# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 02:35:59 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: N-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(carboxyamino)-2-phenylethyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)OC(C)(C)C)C(=O)N1CCC[C@H]1C(=O)N[C@@H](Cc2ccccc2)NC(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
 0EF  0EF  N-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(carboxyamino)-2-phenylethyl]-L-prolinamide  peptide  63  32  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_0EF
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
 0EF  O1    O  O      0  -0.522   5.8460  -0.4903   0.9667
 0EF  C     C  C      0   0.763   5.3090   0.3088   0.2248
 0EF  O2    O  O2     0  -0.505   5.9289   1.2436  -0.4953
 0EF  CT    C  CT     0   0.191   7.3725   1.3982  -0.5109
 0EF  C1    C  CH3    0  -0.674   8.0530   0.1348  -1.0256
 0EF  C2    C  CH3    0  -0.659   7.5816   2.5351  -1.5047
 0EF  C3    C  CH3    0  -0.670   7.8892   1.8103   0.8622
 0EF  N     N  NH1    0  -0.661   3.9808   0.3633   0.0042
 0EF  CA    C  CH1    0  -0.201   3.0478  -0.4973   0.6864
 0EF  C4    C  C      0   0.565   1.8077  -0.6231  -0.1902
 0EF  O     O  O      0  -0.502   1.4519   0.3090  -0.9028
 0EF  CB    C  CH3    0  -0.652   2.6363   0.0564   2.0538
 0EF  N1    N  NT     0  -0.461   1.1162  -1.7646  -0.1161
 0EF  CA1   C  CH1    0  -0.226  -0.1285  -1.8958  -0.8429
 0EF  C5    C  C      0   0.574  -1.2076  -1.0069  -0.2353
 0EF  O3    O  O      0  -0.493  -1.1938  -0.6972   0.9467
 0EF  CB1   C  CH2    0  -0.477  -0.4979  -3.3750  -0.6556
 0EF  CG    C  CH2    0  -0.474   0.1189  -3.7266   0.6941
 0EF  CD    C  CH2    0  -0.279   1.4179  -2.9293   0.7138
 0EF  N2    N  NH1    0  -0.638  -2.1828  -0.6677  -1.0869
 0EF  CA2   C  CH1    0   0.133  -3.4969  -0.1905  -0.6575
 0EF  CB2   C  CH2    0  -0.556  -3.5872   1.3307  -0.8127
 0EF  CG1   C  CR6    0   0.164  -4.8673   1.8815  -0.2533
 0EF  CD1   C  CR16   0  -0.306  -5.0288   2.0158   1.1247
 0EF  CD2   C  CR16   0  -0.321  -5.9254   2.2430  -1.0828
 0EF  CE1   C  CR16   0  -0.241  -6.2167   2.4934   1.6607
 0EF  CE2   C  CR16   0  -0.242  -7.1147   2.7265  -0.5527
 0EF  CZ    C  CR16   0  -0.274  -7.2651   2.8514   0.8220
 0EF  NHO   N  NH1    0  -0.674  -4.5425  -0.8386  -1.3720
 0EF  C6    C  C      0   0.514  -4.7805  -2.2246  -1.2325
 0EF  O4    O  O      0  -0.627  -4.2589  -2.7868  -0.2490
 0EF  OXT   O  OC    -1  -0.651  -5.5142  -2.7360  -2.1027
 0EF  H11   H  HCH3   0   0.235   7.6033  -0.1903  -1.9652
 0EF  H12   H  HCH3   0   0.234   9.1047   0.3475  -1.2212
 0EF  H13   H  HCH3   0   0.246   8.0074  -0.6852  -0.3129
 0EF  H21   H  HCH3   0   0.237   7.0808   3.4473  -1.1765
 0EF  H22   H  HCH3   0   0.230   8.6448   2.7544  -1.5981
 0EF  H23   H  HCH3   0   0.237   7.2057   2.2706  -2.4943
