# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 21:51:25 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: D-phenylalanyl-N-benzyl-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccccc3
#
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
 53U  53U  "D-phenylalanyl-N-benzyl-L-prolinamide"  peptide  51  26  .  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_53U
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
 53U  N1    N  NH2   0  -0.763   2.6611   1.8261   0.9048
 53U  C2    C  CH1   0  -0.215   2.4335   0.4803   0.4372
 53U  C3    C  C     0   0.538   0.9552   0.1640   0.1964
 53U  O1    O  O     0  -0.500   0.1743   1.0405  -0.1574
 53U  C1    C  CH2   0  -0.540   3.1829   0.2467  -0.8871
 53U  C16   C  CR6   0   0.168   4.6708   0.3678  -0.7347
 53U  C17   C  CR16  0  -0.314   5.4197  -0.7151  -0.2797
 53U  C21   C  CR16  0  -0.309   5.3330   1.5574  -1.0239
 53U  C18   C  CR16  0  -0.240   6.7949  -0.6153  -0.1167
 53U  C20   C  CR16  0  -0.244   6.7090   1.6621  -0.8679
 53U  C19   C  CR16  0  -0.273   7.4451   0.5762  -0.4115
 53U  N2    N  NT    0  -0.474   0.5519  -1.1070   0.3415
 53U  C7    C  CH1   0  -0.161  -0.8363  -1.4574   0.0983
 53U  C8    C  C     0   0.567  -1.7704  -0.6379   0.9801
 53U  O2    O  O     0  -0.498  -1.5175  -0.4232   2.1553
 53U  C6    C  CH2   0  -0.480  -0.9026  -2.9490   0.4569
 53U  C5    C  CH2   0  -0.471   0.5285  -3.4310   0.2495
 53U  C4    C  CH2   0  -0.285   1.3587  -2.2546   0.7410
 53U  N3    N  NH1   0  -0.634  -2.9089  -0.2516   0.3917
 53U  C9    C  CH2   0  -0.318  -3.9190   0.5212   1.0913
 53U  C10   C  CR6   0   0.051  -5.1364   0.6793   0.2239
 53U  C11   C  CR16  0  -0.285  -6.1187  -0.3077   0.1970
 53U  C12   C  CR16  0  -0.241  -7.2283  -0.1772  -0.6264
 53U  C13   C  CR16  0  -0.264  -7.3665   0.9432  -1.4364
 53U  C14   C  CR16  0  -0.241  -6.3910   1.9310  -1.4179
 53U  C15   C  CR16  0  -0.289  -5.2822   1.7972  -0.5922
 53U  HN1   H  HNH2  0   0.340   2.2007   2.4856   0.2891
 53U  HN1A  H  HNH2  0   0.351   2.2400   1.9519   1.8167
 53U  H2    H  HCH1  0   0.266   2.8392  -0.1999   1.1914
 53U  H1    H  HCH2  0   0.261   2.9347  -0.7440  -1.2777
 53U  H1A   H  HCH2  0   0.262   2.8161   0.9674  -1.6233
 53U  H17   H  HCR6  0   0.246   4.9221  -1.6523  -0.0542
 53U  H21   H  HCR6  0   0.242   4.7700   2.4097  -1.3841
 53U  H18   H  HCR6  0   0.253   7.3583  -1.4703   0.2347
 53U  H20   H  HCR6  0   0.252   7.2070   2.5939  -1.1046
 53U  H19   H  HCR6  0   0.252   8.5178   0.6566  -0.2913
 53U  H7    H  HCH1  0   0.273  -1.0817  -1.3082  -0.9588
 53U  H6    H  HCH2  0   0.266  -1.6311  -3.4769  -0.1558
 53U  H6A   H  HCH2  0   0.251  -1.1887  -3.0751   1.5031
 53U  H5    H  HCH2  0   0.245   0.7242  -3.6064  -0.8101
 53U  H5A   H  HCH2  0   0.258   0.7524  -4.3489   0.7911
 53U  H4    H  HCH2  0   0.255   2.3475  -2.2332   0.2845
