# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:34:08 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: N-[3-(biphenyl-4-yl)propanoyl]-L-alpha-glutamyl-L-alpha-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](CCC(O)=O)NC(=O)CCc1ccc(cc1)c2ccccc2
#
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
 EEF  EEF  N-[3-(biphenyl-4-yl)propanoyl]-L-alpha-glutamyl-L-alpha-glutamine  peptide  64  35  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EEF
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
 EEF  C1   C  CH2   0  -0.582   1.5001   0.3317   0.4345
 EEF  C2   C  C     0   0.570   0.0741   0.6633   0.8262
 EEF  O2   O  O     0  -0.493  -0.2697   0.8291   1.9865
 EEF  C14  C  CH2   0  -0.502   2.4212   0.1393   1.6358
 EEF  C15  C  CR16  0  -0.292   4.7319   0.8391   0.9144
 EEF  C16  C  CR16  0  -0.294   6.0187   0.5524   0.4865
 EEF  C17  C  CR6   0   0.071   6.4444  -0.7674   0.3276
 EEF  C18  C  CR6   0   0.115   3.8237  -0.1778   1.1986
 EEF  C19  C  CR6   0   0.089   7.8191  -1.0779  -0.1141
 EEF  C20  C  CR16  0  -0.313   8.5120  -2.1667   0.4195
 EEF  C21  C  CR16  0  -0.240   9.8037  -2.4599   0.0075
 EEF  C22  C  CR16  0  -0.240   9.7520  -0.5828  -1.4854
 EEF  C23  C  CR16  0  -0.312   8.4601  -0.2905  -1.0730
 EEF  C27  C  CR16  0  -0.268  10.4297  -1.6691  -0.9471
 EEF  C30  C  CR16  0  -0.294   5.5327  -1.7858   0.6076
 EEF  C31  C  CR16  0  -0.295   4.2462  -1.4943   1.0341
 EEF  N1   N  NH1   0  -0.638  -0.7761   0.7678  -0.2148
 EEF  C3   C  CH1   0  -0.240  -2.1807   1.0534  -0.0789
 EEF  C9   C  C     0   0.586  -2.9838   0.0339  -0.8760
 EEF  O1   O  O     0  -0.483  -2.5930  -0.3959  -1.9491
 EEF  C4   C  CH2   0  -0.410  -2.5507   2.4589  -0.5707
 EEF  C5   C  CH2   0  -0.590  -1.8176   3.5344   0.2101
 EEF  C8   C  C     0   0.556  -2.2010   4.9283  -0.2020
 EEF  O7   O  O     0  -0.443  -3.0028   5.2070  -1.0580
 EEF  O6   O  OH1   0  -0.597  -1.5397   5.8447   0.4985
 EEF  N2   N  NH1   0  -0.634  -4.1542  -0.3216  -0.3239
 EEF  C10  C  CH1   0  -0.198  -5.1398  -1.0697  -1.0573
 EEF  C13  C  C     0   0.519  -5.7232  -0.2125  -2.1874
 EEF  O5   O  O     0  -0.474  -5.7095   1.0056  -2.1391
 EEF  C11  C  CH2   0  -0.460  -6.2554  -1.5291  -0.1179
 EEF  C12  C  CH2   0  -0.580  -5.7407  -2.5011   0.9321
 EEF  C32  C  C     0   0.555  -6.8239  -3.0045   1.8452
 EEF  O34  O  O     0  -0.443  -7.9870  -2.6941   1.7800
 EEF  O33  O  OH1   0  -0.595  -6.3471  -3.8487   2.7537
 EEF  N3   N  NH2   0  -0.800  -6.2656  -0.9165  -3.1879
 EEF  H1   H  HCH2  0   0.277   1.4993  -0.5676  -0.1885
 EEF  H2   H  HCH2  0   0.278   1.8818   1.1338  -0.2045
 EEF  H16  H  HCH2  0   0.250   2.4209   1.0437   2.2466
 EEF  H17  H  HCH2  0   0.250   2.0392  -0.6665   2.2646
 EEF  H19  H  HCR6  0   0.251   6.7064   1.3680   0.2991
 EEF  H20  H  HCR6  0   0.253   8.0464  -2.7814   1.1801
 EEF  H21  H  HCR6  0   0.257  10.3257  -3.3034   0.4407
 EEF  H22  H  HCR6  0   0.257  10.2282   0.0365  -2.2346
