# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 04:57:40 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-3-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(Cl)c(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
 98P  98P  D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-3-yl)methyl]-L-prolinamide  peptide  54  28  .  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_98P
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
 98P  N22   N   NH2   0  -0.778   2.7153  -1.5572  -0.9972
 98P  C3    C   CH1   0  -0.225   2.8390  -0.2637  -0.3639
 98P  C4    C   C     0   0.572   1.4460   0.3154  -0.1580
 98P  O26   O   O     0  -0.488   0.5008  -0.4072   0.1262
 98P  C2    C   CH2   0  -0.543   3.5522  -0.2694   1.0112
 98P  C1    C   CR6   0   0.138   4.9762  -0.7267   0.8963
 98P  C5    C   CR16  0  -0.307   5.9904   0.1862   0.6110
 98P  C9    C   CR16  0  -0.320   5.3113  -2.0737   1.0192
 98P  C6    C   CR16  0  -0.239   7.3046  -0.2326   0.4592
 98P  C8    C   CR16  0  -0.241   6.6255  -2.4981   0.8674
 98P  C7    C   CR16  0  -0.271   7.6267  -1.5783   0.5872
 98P  N23   N   NT    0  -0.478   1.3066   1.6493  -0.2401
 98P  C10   C   CH1   0  -0.174   0.0087   2.2506  -0.0083
 98P  C11   C   C     0   0.581  -1.0261   1.7490  -1.0063
 98P  O27   O   O     0  -0.479  -0.7390   1.5140  -2.1648
 98P  C14   C   CH2   0  -0.479   0.2580   3.7543  -0.2112
 98P  C15   C   CH2   0  -0.470   1.7483   3.9121   0.0680
 98P  C16   C   CH2   0  -0.282   2.3414   2.6389  -0.5163
 98P  C12   C   CH2   0  -0.369  -3.4432   1.4040  -1.3086
 98P  C13   C   CR6   0   0.063  -4.2272   0.2447  -0.7577
 98P  C17   C   CR16  0   0.061  -5.4756   0.4627  -0.2207
 98P  C19   C   CR16  0   0.091  -5.7590  -1.7867   0.3020
 98P  C20   C   CR16  0  -0.310  -4.5229  -2.0880  -0.2125
 98P  C21   C   CR6   0   0.071  -3.7496  -1.0674  -0.7451
 98P  N24   N   NH1   0  -0.634  -2.2775   1.6821  -0.5106
 98P  N25   N   NR6   1  -0.424  -6.2147  -0.5293   0.2922
 98P  CL28  CL  CL    0  -0.007  -2.2180  -1.4260  -1.3869
 98P  HN22  H   HNH2  0   0.355   3.6359  -1.9493  -1.1500
 98P  HN2A  H   HNH2  0   0.342   2.2232  -2.1996  -0.3884
 98P  H3    H   HCH1  0   0.268   3.4128   0.3727  -1.0425
 98P  H2    H   HCH2  0   0.262   2.9948  -0.9233   1.6873
 98P  H2A   H   HCH2  0   0.256   3.5226   0.7324   1.4492
 98P  H5    H   HCR6  0   0.245   5.7522   1.2398   0.5124
 98P  H9    H   HCR6  0   0.251   4.5367  -2.7981   1.2434
 98P  H6    H   HCR6  0   0.255   8.0791   0.4927   0.2445
 98P  H8    H   HCR6  0   0.255   6.8657  -3.5486   0.9710
 98P  H7    H   HCR6  0   0.255   8.6520  -1.9058   0.4720
 98P  H10   H   HCH1  0   0.277  -0.3222   2.0508   1.0162
 98P  H14   H   HCH2  0   0.253   0.0437   4.0407  -1.2431
 98P  H14A  H   HCH2  0   0.267  -0.3720   4.3568   0.4404
 98P  H15   H   HCH2  0   0.259   2.1705   4.8090  -0.3824
 98P  H15A  H   HCH2  0   0.246   1.9347   3.9534   1.1429
 98P  H16   H   HCH2  0   0.250   2.5136   2.7379  -1.5920
 98P  H16A  H   HCH2  0   0.253   3.2872   2.3760  -0.0450
 98P  H12   H   HCH2  0   0.293  -3.1251   1.1872  -2.3276
 98P  H12A  H   HCH2  0   0.291  -4.0928   2.2800  -1.3537
 98P  H17   H   HCR6  0   0.352  -5.9089   1.4526  -0.1901
 98P  H18   H   HCH3  0   0.302  -8.2717  -0.2926  -0.0106
 98P  H18A  H   HCH3  0   0.291  -7.8121  -0.9619   1.5711
