# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:50:45 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: D-phenylalanyl-N-(pyridin-4-ylmethyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccncc3
#
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
 P05  P05  D-phenylalanyl-N-(pyridin-4-ylmethyl)-L-prolinamide  peptide  50  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_P05
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
 P05  N21   N  NH2   0  -0.763  -2.7210   1.8366  -0.8703
 P05  C8    C  CH1   0  -0.215  -2.4869   0.4847  -0.4236
 P05  C9    C  C     0   0.538  -1.0091   0.1783  -0.1672
 P05  O25   O  O     0  -0.500  -0.2426   1.0531   0.2203
 P05  C7    C  CH2   0  -0.540  -3.2542   0.2208   0.8843
 P05  C4    C  CR6   0   0.167  -4.7412   0.3246   0.7102
 P05  C3    C  CR16  0  -0.314  -5.4700  -0.7639   0.2363
 P05  C5    C  CR16  0  -0.308  -5.4224   1.5037   0.9990
 P05  C2    C  CR16  0  -0.240  -6.8441  -0.6803   0.0553
 P05  C6    C  CR16  0  -0.244  -6.7972   1.5922   0.8248
 P05  C1    C  CR16  0  -0.273  -7.5133   0.5006   0.3504
 P05  N22   N  NR5   0  -0.474  -0.5902  -1.0842  -0.3412
 P05  C13   C  CR15  0  -0.162   0.7984  -1.4262  -0.0921
 P05  C14   C  C     0   0.570   1.7338  -0.5738  -0.9396
 P05  O26   O  O     0  -0.496   1.4830  -0.3051  -2.1036
 P05  C12   C  CH2   0  -0.479   0.8854  -2.9063  -0.4928
 P05  C11   C  CH2   0  -0.471  -0.5414  -3.4103  -0.3099
 P05  C10   C  CH2   0  -0.285  -1.3823  -2.2301  -0.7739
 P05  C15   C  CH2   0  -0.310   3.8936   0.5562  -1.0196
 P05  C16   C  CR6   0   0.134   5.0900   0.7168  -0.1255
 P05  C17   C  CR16  0  -0.352   6.0602  -0.2750  -0.0399
 P05  C18   C  CR16  0  -0.057   7.1322  -0.0934   0.8199
 P05  C19   C  CR16  0  -0.056   6.3611   1.9313   1.4969
 P05  C20   C  CR16  0  -0.358   5.2513   1.8444   0.6689
 P05  N23   N  NH1   0  -0.638   2.8756  -0.2181  -0.3367
 P05  N24   N  N     0  -0.406   7.2895   0.9860   1.5782
 P05  HN21  H  HNH2  0   0.340  -2.2927   2.4897  -0.2254
 P05  HN2A  H  HNH2  0   0.351  -2.2721   1.9895  -1.7647
 P05  H8    H  HCH1  0   0.266  -2.8739  -0.1862  -1.1962
 P05  H7    H  HCH2  0   0.262  -2.9096   0.9361   1.6365
 P05  H7A   H  HCH2  0   0.262  -2.9993  -0.7720   1.2650
 P05  H3    H  HCR6  0   0.246  -4.9575  -1.6928   0.0101
 P05  H5    H  HCR6  0   0.242  -4.8749   2.3601   1.3728
 P05  H2    H  HCR6  0   0.253  -7.3916  -1.5396  -0.3104
 P05  H6    H  HCR6  0   0.252  -7.3104   2.5157   1.0616
 P05  H1    H  HCR6  0   0.252  -8.5852   0.5684   0.2162
 P05  H13   H  HCR5  0   0.275   1.0315  -1.3045   0.9712
 P05  H12   H  HCH2  0   0.266   1.6162  -3.4429   0.1095
 P05  H12A  H  HCH2  0   0.251   1.1794  -2.9994  -1.5404
 P05  H11   H  HCH2  0   0.246  -0.7428  -3.6181   0.7427
 P05  H11A  H  HCH2  0   0.259  -0.7499  -4.3146  -0.8798
 P05  H10   H  HCH2  0   0.250  -1.5068  -2.2328  -1.8608
 P05  H10A  H  HCH2  0   0.256  -2.3725  -2.2310  -0.3196
 P05  H15   H  HCH2  0   0.260   3.5019   1.5369  -1.3007
 P05  H15A  H  HCH2  0   0.263   4.1841   0.0479  -1.9412
 P05  H17   H  HCR6  0   0.272   5.9931  -1.1755  -0.6370