 EEF  H23  H  HCR6  0   0.253   7.9379   0.5483  -1.5166
 EEF  H24  H  HCR6  0   0.257  11.4378  -1.8965  -1.2682
 EEF  H25  H  HCR6  0   0.251   5.8230  -2.8209   0.4769
 EEF  H26  H  HCR6  0   0.248   3.5595  -2.3073   1.2408
 EEF  H3   H  HNH1  0   0.399  -0.4274   0.5978  -1.1461
 EEF  H5   H  HCH1  0   0.281  -2.4324   0.9724   0.9803
 EEF  H8   H  HCH2  0   0.248  -2.3216   2.5420  -1.6357
 EEF  H9   H  HCH2  0   0.284  -2.0020   3.4310   1.2835
 EEF  H10  H  HOH1  0   0.480  -1.8050   6.7328   0.2163
 EEF  H4   H  HNH1  0   0.407  -4.4532   0.1557   0.5128
 EEF  H11  H  HCH1  0   0.283  -4.6620  -1.9534  -1.4907
 EEF  H12  H  HCH2  0   0.259  -6.7147  -0.6565   0.3539
 EEF  H13  H  HCH2  0   0.268  -7.0335  -2.0088  -0.7127
 EEF  H14  H  HCH2  0   0.288  -5.2687  -3.3635   0.4513
 EEF  H15  H  HCH2  0   0.287  -4.9613  -2.0482   1.5514
 EEF  H27  H  HOH1  0   0.480  -7.0641  -4.1538   3.3293
 EEF  H6   H  HNH2  0   0.410  -6.2254  -1.9210  -3.2169
 EEF  H7   H  HNH2  0   0.405  -6.7258  -0.4515  -3.9533
 EEF  H28  H  HCH2  0   0.254  -3.6303   2.5853  -0.4698
 EEF  H29  H  HCH2  0   0.284  -0.7359   3.4346   0.0845
 EEF  H18  H  HCR6  0   0.249   4.4336   1.8734   1.0417

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
 EEF  O7   C8   double    1.206  0.020  1.206
 EEF  C8   O6   single    1.330  0.020  1.330
 EEF  C8   C5   single    1.503  0.020  1.503
 EEF  C5   C4   single    1.518  0.020  1.518
 EEF  C1   C2   single    1.515  0.020  1.515
 EEF  C1   C14  single    1.526  0.020  1.526
 EEF  C2   N1   single    1.348  0.020  1.348
 EEF  C2   O2   double    1.221  0.020  1.221
 EEF  C14  C18  single    1.503  0.020  1.503
 EEF  N1   C3   single    1.440  0.020  1.440
 EEF  C4   C3   single    1.534  0.020  1.534
 EEF  C31  C18  aromatic  1.392  0.020  1.392
 EEF  C31  C30  aromatic  1.386  0.020  1.386
 EEF  C18  C15  aromatic  1.393  0.020  1.393
 EEF  C3   C9   single    1.523  0.020  1.523
 EEF  C30  C17  aromatic  1.395  0.020  1.395
 EEF  C15  C16  aromatic  1.386  0.020  1.386
 EEF  C23  C22  aromatic  1.387  0.020  1.387
 EEF  C23  C19  aromatic  1.397  0.020  1.397
 EEF  C17  C16  aromatic  1.396  0.020  1.396
 EEF  C17  C19  single    1.477  0.020  1.477
 EEF  C9   O1   double    1.220  0.020  1.220
 EEF  C9   N2   single    1.342  0.020  1.342
 EEF  C22  C27  aromatic  1.389  0.020  1.389
 EEF  C19  C20  aromatic  1.397  0.020  1.397
 EEF  N2   C10  single    1.438  0.020  1.438
 EEF  O5   C13  double    1.219  0.020  1.219
 EEF  C27  C21  aromatic  1.389  0.020  1.389
 EEF  C20  C21  aromatic  1.387  0.020  1.387
 EEF  C13  C10  single    1.534  0.020  1.534
 EEF  C13  N3   single    1.338  0.020  1.338
 EEF  C10  C11  single    1.529  0.020  1.529
 EEF  C11  C12  single    1.521  0.020  1.521
 EEF  C12  C32  single    1.503  0.020  1.503
 EEF  O34  C32  double    1.206  0.020  1.206
 EEF  C32  O33  single    1.329  0.020  1.329
 EEF  C1   H1   single    0.970  0.020  1.090
 EEF  C1   H2   single    0.970  0.020  1.090
