# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:33:52 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-2-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3
#
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
 02P  02P  D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-2-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_02P
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
 02P  N10   N   NH2   0  -0.763  -3.8021  -1.4316   1.4896
 02P  C8    C   CH1   0  -0.210  -3.4908  -0.3751   0.5587
 02P  C9    C   C     0   0.534  -2.0104  -0.3135   0.1793
 02P  O12   O   O     0  -0.497  -1.3134  -1.3217   0.1915
 02P  C7    C   CH2   0  -0.538  -4.2940  -0.5580  -0.7427
 02P  C4    C   CR6   0   0.170  -5.7757  -0.5093  -0.5087
 02P  C3    C   CR16  0  -0.311  -6.4300   0.7152  -0.3932
 02P  C5    C   CR16  0  -0.309  -6.5234  -1.6763  -0.3823
 02P  C26   C   CR16  0  -0.241  -7.7964   0.7743  -0.1546
 02P  C6    C   CR16  0  -0.244  -7.8914  -1.6239  -0.1489
 02P  C1    C   CR16  0  -0.273  -8.5325  -0.3974  -0.0324
 02P  N11   N   NT    0  -0.461  -1.5097   0.8661  -0.2249
 02P  C13   C   CH1   0  -0.211  -0.1379   0.9310  -0.6843
 02P  C17   C   C     0   0.582   0.8184   0.6132   0.4588
 02P  O28   O   O     0  -0.467   0.6141   0.9831   1.5996
 02P  C15   C   CH2   0  -0.484   0.0124   2.3848  -1.1562
 02P  C16   C   CH2   0  -0.466  -1.0004   3.1489  -0.3109
 02P  C14   C   CH2   0  -0.280  -2.1623   2.1716  -0.1872
 02P  CL2   CL  CL    0  -0.026   7.5583  -2.1393  -0.6104
 02P  N18   N   NH1   0  -0.641   1.9370  -0.0430   0.0776
 02P  C19   C   CH2   0  -0.382   2.9324  -0.4999   1.0114
 02P  C20   C   CR6   0   0.444   4.3252  -0.1694   0.5556
 02P  N21   N   NR6   1  -0.465   4.7360   1.1141   0.4581
 02P  C22   C   CR16  0  -0.327   5.1980  -1.1844   0.2259
 02P  C23   C   CR6   0   0.129   6.4808  -0.8852  -0.2056
 02P  C24   C   CR16  0  -0.306   6.8771   0.4380  -0.3103
 02P  C25   C   CR16  0   0.076   5.9730   1.4099   0.0328
 02P  C27   C   CH3   0  -0.552   3.8414   2.2275   0.7982
 02P  HN10  H   HNH2  0   0.340  -3.4523  -2.3144   1.1368
 02P  HN1A  H   HNH2  0   0.351  -3.3238  -1.2704   2.3671
 02P  H8    H   HCH1  0   0.263  -3.7956   0.5695   1.0169
 02P  H7    H   HCH2  0   0.260  -4.0134  -1.5162  -1.1892
 02P  H7A   H   HCH2  0   0.264  -4.0089   0.2146  -1.4617
 02P  H3    H   HCR6  0   0.242  -5.8646   1.6352  -0.4953
 02P  H5    H   HCR6  0   0.242  -6.0316  -2.6372  -0.4754
 02P  H26   H   HCR6  0   0.252  -8.2872   1.7353  -0.0682
 02P  H6    H   HCR6  0   0.252  -8.4577  -2.5420  -0.0557
 02P  H1    H   HCR6  0   0.253  -9.5989  -0.3546   0.1471
 02P  H13   H   HCH1  0   0.288   0.0253   0.2320  -1.5080
 02P  H15   H   HCH2  0   0.266   1.0313   2.7600  -1.0580
 02P  H15A  H   HCH2  0   0.266  -0.2503   2.4409  -2.2138
 02P  H16   H   HCH2  0   0.260  -1.3055   4.0889  -0.7676
 02P  H16A  H   HCH2  0   0.249  -0.5894   3.3712   0.6741
 02P  H14   H   HCH2  0   0.243  -2.8617   2.2801  -1.0219
 02P  H14A  H   HCH2  0   0.262  -2.7194   2.3128   0.7381
 02P  HN18  H   HNH1  0   0.416   1.9691  -0.4338  -0.8517
 02P  H19   H   HCH2  0   0.315   2.7333  -0.0638   1.9908
 02P  H19A  H   HCH2  0   0.313   2.8742  -1.5818   1.1365
 02P  H22   H   HCR6  0   0.336   4.8639  -2.2086   0.3080
 02P  H24   H   HCR6  0   0.336   7.8630   0.7224  -0.6455