 0EF  H31   H  HCH3   0   0.246   7.8031   1.0116   1.5948
 0EF  H32   H  HCH3   0   0.233   8.9430   2.0806   0.7841
 0EF  H33   H  HCH3   0   0.234   7.3514   2.6851   1.2314
 0EF  H     H  HNH1   0   0.394   3.5992   1.0995  -0.5705
 0EF  HA    H  HCH1   0   0.277   3.5193  -1.4724   0.8180
 0EF  HB1   H  HCH3   0   0.237   2.2103   1.0540   1.9472
 0EF  HB2   H  HCH3   0   0.238   1.8919  -0.5776   2.5354
 0EF  HB3   H  HCH3   0   0.249   3.5037   0.1164   2.7094
 0EF  HA1   H  HCH1   0   0.286   0.0108  -1.6529  -1.8988
 0EF  HB21  H  HCH2   0   0.271  -1.5756  -3.5343  -0.6954
 0EF  HB31  H  HCH2   0   0.255  -0.0405  -3.9636  -1.4530
 0EF  HG2   H  HCH2   0   0.246  -0.5324  -3.4060   1.5075
 0EF  HG3   H  HCH2   0   0.257   0.2984  -4.7940   0.8128
 0EF  HD2   H  HCH2   0   0.250   2.2422  -3.5023   0.2809
 0EF  HD3   H  HCH2   0   0.256   1.7025  -2.6412   1.7252
 0EF  H1    H  HNH1   0   0.388  -2.1152  -0.9816  -2.0431
 0EF  HA2   H  HCH1   0   0.237  -3.5818  -0.4380   0.4013
 0EF  HB22  H  HCH2   0   0.260  -2.7316   1.7689  -0.2943
 0EF  HB32  H  HCH2   0   0.249  -3.4838   1.5972  -1.8690
 0EF  HD1   H  HCR6   0   0.245  -4.2134   1.7440   1.7859
 0EF  HD21  H  HCR6   0   0.244  -5.8175   2.1492  -2.1574
 0EF  HE1   H  HCR6   0   0.252  -6.3228   2.5907   2.7337
 0EF  HE2   H  HCR6   0   0.252  -7.9248   3.0056  -1.2146
 0EF  HZ    H  HCR6   0   0.253  -8.1905   3.2290   1.2371
 0EF  HN    H  HNH1   0   0.351  -4.7823  -0.4435  -2.2687

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
 0EF  O1   C     double    1.215  0.020  1.215
 0EF  C    O2    single    1.333  0.020  1.333
 0EF  O2   CT    single    1.452  0.020  1.452
 0EF  CT   C1    single    1.525  0.020  1.525
 0EF  CT   C2    single    1.524  0.020  1.524
 0EF  CT   C3    single    1.524  0.020  1.524
 0EF  C1   H11   single    0.970  0.020  1.090
 0EF  C1   H12   single    0.970  0.020  1.090
 0EF  C1   H13   single    0.970  0.020  1.090
 0EF  C2   H21   single    0.970  0.020  1.090
 0EF  C2   H22   single    0.970  0.020  1.090
 0EF  C2   H23   single    0.970  0.020  1.090
 0EF  C3   H31   single    0.970  0.020  1.090
 0EF  C3   H32   single    0.970  0.020  1.090
 0EF  C3   H33   single    0.970  0.020  1.090
 0EF  N    CA    single    1.458  0.019  1.458
 0EF  N    H     single    0.860  0.020  0.860
 0EF  CA   C4    single    1.524  0.020  1.524
 0EF  CA   CB    single    1.521  0.033  1.521
 0EF  CA   HA    single    0.970  0.020  0.970
 0EF  C4   O     double    1.226  0.020  1.226
 0EF  CB   HB1   single    0.970  0.020  1.090
 0EF  CB   HB2   single    0.970  0.020  1.090
 0EF  CB   HB3   single    0.970  0.020  1.090
 0EF  N1   CA1   single    1.447  0.020  1.447
 0EF  N1   CD    single    1.462  0.020  1.462
 0EF  CA1  C5    single    1.524  0.020  1.524
 0EF  CA1  CB1   single    1.536  0.020  1.536
 0EF  CA1  HA1   single    0.970  0.020  1.090
