# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 11:22:38 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: D-phenylalanyl-N-[(4-chloropyridin-2-yl)methyl]-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3cc(Cl)ccn3
#
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
 B01  B01  D-phenylalanyl-N-[(4-chloropyridin-2-yl)methyl]-L-prolinamide  peptide  50  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_B01
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
 B01  N21   N   NH2   0  -0.763  -3.4078   1.5248  -1.3659
 B01  C8    C   CH1   0  -0.216  -3.2357   0.3719  -0.5136
 B01  C9    C   C     0   0.543  -1.7718   0.1032  -0.1588
 B01  O25   O   O     0  -0.503  -0.9943   1.0321   0.0301
 B01  C7    C   CH2   0  -0.533  -4.0108   0.5662   0.8014
 B01  C6    C   CR6   0   0.160  -5.4942   0.6332   0.5854
 B01  C1    C   CR16  0  -0.315  -6.2513  -0.5355   0.5425
 B01  C5    C   CR16  0  -0.303  -6.1425   1.8515   0.4002
 B01  C2    C   CR16  0  -0.240  -7.6208  -0.4914   0.3176
 B01  C4    C   CR16  0  -0.245  -7.5124   1.9022   0.1798
 B01  C3    C   CR16  0  -0.273  -8.2562   0.7300   0.1356
 B01  N22   N   NT    0  -0.477  -1.3785  -1.1728  -0.0329
 B01  C10   C   CH1   0  -0.163   0.0065  -1.4829   0.2759
 B01  C11   C   C     0   0.569   0.9557  -0.8309  -0.7210
 B01  O26   O   O     0  -0.499   0.7106  -0.7967  -1.9170
 B01  C14   C   CH2   0  -0.477   0.0616  -3.0128   0.1704
 B01  C15   C   CH2   0  -0.475  -1.3637  -3.4404   0.4981
 B01  C16   C   CH2   0  -0.282  -2.2036  -2.3677  -0.1791
 B01  C12   C   CH2   0  -0.284   3.1331   0.2197  -0.9829
 B01  C13   C   CR6   0   0.230   4.3177   0.5853  -0.1274
 B01  C17   C   CR16  0  -0.053   5.2487   0.7527   1.9489
 B01  C18   C   CR16  0  -0.306   6.4335   1.2652   1.4545
 B01  C19   C   CR6   0   0.079   6.5256   1.4324   0.0801
 B01  C20   C   CR16  0  -0.298   5.4639   1.0918  -0.7337
 B01  N23   N   NH1   0  -0.658   2.0973  -0.3821  -0.1904
 B01  N24   N   N     0  -0.455   4.2153   0.4209   1.1818
 B01  CL27  CL  CL    0  -0.095   7.9695   2.0671  -0.6132
 B01  HN21  H   HNH2  0   0.340  -2.9314   2.3222  -0.9622
 B01  HN2A  H   HNH2  0   0.352  -2.9710   1.3595  -2.2640
 B01  H8    H   HCH1  0   0.268  -3.6558  -0.4888  -1.0407
 B01  H7    H   HCH2  0   0.260  -3.6520   1.4816   1.2802
 B01  H7A   H   HCH2  0   0.261  -3.7783  -0.2517   1.4883
 B01  H1    H   HCR6  0   0.243  -5.7664  -1.4938   0.6953
 B01  H5    H   HCR6  0   0.241  -5.5698   2.7700   0.4374
 B01  H2    H   HCR6  0   0.253  -8.1927  -1.4102   0.2894
 B01  H4    H   HCR6  0   0.252  -8.0002   2.8588   0.0413
 B01  H3    H   HCR6  0   0.253  -9.3246   0.7683  -0.0331
 B01  H10   H   HCH1  0   0.274   0.2476  -1.1627   1.2952
 B01  H14   H   HCH2  0   0.250   0.3116  -3.3119  -0.8497
 B01  H14A  H   HCH2  0   0.266   0.8086  -3.4379   0.8384
 B01  H15   H   HCH2  0   0.259  -1.6027  -4.4391   0.1361
 B01  H15A  H   HCH2  0   0.246  -1.5314  -3.4218   1.5766
 B01  H16   H   HCH2  0   0.249  -2.3710  -2.6020  -1.2344
 B01  H16A  H   HCH2  0   0.253  -3.1762  -2.2499   0.2986
 B01  H12   H   HCH2  0   0.270   2.7688   1.1242  -1.4817
