# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 20:51:45 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: D-phenylalanyl-N-[(1-methylpyridinium-3-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3)c1
#
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
 10P  10P  D-phenylalanyl-N-[(1-methylpyridinium-3-yl)methyl]-L-prolinamide  peptide  54  27  .  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_10P
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
 10P  N22   N  NH2   0  -0.761   3.0206  -1.9544  -0.8107
 10P  C3    C  CH1   0  -0.216   2.6761  -0.6766  -0.2355
 10P  C4    C  C     0   0.539   1.3151  -0.6747   0.4646
 10P  O24   O  O     0  -0.500   0.8783  -1.6890   0.9968
 10P  C2    C  CH2   0  -0.536   3.7401  -0.2569   0.7959
 10P  C1    C  CR6   0   0.158   5.0762  -0.0000   0.1622
 10P  C5    C  CR16  0  -0.317   5.3898   1.2679  -0.3221
 10P  C9    C  CR16  0  -0.299   6.0159  -1.0174   0.0172
 10P  C6    C  CR16  0  -0.240   6.6103   1.5169  -0.9358
 10P  C8    C  CR16  0  -0.245   7.2391  -0.7736  -0.5930
 10P  C7    C  CR16  0  -0.273   7.5399   0.4946  -1.0738
 10P  N23   N  NT    0  -0.473   0.6338   0.4805   0.5133
 10P  C10   C  CH1   0  -0.167  -0.6510   0.5280   1.1835
 10P  C11   C  C     0   0.564  -1.6312  -0.4531   0.5621
 10P  O25   O  O     0  -0.472  -1.6666  -0.6692  -0.6361
 10P  C14   C  CH2   0  -0.485  -1.1284   1.9738   0.9657
 10P  C15   C  CH2   0  -0.468   0.1654   2.7468   0.7344
 10P  C16   C  CH2   0  -0.284   1.0128   1.7660  -0.0614
 10P  C12   C  CH2   0  -0.342  -3.5694  -1.8529   0.9510
 10P  C13   C  CR6   0  -0.014  -4.5773  -1.1376   0.0875
 10P  C17   C  CR16  0   0.079  -4.9641   0.1509   0.3897
 10P  C19   C  CR16  0   0.077  -6.4533   0.2147  -1.4066
 10P  C20   C  CR16  0  -0.334  -6.1148  -1.0710  -1.7582
 10P  C21   C  CR16  0  -0.128  -5.1698  -1.7518  -1.0090
 10P  N26   N  NH1   0  -0.649  -2.5226  -0.9846   1.4179
 10P  N27   N  NR6   1  -0.409  -5.8773   0.7955  -0.3473
 10P  HN22  H  HNH2  0   0.341   2.9256  -2.6807  -0.1110
 10P  HN2A  H  HNH2  0   0.352   2.3697  -2.1883  -1.5498
 10P  H3    H  HCH1  0   0.268   2.6746   0.0562  -1.0473
 10P  H2    H  HCH2  0   0.263   3.8186  -1.0438   1.5513
 10P  H2A   H  HCH2  0   0.262   3.4071   0.6412   1.3223
 10P  H5    H  HCR6  0   0.244   4.6722   2.0743  -0.2151
 10P  H9    H  HCR6  0   0.241   5.7897  -2.0091   0.3889
 10P  H6    H  HCR6  0   0.253   6.8367   2.5103  -1.3018
 10P  H8    H  HCR6  0   0.252   7.9583  -1.5763  -0.6950
 10P  H7    H  HCR6  0   0.253   8.4932   0.6862  -1.5495
 10P  H10   H  HCH1  0   0.282  -0.5294   0.3209   2.2515
 10P  H14   H  HCH2  0   0.250  -1.7605   2.0367   0.0771
 10P  H14A  H  HCH2  0   0.269  -1.7030   2.3407   1.8145
 10P  H15   H  HCH2  0   0.260   0.0086   3.6849   0.2043
 10P  H15A  H  HCH2  0   0.248   0.6506   2.9734   1.6858
 10P  H16   H  HCH2  0   0.251   0.7693   1.8053  -1.1270
 10P  H16A  H  HCH2  0   0.255   2.0780   1.9623   0.0518
 10P  H12   H  HCH2  0   0.305  -4.0769  -2.2614   1.8246
 10P  H12A  H  HCH2  0   0.278  -3.1604  -2.6992   0.3958
 10P  H17   H  HCR6  0   0.335  -4.5545   0.6966   1.2280
 10P  H18   H  HCH3  0   0.300  -5.4994   2.8503  -0.4822
 10P  H18A  H  HCH3  0   0.290  -7.2150   2.4042  -0.3641
 10P  H18B  H  HCH3  0   0.292  -6.1812   2.3070   1.0686
