# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 21:43:50 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: D-phenylalanyl-N-[(1-methylpyridinium-4-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1ccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3)cc1
#
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
 06P  06P  D-phenylalanyl-N-[(1-methylpyridinium-4-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_06P
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
 06P  N4    N  NH2   0  -0.779   1.5222  -1.7245   0.5639
 06P  C3    C  CH1   0  -0.222   1.9040  -0.3685   0.2431
 06P  C5    C  C     0   0.572   0.6871   0.5371   0.3647
 06P  O7    O  O     0  -0.496  -0.1973   0.2989   1.1788
 06P  C2    C  CH2   0  -0.541   3.0187   0.2317   1.1377
 06P  C1    C  CR6   0   0.137   4.2974  -0.5447   1.0240
 06P  C8    C  CR16  0  -0.304   5.1952  -0.2783  -0.0085
 06P  C12   C  CR16  0  -0.318   4.5940  -1.5763   1.9123
 06P  C9    C  CR16  0  -0.240   6.3606  -1.0184  -0.1480
 06P  C11   C  CR16  0  -0.241   5.7593  -2.3206   1.7764
 06P  C10   C  CR16  0  -0.270   6.6460  -2.0443   0.7448
 06P  N6    N  NT    0  -0.460   0.6635   1.6450  -0.3944
 06P  C13   C  CH1   0  -0.229  -0.4077   2.6045  -0.2284
 06P  C14   C  C     0   0.582  -1.7224   2.0226  -0.7281
 06P  O15   O  O     0  -0.471  -1.7830   1.2493  -1.6680
 06P  C19   C  CH2   0  -0.467   0.0435   3.7900  -1.0927
 06P  C20   C  CH2   0  -0.473   0.8620   3.1349  -2.1985
 06P  C21   C  CH2   0  -0.279   1.5701   1.9866  -1.4883
 06P  N16   N  NH1   0  -0.647  -2.8179   2.4563  -0.0784
 06P  C17   C  CH2   0  -0.330  -4.1353   2.0590  -0.4795
 06P  C18   C  CR6   0   0.222  -4.4814   0.6321  -0.1542
 06P  C22   C  CR16  0  -0.378  -5.6508   0.0801  -0.6745
 06P  C23   C  CR16  0   0.102  -5.9962  -1.2104  -0.3698
 06P  N24   N  NR6   1  -0.419  -5.2179  -1.9591   0.4262
 06P  C25   C  CH3   0  -0.532  -5.6364  -3.3254   0.7541
 06P  C26   C  CR16  0   0.088  -4.0885  -1.4567   0.9386
 06P  C27   C  CR16  0  -0.382  -3.6955  -0.1680   0.6655
 06P  HN4   H  HNH2  0   0.355   2.3216  -2.3351   0.4523
 06P  HN4A  H  HNH2  0   0.342   1.2443  -1.7893   1.5355
 06P  H3    H  HCH1  0   0.267   2.2673  -0.3684  -0.7881
 06P  H2    H  HCH2  0   0.261   2.6680   0.2333   2.1736
 06P  H2A   H  HCH2  0   0.259   3.1949   1.2747   0.8603
 06P  H8    H  HCR6  0   0.245   4.9867   0.5235  -0.7082
 06P  H12   H  HCR6  0   0.250   3.9109  -1.7905   2.7260
 06P  H9    H  HCR6  0   0.255   7.0501  -0.7915  -0.9512
 06P  H11   H  HCR6  0   0.255   5.9741  -3.1150   2.4799
 06P  H10   H  HCR6  0   0.255   7.5564  -2.6202   0.6404
 06P  H13   H  HCH1  0   0.289  -0.5056   2.8979   0.8194
 06P  H19   H  HCH2  0   0.265  -0.7924   4.3833  -1.4625
 06P  H19A  H  HCH2  0   0.262   0.6712   4.4463  -0.4877
 06P  H20   H  HCH2  0   0.249   0.2104   2.7478  -2.9818
 06P  H20A  H  HCH2  0   0.260   1.5692   3.8199  -2.6638
 06P  H21   H  HCH2  0   0.243   2.5426   2.3018  -1.1007
 06P  H21A  H  HCH2  0   0.262   1.7305   1.1385  -2.1535
 06P  HN16  H  HNH1  0   0.415  -2.7220   3.0667   0.7164
 06P  H17   H  HCH2  0   0.312  -4.8546   2.7054   0.0256
 06P  H17A  H  HCH2  0   0.286  -4.2785   2.2169  -1.5509
 06P  H22   H  HCR6  0   0.310  -6.2988   0.6512  -1.3247
 06P  H23   H  HCR6  0   0.348  -6.8928  -1.6764  -0.7504