 0EF  C5   O3    double    1.222  0.020  1.222
 0EF  CB1  CG    single    1.525  0.020  1.525
 0EF  CB1  HB21  single    0.970  0.020  1.090
 0EF  CB1  HB31  single    0.970  0.020  1.090
 0EF  CG   CD    single    1.524  0.020  1.524
 0EF  CG   HG2   single    0.970  0.020  1.090
 0EF  CG   HG3   single    0.970  0.020  1.090
 0EF  CD   HD2   single    0.970  0.020  1.090
 0EF  CD   HD3   single    0.970  0.020  1.090
 0EF  N2   CA2   single    1.463  0.020  1.463
 0EF  N2   H1    single    0.890  0.020  1.040
 0EF  CA2  CB2   single    1.532  0.020  1.532
 0EF  CA2  NHO   single    1.423  0.020  1.423
 0EF  CA2  HA2   single    0.970  0.020  1.090
 0EF  CB2  CG1   single    1.502  0.020  1.502
 0EF  CB2  HB22  single    0.970  0.020  1.090
 0EF  CB2  HB32  single    0.970  0.020  1.090
 0EF  CG1  CD1   aromatic  1.394  0.020  1.394
 0EF  CG1  CD2   aromatic  1.392  0.020  1.392
 0EF  CD1  CE1   aromatic  1.388  0.020  1.388
 0EF  CD1  HD1   single    0.930  0.020  1.080
 0EF  CD2  CE2   aromatic  1.389  0.020  1.389
 0EF  CD2  HD21  single    0.930  0.020  1.080
 0EF  CE1  CZ    aromatic  1.389  0.020  1.389
 0EF  CE1  HE1   single    0.930  0.020  1.080
 0EF  CE2  CZ    aromatic  1.389  0.020  1.389
 0EF  CE2  HE2   single    0.930  0.020  1.080
 0EF  CZ   HZ    single    0.930  0.020  1.080
 0EF  NHO  C6    single    1.413  0.020  1.413
 0EF  NHO  HN    single    0.890  0.020  1.040
 0EF  C6   O4    deloc     1.247  0.020  1.247
 0EF  C6   OXT   deloc     1.248  0.020  1.248
 0EF  C    N     single    1.347  0.020  1.347
 0EF  C4   N1    single    1.337  0.020  1.337
 0EF  C5   N2    single    1.338  0.020  1.338

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
 0EF  N     C    O2    109.97  3.000
 0EF  N     C    O1    124.20  3.000
 0EF  O2    C    O1    125.83  3.000
 0EF  CT    O2   C     122.88  3.000
 0EF  C3    CT   C2    109.83  3.000
 0EF  C3    CT   C1    112.14  3.000
 0EF  C2    CT   C1    109.68  3.000
 0EF  C3    CT   O2    110.87  3.000
 0EF  C2    CT   O2    102.87  3.000
 0EF  C1    CT   O2    111.05  3.000
 0EF  H13   C1   H12   107.76  3.000
 0EF  H13   C1   H11   108.81  3.000
 0EF  H12   C1   H11   107.52  3.000
 0EF  H13   C1   CT    112.64  3.000
 0EF  H12   C1   CT    109.23  3.000
 0EF  H11   C1   CT    110.71  3.000
 0EF  H23   C2   H22   107.89  3.000
 0EF  H23   C2   H21   108.50  3.000
 0EF  H22   C2   H21   107.78  3.000
 0EF  H23   C2   CT    111.30  3.000
 0EF  H22   C2   CT    109.87  3.000
 0EF  H21   C2   CT    111.37  3.000
 0EF  H33   C3   H32   107.56  3.000
 0EF  H33   C3   H31   108.78  3.000
 0EF  H32   C3   H31   107.87  3.000
 0EF  H33   C3   CT    110.76  3.000
 0EF  H32   C3   CT    109.27  3.000
 0EF  H31   C3   CT    112.43  3.000
 0EF  H     N    CA    114.00  3.000
 0EF  H     N    C     119.71  3.000
 0EF  CA    N    C     111.00  2.800
 0EF  HA    CA   CB    109.00  3.000