 10P  H19   H  HCR6  0   0.349  -7.1758   0.8007  -1.9536
 10P  H20   H  HCR6  0   0.318  -6.5884  -1.5251  -2.6154
 10P  H21   H  HCR6  0   0.307  -4.8900  -2.7614  -1.2800
 10P  HN26  H  HNH1  0   0.415  -2.4274  -0.8304   2.4080
 10P  C18   C  CH3   0  -0.535  -6.2149   2.1832  -0.0086

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
 10P  C1   C2    single    1.501  0.020  1.501
 10P  C1   C5    aromatic  1.393  0.020  1.393
 10P  C1   C9    aromatic  1.393  0.020  1.393
 10P  C2   C3    single    1.540  0.020  1.540
 10P  C3   C4    single    1.531  0.020  1.531
 10P  C3   N22   single    1.443  0.020  1.443
 10P  C4   N23   single    1.342  0.020  1.342
 10P  C4   O24   double    1.226  0.020  1.226
 10P  C5   C6    aromatic  1.389  0.020  1.389
 10P  C6   C7    aromatic  1.389  0.020  1.389
 10P  C7   C8    aromatic  1.389  0.020  1.389
 10P  C8   C9    aromatic  1.389  0.020  1.389
 10P  C10  C11   single    1.520  0.020  1.520
 10P  C10  C14   single    1.538  0.020  1.538
 10P  C10  N23   single    1.450  0.020  1.450
 10P  C11  O25   double    1.218  0.020  1.218
 10P  C11  N26   single    1.345  0.020  1.345
 10P  C12  C13   single    1.508  0.020  1.508
 10P  C12  N26   single    1.438  0.020  1.438
 10P  C13  C17   aromatic  1.379  0.020  1.379
 10P  C13  C21   aromatic  1.389  0.020  1.389
 10P  C14  C15   single    1.525  0.020  1.525
 10P  C15  C16   single    1.521  0.020  1.521
 10P  C16  N23   single    1.458  0.020  1.458
 10P  C17  N27   aromatic  1.339  0.020  1.339
 10P  C18  N27   single    1.468  0.020  1.468
 10P  C19  C20   aromatic  1.375  0.020  1.375
 10P  C19  N27   aromatic  1.338  0.020  1.338
 10P  C20  C21   aromatic  1.385  0.020  1.385
 10P  C2   H2    single    0.970  0.020  1.090
 10P  C2   H2A   single    0.970  0.020  1.090
 10P  C3   H3    single    0.970  0.020  1.090
 10P  C5   H5    single    0.930  0.020  1.080
 10P  C6   H6    single    0.930  0.020  1.080
 10P  C7   H7    single    0.930  0.020  1.080
 10P  C8   H8    single    0.930  0.020  1.080
 10P  C9   H9    single    0.930  0.020  1.080
 10P  C10  H10   single    0.970  0.020  1.090
 10P  C12  H12   single    0.970  0.020  1.090
 10P  C12  H12A  single    0.970  0.020  1.090
 10P  C14  H14   single    0.970  0.020  1.090
 10P  C14  H14A  single    0.970  0.020  1.090
 10P  C15  H15   single    0.970  0.020  1.090
 10P  C15  H15A  single    0.970  0.020  1.090
 10P  C16  H16   single    0.970  0.020  1.090
 10P  C16  H16A  single    0.970  0.020  1.090
 10P  C17  H17   single    0.930  0.020  1.080
 10P  C18  H18   single    0.970  0.020  1.090
 10P  C18  H18A  single    0.970  0.020  1.090
 10P  C18  H18B  single    0.970  0.020  1.090
 10P  C19  H19   single    0.930  0.020  1.080
 10P  C20  H20   single    0.930  0.020  1.080
 10P  C21  H21   single    0.930  0.020  1.080
 10P  N22  HN22  single    0.890  0.020  1.040
 10P  N22  HN2A  single    0.890  0.020  1.040
 10P  N26  HN26  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
 10P  HN2A  N22  HN22  106.16  3.000
 10P  HN2A  N22  C3    110.01  3.000
 10P  HN22  N22  C3    109.71  3.000
 10P  H3    C3   C2    108.39  3.000
 10P  H3    C3   C4    109.72  3.000
 10P  C2    C3   C4    107.92  3.000
 10P  H3    C3   N22   107.32  3.000
 10P  C4    C3   N22   113.31  3.000
 10P  C2    C3   N22   110.08  3.000
