# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:23:50 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(N)=[NH2+]
#
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
 32U  32U  D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide  peptide  57  29  .  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_32U
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
 32U  N13   N  NH2   0  -0.763  -1.8311  -1.5773  -0.9456
 32U  C5    C  CH1   0  -0.208  -2.2851  -0.3352  -0.3691
 32U  C14   C  C     0   0.535  -1.2003   0.7446  -0.3255
 32U  O32   O  O     0  -0.492  -0.2818   0.7433  -1.1370
 32U  C33   C  CH2   0  -0.540  -3.4747   0.2254  -1.1715
 32U  C6    C  CR6   0   0.168  -4.6466  -0.7123  -1.1842
 32U  C8    C  CR16  0  -0.307  -4.8405  -1.6053  -2.2341
 32U  C12   C  CR16  0  -0.312  -5.5538  -0.7232  -0.1268
 32U  C9    C  CR16  0  -0.245  -5.9149  -2.4847  -2.2323
 32U  C11   C  CR16  0  -0.241  -6.6271  -1.6042  -0.1164
 32U  C10   C  CR16  0  -0.274  -6.8111  -2.4891  -1.1711
 32U  N1    N  NT    0  -0.457  -1.3227   1.7190   0.5919
 32U  C1    C  CH1   0  -0.227  -0.3551   2.7965   0.6326
 32U  C7    C  C     0   0.580   0.9847   2.2824   1.1459
 32U  O22   O  O     0  -0.477   1.0585   1.4271   2.0124
 32U  C2    C  CH2   0  -0.466  -0.9822   3.7924   1.6154
 32U  C3    C  CH2   0  -0.474  -1.7779   2.9086   2.5694
 32U  C4    C  CH2   0  -0.277  -2.2987   1.7856   1.6774
 32U  N23   N  NH1   0  -0.644   2.0634   2.8773   0.6117
 32U  C24   C  CH2   0  -0.328   3.4032   2.5420   1.0107
 32U  C25   C  CR6   0   0.091   3.9084   1.2177   0.4895
 32U  C26   C  CR16  0  -0.284   3.2255   0.4828  -0.4724
 32U  C27   C  CR16  0  -0.256   3.7383  -0.7172  -0.9370
 32U  C28   C  CR6   0   0.001   4.9511  -1.1967  -0.4500
 32U  C21   C  C     0   0.584   5.4976  -2.4652  -0.9492
 32U  N46   N  NC2   1  -0.765   4.6785  -3.4430  -1.2547
 32U  N47   N  NH2   0  -0.765   6.7952  -2.5978  -1.0831
 32U  C29   C  CR16  0  -0.254   5.6436  -0.4627   0.5125
 32U  C30   C  CR16  0  -0.273   5.1188   0.7278   0.9776
 32U  H113  H  HNH2  0   0.339  -1.4229  -1.4022  -1.8562
 32U  H213  H  HNH2  0   0.351  -1.0861  -1.9626  -0.3782
 32U  H5    H  HCH1  0   0.263  -2.6301  -0.5515   0.6458
 32U  H133  H  HCH2  0   0.264  -3.7769   1.1884  -0.7526
 32U  H233  H  HCH2  0   0.260  -3.1401   0.4247  -2.1936
 32U  H8    H  HCR6  0   0.242  -4.1462  -1.6099  -3.0654
 32U  H12A  H  HCR6  0   0.243  -5.4225  -0.0298   0.6965
 32U  H9    H  HCR6  0   0.252  -6.0520  -3.1688  -3.0601
 32U  H11   H  HCR6  0   0.253  -7.3221  -1.5961   0.7135
 32U  H10   H  HCR6  0   0.253  -7.6499  -3.1731  -1.1683
 32U  H1    H  HCH1  0   0.284  -0.2338   3.2430  -0.3570
 32U  H12   H  HCH2  0   0.263  -0.2407   4.4126   2.1186
 32U  H22   H  HCH2  0   0.260  -1.6474   4.4591   1.0638