 53U  H4A   H  HCH2  0   0.249   1.4864  -2.2849   1.8271
 53U  HN3   H  HNH1  0   0.403  -3.0107  -0.3723  -0.6032
 53U  H9    H  HCH2  0   0.256  -4.1806   0.0123   2.0208
 53U  H9A   H  HCH2  0   0.253  -3.5223   1.5028   1.3653
 53U  H11   H  HCR6  0   0.254  -6.0193  -1.1819   0.8298
 53U  H12   H  HCR6  0   0.258  -7.9872  -0.9486  -0.6336
 53U  H13   H  HCR6  0   0.258  -8.2334   1.0473  -2.0761
 53U  H14   H  HCR6  0   0.258  -6.4938   2.8082  -2.0435
 53U  H15   H  HCR6  0   0.255  -4.5251   2.5724  -0.5805

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
 53U  C1   C2    single    1.539  0.020  1.539
 53U  C1   C16   single    1.501  0.020  1.501
 53U  N1   C2    single    1.443  0.020  1.443
 53U  C2   C3    single    1.531  0.020  1.531
 53U  C3   O1    double    1.226  0.020  1.226
 53U  C3   N2    single    1.341  0.020  1.341
 53U  N2   C4    single    1.459  0.020  1.459
 53U  N2   C7    single    1.452  0.020  1.452
 53U  C4   C5    single    1.521  0.020  1.521
 53U  C5   C6    single    1.524  0.020  1.524
 53U  C6   C7    single    1.536  0.020  1.536
 53U  C7   C8    single    1.524  0.020  1.524
 53U  C8   N3    single    1.339  0.020  1.339
 53U  C8   O2    double    1.221  0.020  1.221
 53U  N3   C9    single    1.452  0.020  1.452
 53U  C9   C10   single    1.503  0.020  1.503
 53U  C10  C11   aromatic  1.393  0.020  1.393
 53U  C10  C15   aromatic  1.392  0.020  1.392
 53U  C11  C12   aromatic  1.388  0.020  1.388
 53U  C12  C13   aromatic  1.389  0.020  1.389
 53U  C13  C14   aromatic  1.388  0.020  1.388
 53U  C14  C15   aromatic  1.389  0.020  1.389
 53U  C16  C17   aromatic  1.393  0.020  1.393
 53U  C16  C21   aromatic  1.392  0.020  1.392
 53U  C17  C18   aromatic  1.388  0.020  1.388
 53U  C18  C19   aromatic  1.389  0.020  1.389
 53U  C19  C20   aromatic  1.389  0.020  1.389
 53U  C20  C21   aromatic  1.389  0.020  1.389
 53U  C1   H1    single    0.970  0.020  1.090
 53U  C1   H1A   single    0.970  0.020  1.090
 53U  N1   HN1   single    0.890  0.020  1.040
 53U  N1   HN1A  single    0.890  0.020  1.040
 53U  C2   H2    single    0.970  0.020  1.090
 53U  C4   H4    single    0.970  0.020  1.090
 53U  C4   H4A   single    0.970  0.020  1.090
 53U  C5   H5    single    0.970  0.020  1.090
 53U  C5   H5A   single    0.970  0.020  1.090
 53U  C6   H6    single    0.970  0.020  1.090
 53U  C6   H6A   single    0.970  0.020  1.090
 53U  C7   H7    single    0.970  0.020  1.090
 53U  N3   HN3   single    0.860  0.020  1.020
 53U  C9   H9    single    0.970  0.020  1.090
 53U  C9   H9A   single    0.970  0.020  1.090
 53U  C11  H11   single    0.930  0.020  1.080
 53U  C12  H12   single    0.930  0.020  1.080
 53U  C13  H13   single    0.930  0.020  1.080
 53U  C14  H14   single    0.930  0.020  1.080
 53U  C15  H15   single    0.930  0.020  1.080
 53U  C17  H17   single    0.930  0.020  1.080
 53U  C18  H18   single    0.930  0.020  1.080