 02P  H25   H   HCR6  0   0.360   6.2276   2.4569  -0.0260
 02P  H27   H   HCH3  0   0.294   3.3229   2.0216   1.7284
 02P  H27A  H   HCH3  0   0.302   4.4367   3.1250   0.9219
 02P  H27B  H   HCH3  0   0.297   3.1267   2.3783  -0.0052

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
 02P  C1   C6    aromatic  1.389  0.020  1.389
 02P  C1   C26   aromatic  1.389  0.020  1.389
 02P  CL2  C23   single    1.702  0.020  1.702
 02P  C3   C4    aromatic  1.393  0.020  1.393
 02P  C3   C26   aromatic  1.388  0.020  1.388
 02P  C4   C5    aromatic  1.392  0.020  1.392
 02P  C4   C7    single    1.501  0.020  1.501
 02P  C5   C6    aromatic  1.389  0.020  1.389
 02P  C7   C8    single    1.540  0.020  1.540
 02P  C8   C9    single    1.529  0.020  1.529
 02P  C8   N10   single    1.442  0.020  1.442
 02P  C9   N11   single    1.344  0.020  1.344
 02P  C9   O12   double    1.226  0.020  1.226
 02P  N11  C13   single    1.448  0.020  1.448
 02P  N11  C14   single    1.460  0.020  1.460
 02P  C13  C15   single    1.536  0.020  1.536
 02P  C13  C17   single    1.524  0.020  1.524
 02P  C14  C16   single    1.523  0.020  1.523
 02P  C15  C16   single    1.524  0.020  1.524
 02P  C17  N18   single    1.352  0.020  1.352
 02P  C17  O28   double    1.217  0.020  1.217
 02P  N18  C19   single    1.439  0.020  1.439
 02P  C19  C20   single    1.502  0.020  1.502
 02P  C20  N21   aromatic  1.351  0.020  1.351
 02P  C20  C22   aromatic  1.379  0.020  1.379
 02P  N21  C25   aromatic  1.341  0.020  1.341
 02P  N21  C27   single    1.468  0.020  1.468
 02P  C22  C23   aromatic  1.386  0.020  1.386
 02P  C23  C24   aromatic  1.385  0.020  1.385
 02P  C24  C25   aromatic  1.371  0.020  1.371
 02P  C1   H1    single    0.930  0.020  1.080
 02P  C3   H3    single    0.930  0.020  1.080
 02P  C5   H5    single    0.930  0.020  1.080
 02P  C6   H6    single    0.930  0.020  1.080
 02P  C7   H7    single    0.970  0.020  1.090
 02P  C7   H7A   single    0.970  0.020  1.090
 02P  C8   H8    single    0.970  0.020  1.090
 02P  N10  HN10  single    0.890  0.020  1.040
 02P  N10  HN1A  single    0.890  0.020  1.040
 02P  C13  H13   single    0.970  0.020  1.090
 02P  C14  H14   single    0.970  0.020  1.090
 02P  C14  H14A  single    0.970  0.020  1.090
 02P  C15  H15   single    0.970  0.020  1.090
 02P  C15  H15A  single    0.970  0.020  1.090
 02P  C16  H16   single    0.970  0.020  1.090
 02P  C16  H16A  single    0.970  0.020  1.090
 02P  N18  HN18  single    0.860  0.020  1.020
 02P  C19  H19   single    0.970  0.020  1.090
 02P  C19  H19A  single    0.970  0.020  1.090
 02P  C22  H22   single    0.930  0.020  1.080
 02P  C24  H24   single    0.930  0.020  1.080
 02P  C25  H25   single    0.930  0.020  1.080
 02P  C26  H26   single    0.930  0.020  1.080
 02P  C27  H27   single    0.970  0.020  1.090
 02P  C27  H27A  single    0.970  0.020  1.090
 02P  C27  H27B  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
 02P  HN1A  N10  HN10  106.12  3.000
 02P  HN1A  N10  C8    109.93  3.000
 02P  HN10  N10  C8    109.82  3.000
 02P  H8    C8   C7    108.14  3.000
 02P  H8    C8   C9    109.82  3.000
 02P  C7    C8   C9    107.45  3.000
 02P  H8    C8   N10   107.59  3.000
 02P  C9    C8   N10   113.49  3.000
 02P  C7    C8   N10   110.23  3.000
 02P  N11   C9   O12   120.88  3.000
 02P  O12   C9   C8    120.99  3.000