 P05  H18   H  HCR6  0   0.267   7.8996  -0.8556   0.8961
 P05  H19   H  HCR6  0   0.267   6.5040   2.8077   2.1192
 P05  H20   H  HCR6  0   0.272   4.5293   2.6505   0.6468
 P05  HN23  H  HNH1  0   0.406   2.9958  -0.4131   0.6441

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
 P05  C1   C2    aromatic  1.389  0.020  1.389
 P05  C1   C6    aromatic  1.389  0.020  1.389
 P05  C2   C3    aromatic  1.388  0.020  1.388
 P05  C3   C4    aromatic  1.393  0.020  1.393
 P05  C4   C5    aromatic  1.392  0.020  1.392
 P05  C4   C7    single    1.501  0.020  1.501
 P05  C5   C6    aromatic  1.389  0.020  1.389
 P05  C7   C8    single    1.539  0.020  1.539
 P05  C8   C9    single    1.531  0.020  1.531
 P05  C8   N21   single    1.443  0.020  1.443
 P05  C9   N22   single    1.342  0.020  1.342
 P05  C9   O25   double    1.226  0.020  1.226
 P05  C10  C11   single    1.522  0.020  1.522
 P05  C10  N22   single    1.459  0.020  1.459
 P05  C11  C12   single    1.524  0.020  1.524
 P05  C12  C13   single    1.536  0.020  1.536
 P05  C13  C14   single    1.523  0.020  1.523
 P05  C13  N22   single    1.452  0.020  1.452
 P05  C14  N23   single    1.339  0.020  1.339
 P05  C14  O26   double    1.221  0.020  1.221
 P05  C15  C16   single    1.502  0.020  1.502
 P05  C15  N23   single    1.450  0.020  1.450
 P05  C16  C17   aromatic  1.390  0.020  1.390
 P05  C16  C20   aromatic  1.389  0.020  1.389
 P05  C17  C18   aromatic  1.386  0.020  1.386
 P05  C18  N24   aromatic  1.328  0.020  1.328
 P05  C19  C20   aromatic  1.387  0.020  1.387
 P05  C19  N24   aromatic  1.327  0.020  1.327
 P05  C1   H1    single    0.930  0.020  1.080
 P05  C2   H2    single    0.930  0.020  1.080
 P05  C3   H3    single    0.930  0.020  1.080
 P05  C5   H5    single    0.930  0.020  1.080
 P05  C6   H6    single    0.930  0.020  1.080
 P05  C7   H7    single    0.970  0.020  1.090
 P05  C7   H7A   single    0.970  0.020  1.090
 P05  C8   H8    single    0.970  0.020  1.090
 P05  C10  H10   single    0.970  0.020  1.090
 P05  C10  H10A  single    0.970  0.020  1.090
 P05  C11  H11   single    0.970  0.020  1.090
 P05  C11  H11A  single    0.970  0.020  1.090
 P05  C12  H12   single    0.970  0.020  1.090
 P05  C12  H12A  single    0.970  0.020  1.090
 P05  C13  H13   single    0.970  0.020  1.090
 P05  C15  H15   single    0.970  0.020  1.090
 P05  C15  H15A  single    0.970  0.020  1.090
 P05  C17  H17   single    0.930  0.020  1.080
 P05  C18  H18   single    0.930  0.020  1.080
 P05  C19  H19   single    0.930  0.020  1.080
 P05  C20  H20   single    0.930  0.020  1.080
 P05  N21  HN21  single    0.890  0.020  1.040
 P05  N21  HN2A  single    0.890  0.020  1.040
 P05  N23  HN23  single    0.860  0.020  1.020

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
 P05  HN2A  N21  HN21  106.12  3.000
 P05  HN2A  N21  C8    110.07  3.000
 P05  HN21  N21  C8    109.78  3.000
 P05  H8    C8   C7    108.58  3.000
 P05  H8    C8   C9    109.70  3.000
 P05  C7    C8   C9    107.73  3.000
 P05  H8    C8   N21   107.37  3.000
 P05  C9    C8   N21   113.33  3.000
 P05  C7    C8   N21   110.05  3.000