 53U  C19  H19   single    0.930  0.020  1.080
 53U  C20  H20   single    0.930  0.020  1.080
 53U  C21  H21   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
 53U  HN1A  N1   HN1  106.12  3.000
 53U  HN1A  N1   C2   110.02  3.000
 53U  HN1   N1   C2   109.79  3.000
 53U  H2    C2   C1   108.56  3.000
 53U  H2    C2   C3   109.76  3.000
 53U  C1    C2   C3   107.66  3.000
 53U  H2    C2   N1   107.35  3.000
 53U  C3    C2   N1   113.33  3.000
 53U  C1    C2   N1   110.10  3.000
 53U  N2    C3   O1   121.14  3.000
 53U  N2    C3   C2   117.98  3.000
 53U  O1    C3   C2   120.84  3.000
 53U  H1A   C1   H1   106.29  3.000
 53U  H1A   C1   C16  110.35  3.000
 53U  H1    C1   C16  109.54  3.000
 53U  H1A   C1   C2   108.41  3.000
 53U  H1    C1   C2   109.53  3.000
 53U  C16   C1   C2   112.52  3.000
 53U  C21   C16  C17  118.45  3.000
 53U  C21   C16  C1   121.31  3.000
 53U  C17   C16  C1   120.23  3.000
 53U  H17   C17  C18  119.48  3.000
 53U  H17   C17  C16  119.53  3.000
 53U  C18   C17  C16  120.99  3.000
 53U  H21   C21  C20  119.54  3.000
 53U  H21   C21  C16  119.62  3.000
 53U  C20   C21  C16  120.83  3.000
 53U  H18   C18  C19  120.18  3.000
 53U  H18   C18  C17  119.79  3.000
 53U  C19   C18  C17  120.02  3.000
 53U  H20   C20  C19  120.06  3.000
 53U  H20   C20  C21  119.74  3.000
 53U  C19   C20  C21  120.21  3.000
 53U  H19   C19  C20  120.24  3.000
 53U  H19   C19  C18  120.27  3.000
 53U  C20   C19  C18  119.49  3.000
 53U  C4    N2   C7   112.63  3.000
 53U  C7    N2   C3   119.86  3.000
 53U  C4    N2   C3   127.51  3.000
 53U  H7    C7   C6   110.36  3.000
 53U  H7    C7   C8   110.36  3.000
 53U  C6    C7   C8   111.15  3.000
 53U  H7    C7   N2   110.05  3.000
 53U  C8    C7   N2   111.06  3.000
 53U  C6    C7   N2   103.68  3.000
 53U  N3    C8   O2   123.26  3.000
 53U  O2    C8   C7   121.64  3.000
 53U  N3    C8   C7   114.98  3.000
 53U  H6A   C6   H6   107.94  3.000
 53U  H6A   C6   C5   109.87  3.000
 53U  H6    C6   C5   113.48  3.000
 53U  H6A   C6   C7   110.32  3.000
 53U  H6    C6   C7   111.62  3.000
 53U  C5    C6   C7   103.58  3.000
 53U  H5A   C5   H5   108.09  3.000
 53U  H5A   C5   C4   112.26  3.000
 53U  H5    C5   C4   109.87  3.000
 53U  H5A   C5   C6   113.07  3.000
 53U  H5    C5   C6   110.56  3.000
 53U  C4    C5   C6   102.94  3.000
 53U  H4A   C4   H4   108.10  3.000
 53U  H4A   C4   C5   111.29  3.000
 53U  H4    C4   C5   112.03  3.000
 53U  H4A   C4   N2   110.99  3.000
 53U  H4    C4   N2   111.83  3.000
 53U  C5    C4   N2   102.59  3.000
 53U  HN3   N3   C9   118.00  3.000
 53U  HN3   N3   C8   119.04  3.000
 53U  C9    N3   C8   122.25  3.000
 53U  H9A   C9   H9   106.99  3.000
 53U  H9A   C9   C10  110.12  3.000
 53U  H9    C9   C10  110.26  3.000
 53U  H9A   C9   N3   110.26  3.000
 53U  H9    C9   N3   109.21  3.000
 53U  C10   C9   N3   109.96  3.000
 53U  C15   C10  C11  118.95  3.000