 32U  H13   H  HCH2  0   0.248  -1.1319   2.5025   3.3471
 32U  H23   H  HCH2  0   0.258  -2.5894   3.4453   3.0583
 32U  H14   H  HCH2  0   0.243  -3.2944   2.0196   1.2911
 32U  H24   H  HCH2  0   0.259  -2.3607   0.8409   2.2176
 32U  HN23  H  HNH1  0   0.410   1.9439   3.5312  -0.1441
 32U  H124  H  HCH2  0   0.289   4.0601   3.3346   0.6500
 32U  H224  H  HCH2  0   0.269   3.4819   2.5506   2.0999
 32U  H26   H  HCR6  0   0.275   2.2836   0.8364  -0.8688
 32U  H27   H  HCR6  0   0.277   3.1956  -1.2588  -1.7012
 32U  H146  H  HNC2  0   0.438   5.0022  -4.3068  -1.6635
 32U  H147  H  HNH2  0   0.447   7.4098  -1.8096  -0.9599
 32U  H247  H  HNH2  0   0.438   7.2200  -3.4664  -1.3709
 32U  H29   H  HCR6  0   0.280   6.5761  -0.8269   0.9246
 32U  H30   H  HCR6  0   0.268   5.6575   1.2829   1.7358
 32U  H246  H  HNC2  0   0.446   3.6990  -3.3856  -1.0286

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
 32U  C24  N23   single    1.438  0.020  1.438
 32U  C24  C25   single    1.510  0.020  1.510
 32U  O22  C7    double    1.220  0.020  1.220
 32U  C2   C3    single    1.525  0.020  1.525
 32U  C2   C1    single    1.533  0.020  1.533
 32U  C7   N23   single    1.343  0.020  1.343
 32U  C7   C1    single    1.524  0.020  1.524
 32U  C3   C4    single    1.526  0.020  1.526
 32U  C25  C30   aromatic  1.394  0.020  1.394
 32U  C25  C26   aromatic  1.390  0.020  1.390
 32U  C1   N1    single    1.449  0.020  1.449
 32U  C30  C29   aromatic  1.382  0.020  1.382
 32U  C4   N1    single    1.461  0.020  1.461
 32U  C26  C27   aromatic  1.385  0.020  1.385
 32U  N1   C14   single    1.344  0.020  1.344
 32U  C29  C28   aromatic  1.395  0.020  1.395
 32U  C27  C28   aromatic  1.392  0.020  1.392
 32U  C14  O32   double    1.226  0.020  1.226
 32U  C14  C5    single    1.531  0.020  1.531
 32U  C28  C21   single    1.469  0.020  1.469
 32U  N13  C5    single    1.443  0.020  1.443
 32U  C5   C33   single    1.541  0.020  1.541
 32U  C21  N47   single    1.311  0.020  1.311
 32U  C21  N46   double    1.312  0.020  1.312
 32U  C8   C9    aromatic  1.388  0.020  1.388
 32U  C8   C6    aromatic  1.392  0.020  1.392
 32U  C9   C10   aromatic  1.389  0.020  1.389
 32U  C33  C6    single    1.501  0.020  1.501
 32U  C6   C12   aromatic  1.393  0.020  1.393
 32U  C10  C11   aromatic  1.389  0.020  1.389
 32U  C12  C11   aromatic  1.389  0.020  1.389
 32U  C1   H1    single    0.970  0.020  1.090
 32U  N23  HN23  single    0.860  0.020  1.020
 32U  C24  H124  single    0.970  0.020  1.090
 32U  C24  H224  single    0.970  0.020  1.090
 32U  C26  H26   single    0.930  0.020  1.080
 32U  C27  H27   single    0.930  0.020  1.080
 32U  N46  H146  single    0.860  0.020  1.020
 32U  N46  H246  single    0.860  0.020  1.020
 32U  N47  H147  single    0.860  0.020  1.020