 P05  N22   C9   O25   121.15  3.000
 P05  O25   C9   C8    120.91  3.000
 P05  N22   C9   C8    117.91  3.000
 P05  H7A   C7   H7    106.32  3.000
 P05  H7A   C7   C4    109.52  3.000
 P05  H7    C7   C4    110.29  3.000
 P05  H7A   C7   C8    109.59  3.000
 P05  H7    C7   C8    108.37  3.000
 P05  C4    C7   C8    112.55  3.000
 P05  C5    C4   C3    118.45  3.000
 P05  C5    C4   C7    121.29  3.000
 P05  C3    C4   C7    120.25  3.000
 P05  H3    C3   C2    119.47  3.000
 P05  H3    C3   C4    119.53  3.000
 P05  C2    C3   C4    121.00  3.000
 P05  H5    C5   C6    119.57  3.000
 P05  H5    C5   C4    119.60  3.000
 P05  C6    C5   C4    120.83  3.000
 P05  H2    C2   C1    120.19  3.000
 P05  H2    C2   C3    119.79  3.000
 P05  C1    C2   C3    120.02  3.000
 P05  H6    C6   C1    120.05  3.000
 P05  H6    C6   C5    119.75  3.000
 P05  C1    C6   C5    120.20  3.000
 P05  H1    C1   C6    120.23  3.000
 P05  H1    C1   C2    120.27  3.000
 P05  C6    C1   C2    119.49  3.000
 P05  C10   N22  C13   112.66  3.000
 P05  C13   N22  C9    119.88  3.000
 P05  C10   N22  C9    127.46  3.000
 P05  H13   C13  C12   110.38  3.000
 P05  H13   C13  C14   110.32  3.000
 P05  C12   C13  C14   111.07  3.000
 P05  H13   C13  N22   110.12  3.000
 P05  C14   C13  N22   111.11  3.000
 P05  C12   C13  N22   103.68  3.000
 P05  N23   C14  O26   123.09  3.000
 P05  O26   C14  C13   121.85  3.000
 P05  N23   C14  C13   114.94  3.000
 P05  H12A  C12  H12   107.94  3.000
 P05  H12A  C12  C11   109.81  3.000
 P05  H12   C12  C11   113.52  3.000
 P05  H12A  C12  C13   110.35  3.000
 P05  H12   C12  C13   111.64  3.000
 P05  C11   C12  C13   103.55  3.000
 P05  H11A  C11  H11   108.13  3.000
 P05  H11A  C11  C10   112.25  3.000
 P05  H11   C11  C10   109.86  3.000
 P05  H11A  C11  C12   113.01  3.000
 P05  H11   C11  C12   110.57  3.000
 P05  C10   C11  C12   102.96  3.000
 P05  H10A  C10  H10   108.12  3.000
 P05  H10A  C10  C11   111.99  3.000
 P05  H10   C10  C11   111.34  3.000
 P05  H10A  C10  N22   111.75  3.000
 P05  H10   C10  N22   111.00  3.000
 P05  C11   C10  N22   102.63  3.000
 P05  H15A  C15  H15   107.22  3.000
 P05  H15A  C15  N23   109.62  3.000
 P05  H15   C15  N23   110.41  3.000
 P05  H15A  C15  C16   109.90  3.000
 P05  H15   C15  C16   110.03  3.000
 P05  N23   C15  C16   109.63  3.000
 P05  C20   C16  C17   117.58  3.000
 P05  C20   C16  C15   121.32  3.000
 P05  C17   C16  C15   121.08  3.000
 P05  H17   C17  C18   119.93  3.000
 P05  H17   C17  C16   121.08  3.000
 P05  C18   C17  C16   118.98  3.000
 P05  H18   C18  N24   116.57  3.000
 P05  H18   C18  C17   119.92  3.000
 P05  N24   C18  C17   123.50  3.000
 P05  H19   C19  N24   116.63  3.000
 P05  H19   C19  C20   119.91  3.000
 P05  N24   C19  C20   123.46  3.000
 P05  H20   C20  C19   119.94  3.000
 P05  H20   C20  C16   121.04  3.000
 P05  C19   C20  C16   119.02  3.000
 P05  HN23  N23  C15   118.57  3.000
 P05  HN23  N23  C14   119.26  3.000
 P05  C15   N23  C14   121.90  3.000
 P05  C19   N24  C18   117.44  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