 EEF  N1   H3   single    0.860  0.020  1.020
 EEF  N2   H4   single    0.860  0.020  1.020
 EEF  C3   H5   single    0.970  0.020  1.090
 EEF  N3   H6   single    0.860  0.020  1.020
 EEF  N3   H7   single    0.860  0.020  1.020
 EEF  C4   H8   single    0.970  0.020  1.090
 EEF  C5   H9   single    0.970  0.020  1.090
 EEF  O6   H10  single    0.850  0.020  0.980
 EEF  C10  H11  single    0.970  0.020  1.090
 EEF  C11  H12  single    0.970  0.020  1.090
 EEF  C11  H13  single    0.970  0.020  1.090
 EEF  C12  H14  single    0.970  0.020  1.090
 EEF  C12  H15  single    0.970  0.020  1.090
 EEF  C14  H16  single    0.970  0.020  1.090
 EEF  C14  H17  single    0.970  0.020  1.090
 EEF  C15  H18  single    0.930  0.020  1.080
 EEF  C16  H19  single    0.930  0.020  1.080
 EEF  C20  H20  single    0.930  0.020  1.080
 EEF  C21  H21  single    0.930  0.020  1.080
 EEF  C22  H22  single    0.930  0.020  1.080
 EEF  C23  H23  single    0.930  0.020  1.080
 EEF  C27  H24  single    0.930  0.020  1.080
 EEF  C30  H25  single    0.930  0.020  1.080
 EEF  C31  H26  single    0.930  0.020  1.080
 EEF  O33  H27  single    0.850  0.020  0.980
 EEF  C4   H28  single    0.970  0.020  1.090
 EEF  C5   H29  single    0.970  0.020  1.090

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
 EEF  H2   C1   H1   105.68  3.000
 EEF  H2   C1   C14  109.97  3.000
 EEF  H1   C1   C14  110.19  3.000
 EEF  H2   C1   C2   108.59  3.000
 EEF  H1   C1   C2   109.05  3.000
 EEF  C14  C1   C2   113.08  3.000
 EEF  N1   C2   O2   123.06  3.000
 EEF  O2   C2   C1   122.69  3.000
 EEF  N1   C2   C1   114.25  3.000
 EEF  H17  C14  H16  106.82  3.000
 EEF  H17  C14  C18  109.79  3.000
 EEF  H16  C14  C18  109.75  3.000
 EEF  H17  C14  C1   109.60  3.000
 EEF  H16  C14  C1   109.63  3.000
 EEF  C18  C14  C1   111.15  3.000
 EEF  H18  C15  C18  119.55  3.000
 EEF  H18  C15  C16  119.28  3.000
 EEF  C18  C15  C16  121.16  3.000
 EEF  H19  C16  C17  119.91  3.000
 EEF  H19  C16  C15  119.15  3.000
 EEF  C17  C16  C15  120.92  3.000
 EEF  C30  C17  C19  120.98  3.000
 EEF  C19  C17  C16  121.11  3.000
 EEF  C30  C17  C16  117.91  3.000
 EEF  C31  C18  C15  117.93  3.000
 EEF  C15  C18  C14  120.92  3.000
 EEF  C31  C18  C14  121.13  3.000
 EEF  C23  C19  C20  118.31  3.000
 EEF  C20  C19  C17  120.76  3.000
 EEF  C23  C19  C17  120.94  3.000
 EEF  H20  C20  C21  119.27  3.000
 EEF  H20  C20  C19  119.83  3.000
 EEF  C21  C20  C19  120.88  3.000
 EEF  H21  C21  C27  120.10  3.000
 EEF  H21  C21  C20  119.66  3.000
 EEF  C27  C21  C20  120.24  3.000
 EEF  H22  C22  C27  120.07  3.000
 EEF  H22  C22  C23  119.67  3.000
 EEF  C27  C22  C23  120.26  3.000
 EEF  H23  C23  C22  119.36  3.000
 EEF  H23  C23  C19  119.78  3.000
 EEF  C22  C23  C19  120.85  3.000
 EEF  H24  C27  C22  120.26  3.000
 EEF  H24  C27  C21  120.28  3.000
 EEF  C22  C27  C21  119.46  3.000
 EEF  H25  C30  C31  119.14  3.000
 EEF  H25  C30  C17  119.88  3.000
 EEF  C31  C30  C17  120.97  3.000
 EEF  H26  C31  C30  119.26  3.000