 98P  H18B  H   HCH3  0   0.292  -7.5658   0.7586   1.2383
 98P  H19   H   HCR6  0   0.359  -6.4016  -2.5415   0.7290
 98P  H20   H   HCR6  0   0.336  -4.1769  -3.1105  -0.1937
 98P  HN24  H   HNH1  0   0.409  -2.4280   1.9299   0.4549
 98P  C18   C   CH3   0  -0.532  -7.5576  -0.2364   0.8064

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
 98P  C1   C2    single    1.500  0.020  1.500
 98P  C1   C5    aromatic  1.394  0.020  1.394
 98P  C1   C9    aromatic  1.393  0.020  1.393
 98P  C2   C3    single    1.549  0.020  1.549
 98P  C3   C4    single    1.522  0.020  1.522
 98P  C3   N22   single    1.446  0.020  1.446
 98P  C4   N23   single    1.344  0.020  1.344
 98P  C4   O26   double    1.223  0.020  1.223
 98P  C5   C6    aromatic  1.388  0.020  1.388
 98P  C6   C7    aromatic  1.390  0.020  1.390
 98P  C7   C8    aromatic  1.388  0.020  1.388
 98P  C8   C9    aromatic  1.389  0.020  1.389
 98P  C10  C11   single    1.523  0.020  1.523
 98P  C10  C14   single    1.538  0.020  1.538
 98P  C10  N23   single    1.449  0.020  1.449
 98P  C11  N24   single    1.348  0.020  1.348
 98P  C11  O27   double    1.216  0.020  1.216
 98P  C12  C13   single    1.504  0.020  1.504
 98P  C12  N24   single    1.440  0.020  1.440
 98P  C13  C17   aromatic  1.376  0.020  1.376
 98P  C13  C21   aromatic  1.396  0.020  1.396
 98P  C14  C15   single    1.524  0.020  1.524
 98P  C15  C16   single    1.521  0.020  1.521
 98P  C16  N23   single    1.458  0.020  1.458
 98P  C17  N25   aromatic  1.339  0.020  1.339
 98P  C18  N25   single    1.467  0.020  1.467
 98P  C19  C20   aromatic  1.372  0.020  1.372
 98P  C19  N25   aromatic  1.337  0.020  1.337
 98P  C20  C21   aromatic  1.387  0.020  1.387
 98P  C21  CL28  single    1.699  0.020  1.699
 98P  C2   H2    single    0.970  0.020  1.090
 98P  C2   H2A   single    0.970  0.020  1.090
 98P  C3   H3    single    0.970  0.020  1.090
 98P  C5   H5    single    0.930  0.020  1.080
 98P  C6   H6    single    0.930  0.020  1.080
 98P  C7   H7    single    0.930  0.020  1.080
 98P  C8   H8    single    0.930  0.020  1.080
 98P  C9   H9    single    0.930  0.020  1.080
 98P  C10  H10   single    0.970  0.020  1.090
 98P  C12  H12   single    0.970  0.020  1.090
 98P  C12  H12A  single    0.970  0.020  1.090
 98P  C14  H14   single    0.970  0.020  1.090
 98P  C14  H14A  single    0.970  0.020  1.090
 98P  C15  H15   single    0.970  0.020  1.090
 98P  C15  H15A  single    0.970  0.020  1.090
 98P  C16  H16   single    0.970  0.020  1.090
 98P  C16  H16A  single    0.970  0.020  1.090
 98P  C17  H17   single    0.930  0.020  1.080
 98P  C18  H18   single    0.970  0.020  1.090
 98P  C18  H18A  single    0.970  0.020  1.090
 98P  C18  H18B  single    0.970  0.020  1.090
 98P  C19  H19   single    0.930  0.020  1.080
 98P  C20  H20   single    0.930  0.020  1.080
 98P  N22  HN22  single    0.890  0.020  1.040
 98P  N22  HN2A  single    0.890  0.020  1.040
 98P  N24  HN24  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
 98P  HN2A  N22  HN22  106.68  3.000
 98P  HN2A  N22  C3    110.23  3.000
 98P  HN22  N22  C3    109.57  3.000
 98P  H3    C3   C2    108.15  3.000
 98P  H3    C3   C4    110.05  3.000
 98P  C2    C3   C4    107.62  3.000
 98P  H3    C3   N22   107.09  3.000
 98P  C4    C3   N22   108.74  3.000
 98P  C2    C3   N22   115.15  3.000
