# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 21:22:31 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: D-phenylalanyl-N-(3-fluorobenzyl)-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(F)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
 37U  37U  "D-phenylalanyl-N-(3-fluorobenzyl)-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_37U
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
 37U  N25   N  NH2   0  -0.761  -3.3259  -1.7662   1.0691
 37U  C7    C  CH1   0  -0.217  -2.9844  -0.5489   0.3727
 37U  C6    C  C     0   0.539  -1.5301  -0.5184  -0.1036
 37U  O27   O  O     0  -0.502  -0.9586  -1.5497  -0.4396
 37U  C8    C  CH2   0  -0.532  -3.8905  -0.3674  -0.8595
 37U  C9    C  CR6   0   0.158  -5.3301  -0.1746  -0.4820
 37U  C10   C  CR16  0  -0.317  -5.8230   1.1032  -0.2267
 37U  C14   C  CR16  0  -0.299  -6.1942  -1.2584  -0.3463
 37U  C11   C  CR16  0  -0.240  -7.1436   1.2968   0.1555
 37U  C13   C  CR16  0  -0.245  -7.5166  -1.0706   0.0319
 37U  C12   C  CR16  0  -0.273  -7.9959   0.2083   0.2864
 37U  N15   N  NR5   0  -0.473  -0.9156   0.6720  -0.1783
 37U  C5    C  CR15  0  -0.170   0.4628   0.7465  -0.6217
 37U  C4    C  C     0   0.556   1.3796  -0.0765   0.2727
 37U  O26   O  O     0  -0.486   1.1891  -0.1662   1.4739
 37U  C17   C  CH2   0  -0.486   0.8062   2.2413  -0.5051
 37U  C16   C  CH2   0  -0.466  -0.5510   2.9291  -0.5951
 37U  C15   C  CH2   0  -0.287  -1.4607   1.9789   0.1683
 37U  C1    C  CR16  0  -0.305   4.8067   0.8754   0.5471
 37U  C2    C  CR6   0   0.121   4.8052  -0.4970   0.3100
 37U  C3    C  CH2   0  -0.351   3.5204  -1.2904   0.2926
 37U  N9    N  NH1   0  -0.632   2.4383  -0.6030  -0.3645
 37U  C18   C  CR16  0  -0.466   6.0152  -1.1534   0.1142
 37U  C19   C  CR6   0   0.541   7.1913  -0.4291   0.1617
 37U  F7    F  F     0  -0.317   8.3519  -1.0768  -0.0339
 37U  C20   C  CR16  0  -0.424   7.2155   0.9314   0.3930
 37U  C21   C  CR16  0  -0.223   6.0014   1.5787   0.5883
 37U  HN25  H  HNH2  0   0.340  -3.0515  -2.5663   0.5115
 37U  HN2A  H  HNH2  0   0.351  -2.7960  -1.8299   1.9294
 37U  H7    H  HCH1  0   0.267  -3.1647   0.2815   1.0609
 37U  H8    H  HCH2  0   0.260  -3.5459   0.4898  -1.4433
 37U  H8A   H  HCH2  0   0.261  -3.7765  -1.2437  -1.5035
 37U  H10   H  HCR6  0   0.245  -5.1663   1.9601  -0.3315
 37U  H14   H  HCR6  0   0.241  -5.8305  -2.2589  -0.5438
 37U  H11   H  HCR6  0   0.253  -7.5076   2.2982   0.3467
 37U  H13   H  HCR6  0   0.251  -8.1747  -1.9247   0.1293
 37U  H12   H  HCR6  0   0.253  -9.0274   0.3559   0.5796
 37U  H5    H  HCR5  0   0.279   0.5445   0.4140  -1.6618
 37U  H17   H  HCH2  0   0.252   1.2565   2.4554   0.4670
 37U  H17A  H  HCH2  0   0.268   1.5083   2.5556  -1.2752
 37U  H16   H  HCH2  0   0.246  -0.8772   3.0058  -1.6340
 37U  H16A  H  HCH2  0   0.259  -0.5465   3.9308  -0.1680
 37U  H15   H  HCH2  0   0.256  -2.5021   2.0797  -0.1330
 37U  H15A  H  HCH2  0   0.249  -1.4013   2.1543   1.2464
 37U  H3    H  HCH2  0   0.271   3.6893  -2.2509  -0.1976
 37U  H3A   H  HCH2  0   0.275   3.2091  -1.5109   1.3140
 37U  HN9   H  HNH1  0   0.405   2.5062  -0.4861  -1.3631
