# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:59:38 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3cccc(Cl)c3
#
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
 22U  22U  D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide  peptide  51  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_22U
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
 22U  N1    N   NH2   0  -0.779   3.6988   1.5831   1.2252
 22U  C2    C   CH1   0  -0.227   3.3840   0.4037   0.4501
 22U  C3    C   C     0   0.574   1.9397   0.4988  -0.0200
 22U  O1    O   O     0  -0.502   1.4575   1.5770  -0.3455
 22U  C1    C   CH2   0  -0.541   4.2672   0.1844  -0.8042
 22U  C16   C   CR6   0   0.137   5.7118   0.0071  -0.4414
 22U  C17   C   CR16  0  -0.307   6.2023  -1.2515  -0.0965
 22U  C21   C   CR16  0  -0.320   6.5799   1.0958  -0.3879
 22U  C18   C   CR16  0  -0.239   7.5246  -1.4203   0.2884
 22U  C20   C   CR16  0  -0.241   7.9045   0.9319  -0.0023
 22U  C19   C   CR16  0  -0.270   8.3807  -0.3269   0.3378
 22U  N2    N   NT    0  -0.479   1.2366  -0.6386  -0.1224
 22U  C7    C   CH1   0  -0.171  -0.1262  -0.5994  -0.6196
 22U  C8    C   C     0   0.559  -1.0039   0.3115   0.2277
 22U  O2    O   O     0  -0.485  -0.9002   0.3470   1.4420
 22U  C6    C   CH2   0  -0.483  -0.5958  -2.0575  -0.5059
 22U  C5    C   CH2   0  -0.470   0.7001  -2.8550  -0.5874
 22U  C4    C   CH2   0  -0.283   1.6783  -1.9924   0.1962
 22U  N3    N   NH1   0  -0.638  -1.9370   0.9807  -0.4700
 22U  C9    C   CH2   0  -0.336  -2.9502   1.8141   0.1224
 22U  C10   C   CR6   0   0.089  -4.3529   1.3100  -0.1168
 22U  C15   C   CR16  0  -0.296  -5.4012   2.2153  -0.2473
 22U  C14   C   CR16  0  -0.246  -6.7024   1.7678  -0.4242
 22U  C13   C   CR16  0  -0.231  -6.9811   0.4099  -0.4807
 22U  C12   C   CR6   0  -0.018  -5.9291  -0.4837  -0.3554
 22U  C11   C   CR16  0  -0.251  -4.6248  -0.0529  -0.1748
 22U  CL1   CL  CL    0  -0.130  -6.2486  -2.1878  -0.4296
 22U  HN1   H   HNH2  0   0.357   4.6376   1.5040   1.5951
 22U  HN1A  H   HNH2  0   0.342   3.6902   2.4049   0.6334
 22U  H2    H   HCH1  0   0.270   3.5092  -0.4567   1.1123
 22U  H1    H   HCH2  0   0.255   3.9144  -0.6910  -1.3563
 22U  H1A   H   HCH2  0   0.263   4.1431   1.0447  -1.4672
 22U  H17   H   HCR6  0   0.248   5.5419  -2.1109  -0.1350
 22U  H21   H   HCR6  0   0.250   6.2203   2.0810  -0.6615
 22U  H18   H   HCR6  0   0.255   7.8884  -2.4062   0.5475
 22U  H20   H   HCR6  0   0.255   8.5650   1.7887   0.0311
 22U  H19   H   HCR6  0   0.255   9.4131  -0.4567   0.6359
 22U  H7    H   HCH1  0   0.278  -0.1350  -0.2765  -1.6662
 22U  H6    H   HCH2  0   0.267  -1.3162  -2.3111  -1.2817
 22U  H6A   H   HCH2  0   0.253  -1.0690  -2.2290   0.4633
 22U  H5    H   HCH2  0   0.247   1.0312  -2.9481  -1.6235
 22U  H5A   H   HCH2  0   0.260   0.6082  -3.8575  -0.1723
 22U  H4    H   HCH2  0   0.254   2.7087  -2.1653  -0.1101
 22U  H4A   H   HCH2  0   0.252   1.6063  -2.1829   1.2705
 22U  HN3   H   HNH1  0   0.405  -1.9115   0.9309  -1.4762
 22U  H9    H   HCH2  0   0.278  -2.7582   1.8665   1.1945
 22U  H9A   H   HCH2  0   0.270  -2.8593   2.8330  -0.2601