 B01  H12A  H   HCH2  0   0.269   3.4588  -0.4562  -1.7785
 B01  H17   H   HCR6  0   0.280   5.1293   0.6042   3.0153
 B01  H18   H   HCR6  0   0.296   7.2471   1.5217   2.1174
 B01  H20   H   HCR6  0   0.295   5.5161   1.2122  -1.8076
 B01  HN23  H   HNH1  0   0.405   2.2385  -0.3842   0.8096

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
 B01  C1   C2    aromatic  1.389  0.020  1.389
 B01  C1   C6    aromatic  1.393  0.020  1.393
 B01  C2   C3    aromatic  1.389  0.020  1.389
 B01  C3   C4    aromatic  1.389  0.020  1.389
 B01  C4   C5    aromatic  1.388  0.020  1.388
 B01  C5   C6    aromatic  1.392  0.020  1.392
 B01  C6   C7    single    1.501  0.020  1.501
 B01  C7   C8    single    1.539  0.020  1.539
 B01  C8   C9    single    1.530  0.020  1.530
 B01  C8   N21   single    1.444  0.020  1.444
 B01  C9   N22   single    1.341  0.020  1.341
 B01  C9   O25   double    1.226  0.020  1.226
 B01  C10  C11   single    1.523  0.020  1.523
 B01  C10  C14   single    1.535  0.020  1.535
 B01  C10  N22   single    1.452  0.020  1.452
 B01  C11  N23   single    1.336  0.020  1.336
 B01  C11  O26   double    1.221  0.020  1.221
 B01  C12  C13   single    1.506  0.020  1.506
 B01  C12  N23   single    1.436  0.020  1.436
 B01  C13  C20   aromatic  1.392  0.020  1.392
 B01  C13  N24   aromatic  1.323  0.020  1.323
 B01  C14  C15   single    1.524  0.020  1.524
 B01  C15  C16   single    1.521  0.020  1.521
 B01  C16  N22   single    1.459  0.020  1.459
 B01  C17  C18   aromatic  1.382  0.020  1.382
 B01  C17  N24   aromatic  1.329  0.020  1.329
 B01  C18  C19   aromatic  1.388  0.020  1.388
 B01  C19  C20   aromatic  1.380  0.020  1.380
 B01  C19  CL27  single    1.723  0.020  1.723
 B01  C1   H1    single    0.930  0.020  1.080
 B01  C2   H2    single    0.930  0.020  1.080
 B01  C3   H3    single    0.930  0.020  1.080
 B01  C4   H4    single    0.930  0.020  1.080
 B01  C5   H5    single    0.930  0.020  1.080
 B01  C7   H7    single    0.970  0.020  1.090
 B01  C7   H7A   single    0.970  0.020  1.090
 B01  C8   H8    single    0.970  0.020  1.090
 B01  C10  H10   single    0.970  0.020  1.090
 B01  C12  H12   single    0.970  0.020  1.090
 B01  C12  H12A  single    0.970  0.020  1.090
 B01  C14  H14   single    0.970  0.020  1.090
 B01  C14  H14A  single    0.970  0.020  1.090
 B01  C15  H15   single    0.970  0.020  1.090
 B01  C15  H15A  single    0.970  0.020  1.090
 B01  C16  H16   single    0.970  0.020  1.090
 B01  C16  H16A  single    0.970  0.020  1.090
 B01  C17  H17   single    0.930  0.020  1.080
 B01  C18  H18   single    0.930  0.020  1.080
 B01  C20  H20   single    0.930  0.020  1.080
 B01  N21  HN21  single    0.890  0.020  1.040
 B01  N21  HN2A  single    0.890  0.020  1.040
 B01  N23  HN23  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
 B01  HN2A  N21  HN21  106.22  3.000
 B01  HN2A  N21  C8    109.98  3.000
 B01  HN21  N21  C8    109.71  3.000
 B01  H8    C8   C7    108.54  3.000
 B01  H8    C8   C9    109.95  3.000
 B01  C7    C8   C9    107.81  3.000
 B01  H8    C8   N21   107.35  3.000
 B01  C9    C8   N21   113.02  3.000
 B01  C7    C8   N21   110.09  3.000