 EEF  H26  C31  C18  119.63  3.000
 EEF  C30  C31  C18  121.12  3.000
 EEF  H3   N1   C3   117.24  3.000
 EEF  H3   N1   C2   118.80  3.000
 EEF  C3   N1   C2   123.90  3.000
 EEF  H5   C3   C4   108.87  3.000
 EEF  H5   C3   C9   109.67  3.000
 EEF  C4   C3   C9   108.56  3.000
 EEF  H5   C3   N1   107.57  3.000
 EEF  C9   C3   N1   109.41  3.000
 EEF  C4   C3   N1   112.74  3.000
 EEF  N2   C9   O1   123.22  3.000
 EEF  N2   C9   C3   114.95  3.000
 EEF  O1   C9   C3   121.81  3.000
 EEF  H28  C4   H8   106.78  3.000
 EEF  H28  C4   C5   110.37  3.000
 EEF  H8   C4   C5   110.26  3.000
 EEF  H28  C4   C3   108.35  3.000
 EEF  H8   C4   C3   109.36  3.000
 EEF  C5   C4   C3   111.58  3.000
 EEF  H29  C5   H9   105.71  3.000
 EEF  H29  C5   C8   107.78  3.000
 EEF  H9   C5   C8   108.28  3.000
 EEF  H29  C5   C4   110.74  3.000
 EEF  H9   C5   C4   110.88  3.000
 EEF  C8   C5   C4   113.13  3.000
 EEF  O6   C8   O7   123.06  3.000
 EEF  O6   C8   C5   111.58  3.000
 EEF  O7   C8   C5   125.35  3.000
 EEF  H10  O6   C8   110.01  3.000
 EEF  H4   N2   C10  117.78  3.000
 EEF  H4   N2   C9   118.32  3.000
 EEF  C10  N2   C9   121.71  3.000
 EEF  H11  C10  C11  108.62  3.000
 EEF  H11  C10  C13  109.00  3.000
 EEF  C11  C10  C13  110.06  3.000
 EEF  H11  C10  N2   108.84  3.000
 EEF  C11  C10  N2   110.06  3.000
 EEF  C13  C10  N2   110.22  3.000
 EEF  N3   C13  O5   124.04  3.000
 EEF  N3   C13  C10  114.27  3.000
 EEF  O5   C13  C10  121.67  3.000
 EEF  H13  C11  H12  106.66  3.000
 EEF  H13  C11  C12  109.69  3.000
 EEF  H12  C11  C12  110.76  3.000
 EEF  H13  C11  C10  108.52  3.000
 EEF  H12  C11  C10  109.38  3.000
 EEF  C12  C11  C10  111.67  3.000
 EEF  H15  C12  H14  105.52  3.000
 EEF  H15  C12  C32  107.95  3.000
 EEF  H14  C12  C32  108.28  3.000
 EEF  H15  C12  C11  111.56  3.000
 EEF  H14  C12  C11  110.26  3.000
 EEF  C32  C12  C11  112.93  3.000
 EEF  O33  C32  O34  123.15  3.000
 EEF  O33  C32  C12  111.69  3.000
 EEF  O34  C32  C12  125.17  3.000
 EEF  H27  O33  C32  109.92  3.000
 EEF  H7   N3   H6   117.24  3.000
 EEF  H7   N3   C13  120.70  3.000
 EEF  H6   N3   C13  122.06  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
 EEF  CONST_01  C30  C31  C18  C15     0.00   0.0  0
 EEF  CONST_02  C30  C17  C16  C15     0.00   0.0  0
 EEF  CONST_03  C19  C17  C16  C15   180.00   0.0  0
 EEF  CONST_04  C31  C18  C15  C16     0.00   0.0  0
 EEF  CONST_05  C31  C30  C17  C16     0.00   0.0  0
 EEF  CONST_08  C18  C31  C30  C17     0.00   0.0  0
 EEF  CONST_09  C18  C15  C16  C17     0.00   0.0  0
 EEF  CONST_10  C22  C23  C19  C17   180.00   0.0  0
 EEF  CONST_11  C21  C20  C19  C17   180.00   0.0  0
 EEF  CONST_12  C27  C22  C23  C19     0.00   0.0  0
 EEF  CONST_13  C31  C30  C17  C19   180.00   0.0  0
 EEF  CONST_14  C27  C21  C20  C19     0.00   0.0  0
 EEF  CONST_15  C22  C23  C19  C20     0.00   0.0  0
 EEF  CONST_17  C22  C27  C21  C20     0.00   0.0  0
 EEF  CONST_18  C23  C22  C27  C21     0.00   0.0  0