 02P  N11   C9   C8    118.07  3.000
 02P  H7A   C7   H7    106.48  3.000
 02P  H7A   C7   C4    109.70  3.000
 02P  H7    C7   C4    110.20  3.000
 02P  H7A   C7   C8    109.62  3.000
 02P  H7    C7   C8    108.37  3.000
 02P  C4    C7   C8    112.29  3.000
 02P  C5    C4   C3    118.50  3.000
 02P  C5    C4   C7    121.15  3.000
 02P  C3    C4   C7    120.34  3.000
 02P  H3    C3   C26   119.54  3.000
 02P  H3    C3   C4    119.53  3.000
 02P  C26   C3   C4    120.92  3.000
 02P  H5    C5   C6    119.68  3.000
 02P  H5    C5   C4    119.47  3.000
 02P  C6    C5   C4    120.85  3.000
 02P  H26   C26  C1    120.10  3.000
 02P  H26   C26  C3    119.85  3.000
 02P  C1    C26  C3    120.05  3.000
 02P  H6    C6   C1    120.01  3.000
 02P  H6    C6   C5    119.85  3.000
 02P  C1    C6   C5    120.14  3.000
 02P  H1    C1   C6    120.24  3.000
 02P  H1    C1   C26   120.22  3.000
 02P  C6    C1   C26   119.54  3.000
 02P  C14   N11  C13   113.05  3.000
 02P  C14   N11  C9    127.64  3.000
 02P  C13   N11  C9    119.19  3.000
 02P  H13   C13  C15   111.06  3.000
 02P  H13   C13  C17   109.78  3.000
 02P  C15   C13  C17   111.50  3.000
 02P  H13   C13  N11   110.61  3.000
 02P  C17   C13  N11   110.31  3.000
 02P  C15   C13  N11   103.45  3.000
 02P  N18   C17  O28   123.44  3.000
 02P  O28   C17  C13   122.32  3.000
 02P  N18   C17  C13   114.14  3.000
 02P  H15A  C15  H15   107.13  3.000
 02P  H15A  C15  C16   110.59  3.000
 02P  H15   C15  C16   113.48  3.000
 02P  H15A  C15  C13   108.84  3.000
 02P  H15   C15  C13   112.93  3.000
 02P  C16   C15  C13   103.83  3.000
 02P  H16A  C16  H16   107.97  3.000
 02P  H16A  C16  C14   110.18  3.000
 02P  H16   C16  C14   111.98  3.000
 02P  H16A  C16  C15   110.65  3.000
 02P  H16   C16  C15   112.73  3.000
 02P  C14   C16  C15   103.31  3.000
 02P  H14A  C14  H14   107.95  3.000
 02P  H14A  C14  C16   112.08  3.000
 02P  H14   C14  C16   111.22  3.000
 02P  H14A  C14  N11   111.49  3.000
 02P  H14   C14  N11   110.77  3.000
 02P  C16   C14  N11   103.33  3.000
 02P  HN18  N18  C19   116.92  3.000
 02P  HN18  N18  C17   118.31  3.000
 02P  C19   N18  C17   122.92  3.000
 02P  H19A  C19  H19   106.50  3.000
 02P  H19A  C19  C20   107.60  3.000
 02P  H19   C19  C20   110.72  3.000
 02P  H19A  C19  N18   110.63  3.000
 02P  H19   C19  N18   109.24  3.000
 02P  C20   C19  N18   111.99  3.000
 02P  C22   C20  N21   119.32  3.000
 02P  C22   C20  C19   119.84  3.000
 02P  N21   C20  C19   120.84  3.000
 02P  C27   N21  C25   117.92  3.000
 02P  C27   N21  C20   121.23  3.000
 02P  C25   N21  C20   120.85  3.000
 02P  H22   C22  C23   120.96  3.000
 02P  H22   C22  C20   118.95  3.000
 02P  C23   C22  C20   120.09  3.000
 02P  C24   C23  C22   119.64  3.000
 02P  C24   C23  CL2   120.31  3.000
 02P  C22   C23  CL2   120.05  3.000
 02P  H24   C24  C25   119.55  3.000
 02P  H24   C24  C23   122.44  3.000
 02P  C25   C24  C23   118.00  3.000
 02P  H25   C25  C24   121.24  3.000
 02P  H25   C25  N21   116.67  3.000
 02P  C24   C25  N21   122.09  3.000
 02P  H27B  C27  H27A  109.32  3.000
 02P  H27B  C27  H27   110.26  3.000
 02P  H27A  C27  H27   108.78  3.000
 02P  H27B  C27  N21   109.57  3.000
 02P  H27A  C27  N21   108.64  3.000
 02P  H27   C27  N21   110.24  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
 02P  CONST_01  C1    C26  C3   C4      0.00   0.0  0