 06P  H25   H  HCH3  0   0.291  -5.9646  -3.8265  -0.1510
 06P  H25A  H  HCH3  0   0.286  -4.7975  -3.8651   1.1790
 06P  H25B  H  HCH3  0   0.297  -6.4503  -3.2878   1.4730
 06P  H26   H  HCR6  0   0.348  -3.5085  -2.1116   1.5709
 06P  H27   H  HCR6  0   0.309  -2.7715   0.1893   1.0964

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
 06P  C1   C2    single    1.500  0.020  1.500
 06P  C1   C8    aromatic  1.394  0.020  1.394
 06P  C1   C12   aromatic  1.393  0.020  1.393
 06P  C2   C3    single    1.550  0.020  1.550
 06P  C3   N4    single    1.445  0.020  1.445
 06P  C3   C5    single    1.522  0.020  1.522
 06P  C5   N6    single    1.343  0.020  1.343
 06P  C5   O7    double    1.225  0.020  1.225
 06P  N6   C13   single    1.448  0.020  1.448
 06P  N6   C21   single    1.461  0.020  1.461
 06P  C8   C9    aromatic  1.388  0.020  1.388
 06P  C9   C10   aromatic  1.390  0.020  1.390
 06P  C10  C11   aromatic  1.388  0.020  1.388
 06P  C11  C12   aromatic  1.389  0.020  1.389
 06P  C13  C14   single    1.522  0.020  1.522
 06P  C13  C19   single    1.535  0.020  1.535
 06P  C14  O15   double    1.219  0.020  1.219
 06P  C14  N16   single    1.345  0.020  1.345
 06P  N16  C17   single    1.433  0.020  1.433
 06P  C17  C18   single    1.504  0.020  1.504
 06P  C18  C22   aromatic  1.394  0.020  1.394
 06P  C18  C27   aromatic  1.389  0.020  1.389
 06P  C19  C20   single    1.524  0.020  1.524
 06P  C20  C21   single    1.525  0.020  1.525
 06P  C22  C23   aromatic  1.370  0.020  1.370
 06P  C23  N24   aromatic  1.342  0.020  1.342
 06P  N24  C25   single    1.466  0.020  1.466
 06P  N24  C26   aromatic  1.338  0.020  1.338
 06P  C26  C27   aromatic  1.375  0.020  1.375
 06P  C2   H2    single    0.970  0.020  1.090
 06P  C2   H2A   single    0.970  0.020  1.090
 06P  C3   H3    single    0.970  0.020  1.090
 06P  N4   HN4   single    0.890  0.020  1.040
 06P  N4   HN4A  single    0.890  0.020  1.040
 06P  C8   H8    single    0.930  0.020  1.080
 06P  C9   H9    single    0.930  0.020  1.080
 06P  C10  H10   single    0.930  0.020  1.080
 06P  C11  H11   single    0.930  0.020  1.080
 06P  C12  H12   single    0.930  0.020  1.080
 06P  C13  H13   single    0.970  0.020  1.090
 06P  N16  HN16  single    0.860  0.020  1.020
 06P  C17  H17   single    0.970  0.020  1.090
 06P  C17  H17A  single    0.970  0.020  1.090
 06P  C19  H19   single    0.970  0.020  1.090
 06P  C19  H19A  single    0.970  0.020  1.090
 06P  C20  H20   single    0.970  0.020  1.090
 06P  C20  H20A  single    0.970  0.020  1.090
 06P  C21  H21   single    0.970  0.020  1.090
 06P  C21  H21A  single    0.970  0.020  1.090
 06P  C22  H22   single    0.930  0.020  1.080
 06P  C23  H23   single    0.930  0.020  1.080
 06P  C25  H25   single    0.970  0.020  1.090
 06P  C25  H25A  single    0.970  0.020  1.090
 06P  C25  H25B  single    0.970  0.020  1.090
 06P  C26  H26   single    0.930  0.020  1.080
 06P  C27  H27   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
 06P  HN4A  N4   HN4   106.49  3.000
 06P  HN4A  N4   C3    110.22  3.000
 06P  HN4   N4   C3    109.45  3.000
 06P  H3    C3   C2    107.78  3.000
 06P  H3    C3   C5    109.94  3.000
 06P  C2    C3   C5    107.37  3.000
 06P  H3    C3   N4    107.30  3.000
 06P  C5    C3   N4    109.23  3.000
 06P  C2    C3   N4    115.17  3.000
