG    CG1  CD2   107.60  3.000
 2ZF  HG    CG1  CD1   108.17  3.000
 2ZF  CD2   CG1  CD1   110.37  3.000
 2ZF  HG    CG1  CB1   108.88  3.000
 2ZF  CD2   CG1  CB1   109.17  3.000
 2ZF  CD1   CG1  CB1   112.52  3.000
 2ZF  HD13  CD1  HD12  107.82  3.000
 2ZF  HD13  CD1  HD11  107.68  3.000
 2ZF  HD12  CD1  HD11  106.75  3.000
 2ZF  HD13  CD1  CG1   110.91  3.000
 2ZF  HD12  CD1  CG1   112.82  3.000
 2ZF  HD11  CD1  CG1   110.63  3.000
 2ZF  HD23  CD2  HD22  107.61  3.000
 2ZF  HD23  CD2  HD21  107.70  3.000
 2ZF  HD22  CD2  HD21  107.77  3.000
 2ZF  HD23  CD2  CG1   110.89  3.000
 2ZF  HD22  CD2  CG1   111.21  3.000
 2ZF  HD21  CD2  CG1   111.49  3.000
 2ZF  H14   N2   CA2   116.98  3.000
 2ZF  H14   N2   C5    118.24  3.000
 2ZF  CA2   N2   C5    124.41  3.000
 2ZF  HA2   CA2  CB2   109.35  3.000
 2ZF  HA2   CA2  C6    108.07  3.000
 2ZF  CB2   CA2  C6    109.20  3.000
 2ZF  HA2   CA2  N2    108.46  3.000
 2ZF  CB2   CA2  N2    111.32  3.000
 2ZF  C6    CA2  N2    110.39  3.000
 2ZF  CD3   C6   O4    121.84  3.000
 2ZF  CD3   C6   CA2   117.08  3.000
 2ZF  O4    C6   CA2   121.08  3.000
 2ZF  HB1   CB2  HB22  107.82  3.000
 2ZF  HB1   CB2  CG2   109.16  3.000
 2ZF  HB22  CB2  CG2   107.88  3.000
 2ZF  HB1   CB2  CA2   109.60  3.000
 2ZF  HB22  CB2  CA2   109.68  3.000
 2ZF  CG2   CB2  CA2   112.57  3.000
 2ZF  HG1   CG2  F2    108.04  3.000
 2ZF  HG1   CG2  F1    107.84  3.000
 2ZF  F2    CG2  F1    106.33  3.000
 2ZF  HG1   CG2  CB2   113.90  3.000
 2ZF  F2    CG2  CB2   110.74  3.000
 2ZF  F1    CG2  CB2   109.68  3.000
 2ZF  OE21  CD3  OE11  129.55  3.000
 2ZF  OE21  CD3  C6    114.90  3.000
 2ZF  OE11  CD3  C6    115.55  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
 2ZF  CONST_01  CA1   N1   C4   CA    180.00   0.0  0
 2ZF  CONST_02  CA1   N1   C4   O       0.00   0.0  0
 2ZF  CONST_03  CA2   N2   C5   CA1   180.00   0.0  0
 2ZF  CONST_04  CA2   N2   C5   O3      0.00   0.0  0
 2ZF  CONST_05  H1    N1   C4   CA      0.00   0.0  0
 2ZF  CONST_06  H14   N2   C5   CA1     0.00   0.0  0
 2ZF  Var_01    CA    N    C    O1      0.35  30.0  2
 2ZF  Var_02    C1    CT   O2   C      63.15  30.0  3
 2ZF  Var_03    N     C    O2   CT    175.64  30.0  1
 2ZF  Var_04    CD    CG   CB   CA   -178.38  30.0  3
 2ZF  Var_05    OE1   CD   CG   CB     -0.14  30.0  3
 2ZF  Var_06    CD1   CG1  CB1  CA1    61.29  30.0  3
 2ZF  Var_07    OE11  CD3  C6   CA2   164.13  30.0  2
 2ZF  Var_08    F1    CG2  CB2  CA2  -179.54  30.0  3
 2ZF  Var_09    H11   C1   CT   O2     51.59  30.0  3
 2ZF  Var_10    H21   C2   CT   O2     59.35  30.0  3
 2ZF  Var_11    H31   C3   CT   O2     70.59  30.0  3
 2ZF  Var_12    HD11  CD1  CG1  CB1   174.76  30.0  3
 2ZF  Var_13    HD21  CD2  CG1  CB1    57.24  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
 2ZF  chir_01  CA   N   C4   CB   positiv
 2ZF  chir_02  CA1  N1  CB1  C5   negativ
 2ZF  chir_03  CA2  N2  C6   CB2  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
 2ZF  plan-1  CA    0.020
 2ZF  plan-1  C4    0.020
 2ZF  plan-1  O     0.020
 2ZF  plan-1  N1    0.020
 2ZF  plan-1  CA1   0.020
 2ZF  plan-1  H1    0.020
 2ZF  plan-2  CA1   0.020
 2ZF  plan-2  C5    0.020
 2ZF  plan-2  O3    0.020
 2ZF  plan-2  N2    0.020
 2ZF  plan-2  CA2   0.020
 2ZF  plan-2  H14   0.020
 2ZF  plan-3  CA2   0.020
 2ZF  plan-3  C6    0.020
 2ZF  plan-3  O4    0.020
 2ZF  plan-3  CD3   0.020
 2ZF  plan-4  CG    0.020
 2ZF  plan-4  CD    0.020
 2ZF  plan-4  OE1   0.020
 2ZF  plan-4  OE2   0.020
 2ZF  plan-5  C6    0.020
 2ZF  plan-5  CD3   0.020
 2ZF  plan-5  OE11  0.020
 2ZF  plan-5  OE21  0.020
 2ZF  plan-6  O1    0.020
 2ZF  plan-6  C     0.020
 2ZF  plan-6  O2    0.020
 2ZF  plan-6  N     0.020