 P05  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 P05  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 P05  CONST_03  C6    C1   C2   C3      0.00   0.0  0
 P05  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 P05  CONST_05  C2    C3   C4   C5      0.00   0.0  0
 P05  CONST_06  C2    C1   C6   C5      0.00   0.0  0
 P05  CONST_07  N24   C18  C17  C16     0.00   0.0  0
 P05  CONST_08  N24   C19  C20  C16     0.00   0.0  0
 P05  CONST_09  C19   C20  C16  C17     0.00   0.0  0
 P05  CONST_10  C19   N24  C18  C17     0.00   0.0  0
 P05  CONST_11  C20   C16  C17  C18     0.00   0.0  0
 P05  CONST_12  C20   C19  N24  C18     0.00   0.0  0
 P05  CONST_13  C2    C3   C4   C7    180.00   0.0  0
 P05  CONST_14  C6    C5   C4   C7    180.00   0.0  0
 P05  CONST_15  C18   C17  C16  C15   180.00   0.0  0
 P05  CONST_16  C19   C20  C16  C15   180.00   0.0  0
 P05  CONST_17  H2    C2   C3   C4    180.00   0.0  0
 P05  CONST_18  H6    C6   C5   C4    180.00   0.0  0
 P05  CONST_19  H1    C1   C2   C3    180.00   0.0  0
 P05  CONST_20  H5    C5   C4   C3    180.00   0.0  0
 P05  CONST_21  H3    C3   C4   C5    180.00   0.0  0
 P05  CONST_22  H18   C18  C17  C16   180.00   0.0  0
 P05  CONST_23  H19   C19  C20  C16   180.00   0.0  0
 P05  CONST_24  H20   C20  C16  C17   180.00   0.0  0
 P05  CONST_25  H17   C17  C16  C20   180.00   0.0  0
 P05  CONST_26  C10   N22  C9   C8      0.00   0.0  0
 P05  CONST_27  C13   N22  C9   C8    180.00   0.0  0
 P05  CONST_28  C10   N22  C9   O25   180.00   0.0  0
 P05  CONST_29  C13   N22  C9   O25     0.00   0.0  0
 P05  CONST_30  C15   N23  C14  C13   180.00   0.0  0
 P05  CONST_31  HN23  N23  C14  C13     0.00   0.0  0
 P05  CONST_32  C15   N23  C14  O26     0.00   0.0  0
 P05  Var_01    C12   C11  C10  N22   -34.73  30.0  1
 P05  Var_02    C10   C11  C12  C13    37.49  30.0  1
 P05  Var_03    C11   C10  N22  C13    19.66  30.0  1
 P05  Var_04    C3    C4   C7   C8     83.70  30.0  2
 P05  Var_05    N23   C15  C16  C17    83.35  30.0  2
 P05  Var_06    C16   C15  N23  C14  -176.10  30.0  1

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
 P05  chir_01  C8   C7   C9   N21  positiv
 P05  chir_02  C13  N22  C12  C14  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
 P05  plan-1  C7    0.020
 P05  plan-1  C4    0.020
 P05  plan-1  C3    0.020
 P05  plan-1  C5    0.020
 P05  plan-1  C2    0.020
 P05  plan-1  C6    0.020
 P05  plan-1  C1    0.020
 P05  plan-1  H3    0.020
 P05  plan-1  H5    0.020
 P05  plan-1  H2    0.020
 P05  plan-1  H6    0.020
 P05  plan-1  H1    0.020
 P05  plan-2  C15   0.020
 P05  plan-2  C16   0.020
 P05  plan-2  C17   0.020
 P05  plan-2  C18   0.020
 P05  plan-2  C19   0.020
 P05  plan-2  C20   0.020
 P05  plan-2  N24   0.020
 P05  plan-2  H17   0.020
 P05  plan-2  H18   0.020
 P05  plan-2  H19   0.020
 P05  plan-2  H20   0.020
 P05  plan-3  C13   0.020
 P05  plan-3  C14   0.020
 P05  plan-3  O26   0.020
 P05  plan-3  C15   0.020
 P05  plan-3  N23   0.020
 P05  plan-3  HN23  0.020
 P05  plan-4  C8    0.020
 P05  plan-4  C9    0.020
 P05  plan-4  O25   0.020
 P05  plan-4  N22   0.020
 P05  plan-4  C13   0.020
 P05  plan-4  C10   0.020