 32U  N47  H247  single    0.860  0.020  1.020
 32U  C29  H29   single    0.930  0.020  1.080
 32U  C30  H30   single    0.930  0.020  1.080
 32U  C2   H12   single    0.970  0.020  1.090
 32U  C2   H22   single    0.970  0.020  1.090
 32U  C3   H13   single    0.970  0.020  1.090
 32U  C3   H23   single    0.970  0.020  1.090
 32U  C4   H14   single    0.970  0.020  1.090
 32U  C4   H24   single    0.970  0.020  1.090
 32U  C5   H5    single    0.970  0.020  1.090
 32U  N13  H113  single    0.890  0.020  1.040
 32U  N13  H213  single    0.890  0.020  1.040
 32U  C33  H133  single    0.970  0.020  1.090
 32U  C33  H233  single    0.970  0.020  1.090
 32U  C8   H8    single    0.930  0.020  1.080
 32U  C9   H9    single    0.930  0.020  1.080
 32U  C10  H10   single    0.930  0.020  1.080
 32U  C11  H11   single    0.930  0.020  1.080
 32U  C12  H12A  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
 32U  H213  N13  H113  105.84  3.000
 32U  H213  N13  C5    109.58  3.000
 32U  H113  N13  C5    109.70  3.000
 32U  H5    C5   C33   108.16  3.000
 32U  H5    C5   C14   109.67  3.000
 32U  C33   C5   C14   107.78  3.000
 32U  H5    C5   N13   107.45  3.000
 32U  C33   C5   N13   110.38  3.000
 32U  C14   C5   N13   113.30  3.000
 32U  N1    C14  O32   121.39  3.000
 32U  O32   C14  C5    120.76  3.000
 32U  N1    C14  C5    117.79  3.000
 32U  H233  C33  H133  106.40  3.000
 32U  H233  C33  C6    110.17  3.000
 32U  H133  C33  C6    109.75  3.000
 32U  H233  C33  C5    108.47  3.000
 32U  H133  C33  C5    109.54  3.000
 32U  C6    C33  C5    112.33  3.000
 32U  C12   C6   C8    118.47  3.000
 32U  C12   C6   C33   120.46  3.000
 32U  C8    C6   C33   121.06  3.000
 32U  H8    C8   C9    119.63  3.000
 32U  H8    C8   C6    119.50  3.000
 32U  C9    C8   C6    120.88  3.000
 32U  H12A  C12  C11   119.58  3.000
 32U  H12A  C12  C6    119.49  3.000
 32U  C11   C12  C6    120.93  3.000
 32U  H9    C9   C10   120.03  3.000
 32U  H9    C9   C8    119.82  3.000
 32U  C10   C9   C8    120.15  3.000
 32U  H11   C11  C10   120.12  3.000
 32U  H11   C11  C12   119.82  3.000
 32U  C10   C11  C12   120.05  3.000
 32U  H10   C10  C11   120.22  3.000
 32U  H10   C10  C9    120.26  3.000
 32U  C11   C10  C9    119.52  3.000
 32U  C4    N1   C1    113.04  3.000
 32U  C4    N1   C14   126.94  3.000
 32U  C1    N1   C14   119.84  3.000
 32U  H1    C1   C2    111.14  3.000
 32U  H1    C1   C7    110.20  3.000
 32U  C2    C1   C7    111.27  3.000
 32U  H1    C1   N1    110.66  3.000
 32U  C7    C1   N1    110.22  3.000
 32U  C2    C1   N1    103.17  3.000
 32U  N23   C7   O22   123.00  3.000
 32U  N23   C7   C1    115.01  3.000
 32U  O22   C7   C1    121.94  3.000
 32U  H22   C2   H12   107.48  3.000
 32U  H22   C2   C3    110.63  3.000
 32U  H12   C2   C3    113.34  3.000
 32U  H22   C2   C1    108.79  3.000