 0EF  HA    CA   C4    110.32  3.000
 0EF  CB    CA   C4    108.96  3.000
 0EF  HA    CA   N     110.00  3.000
 0EF  CB    CA   N     110.40  1.500
 0EF  C4    CA   N     107.69  3.000
 0EF  N1    C4   O     122.10  3.000
 0EF  N1    C4   CA    117.36  3.000
 0EF  O     C4   CA    120.51  3.000
 0EF  HB3   CB   HB2   108.06  3.000
 0EF  HB3   CB   HB1   108.65  3.000
 0EF  HB2   CB   HB1   107.98  3.000
 0EF  HB3   CB   CA    110.09  3.000
 0EF  HB2   CB   CA    111.57  3.000
 0EF  HB1   CB   CA    110.40  3.000
 0EF  CD    N1   CA1   112.98  3.000
 0EF  CD    N1   C4    127.24  3.000
 0EF  CA1   N1   C4    119.64  3.000
 0EF  HA1   CA1  CB1   111.26  3.000
 0EF  HA1   CA1  C5    110.23  3.000
 0EF  CB1   CA1  C5    110.04  3.000
 0EF  HA1   CA1  N1    110.83  3.000
 0EF  CB1   CA1  N1    103.47  3.000
 0EF  C5    CA1  N1    110.84  3.000
 0EF  N2    C5   O3    124.02  3.000
 0EF  N2    C5   CA1   114.21  3.000
 0EF  O3    C5   CA1   121.69  3.000
 0EF  HB31  CB1  HB21  107.98  3.000
 0EF  HB31  CB1  CG    110.65  3.000
 0EF  HB21  CB1  CG    113.48  3.000
 0EF  HB31  CB1  CA1   109.23  3.000
 0EF  HB21  CB1  CA1   111.97  3.000
 0EF  CG    CB1  CA1   103.45  3.000
 0EF  HG3   CG   HG2   107.78  3.000
 0EF  HG3   CG   CD    111.76  3.000
 0EF  HG2   CG   CD    110.22  3.000
 0EF  HG3   CG   CB1   112.90  3.000
 0EF  HG2   CG   CB1   110.54  3.000
 0EF  CD    CG   CB1   103.63  3.000
 0EF  HD3   CD   HD2   108.02  3.000
 0EF  HD3   CD   CG    111.90  3.000
 0EF  HD2   CD   CG    111.30  3.000
 0EF  HD3   CD   N1    111.74  3.000
 0EF  HD2   CD   N1    110.39  3.000
 0EF  CG    CD   N1    103.50  3.000
 0EF  H1    N2   CA2   116.11  3.000
 0EF  H1    N2   C5    118.39  3.000
 0EF  CA2   N2   C5    123.41  3.000
 0EF  HA2   CA2  NHO   109.09  3.000
 0EF  HA2   CA2  CB2   108.61  3.000
 0EF  NHO   CA2  CB2   110.99  3.000
 0EF  HA2   CA2  N2    106.31  3.000
 0EF  NHO   CA2  N2    111.37  3.000
 0EF  CB2   CA2  N2    110.32  3.000
 0EF  HB32  CB2  HB22  106.65  3.000
 0EF  HB32  CB2  CG1   110.54  3.000
 0EF  HB22  CB2  CG1   110.11  3.000
 0EF  HB32  CB2  CA2   109.52  3.000
 0EF  HB22  CB2  CA2   107.71  3.000
 0EF  CG1   CB2  CA2   112.13  3.000
 0EF  CD2   CG1  CD1   118.42  3.000
 0EF  CD2   CG1  CB2   121.41  3.000
 0EF  CD1   CG1  CB2   120.16  3.000
 0EF  HD1   CD1  CE1   119.63  3.000
 0EF  HD1   CD1  CG1   119.44  3.000
 0EF  CE1   CD1  CG1   120.93  3.000
 0EF  HD21  CD2  CE2   119.58  3.000
 0EF  HD21  CD2  CG1   119.50  3.000
 0EF  CE2   CD2  CG1   120.91  3.000
 0EF  HE1   CE1  CZ    120.08  3.000
 0EF  HE1   CE1  CD1   119.83  3.000
 0EF  CZ    CE1  CD1   120.09  3.000
 0EF  HE2   CE2  CZ    120.07  3.000
 0EF  HE2   CE2  CD2   119.81  3.000
 0EF  CZ    CE2  CD2   120.13  3.000
 0EF  HZ    CZ   CE2   120.25  3.000
 0EF  HZ    CZ   CE1   120.24  3.000
 0EF  CE2   CZ   CE1   119.52  3.000
 0EF  HN    NHO  C6    115.58  3.000