 B01  N22   C9   O25   121.36  3.000
 B01  O25   C9   C8    120.62  3.000
 B01  N22   C9   C8    118.00  3.000
 B01  H7A   C7   H7    106.34  3.000
 B01  H7A   C7   C6    109.52  3.000
 B01  H7    C7   C6    110.49  3.000
 B01  H7A   C7   C8    109.60  3.000
 B01  H7    C7   C8    108.34  3.000
 B01  C6    C7   C8    112.37  3.000
 B01  C5    C6   C1    118.49  3.000
 B01  C5    C6   C7    121.23  3.000
 B01  C1    C6   C7    120.28  3.000
 B01  H1    C1   C2    119.45  3.000
 B01  H1    C1   C6    119.60  3.000
 B01  C2    C1   C6    120.95  3.000
 B01  H5    C5   C4    119.74  3.000
 B01  H5    C5   C6    119.43  3.000
 B01  C4    C5   C6    120.83  3.000
 B01  H2    C2   C3    120.08  3.000
 B01  H2    C2   C1    119.89  3.000
 B01  C3    C2   C1    120.03  3.000
 B01  H4    C4   C3    120.02  3.000
 B01  H4    C4   C5    119.81  3.000
 B01  C3    C4   C5    120.17  3.000
 B01  H3    C3   C4    120.24  3.000
 B01  H3    C3   C2    120.22  3.000
 B01  C4    C3   C2    119.54  3.000
 B01  C16   N22  C10   112.68  3.000
 B01  C16   N22  C9    127.14  3.000
 B01  C10   N22  C9    120.18  3.000
 B01  H10   C10  C14   110.34  3.000
 B01  H10   C10  C11   110.28  3.000
 B01  C14   C10  C11   111.06  3.000
 B01  H10   C10  N22   110.20  3.000
 B01  C14   C10  N22   103.45  3.000
 B01  C11   C10  N22   111.33  3.000
 B01  N23   C11  O26   123.42  3.000
 B01  O26   C11  C10   121.86  3.000
 B01  N23   C11  C10   114.60  3.000
 B01  H14A  C14  H14   108.01  3.000
 B01  H14A  C14  C15   113.60  3.000
 B01  H14   C14  C15   109.76  3.000
 B01  H14A  C14  C10   111.83  3.000
 B01  H14   C14  C10   110.21  3.000
 B01  C15   C14  C10   103.38  3.000
 B01  H15A  C15  H15   108.08  3.000
 B01  H15A  C15  C16   110.05  3.000
 B01  H15   C15  C16   112.19  3.000
 B01  H15A  C15  C14   110.57  3.000
 B01  H15   C15  C14   113.03  3.000
 B01  C16   C15  C14   102.87  3.000
 B01  H16A  C16  H16   108.02  3.000
 B01  H16A  C16  C15   111.94  3.000
 B01  H16   C16  C15   111.28  3.000
 B01  H16A  C16  N22   111.85  3.000
 B01  H16   C16  N22   111.01  3.000
 B01  C15   C16  N22   102.74  3.000
 B01  H12A  C12  H12   106.15  3.000
 B01  H12A  C12  N23   110.93  3.000
 B01  H12   C12  N23   110.94  3.000
 B01  H12A  C12  C13   109.21  3.000
 B01  H12   C12  C13   108.65  3.000
 B01  N23   C12  C13   110.82  3.000
 B01  N24   C13  C20   122.67  3.000
 B01  N24   C13  C12   118.09  3.000
 B01  C20   C13  C12   119.24  3.000
 B01  H17   C17  N24   116.63  3.000
 B01  H17   C17  C18   119.83  3.000
 B01  N24   C17  C18   123.55  3.000
 B01  H18   C18  C19   121.95  3.000
 B01  H18   C18  C17   120.94  3.000
 B01  C19   C18  C17   117.12  3.000
 B01  CL27  C19  C20   119.88  3.000
 B01  CL27  C19  C18   119.91  3.000
 B01  C20   C19  C18   120.21  3.000
 B01  H20   C20  C19   121.38  3.000
 B01  H20   C20  C13   120.83  3.000
 B01  C19   C20  C13   117.79  3.000
 B01  HN23  N23  C12   116.51  3.000
 B01  HN23  N23  C11   120.79  3.000
 B01  C12   N23  C11   122.52  3.000
 B01  C17   N24  C13   118.67  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
 B01  CONST_01  C3    C2   C1   C6      0.00   0.0  0