 53U  C15   C10  C9   120.51  3.000
 53U  C11   C10  C9   120.52  3.000
 53U  H11   C11  C12  119.71  3.000
 53U  H11   C11  C10  119.72  3.000
 53U  C12   C11  C10  120.57  3.000
 53U  H12   C12  C13  120.08  3.000
 53U  H12   C12  C11  119.84  3.000
 53U  C13   C12  C11  120.08  3.000
 53U  H13   C13  C14  120.14  3.000
 53U  H13   C13  C12  120.12  3.000
 53U  C14   C13  C12  119.74  3.000
 53U  H14   C14  C15  119.83  3.000
 53U  H14   C14  C13  120.14  3.000
 53U  C15   C14  C13  120.02  3.000
 53U  H15   C15  C14  119.69  3.000
 53U  H15   C15  C10  119.68  3.000
 53U  C14   C15  C10  120.63  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
 53U  CONST_01  C19  C18  C17  C16     0.00   0.0  0
 53U  CONST_02  C19  C20  C21  C16     0.00   0.0  0
 53U  CONST_03  C20  C21  C16  C17     0.00   0.0  0
 53U  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 53U  CONST_05  C18  C17  C16  C21     0.00   0.0  0
 53U  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 53U  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 53U  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 53U  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 53U  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 53U  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 53U  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 53U  CONST_13  C18  C17  C16  C1    180.00   0.0  0
 53U  CONST_14  C20  C21  C16  C1    180.00   0.0  0
 53U  CONST_15  C12  C11  C10  C9    180.00   0.0  0
 53U  CONST_16  C14  C15  C10  C9    180.00   0.0  0
 53U  CONST_17  H18  C18  C17  C16   180.00   0.0  0
 53U  CONST_18  H20  C20  C21  C16   180.00   0.0  0
 53U  CONST_19  H21  C21  C16  C17   180.00   0.0  0
 53U  CONST_20  H19  C19  C18  C17   180.00   0.0  0
 53U  CONST_21  H17  C17  C16  C21   180.00   0.0  0
 53U  CONST_22  H19  C19  C20  C21   180.00   0.0  0
 53U  CONST_23  H20  C20  C19  C18   180.00   0.0  0
 53U  CONST_24  H18  C18  C19  C20   180.00   0.0  0
 53U  CONST_25  H17  C17  C18  C19   180.00   0.0  0
 53U  CONST_26  H21  C21  C20  C19   180.00   0.0  0
 53U  CONST_27  H12  C12  C11  C10   180.00   0.0  0
 53U  CONST_28  H14  C14  C15  C10   180.00   0.0  0
 53U  CONST_29  H15  C15  C10  C11   180.00   0.0  0
 53U  CONST_30  H13  C13  C12  C11   180.00   0.0  0
 53U  CONST_31  H14  C14  C13  C12   180.00   0.0  0
 53U  CONST_32  H11  C11  C12  C13   180.00   0.0  0
 53U  CONST_33  H15  C15  C14  C13   180.00   0.0  0
 53U  CONST_34  H12  C12  C13  C14   180.00   0.0  0
 53U  CONST_35  H11  C11  C10  C15   180.00   0.0  0
 53U  CONST_36  H13  C13  C14  C15   180.00   0.0  0
 53U  CONST_37  C4   N2   C3   C2      0.00   0.0  0
 53U  CONST_38  C7   N2   C3   C2    180.00   0.0  0
 53U  CONST_39  C4   N2   C3   O1    180.00   0.0  0
 53U  CONST_40  C7   N2   C3   O1      0.00   0.0  0
 53U  CONST_41  C9   N3   C8   C7    180.00   0.0  0