 32U  H12   C2   C1    112.78  3.000
 32U  C3    C2   C1    103.77  3.000
 32U  H23   C3   H13   107.77  3.000
 32U  H23   C3   C4    111.77  3.000
 32U  H13   C3   C4    110.20  3.000
 32U  H23   C3   C2    112.59  3.000
 32U  H13   C3   C2    110.68  3.000
 32U  C4    C3   C2    103.83  3.000
 32U  H24   C4   H14   107.98  3.000
 32U  H24   C4   C3    111.57  3.000
 32U  H14   C4   C3    111.09  3.000
 32U  H24   C4   N1    111.51  3.000
 32U  H14   C4   N1    110.83  3.000
 32U  C3    C4   N1    103.88  3.000
 32U  HN23  N23  C24   118.07  3.000
 32U  HN23  N23  C7    119.42  3.000
 32U  C24   N23  C7    122.34  3.000
 32U  H224  C24  H124  106.31  3.000
 32U  H224  C24  C25   109.09  3.000
 32U  H124  C24  C25   108.76  3.000
 32U  H224  C24  N23   110.01  3.000
 32U  H124  C24  N23   107.46  3.000
 32U  C25   C24  N23   114.86  3.000
 32U  C30   C25  C26   118.89  3.000
 32U  C26   C25  C24   122.56  3.000
 32U  C30   C25  C24   118.54  3.000
 32U  H26   C26  C27   118.87  3.000
 32U  H26   C26  C25   120.58  3.000
 32U  C27   C26  C25   120.55  3.000
 32U  H27   C27  C28   120.75  3.000
 32U  H27   C27  C26   118.99  3.000
 32U  C28   C27  C26   120.24  3.000
 32U  C29   C28  C21   120.29  3.000
 32U  C21   C28  C27   120.19  3.000
 32U  C29   C28  C27   119.52  3.000
 32U  N47   C21  N46   121.26  3.000
 32U  N46   C21  C28   119.39  3.000
 32U  N47   C21  C28   119.36  3.000
 32U  H246  N46  H146  116.87  3.000
 32U  H246  N46  C21   120.84  3.000
 32U  H146  N46  C21   122.16  3.000
 32U  H247  N47  H147  116.86  3.000
 32U  H247  N47  C21   122.20  3.000
 32U  H147  N47  C21   120.82  3.000
 32U  H29   C29  C30   119.27  3.000
 32U  H29   C29  C28   120.89  3.000
 32U  C30   C29  C28   119.82  3.000
 32U  H30   C30  C29   119.22  3.000
 32U  H30   C30  C25   119.80  3.000
 32U  C29   C30  C25   120.98  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
 32U  CONST_01  C10   C9   C8   C6      0.00   0.0  0
 32U  CONST_02  C10   C11  C12  C6      0.00   0.0  0
 32U  CONST_03  C11   C10  C9   C8      0.00   0.0  0
 32U  CONST_04  C11   C12  C6   C8      0.00   0.0  0
 32U  CONST_05  C9    C8   C6   C12     0.00   0.0  0
 32U  CONST_06  C9    C10  C11  C12     0.00   0.0  0
 32U  CONST_07  C28   C29  C30  C25     0.00   0.0  0
 32U  CONST_08  C28   C27  C26  C25     0.00   0.0  0
 32U  CONST_09  C29   C30  C25  C26     0.00   0.0  0
 32U  CONST_10  C29   C28  C27  C26     0.00   0.0  0
 32U  CONST_11  C30   C25  C26  C27     0.00   0.0  0
 32U  CONST_12  C30   C29  C28  C27     0.00   0.0  0
 32U  CONST_13  C9    C8   C6   C33   180.00   0.0  0
 32U  CONST_14  C11   C12  C6   C33   180.00   0.0  0
 32U  CONST_15  C29   C30  C25  C24   180.00   0.0  0
 32U  CONST_16  C27   C26  C25  C24   180.00   0.0  0
 32U  CONST_17  C21   C28  C27  C26   180.00   0.0  0