 B01  CONST_02  C3    C4   C5   C6      0.00   0.0  0
 B01  CONST_03  C4    C3   C2   C1      0.00   0.0  0
 B01  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 B01  CONST_05  C2    C3   C4   C5      0.00   0.0  0
 B01  CONST_06  C2    C1   C6   C5      0.00   0.0  0
 B01  CONST_07  C18   C19  C20  C13     0.00   0.0  0
 B01  CONST_08  C18   C17  N24  C13     0.00   0.0  0
 B01  CONST_09  C20   C19  C18  C17     0.00   0.0  0
 B01  CONST_10  C20   C13  N24  C17     0.00   0.0  0
 B01  CONST_11  N24   C17  C18  C19     0.00   0.0  0
 B01  CONST_12  N24   C13  C20  C19     0.00   0.0  0
 B01  CONST_13  C2    C1   C6   C7    180.00   0.0  0
 B01  CONST_14  C4    C5   C6   C7    180.00   0.0  0
 B01  CONST_15  C19   C20  C13  C12   180.00   0.0  0
 B01  CONST_16  C17   N24  C13  C12   180.00   0.0  0
 B01  CONST_17  CL27  C19  C20  C13   180.00   0.0  0
 B01  CONST_18  CL27  C19  C18  C17   180.00   0.0  0
 B01  CONST_19  H2    C2   C1   C6    180.00   0.0  0
 B01  CONST_20  H4    C4   C5   C6    180.00   0.0  0
 B01  CONST_21  H3    C3   C2   C1    180.00   0.0  0
 B01  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 B01  CONST_23  H1    C1   C6   C5    180.00   0.0  0
 B01  CONST_24  H17   C17  N24  C13   180.00   0.0  0
 B01  CONST_25  H20   C20  C19  C18   180.00   0.0  0
 B01  CONST_26  H18   C18  C19  C20   180.00   0.0  0
 B01  CONST_27  C10   N22  C9   C8    180.00   0.0  0
 B01  CONST_28  C16   N22  C9   C8      0.00   0.0  0
 B01  CONST_29  C10   N22  C9   O25     0.00   0.0  0
 B01  CONST_30  C16   N22  C9   O25   180.00   0.0  0
 B01  CONST_31  C12   N23  C11  C10   180.00   0.0  0
 B01  CONST_32  HN23  N23  C11  C10     0.00   0.0  0
 B01  CONST_33  C12   N23  C11  O26     0.00   0.0  0
 B01  Var_01    C14   C15  C16  N22   -34.22  30.0  1
 B01  Var_02    C16   C15  C14  C10    38.35  30.0  1
 B01  Var_03    C15   C16  N22  C10    17.86  30.0  1
 B01  Var_04    C1    C6   C7   C8     86.38  30.0  2
 B01  Var_05    N23   C12  C13  C20   175.31  30.0  2
 B01  Var_06    C13   C12  N23  C11  -178.04  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
 B01  chir_01  C8   C7   C9   N21  positiv
 B01  chir_02  C10  N22  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
 B01  plan-1  C7    0.020
 B01  plan-1  C6    0.020
 B01  plan-1  C1    0.020
 B01  plan-1  C5    0.020
 B01  plan-1  C2    0.020
 B01  plan-1  C4    0.020
 B01  plan-1  C3    0.020
 B01  plan-1  H1    0.020
 B01  plan-1  H5    0.020
 B01  plan-1  H2    0.020
 B01  plan-1  H4    0.020
 B01  plan-1  H3    0.020
 B01  plan-2  C12   0.020
 B01  plan-2  C13   0.020
 B01  plan-2  C17   0.020
 B01  plan-2  C18   0.020
 B01  plan-2  C19   0.020
 B01  plan-2  C20   0.020
 B01  plan-2  N24   0.020
 B01  plan-2  CL27  0.020
 B01  plan-2  H17   0.020
 B01  plan-2  H18   0.020
 B01  plan-2  H20   0.020
 B01  plan-3  C10   0.020
 B01  plan-3  C11   0.020
 B01  plan-3  O26   0.020
 B01  plan-3  C12   0.020
 B01  plan-3  N23   0.020
 B01  plan-3  HN23  0.020
 B01  plan-4  C8    0.020
 B01  plan-4  C9    0.020
 B01  plan-4  O25   0.020
 B01  plan-4  N22   0.020
 B01  plan-4  C10   0.020
 B01  plan-4  C16   0.020