 53U  CONST_42  HN3  N3   C8   C7      0.00   0.0  0
 53U  CONST_43  C9   N3   C8   O2      0.00   0.0  0
 53U  CONST_44  HN3  N3   C8   O2    180.00   0.0  0
 53U  Var_01    C6   C5   C4   N2    -34.95  30.0  1
 53U  Var_02    C5   C4   N2   C7     20.06  30.0  1
 53U  Var_03    C4   C5   C6   C7     37.48  30.0  1
 53U  Var_04    C5   C4   N2   C3   -160.33  30.0  1
 53U  Var_05    H5   C5   C4   N2     82.84  30.0  1
 53U  Var_06    H5A  C5   C4   N2   -156.85  30.0  1
 53U  Var_07    H4   C4   N2   C7    140.29  30.0  1
 53U  Var_08    H4A  C4   N2   C7    -98.90  30.0  1
 53U  Var_09    H5   C5   C6   C7    -79.82  30.0  1
 53U  Var_10    H5A  C5   C6   C7    158.84  30.0  1
 53U  Var_11    H4   C4   C5   C6   -155.04  30.0  1
 53U  Var_12    H4A  C4   C5   C6     83.80  30.0  1
 53U  Var_13    H6   C6   C5   C4    158.70  30.0  1
 53U  Var_14    H6A  C6   C5   C4    -80.37  30.0  1
 53U  Var_15    C17  C16  C1   C2     83.22  30.0  2
 53U  Var_16    C21  C16  C1   C2    -95.93  30.0  2
 53U  Var_17    C11  C10  C9   N3     85.09  30.0  2
 53U  Var_18    C15  C10  C9   N3    -93.16  30.0  2
 53U  Var_19    H4   C4   N2   C3    -40.10  30.0  1
 53U  Var_20    H4A  C4   N2   C3     80.71  30.0  1
 53U  Var_21    H1   C1   C16  C17   -38.87  30.0  2
 53U  Var_22    H1A  C1   C16  C17  -155.55  30.0  2
 53U  Var_23    H1   C1   C16  C21   141.98  30.0  2
 53U  Var_24    H1A  C1   C16  C21    25.30  30.0  2
 53U  Var_25    H9   C9   C10  C11   -35.39  30.0  2
 53U  Var_26    H9A  C9   C10  C11  -153.22  30.0  2
 53U  Var_27    H9   C9   C10  C15   146.37  30.0  2
 53U  Var_28    H9A  C9   C10  C15    28.54  30.0  2
 53U  Var_29    C10  C9   N3   C8   -174.12  30.0  3
 53U  Var_30    HN3  N3   C9   C10    15.56  30.0  1
 53U  Var_31    H9   C9   N3   C8    -53.01  30.0  3
 53U  Var_32    H9A  C9   N3   C8     64.27  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
 53U  chir_01  C2  C1  N1  C3  negativ
 53U  chir_02  C7  N2  C6  C8  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
 53U  plan-1  C1   0.020
 53U  plan-1  C16  0.020
 53U  plan-1  C17  0.020
 53U  plan-1  C21  0.020
 53U  plan-1  C18  0.020
 53U  plan-1  C20  0.020
 53U  plan-1  C19  0.020
 53U  plan-1  H17  0.020
 53U  plan-1  H21  0.020
 53U  plan-1  H18  0.020
 53U  plan-1  H20  0.020
 53U  plan-1  H19  0.020
 53U  plan-2  C9   0.020
 53U  plan-2  C10  0.020
 53U  plan-2  C11  0.020
 53U  plan-2  C12  0.020
 53U  plan-2  C13  0.020
 53U  plan-2  C14  0.020
 53U  plan-2  C15  0.020
 53U  plan-2  H11  0.020
 53U  plan-2  H12  0.020
 53U  plan-2  H13  0.020
 53U  plan-2  H14  0.020
 53U  plan-2  H15  0.020
 53U  plan-3  C7   0.020
 53U  plan-3  C8   0.020
 53U  plan-3  O2   0.020
 53U  plan-3  N3   0.020
 53U  plan-3  C9   0.020
 53U  plan-3  HN3  0.020
 53U  plan-4  C2   0.020
 53U  plan-4  C3   0.020
 53U  plan-4  O1   0.020
 53U  plan-4  N2   0.020
 53U  plan-4  C7   0.020
 53U  plan-4  C4   0.020