 98P  N23   C4   O26   121.36  3.000
 98P  O26   C4   C3    120.91  3.000
 98P  N23   C4   C3    117.66  3.000
 98P  H2A   C2   H2    106.63  3.000
 98P  H2A   C2   C1    109.61  3.000
 98P  H2    C2   C1    110.43  3.000
 98P  H2A   C2   C3    109.85  3.000
 98P  H2    C2   C3    108.45  3.000
 98P  C1    C2   C3    111.73  3.000
 98P  C9    C1   C5    118.43  3.000
 98P  C9    C1   C2    121.08  3.000
 98P  C5    C1   C2    120.44  3.000
 98P  H5    C5   C6    119.42  3.000
 98P  H5    C5   C1    119.67  3.000
 98P  C6    C5   C1    120.91  3.000
 98P  H9    C9   C8    119.63  3.000
 98P  H9    C9   C1    119.50  3.000
 98P  C8    C9   C1    120.87  3.000
 98P  H6    C6   C7    120.08  3.000
 98P  H6    C6   C5    119.81  3.000
 98P  C7    C6   C5    120.11  3.000
 98P  H8    C8   C7    120.15  3.000
 98P  H8    C8   C9    119.72  3.000
 98P  C7    C8   C9    120.13  3.000
 98P  H7    C7   C8    120.28  3.000
 98P  H7    C7   C6    120.18  3.000
 98P  C8    C7   C6    119.54  3.000
 98P  C16   N23  C10   112.60  3.000
 98P  C16   N23  C4    127.71  3.000
 98P  C10   N23  C4    119.68  3.000
 98P  H10   C10  C14   110.55  3.000
 98P  H10   C10  C11   110.35  3.000
 98P  C14   C10  C11   110.23  3.000
 98P  H10   C10  N23   110.16  3.000
 98P  C14   C10  N23   103.86  3.000
 98P  C11   C10  N23   111.54  3.000
 98P  N24   C11  O27   124.04  3.000
 98P  O27   C11  C10   121.83  3.000
 98P  N24   C11  C10   113.98  3.000
 98P  H14A  C14  H14   107.87  3.000
 98P  H14A  C14  C15   113.51  3.000
 98P  H14   C14  C15   109.74  3.000
 98P  H14A  C14  C10   111.62  3.000
 98P  H14   C14  C10   110.45  3.000
 98P  C15   C14  C10   103.62  3.000
 98P  H15A  C15  H15   108.05  3.000
 98P  H15A  C15  C16   110.08  3.000
 98P  H15   C15  C16   112.30  3.000
 98P  H15A  C15  C14   110.55  3.000
 98P  H15   C15  C14   112.86  3.000
 98P  C16   C15  C14   102.95  3.000
 98P  H16A  C16  H16   108.10  3.000
 98P  H16A  C16  C15   111.99  3.000
 98P  H16   C16  C15   111.30  3.000
 98P  H16A  C16  N23   111.75  3.000
 98P  H16   C16  N23   111.06  3.000
 98P  C15   C16  N23   102.63  3.000
 98P  H12A  C12  H12   107.15  3.000
 98P  H12A  C12  N24   110.47  3.000
 98P  H12   C12  N24   108.69  3.000
 98P  H12A  C12  C13   108.88  3.000
 98P  H12   C12  C13   109.96  3.000
 98P  N24   C12  C13   111.59  3.000
 98P  C21   C13  C17   117.10  3.000
 98P  C21   C13  C12   123.32  3.000
 98P  C17   C13  C12   119.58  3.000
 98P  H17   C17  N25   116.50  3.000
 98P  H17   C17  C13   121.31  3.000
 98P  N25   C17  C13   122.19  3.000
 98P  H19   C19  N25   117.22  3.000
 98P  H19   C19  C20   122.07  3.000
 98P  N25   C19  C20   120.70  3.000
 98P  H20   C20  C21   121.66  3.000
 98P  H20   C20  C19   119.35  3.000
 98P  C21   C20  C19   118.99  3.000
 98P  CL28  C21  C20   119.50  3.000
 98P  CL28  C21  C13   120.22  3.000
 98P  C20   C21  C13   120.28  3.000
 98P  HN24  N24  C12   117.22  3.000
 98P  HN24  N24  C11   118.60  3.000
 98P  C12   N24  C11   123.89  3.000
 98P  C19   N25  C18   119.80  3.000
 98P  C19   N25  C17   120.74  3.000
 98P  C18   N25  C17   119.43  3.000
 98P  H18B  C18  H18A  109.34  3.000
 98P  H18B  C18  H18   110.00  3.000
 98P  H18A  C18  H18   109.96  3.000
 98P  H18B  C18  N25   109.24  3.000
 98P  H18A  C18  N25   109.16  3.000
 98P  H18   C18  N25   109.12  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