 02P  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 02P  CONST_03  C6    C5   C4   C3      0.00   0.0  0
 02P  CONST_04  C6    C1   C26  C3      0.00   0.0  0
 02P  CONST_05  C26   C3   C4   C5      0.00   0.0  0
 02P  CONST_06  C26   C1   C6   C5      0.00   0.0  0
 02P  CONST_07  C24   C25  N21  C20     0.00   0.0  0
 02P  CONST_08  C24   C23  C22  C20     0.00   0.0  0
 02P  CONST_09  C23   C22  C20  N21     0.00   0.0  0
 02P  CONST_10  C23   C24  C25  N21     0.00   0.0  0
 02P  CONST_11  C25   N21  C20  C22     0.00   0.0  0
 02P  CONST_12  C25   C24  C23  C22     0.00   0.0  0
 02P  CONST_13  C26   C3   C4   C7    180.00   0.0  0
 02P  CONST_14  C6    C5   C4   C7    180.00   0.0  0
 02P  CONST_15  C20   C22  C23  CL2   180.00   0.0  0
 02P  CONST_16  C25   C24  C23  CL2   180.00   0.0  0
 02P  CONST_17  C25   N21  C20  C19   180.00   0.0  0
 02P  CONST_18  C23   C22  C20  C19   180.00   0.0  0
 02P  CONST_19  C27   N21  C20  C22   180.00   0.0  0
 02P  CONST_20  C27   N21  C25  C24   180.00   0.0  0
 02P  CONST_21  H26   C26  C3   C4    180.00   0.0  0
 02P  CONST_22  H6    C6   C5   C4    180.00   0.0  0
 02P  CONST_23  H5    C5   C4   C3    180.00   0.0  0
 02P  CONST_24  H1    C1   C26  C3    180.00   0.0  0
 02P  CONST_25  H3    C3   C4   C5    180.00   0.0  0
 02P  CONST_26  H25   C25  N21  C20   180.00   0.0  0
 02P  CONST_27  H22   C22  C20  N21   180.00   0.0  0
 02P  CONST_28  H24   C24  C25  N21   180.00   0.0  0
 02P  CONST_29  C13   N11  C9   C8    180.00   0.0  0
 02P  CONST_30  C14   N11  C9   C8      0.00   0.0  0
 02P  CONST_31  C13   N11  C9   O12     0.00   0.0  0
 02P  CONST_32  C14   N11  C9   O12   180.00   0.0  0
 02P  CONST_33  C19   N18  C17  C13   180.00   0.0  0
 02P  CONST_34  HN18  N18  C17  C13     0.00   0.0  0
 02P  CONST_35  C19   N18  C17  O28     0.00   0.0  0
 02P  Var_01    C15   C16  C14  N11    30.90  30.0  1
 02P  Var_02    C16   C14  N11  C13   -14.37  30.0  1
 02P  Var_03    C14   C16  C15  C13   -36.26  30.0  1
 02P  Var_04    C3    C4   C7   C8     81.28  30.0  3
 02P  Var_05    N21   C20  C19  N18    65.51  30.0  2
 02P  Var_06    H27   C27  N21  C20    45.05  30.0  2
 02P  Var_07    C20   C19  N18  C17  -134.18  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
 02P  chir_01  C8   C7   C9   N10  positiv
 02P  chir_02  C13  N11  C17  C15  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
 02P  plan-1  C7    0.020
 02P  plan-1  C4    0.020
 02P  plan-1  C3    0.020
 02P  plan-1  C5    0.020
 02P  plan-1  C26   0.020
 02P  plan-1  C6    0.020
 02P  plan-1  C1    0.020
 02P  plan-1  H3    0.020
 02P  plan-1  H5    0.020
 02P  plan-1  H26   0.020
 02P  plan-1  H6    0.020
 02P  plan-1  H1    0.020
 02P  plan-2  CL2   0.020
 02P  plan-2  C19   0.020
 02P  plan-2  C20   0.020
 02P  plan-2  N21   0.020
 02P  plan-2  C22   0.020
 02P  plan-2  C23   0.020
 02P  plan-2  C24   0.020
 02P  plan-2  C25   0.020
 02P  plan-2  C27   0.020
 02P  plan-2  H22   0.020
 02P  plan-2  H24   0.020
 02P  plan-2  H25   0.020
 02P  plan-3  C13   0.020
 02P  plan-3  C17   0.020
 02P  plan-3  O28   0.020
 02P  plan-3  N18   0.020
 02P  plan-3  C19   0.020
 02P  plan-3  HN18  0.020
 02P  plan-4  C8    0.020
 02P  plan-4  C9    0.020
 02P  plan-4  O12   0.020
 02P  plan-4  N11   0.020
 02P  plan-4  C13   0.020
 02P  plan-4  C14   0.020