 32U  CONST_18  C30   C29  C28  C21   180.00   0.0  0
 32U  CONST_19  H9    C9   C8   C6    180.00   0.0  0
 32U  CONST_20  H11   C11  C12  C6    180.00   0.0  0
 32U  CONST_21  H10   C10  C9   C8    180.00   0.0  0
 32U  CONST_22  H12A  C12  C6   C8    180.00   0.0  0
 32U  CONST_23  H8    C8   C6   C12   180.00   0.0  0
 32U  CONST_24  H29   C29  C30  C25   180.00   0.0  0
 32U  CONST_25  H27   C27  C26  C25   180.00   0.0  0
 32U  CONST_26  H30   C30  C25  C26   180.00   0.0  0
 32U  CONST_27  H26   C26  C27  C28   180.00   0.0  0
 32U  CONST_28  C1    N1   C14  C5    180.00   0.0  0
 32U  CONST_29  C4    N1   C14  C5      0.00   0.0  0
 32U  CONST_30  C1    N1   C14  O32     0.00   0.0  0
 32U  CONST_31  C4    N1   C14  O32   180.00   0.0  0
 32U  CONST_32  C24   N23  C7   C1    180.00   0.0  0
 32U  CONST_33  HN23  N23  C7   C1      0.00   0.0  0
 32U  CONST_34  H147  N47  C21  C28     0.00   0.0  0
 32U  CONST_35  H247  N47  C21  C28   180.00   0.0  0
 32U  CONST_36  H146  N46  C21  C28   180.00   0.0  0
 32U  CONST_37  H246  N46  C21  C28     0.00   0.0  0
 32U  CONST_38  C24   N23  C7   O22     0.00   0.0  0
 32U  Var_01    C2    C3   C4   N1     26.41  30.0  1
 32U  Var_02    C4    C3   C2   C1    -35.26  30.0  1
 32U  Var_03    C3    C4   N1   C1     -7.55  30.0  1
 32U  Var_04    C8    C6   C33  C5    -95.14  30.0  2
 32U  Var_05    C30   C25  C24  N23  -171.10  30.0  2
 32U  Var_06    N47   C21  C28  C27   144.68  30.0  2
 32U  Var_07    C25   C24  N23  C7     74.30  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
 32U  chir_01  C5  C14  N13  C33  positiv
 32U  chir_02  C1  N1   C2   C7   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
 32U  plan-1  C33   0.020
 32U  plan-1  C6    0.020
 32U  plan-1  C8    0.020
 32U  plan-1  C12   0.020
 32U  plan-1  C9    0.020
 32U  plan-1  C11   0.020
 32U  plan-1  C10   0.020
 32U  plan-1  H8    0.020
 32U  plan-1  H12A  0.020
 32U  plan-1  H9    0.020
 32U  plan-1  H11   0.020
 32U  plan-1  H10   0.020
 32U  plan-2  C24   0.020
 32U  plan-2  C25   0.020
 32U  plan-2  C26   0.020
 32U  plan-2  C27   0.020
 32U  plan-2  C28   0.020
 32U  plan-2  C21   0.020
 32U  plan-2  C29   0.020
 32U  plan-2  C30   0.020
 32U  plan-2  H26   0.020
 32U  plan-2  H27   0.020
 32U  plan-2  H29   0.020
 32U  plan-2  H30   0.020
 32U  plan-3  C1    0.020
 32U  plan-3  C7    0.020
 32U  plan-3  O22   0.020
 32U  plan-3  N23   0.020
 32U  plan-3  C24   0.020
 32U  plan-3  HN23  0.020
 32U  plan-4  C5    0.020
 32U  plan-4  C14   0.020
 32U  plan-4  O32   0.020
 32U  plan-4  N1    0.020
 32U  plan-4  C1    0.020
 32U  plan-4  C4    0.020
 32U  plan-5  C28   0.020
 32U  plan-5  C21   0.020
 32U  plan-5  N46   0.020
 32U  plan-5  N47   0.020
 32U  plan-5  H146  0.020
 32U  plan-5  H147  0.020
 32U  plan-5  H247  0.020
 32U  plan-5  H246  0.020