 22U  H15   H   HCR6  0   0.259  -5.2010   3.2794  -0.2153
 22U  H14   H   HCR6  0   0.269  -7.5092   2.4810  -0.5273
 22U  H13   H   HCR6  0   0.280  -7.9931   0.0573  -0.6256
 22U  H11   H   HCR6  0   0.264  -3.8261  -0.7777  -0.0877

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
 22U  C1   C2    single    1.550  0.020  1.550
 22U  C1   C16   single    1.500  0.020  1.500
 22U  N1   C2    single    1.446  0.020  1.446
 22U  C2   C3    single    1.522  0.020  1.522
 22U  C3   O1    double    1.225  0.020  1.225
 22U  C3   N2    single    1.341  0.020  1.341
 22U  N2   C4    single    1.459  0.020  1.459
 22U  N2   C7    single    1.451  0.020  1.451
 22U  C4   C5    single    1.521  0.020  1.521
 22U  C5   C6    single    1.524  0.020  1.524
 22U  C6   C7    single    1.536  0.020  1.536
 22U  C7   C8    single    1.523  0.020  1.523
 22U  C8   N3    single    1.344  0.020  1.344
 22U  C8   O2    double    1.219  0.020  1.219
 22U  N3   C9    single    1.439  0.020  1.439
 22U  C9   C10   single    1.510  0.020  1.510
 22U  C10  C11   aromatic  1.391  0.020  1.391
 22U  C10  C15   aromatic  1.391  0.020  1.391
 22U  C11  C12   aromatic  1.385  0.020  1.385
 22U  C12  C13   aromatic  1.386  0.020  1.386
 22U  C12  CL1   single    1.735  0.020  1.735
 22U  C13  C14   aromatic  1.387  0.020  1.387
 22U  C14  C15   aromatic  1.387  0.020  1.387
 22U  C16  C17   aromatic  1.394  0.020  1.394
 22U  C16  C21   aromatic  1.394  0.020  1.394
 22U  C17  C18   aromatic  1.388  0.020  1.388
 22U  C18  C19   aromatic  1.390  0.020  1.390
 22U  C19  C20   aromatic  1.388  0.020  1.388
 22U  C20  C21   aromatic  1.389  0.020  1.389
 22U  C1   H1    single    0.970  0.020  1.090
 22U  C1   H1A   single    0.970  0.020  1.090
 22U  N1   HN1   single    0.890  0.020  1.040
 22U  N1   HN1A  single    0.890  0.020  1.040
 22U  C2   H2    single    0.970  0.020  1.090
 22U  C4   H4    single    0.970  0.020  1.090
 22U  C4   H4A   single    0.970  0.020  1.090
 22U  C5   H5    single    0.970  0.020  1.090
 22U  C5   H5A   single    0.970  0.020  1.090
 22U  C6   H6    single    0.970  0.020  1.090
 22U  C6   H6A   single    0.970  0.020  1.090
 22U  C7   H7    single    0.970  0.020  1.090
 22U  N3   HN3   single    0.860  0.020  1.020
 22U  C9   H9    single    0.970  0.020  1.090
 22U  C9   H9A   single    0.970  0.020  1.090
 22U  C11  H11   single    0.930  0.020  1.080
 22U  C13  H13   single    0.930  0.020  1.080
 22U  C14  H14   single    0.930  0.020  1.080
 22U  C15  H15   single    0.930  0.020  1.080
 22U  C17  H17   single    0.930  0.020  1.080
 22U  C18  H18   single    0.930  0.020  1.080
 22U  C19  H19   single    0.930  0.020  1.080
 22U  C20  H20   single    0.930  0.020  1.080
 22U  C21  H21   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
 22U  HN1A  N1   HN1  106.56  3.000
 22U  HN1A  N1   C2   110.29  3.000
 22U  HN1   N1   C2   109.52  3.000
 22U  H2    C2   C1   108.28  3.000
 22U  H2    C2   C3   110.18  3.000
 22U  C1    C2   C3   107.44  3.000
 22U  H2    C2   N1   107.00  3.000
 22U  C3    C2   N1   108.74  3.000
 22U  C1    C2   N1   115.17  3.000