 98P  CONST_01  C7    C6   C5   C1     0.00   0.0  0
 98P  CONST_02  C7    C8   C9   C1     0.00   0.0  0
 98P  CONST_03  C8    C9   C1   C5     0.00   0.0  0
 98P  CONST_04  C8    C7   C6   C5     0.00   0.0  0
 98P  CONST_05  C6    C5   C1   C9     0.00   0.0  0
 98P  CONST_06  C6    C7   C8   C9     0.00   0.0  0
 98P  CONST_07  C19   N25  C17  C13    0.00   0.0  0
 98P  CONST_08  C19   C20  C21  C13    0.00   0.0  0
 98P  CONST_09  C20   C21  C13  C17    0.00   0.0  0
 98P  CONST_10  C20   C19  N25  C17    0.00   0.0  0
 98P  CONST_11  N25   C17  C13  C21    0.00   0.0  0
 98P  CONST_12  N25   C19  C20  C21    0.00   0.0  0
 98P  CONST_13  C6    C5   C1   C2   180.00   0.0  0
 98P  CONST_14  C8    C9   C1   C2   180.00   0.0  0
 98P  CONST_15  N25   C17  C13  C12  180.00   0.0  0
 98P  CONST_16  C20   C21  C13  C12  180.00   0.0  0
 98P  CONST_17  C18   N25  C17  C13  180.00   0.0  0
 98P  CONST_18  CL28  C21  C13  C17  180.00   0.0  0
 98P  CONST_19  C20   C19  N25  C18  180.00   0.0  0
 98P  CONST_20  CL28  C21  C20  C19  180.00   0.0  0
 98P  CONST_21  H6    C6   C5   C1   180.00   0.0  0
 98P  CONST_22  H8    C8   C9   C1   180.00   0.0  0
 98P  CONST_23  H9    C9   C1   C5   180.00   0.0  0
 98P  CONST_24  H7    C7   C6   C5   180.00   0.0  0
 98P  CONST_25  H5    C5   C1   C9   180.00   0.0  0
 98P  CONST_26  H20   C20  C21  C13  180.00   0.0  0
 98P  CONST_27  H19   C19  N25  C17  180.00   0.0  0
 98P  CONST_28  H17   C17  N25  C19  180.00   0.0  0
 98P  CONST_29  C10   N23  C4   C3   180.00   0.0  0
 98P  CONST_30  C16   N23  C4   C3     0.00   0.0  0
 98P  CONST_31  C10   N23  C4   O26    0.00   0.0  0
 98P  CONST_32  C16   N23  C4   O26  180.00   0.0  0
 98P  CONST_33  C12   N24  C11  C10  180.00   0.0  0
 98P  CONST_34  HN24  N24  C11  C10    0.00   0.0  0
 98P  CONST_35  C12   N24  C11  O27    0.00   0.0  0
 98P  Var_01    C14   C15  C16  N23  -35.08  30.0  1
 98P  Var_02    C16   C15  C14  C10   36.91  30.0  1
 98P  Var_03    C15   C16  N23  C10   20.85  30.0  1
 98P  Var_04    C5    C1   C2   C3    87.37  30.0  2
 98P  Var_05    N24   C12  C13  C17  112.23  30.0  2
 98P  Var_06    H18   C18  N25  C17   86.67  30.0  2
 98P  Var_07    C13   C12  N24  C11  125.83  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
 98P  chir_01  C3   C2   C4   N22  positiv
 98P  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
 98P  plan-1  C2    0.020
 98P  plan-1  C1    0.020
 98P  plan-1  C5    0.020
 98P  plan-1  C9    0.020
 98P  plan-1  C6    0.020
 98P  plan-1  C8    0.020
 98P  plan-1  C7    0.020
 98P  plan-1  H5    0.020
 98P  plan-1  H9    0.020
 98P  plan-1  H6    0.020
 98P  plan-1  H8    0.020
 98P  plan-1  H7    0.020
 98P  plan-2  C12   0.020
 98P  plan-2  C13   0.020
 98P  plan-2  C17   0.020
 98P  plan-2  C19   0.020
 98P  plan-2  C20   0.020
 98P  plan-2  C21   0.020
 98P  plan-2  N25   0.020
 98P  plan-2  CL28  0.020
 98P  plan-2  H17   0.020
 98P  plan-2  H19   0.020
 98P  plan-2  H20   0.020
 98P  plan-2  C18   0.020
 98P  plan-3  C10   0.020
 98P  plan-3  C11   0.020
 98P  plan-3  O27   0.020
 98P  plan-3  C12   0.020
 98P  plan-3  N24   0.020
 98P  plan-3  HN24  0.020
 98P  plan-4  C3    0.020
 98P  plan-4  C4    0.020
 98P  plan-4  O26   0.020
 98P  plan-4  N23   0.020
 98P  plan-4  C10   0.020
 98P  plan-4  C16   0.020