 06P  N6    C5   O7    121.54  3.000
 06P  O7    C5   C3    120.97  3.000
 06P  N6    C5   C3    117.37  3.000
 06P  H2A   C2   H2    106.89  3.000
 06P  H2A   C2   C1    109.70  3.000
 06P  H2    C2   C1    110.24  3.000
 06P  H2A   C2   C3    109.80  3.000
 06P  H2    C2   C3    108.46  3.000
 06P  C1    C2   C3    111.64  3.000
 06P  C12   C1   C8    118.47  3.000
 06P  C12   C1   C2    121.08  3.000
 06P  C8    C1   C2    120.41  3.000
 06P  H8    C8   C9    119.40  3.000
 06P  H8    C8   C1    119.70  3.000
 06P  C9    C8   C1    120.90  3.000
 06P  H12   C12  C11   119.74  3.000
 06P  H12   C12  C1    119.40  3.000
 06P  C11   C12  C1    120.85  3.000
 06P  H9    C9   C10   120.04  3.000
 06P  H9    C9   C8    119.85  3.000
 06P  C10   C9   C8    120.11  3.000
 06P  H11   C11  C10   120.15  3.000
 06P  H11   C11  C12   119.73  3.000
 06P  C10   C11  C12   120.11  3.000
 06P  H10   C10  C11   120.20  3.000
 06P  H10   C10  C9    120.24  3.000
 06P  C11   C10  C9    119.56  3.000
 06P  C21   N6   C13   112.95  3.000
 06P  C21   N6   C5    127.23  3.000
 06P  C13   N6   C5    119.66  3.000
 06P  H13   C13  C19   111.03  3.000
 06P  H13   C13  C14   109.89  3.000
 06P  C19   C13  C14   111.37  3.000
 06P  H13   C13  N6    110.75  3.000
 06P  C19   C13  N6    103.29  3.000
 06P  C14   C13  N6    110.37  3.000
 06P  N16   C14  O15   122.45  3.000
 06P  N16   C14  C13   114.93  3.000
 06P  O15   C14  C13   122.60  3.000
 06P  H19A  C19  H19   107.57  3.000
 06P  H19A  C19  C20   110.61  3.000
 06P  H19   C19  C20   113.57  3.000
 06P  H19A  C19  C13   108.75  3.000
 06P  H19   C19  C13   112.71  3.000
 06P  C20   C19  C13   103.56  3.000
 06P  H20A  C20  H20   107.73  3.000
 06P  H20A  C20  C21   111.79  3.000
 06P  H20   C20  C21   110.17  3.000
 06P  H20A  C20  C19   112.86  3.000
 06P  H20   C20  C19   110.68  3.000
 06P  C21   C20  C19   103.60  3.000
 06P  H21A  C21  H21   108.05  3.000
 06P  H21A  C21  C20   111.73  3.000
 06P  H21   C21  C20   111.16  3.000
 06P  H21A  C21  N6    111.49  3.000
 06P  H21   C21  N6    110.72  3.000
 06P  C20   C21  N6    103.69  3.000
 06P  HN16  N16  C17   118.46  3.000
 06P  HN16  N16  C14   119.95  3.000
 06P  C17   N16  C14   121.59  3.000
 06P  H17A  C17  H17   106.38  3.000
 06P  H17A  C17  C18   108.61  3.000
 06P  H17   C17  C18   108.07  3.000
 06P  H17A  C17  N16   110.79  3.000
 06P  H17   C17  N16   108.19  3.000
 06P  C18   C17  N16   114.46  3.000
 06P  C27   C18  C22   117.83  3.000
 06P  C27   C18  C17   122.95  3.000
 06P  C22   C18  C17   119.22  3.000
 06P  H22   C22  C23   118.70  3.000
 06P  H22   C22  C18   121.21  3.000
 06P  C23   C22  C18   120.09  3.000
 06P  H23   C23  N24   116.74  3.000
 06P  H23   C23  C22   122.51  3.000
 06P  N24   C23  C22   120.75  3.000
 06P  C26   N24  C25   120.35  3.000
 06P  C26   N24  C23   120.48  3.000
 06P  C25   N24  C23   119.16  3.000
 06P  H25B  C25  H25A  109.73  3.000
 06P  H25B  C25  H25   109.95  3.000
 06P  H25A  C25  H25   109.32  3.000
 06P  H25B  C25  N24   109.24  3.000
 06P  H25A  C25  N24   109.31  3.000
 06P  H25   C25  N24   109.28  3.000
 06P  H26   C26  C27   122.11  3.000
 06P  H26   C26  N24   116.74  3.000
 06P  C27   C26  N24   121.15  3.000
 06P  H27   C27  C26   118.38  3.000
 06P  H27   C27  C18   121.92  3.000
 06P  C26   C27  C18   119.70  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