 22U  N2    C3   O1   121.32  3.000
 22U  N2    C3   C2   117.91  3.000
 22U  O1    C3   C2   120.70  3.000
 22U  H1A   C1   H1   106.69  3.000
 22U  H1A   C1   C16  110.43  3.000
 22U  H1    C1   C16  109.77  3.000
 22U  H1A   C1   C2   108.35  3.000
 22U  H1    C1   C2   109.76  3.000
 22U  C16   C1   C2   111.71  3.000
 22U  C21   C16  C17  118.47  3.000
 22U  C21   C16  C1   121.12  3.000
 22U  C17   C16  C1   120.36  3.000
 22U  H17   C17  C18  119.59  3.000
 22U  H17   C17  C16  119.50  3.000
 22U  C18   C17  C16  120.92  3.000
 22U  H21   C21  C20  119.58  3.000
 22U  H21   C21  C16  119.59  3.000
 22U  C20   C21  C16  120.83  3.000
 22U  H18   C18  C19  120.08  3.000
 22U  H18   C18  C17  119.84  3.000
 22U  C19   C18  C17  120.08  3.000
 22U  H20   C20  C19  120.06  3.000
 22U  H20   C20  C21  119.80  3.000
 22U  C19   C20  C21  120.14  3.000
 22U  H19   C19  C20  120.23  3.000
 22U  H19   C19  C18  120.20  3.000
 22U  C20   C19  C18  119.57  3.000
 22U  C4    N2   C7   112.59  3.000
 22U  C7    N2   C3   119.71  3.000
 22U  C4    N2   C3   127.69  3.000
 22U  H7    C7   C6   110.38  3.000
 22U  H7    C7   C8   110.53  3.000
 22U  C6    C7   C8   110.52  3.000
 22U  H7    C7   N2   110.05  3.000
 22U  C8    C7   N2   111.52  3.000
 22U  C6    C7   N2   103.65  3.000
 22U  N3    C8   O2   124.18  3.000
 22U  O2    C8   C7   121.51  3.000
 22U  N3    C8   C7   114.16  3.000
 22U  H6A   C6   H6   108.01  3.000
 22U  H6A   C6   C5   109.50  3.000
 22U  H6    C6   C5   113.75  3.000
 22U  H6A   C6   C7   110.32  3.000
 22U  H6    C6   C7   111.75  3.000
 22U  C5    C6   C7   103.46  3.000
 22U  H5A   C5   H5   108.00  3.000
 22U  H5A   C5   C4   112.33  3.000
 22U  H5    C5   C4   110.01  3.000
 22U  H5A   C5   C6   112.93  3.000
 22U  H5    C5   C6   110.69  3.000
 22U  C4    C5   C6   102.86  3.000
 22U  H4A   C4   H4   108.12  3.000
 22U  H4A   C4   C5   111.40  3.000
 22U  H4    C4   C5   111.93  3.000
 22U  H4A   C4   N2   110.87  3.000
 22U  H4    C4   N2   111.86  3.000
 22U  C5    C4   N2   102.65  3.000
 22U  HN3   N3   C9   117.21  3.000
 22U  HN3   N3   C8   118.44  3.000
 22U  C9    N3   C8   124.30  3.000
 22U  H9A   C9   H9   106.55  3.000
 22U  H9A   C9   C10  109.48  3.000
 22U  H9    C9   C10  109.60  3.000
 22U  H9A   C9   N3   109.72  3.000
 22U  H9    C9   N3   107.97  3.000
 22U  C10   C9   N3   113.30  3.000
 22U  C11   C10  C15  119.11  3.000
 22U  C15   C10  C9   119.84  3.000
 22U  C11   C10  C9   121.03  3.000
 22U  H15   C15  C14  119.60  3.000
 22U  H15   C15  C10  119.82  3.000
 22U  C14   C15  C10  120.58  3.000
 22U  H14   C14  C13  119.44  3.000
 22U  H14   C14  C15  119.94  3.000
 22U  C13   C14  C15  120.62  3.000
 22U  H13   C13  C12  120.81  3.000
 22U  H13   C13  C14  120.83  3.000
 22U  C12   C13  C14  118.35  3.000
 22U  CL1   C12  C11  118.96  3.000
 22U  CL1   C12  C13  119.31  3.000
 22U  C11   C12  C13  121.73  3.000
 22U  H11   C11  C12  119.81  3.000
 22U  H11   C11  C10  120.58  3.000
 22U  C12   C11  C10  119.61  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
 22U  CONST_01  C19  C18  C17  C16     0.00   0.0  0