 EEF  CONST_19  C23  C19  C20  C21     0.00   0.0  0
 EEF  CONST_21  C30  C31  C18  C14   180.00   0.0  0
 EEF  CONST_22  C16  C15  C18  C14   180.00   0.0  0
 EEF  CONST_23  H26  C31  C18  C15   180.00   0.0  0
 EEF  CONST_24  H25  C30  C17  C16   180.00   0.0  0
 EEF  CONST_25  H18  C15  C16  C17   180.00   0.0  0
 EEF  CONST_26  H23  C23  C19  C17     0.00   0.0  0
 EEF  CONST_27  H20  C20  C19  C17     0.00   0.0  0
 EEF  CONST_28  H19  C16  C15  C18   180.00   0.0  0
 EEF  CONST_29  H22  C22  C23  C19   180.00   0.0  0
 EEF  CONST_30  H21  C21  C20  C19   180.00   0.0  0
 EEF  CONST_31  H24  C27  C21  C20   180.00   0.0  0
 EEF  CONST_32  C3   N1   C2   C1    180.00   0.0  0
 EEF  CONST_33  C3   N1   C2   O2      0.00   0.0  0
 EEF  CONST_34  C10  N2   C9   C3    180.00   0.0  0
 EEF  CONST_35  C10  N2   C9   O1      0.00   0.0  0
 EEF  CONST_36  H3   N1   C2   C1      0.00   0.0  0
 EEF  CONST_37  H4   N2   C9   C3      0.00   0.0  0
 EEF  CONST_38  H6   N3   C13  C10     0.00   0.0  0
 EEF  CONST_39  H7   N3   C13  C10   180.00   0.0  0
 EEF  CONST_40  H10  O6   C8   C5    180.00   0.0  0
 EEF  CONST_41  H27  O33  C32  C12   180.00   0.0  0
 EEF  Var_01    C31  C18  C14  C1    -91.64  30.0  2
 EEF  Var_02    C18  C14  C1   C2   -179.61  30.0  3
 EEF  Var_03    C14  C1   C2   O2      3.80  30.0  2
 EEF  Var_04    C8   C5   C4   C3   -177.42  30.0  1
 EEF  Var_05    O7   C8   C5   C4      0.03  30.0  1
 EEF  Var_06    C32  C12  C11  C10  -178.21  30.0  3
 EEF  Var_07    O34  C32  C12  C11     0.12  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
 EEF  chir_01  C3   N1  C4   C9   negativ
 EEF  chir_02  C10  N2  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
 EEF  plan-1  C17  0.020
 EEF  plan-1  C19  0.020
 EEF  plan-1  C20  0.020
 EEF  plan-1  C21  0.020
 EEF  plan-1  C22  0.020
 EEF  plan-1  C23  0.020
 EEF  plan-1  C27  0.020
 EEF  plan-1  H20  0.020
 EEF  plan-1  H21  0.020
 EEF  plan-1  H22  0.020
 EEF  plan-1  H23  0.020
 EEF  plan-1  H24  0.020
 EEF  plan-2  C12  0.020
 EEF  plan-2  C32  0.020
 EEF  plan-2  O34  0.020
 EEF  plan-2  O33  0.020
 EEF  plan-2  H27  0.020
 EEF  plan-3  C14  0.020
 EEF  plan-3  C15  0.020
 EEF  plan-3  C16  0.020
 EEF  plan-3  C17  0.020
 EEF  plan-3  C18  0.020
 EEF  plan-3  C19  0.020
 EEF  plan-3  C30  0.020
 EEF  plan-3  C31  0.020
 EEF  plan-3  H19  0.020
 EEF  plan-3  H25  0.020
 EEF  plan-3  H26  0.020
 EEF  plan-3  H18  0.020
 EEF  plan-4  C1   0.020
 EEF  plan-4  C2   0.020
 EEF  plan-4  O2   0.020
 EEF  plan-4  N1   0.020
 EEF  plan-4  C3   0.020
 EEF  plan-4  H3   0.020
 EEF  plan-5  C3   0.020
 EEF  plan-5  C9   0.020
 EEF  plan-5  O1   0.020
 EEF  plan-5  N2   0.020
 EEF  plan-5  C10  0.020
 EEF  plan-5  H4   0.020
 EEF  plan-6  C10  0.020
 EEF  plan-6  C13  0.020
 EEF  plan-6  O5   0.020
 EEF  plan-6  N3   0.020
 EEF  plan-6  H6   0.020
 EEF  plan-6  H7   0.020
 EEF  plan-7  C5   0.020
 EEF  plan-7  C8   0.020
 EEF  plan-7  O7   0.020
 EEF  plan-7  O6   0.020
 EEF  plan-7  H10  0.020