 0EF  HN    NHO  CA2   116.28  3.000
 0EF  C6    NHO  CA2   121.40  3.000
 0EF  OXT   C6   O4    127.67  3.000
 0EF  OXT   C6   NHO   115.60  3.000
 0EF  O4    C6   NHO   116.71  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
 0EF  CONST_01  CZ    CE1  CD1  CG1     0.00   0.0  0
 0EF  CONST_02  CZ    CE2  CD2  CG1     0.00   0.0  0
 0EF  CONST_03  CE2   CD2  CG1  CD1     0.00   0.0  0
 0EF  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 0EF  CONST_05  CE1   CD1  CG1  CD2     0.00   0.0  0
 0EF  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 0EF  CONST_07  CE1   CD1  CG1  CB2   180.00   0.0  0
 0EF  CONST_08  CE2   CD2  CG1  CB2   180.00   0.0  0
 0EF  CONST_09  HE1   CE1  CD1  CG1   180.00   0.0  0
 0EF  CONST_10  HE2   CE2  CD2  CG1   180.00   0.0  0
 0EF  CONST_11  HD21  CD2  CG1  CD1   180.00   0.0  0
 0EF  CONST_12  HZ    CZ   CE1  CD1   180.00   0.0  0
 0EF  CONST_13  HD1   CD1  CG1  CD2   180.00   0.0  0
 0EF  CONST_14  CA1   N1   C4   CA    180.00   0.0  0
 0EF  CONST_15  CD    N1   C4   CA      0.00   0.0  0
 0EF  CONST_16  CA1   N1   C4   O       0.00   0.0  0
 0EF  CONST_17  CD    N1   C4   O     180.00   0.0  0
 0EF  CONST_19  H1    N2   C5   CA1     0.00   0.0  0
 0EF  Var_01    CB1   CG   CD   N1     29.22  30.0  1
 0EF  Var_02    CG    CD   N1   CA1   -11.25  30.0  1
 0EF  Var_03    CD    CG   CB1  CA1   -36.29  30.0  1
 0EF  Var_04    CD1   CG1  CB2  CA2    76.50  30.0  2
 0EF  Var_05    CA    N    C    O1      2.95  30.0  2
 0EF  Var_06    C1    CT   O2   C      60.48  30.0  3
 0EF  Var_07    N     C    O2   CT   -177.44  30.0  1
 0EF  Var_08    O4    C6   NHO  CA2    16.17  30.0  2
 0EF  Var_09    H11   C1   CT   O2     50.16  30.0  3
 0EF  Var_10    H21   C2   CT   O2     60.16  30.0  3
 0EF  Var_11    H31   C3   CT   O2     69.66  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
 0EF  chir_01  CA   N   C4   CB   positiv
 0EF  chir_02  CA1  N1  CB1  C5   negativ
 0EF  chir_03  CA2  N2  NHO  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
 0EF  plan-1  CB2   0.020
 0EF  plan-1  CG1   0.020
 0EF  plan-1  CD1   0.020
 0EF  plan-1  CD2   0.020
 0EF  plan-1  CE1   0.020
 0EF  plan-1  CE2   0.020
 0EF  plan-1  CZ    0.020
 0EF  plan-1  HD1   0.020
 0EF  plan-1  HD21  0.020
 0EF  plan-1  HE1   0.020
 0EF  plan-1  HE2   0.020
 0EF  plan-1  HZ    0.020
 0EF  plan-2  CA1   0.020
 0EF  plan-2  C5    0.020
 0EF  plan-2  O3    0.020
 0EF  plan-2  N2    0.020
 0EF  plan-2  CA2   0.020
 0EF  plan-2  H1    0.020
 0EF  plan-3  CA    0.020
 0EF  plan-3  C4    0.020
 0EF  plan-3  O     0.020
 0EF  plan-3  N1    0.020
 0EF  plan-3  CA1   0.020
 0EF  plan-3  CD    0.020
 0EF  plan-4  NHO   0.020
 0EF  plan-4  C6    0.020
 0EF  plan-4  O4    0.020
 0EF  plan-4  OXT   0.020
 0EF  plan-5  O1    0.020
 0EF  plan-5  C     0.020
 0EF  plan-5  O2    0.020
 0EF  plan-5  N     0.020