 22U  CONST_02  C19  C20  C21  C16     0.00   0.0  0
 22U  CONST_03  C20  C21  C16  C17     0.00   0.0  0
 22U  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 22U  CONST_05  C18  C17  C16  C21     0.00   0.0  0
 22U  CONST_06  C18  C19  C20  C21     0.00   0.0  0
 22U  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 22U  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 22U  CONST_09  C12  C11  C10  C15     0.00   0.0  0
 22U  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 22U  CONST_11  C11  C12  C13  C14     0.00   0.0  0
 22U  CONST_12  C11  C10  C15  C14     0.00   0.0  0
 22U  CONST_13  C18  C17  C16  C1    180.00   0.0  0
 22U  CONST_14  C20  C21  C16  C1    180.00   0.0  0
 22U  CONST_15  C12  C11  C10  C9    180.00   0.0  0
 22U  CONST_16  C14  C15  C10  C9    180.00   0.0  0
 22U  CONST_17  CL1  C12  C11  C10   180.00   0.0  0
 22U  CONST_18  CL1  C12  C13  C14   180.00   0.0  0
 22U  CONST_19  H18  C18  C17  C16   180.00   0.0  0
 22U  CONST_20  H20  C20  C21  C16   180.00   0.0  0
 22U  CONST_21  H21  C21  C16  C17   180.00   0.0  0
 22U  CONST_22  H19  C19  C18  C17   180.00   0.0  0
 22U  CONST_23  H17  C17  C16  C21   180.00   0.0  0
 22U  CONST_24  H14  C14  C15  C10   180.00   0.0  0
 22U  CONST_25  H11  C11  C10  C15   180.00   0.0  0
 22U  CONST_26  H13  C13  C14  C15   180.00   0.0  0
 22U  CONST_27  H15  C15  C14  C13   180.00   0.0  0
 22U  CONST_28  C4   N2   C3   C2      0.00   0.0  0
 22U  CONST_29  C7   N2   C3   C2    180.00   0.0  0
 22U  CONST_30  C4   N2   C3   O1    180.00   0.0  0
 22U  CONST_31  C7   N2   C3   O1      0.00   0.0  0
 22U  CONST_32  C9   N3   C8   C7    180.00   0.0  0
 22U  CONST_33  HN3  N3   C8   C7      0.00   0.0  0
 22U  CONST_34  C9   N3   C8   O2      0.00   0.0  0
 22U  Var_01    C6   C5   C4   N2    -34.92  30.0  1
 22U  Var_02    C5   C4   N2   C7     19.54  30.0  1
 22U  Var_03    C4   C5   C6   C7     37.88  30.0  1
 22U  Var_04    C17  C16  C1   C2     85.79  30.0  2
 22U  Var_05    C11  C10  C9   N3     34.23  30.0  2
 22U  Var_06    C10  C9   N3   C8   -116.49  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
 22U  chir_01  C2  C1  N1  C3  negativ
 22U  chir_02  C7  N2  C6  C8  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
 22U  plan-1  C1   0.020
 22U  plan-1  C16  0.020
 22U  plan-1  C17  0.020
 22U  plan-1  C21  0.020
 22U  plan-1  C18  0.020
 22U  plan-1  C20  0.020
 22U  plan-1  C19  0.020
 22U  plan-1  H17  0.020
 22U  plan-1  H21  0.020
 22U  plan-1  H18  0.020
 22U  plan-1  H20  0.020
 22U  plan-1  H19  0.020
 22U  plan-2  C9   0.020
 22U  plan-2  C10  0.020
 22U  plan-2  C15  0.020
 22U  plan-2  C14  0.020
 22U  plan-2  C13  0.020
 22U  plan-2  C12  0.020
 22U  plan-2  C11  0.020
 22U  plan-2  CL1  0.020
 22U  plan-2  H15  0.020
 22U  plan-2  H14  0.020
 22U  plan-2  H13  0.020
 22U  plan-2  H11  0.020
 22U  plan-3  C7   0.020
 22U  plan-3  C8   0.020
 22U  plan-3  O2   0.020
 22U  plan-3  N3   0.020
 22U  plan-3  C9   0.020
 22U  plan-3  HN3  0.020
 22U  plan-4  C2   0.020
 22U  plan-4  C3   0.020
 22U  plan-4  O1   0.020
 22U  plan-4  N2   0.020
 22U  plan-4  C7   0.020
 22U  plan-4  C4   0.020