 10P  N23   C4   O24   121.04  3.000
 10P  O24   C4   C3    120.96  3.000
 10P  N23   C4   C3    117.97  3.000
 10P  H2A   C2   H2    106.29  3.000
 10P  H2A   C2   C1    109.51  3.000
 10P  H2    C2   C1    110.53  3.000
 10P  H2A   C2   C3    109.64  3.000
 10P  H2    C2   C3    108.43  3.000
 10P  C1    C2   C3    112.27  3.000
 10P  C9    C1   C5    118.48  3.000
 10P  C9    C1   C2    121.31  3.000
 10P  C5    C1   C2    120.19  3.000
 10P  H5    C5   C6    119.45  3.000
 10P  H5    C5   C1    119.57  3.000
 10P  C6    C5   C1    120.98  3.000
 10P  H9    C9   C8    119.71  3.000
 10P  H9    C9   C1    119.50  3.000
 10P  C8    C9   C1    120.79  3.000
 10P  H6    C6   C7    120.13  3.000
 10P  H6    C6   C5    119.85  3.000
 10P  C7    C6   C5    120.02  3.000
 10P  H8    C8   C7    120.03  3.000
 10P  H8    C8   C9    119.76  3.000
 10P  C7    C8   C9    120.21  3.000
 10P  H7    C7   C8    120.29  3.000
 10P  H7    C7   C6    120.19  3.000
 10P  C8    C7   C6    119.52  3.000
 10P  C16   N23  C10   112.56  3.000
 10P  C16   N23  C4    127.78  3.000
 10P  C10   N23  C4    119.65  3.000
 10P  H10   C10  C14   110.52  3.000
 10P  H10   C10  C11   110.39  3.000
 10P  C14   C10  C11   110.41  3.000
 10P  H10   C10  N23   110.27  3.000
 10P  C14   C10  N23   103.91  3.000
 10P  C11   C10  N23   111.19  3.000
 10P  N26   C11  O25   122.45  3.000
 10P  N26   C11  C10   114.98  3.000
 10P  O25   C11  C10   122.38  3.000
 10P  H14A  C14  H14   108.02  3.000
 10P  H14A  C14  C15   113.28  3.000
 10P  H14   C14  C15   109.78  3.000
 10P  H14A  C14  C10   111.73  3.000
 10P  H14   C14  C10   110.42  3.000
 10P  C15   C14  C10   103.57  3.000
 10P  H15A  C15  H15   108.02  3.000
 10P  H15A  C15  C16   110.01  3.000
 10P  H15   C15  C16   112.40  3.000
 10P  H15A  C15  C14   110.49  3.000
 10P  H15   C15  C14   112.85  3.000
 10P  C16   C15  C14   103.02  3.000
 10P  H16A  C16  H16   108.21  3.000
 10P  H16A  C16  C15   111.99  3.000
 10P  H16   C16  C15   111.26  3.000
 10P  H16A  C16  N23   111.85  3.000
 10P  H16   C16  N23   110.96  3.000
 10P  C15   C16  N23   102.56  3.000
 10P  H12A  C12  H12   106.96  3.000
 10P  H12A  C12  N26   111.14  3.000
 10P  H12   C12  N26   107.76  3.000
 10P  H12A  C12  C13   109.09  3.000
 10P  H12   C12  C13   109.00  3.000
 10P  N26   C12  C13   112.71  3.000
 10P  C21   C13  C17   117.81  3.000
 10P  C21   C13  C12   121.82  3.000
 10P  C17   C13  C12   120.35  3.000
 10P  H17   C17  N27   116.26  3.000
 10P  H17   C17  C13   122.38  3.000
 10P  N27   C17  C13   121.37  3.000
 10P  H19   C19  N27   116.98  3.000
 10P  H19   C19  C20   122.88  3.000
 10P  N27   C19  C20   120.14  3.000
 10P  H20   C20  C21   121.48  3.000
 10P  H20   C20  C19   119.23  3.000
 10P  C21   C20  C19   119.29  3.000
 10P  H21   C21  C20   119.97  3.000
 10P  H21   C21  C13   119.99  3.000
 10P  C20   C21  C13   120.04  3.000
 10P  HN26  N26  C12   118.74  3.000
 10P  HN26  N26  C11   120.17  3.000
 10P  C12   N26  C11   120.96  3.000
 10P  C19   N27  C18   119.59  3.000
 10P  C19   N27  C17   121.36  3.000
 10P  C18   N27  C17   119.02  3.000
 10P  H18B  C18  H18A  109.33  3.000
 10P  H18B  C18  H18   110.01  3.000
 10P  H18A  C18  H18   109.84  3.000
 10P  H18B  C18  N27   109.26  3.000
 10P  H18A  C18  N27   109.22  3.000