 06P  CONST_01  C10   C9   C8   C1      0.00   0.0  0
 06P  CONST_02  C10   C11  C12  C1      0.00   0.0  0
 06P  CONST_03  C11   C12  C1   C8      0.00   0.0  0
 06P  CONST_04  C11   C10  C9   C8      0.00   0.0  0
 06P  CONST_05  C9    C8   C1   C12     0.00   0.0  0
 06P  CONST_06  C9    C10  C11  C12     0.00   0.0  0
 06P  CONST_07  N24   C23  C22  C18     0.00   0.0  0
 06P  CONST_08  N24   C26  C27  C18     0.00   0.0  0
 06P  CONST_09  C26   C27  C18  C22     0.00   0.0  0
 06P  CONST_10  C26   N24  C23  C22     0.00   0.0  0
 06P  CONST_11  C27   C18  C22  C23     0.00   0.0  0
 06P  CONST_12  C27   C26  N24  C23     0.00   0.0  0
 06P  CONST_13  C9    C8   C1   C2    180.00   0.0  0
 06P  CONST_14  C11   C12  C1   C2    180.00   0.0  0
 06P  CONST_15  C23   C22  C18  C17   180.00   0.0  0
 06P  CONST_16  C26   C27  C18  C17   180.00   0.0  0
 06P  CONST_17  C25   N24  C23  C22   180.00   0.0  0
 06P  CONST_18  C27   C26  N24  C25   180.00   0.0  0
 06P  CONST_19  H9    C9   C8   C1    180.00   0.0  0
 06P  CONST_20  H11   C11  C12  C1    180.00   0.0  0
 06P  CONST_21  H12   C12  C1   C8    180.00   0.0  0
 06P  CONST_22  H10   C10  C9   C8    180.00   0.0  0
 06P  CONST_23  H8    C8   C1   C12   180.00   0.0  0
 06P  CONST_24  H23   C23  C22  C18   180.00   0.0  0
 06P  CONST_25  H26   C26  C27  C18   180.00   0.0  0
 06P  CONST_26  H27   C27  C18  C22   180.00   0.0  0
 06P  CONST_27  H22   C22  C23  N24   180.00   0.0  0
 06P  CONST_28  C13   N6   C5   C3    180.00   0.0  0
 06P  CONST_29  C21   N6   C5   C3      0.00   0.0  0
 06P  CONST_30  C13   N6   C5   O7      0.00   0.0  0
 06P  CONST_31  C21   N6   C5   O7    180.00   0.0  0
 06P  CONST_32  C17   N16  C14  C13   180.00   0.0  0
 06P  CONST_33  HN16  N16  C14  C13     0.00   0.0  0
 06P  CONST_34  C17   N16  C14  O15     0.00   0.0  0
 06P  Var_01    C19   C20  C21  N6     28.27  30.0  1
 06P  Var_02    C20   C21  N6   C13    -9.74  30.0  1
 06P  Var_03    C21   C20  C19  C13   -36.18  30.0  1
 06P  Var_04    C8    C1   C2   C3     84.49  30.0  2
 06P  Var_05    C22   C18  C17  N16  -170.37  30.0  2
 06P  Var_06    H25   C25  N24  C23    45.93  30.0  2
 06P  Var_07    C18   C17  N16  C14    72.67  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
 06P  chir_01  C3   C2  N4   C5   negativ
 06P  chir_02  C13  N6  C14  C19  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
 06P  plan-1  C2    0.020
 06P  plan-1  C1    0.020
 06P  plan-1  C8    0.020
 06P  plan-1  C12   0.020
 06P  plan-1  C9    0.020
 06P  plan-1  C11   0.020
 06P  plan-1  C10   0.020
 06P  plan-1  H8    0.020
 06P  plan-1  H12   0.020
 06P  plan-1  H9    0.020
 06P  plan-1  H11   0.020
 06P  plan-1  H10   0.020
 06P  plan-2  C17   0.020
 06P  plan-2  C18   0.020
 06P  plan-2  C22   0.020
 06P  plan-2  C23   0.020
 06P  plan-2  N24   0.020
 06P  plan-2  C25   0.020
 06P  plan-2  C26   0.020
 06P  plan-2  C27   0.020
 06P  plan-2  H22   0.020
 06P  plan-2  H23   0.020
 06P  plan-2  H26   0.020
 06P  plan-2  H27   0.020
 06P  plan-3  C13   0.020
 06P  plan-3  C14   0.020
 06P  plan-3  O15   0.020
 06P  plan-3  N16   0.020
 06P  plan-3  C17   0.020
 06P  plan-3  HN16  0.020
 06P  plan-4  C3    0.020
 06P  plan-4  C5    0.020
 06P  plan-4  O7    0.020
 06P  plan-4  N6    0.020
 06P  plan-4  C13   0.020
 06P  plan-4  C21   0.020