 10P  H18   C18  N27   109.16  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
 10P  CONST_01  C7    C6   C5   C1     0.00   0.0  0
 10P  CONST_02  C7    C8   C9   C1     0.00   0.0  0
 10P  CONST_03  C8    C9   C1   C5     0.00   0.0  0
 10P  CONST_04  C8    C7   C6   C5     0.00   0.0  0
 10P  CONST_05  C6    C5   C1   C9     0.00   0.0  0
 10P  CONST_06  C6    C7   C8   C9     0.00   0.0  0
 10P  CONST_07  C19   N27  C17  C13    0.00   0.0  0
 10P  CONST_08  C19   C20  C21  C13    0.00   0.0  0
 10P  CONST_09  C20   C21  C13  C17    0.00   0.0  0
 10P  CONST_10  C20   C19  N27  C17    0.00   0.0  0
 10P  CONST_11  N27   C17  C13  C21    0.00   0.0  0
 10P  CONST_12  N27   C19  C20  C21    0.00   0.0  0
 10P  CONST_13  C6    C5   C1   C2   180.00   0.0  0
 10P  CONST_14  C8    C9   C1   C2   180.00   0.0  0
 10P  CONST_15  N27   C17  C13  C12  180.00   0.0  0
 10P  CONST_16  C20   C21  C13  C12  180.00   0.0  0
 10P  CONST_17  C18   N27  C17  C13  180.00   0.0  0
 10P  CONST_18  C20   C19  N27  C18  180.00   0.0  0
 10P  CONST_19  H6    C6   C5   C1   180.00   0.0  0
 10P  CONST_20  H8    C8   C9   C1   180.00   0.0  0
 10P  CONST_21  H9    C9   C1   C5   180.00   0.0  0
 10P  CONST_22  H7    C7   C6   C5   180.00   0.0  0
 10P  CONST_23  H5    C5   C1   C9   180.00   0.0  0
 10P  CONST_24  H20   C20  C21  C13  180.00   0.0  0
 10P  CONST_25  H21   C21  C13  C17  180.00   0.0  0
 10P  CONST_26  H19   C19  N27  C17  180.00   0.0  0
 10P  CONST_27  H17   C17  N27  C19  180.00   0.0  0
 10P  CONST_28  C10   N23  C4   C3   180.00   0.0  0
 10P  CONST_29  C16   N23  C4   C3     0.00   0.0  0
 10P  CONST_30  C10   N23  C4   O24    0.00   0.0  0
 10P  CONST_31  C16   N23  C4   O24  180.00   0.0  0
 10P  CONST_32  C12   N26  C11  C10  180.00   0.0  0
 10P  CONST_33  HN26  N26  C11  C10    0.00   0.0  0
 10P  CONST_34  C12   N26  C11  O25    0.00   0.0  0
 10P  Var_01    C14   C15  C16  N23  -35.29  30.0  1
 10P  Var_02    C16   C15  C14  C10   36.85  30.0  1
 10P  Var_03    C15   C16  N23  C10   21.25  30.0  1
 10P  Var_04    C5    C1   C2   C3    88.58  30.0  2
 10P  Var_05    N26   C12  C13  C17  -38.10  30.0  2
 10P  Var_06    H18   C18  N27  C17   84.94  30.0  2
 10P  Var_07    C13   C12  N26  C11  -67.13  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
 10P  chir_01  C3   C2   C4   N22  positiv
 10P  chir_02  C10  N23  C11  C14  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
 10P  plan-1  C2    0.020
 10P  plan-1  C1    0.020
 10P  plan-1  C5    0.020
 10P  plan-1  C9    0.020
 10P  plan-1  C6    0.020
 10P  plan-1  C8    0.020
 10P  plan-1  C7    0.020
 10P  plan-1  H5    0.020
 10P  plan-1  H9    0.020
 10P  plan-1  H6    0.020
 10P  plan-1  H8    0.020
 10P  plan-1  H7    0.020
 10P  plan-2  C12   0.020
 10P  plan-2  C13   0.020
 10P  plan-2  C17   0.020
 10P  plan-2  C19   0.020
 10P  plan-2  C20   0.020
 10P  plan-2  C21   0.020
 10P  plan-2  N27   0.020
 10P  plan-2  H17   0.020
 10P  plan-2  H19   0.020
 10P  plan-2  H20   0.020
 10P  plan-2  H21   0.020
 10P  plan-2  C18   0.020
 10P  plan-3  C10   0.020
 10P  plan-3  C11   0.020
 10P  plan-3  O25   0.020
 10P  plan-3  C12   0.020
 10P  plan-3  N26   0.020
 10P  plan-3  HN26  0.020
 10P  plan-4  C3    0.020
 10P  plan-4  C4    0.020
 10P  plan-4  O24   0.020
 10P  plan-4  N23   0.020
 10P  plan-4  C10   0.020
 10P  plan-4  C16   0.020