 37U  H18   H  HCR6  0   0.275   6.0432  -2.2195  -0.0778
 37U  H20   H  HCR6  0   0.280   8.1520   1.4727   0.4212
 37U  H21   H  HCR6  0   0.269   5.9924   2.6449   0.7714
 37U  H1    H  HCR6  0   0.252   3.8746   1.4041   0.7006

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
 37U  C1   C2    aromatic  1.393  0.020  1.393
 37U  C1   C21   aromatic  1.387  0.020  1.387
 37U  C2   C3    single    1.510  0.020  1.510
 37U  C2   C18   aromatic  1.390  0.020  1.390
 37U  C3   N9    single    1.441  0.020  1.441
 37U  N9   C4    single    1.343  0.020  1.343
 37U  C4   O26   double    1.219  0.020  1.219
 37U  C4   C5    single    1.522  0.020  1.522
 37U  C5   N15   single    1.450  0.020  1.450
 37U  C5   C17   single    1.538  0.020  1.538
 37U  N15  C6    single    1.342  0.020  1.342
 37U  N15  C15   single    1.458  0.020  1.458
 37U  C6   O27   double    1.226  0.020  1.226
 37U  C6   C7    single    1.531  0.020  1.531
 37U  C7   N25   single    1.443  0.020  1.443
 37U  C7   C8    single    1.540  0.020  1.540
 37U  C8   C9    single    1.501  0.020  1.501
 37U  C9   C10   aromatic  1.393  0.020  1.393
 37U  C9   C14   aromatic  1.393  0.020  1.393
 37U  C10  C11   aromatic  1.388  0.020  1.388
 37U  C11  C12   aromatic  1.389  0.020  1.389
 37U  C12  C13   aromatic  1.389  0.020  1.389
 37U  C13  C14   aromatic  1.388  0.020  1.388
 37U  C15  C16   single    1.521  0.020  1.521
 37U  C16  C17   single    1.524  0.020  1.524
 37U  C18  C19   aromatic  1.382  0.020  1.382
 37U  C19  F7    single    1.343  0.020  1.343
 37U  C19  C20   aromatic  1.380  0.020  1.380
 37U  C20  C21   aromatic  1.390  0.020  1.390
 37U  C1   H1    single    0.930  0.020  1.080
 37U  C3   H3    single    0.970  0.020  1.090
 37U  C3   H3A   single    0.970  0.020  1.090
 37U  N9   HN9   single    0.860  0.020  1.020
 37U  C5   H5    single    0.970  0.020  1.090
 37U  C7   H7    single    0.970  0.020  1.090
 37U  N25  HN25  single    0.890  0.020  1.040
 37U  N25  HN2A  single    0.890  0.020  1.040
 37U  C8   H8    single    0.970  0.020  1.090
 37U  C8   H8A   single    0.970  0.020  1.090
 37U  C10  H10   single    0.930  0.020  1.080
 37U  C11  H11   single    0.930  0.020  1.080
 37U  C12  H12   single    0.930  0.020  1.080
 37U  C13  H13   single    0.930  0.020  1.080
 37U  C14  H14   single    0.930  0.020  1.080
 37U  C15  H15   single    0.970  0.020  1.090
 37U  C15  H15A  single    0.970  0.020  1.090
 37U  C16  H16   single    0.970  0.020  1.090
 37U  C16  H16A  single    0.970  0.020  1.090
 37U  C17  H17   single    0.970  0.020  1.090
 37U  C17  H17A  single    0.970  0.020  1.090
 37U  C18  H18   single    0.930  0.020  1.080
 37U  C20  H20   single    0.930  0.020  1.080
 37U  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
 37U  HN2A  N25  HN25  106.04  3.000
 37U  HN2A  N25  C7    109.83  3.000
 37U  HN25  N25  C7    109.66  3.000
 37U  H7    C7   C8    108.48  3.000
 37U  H7    C7   C6    109.72  3.000
 37U  C8    C7   C6    107.92  3.000
 37U  H7    C7   N25   107.32  3.000
 37U  C8    C7   N25   110.25  3.000
 37U  C6    C7   N25   113.06  3.000
 37U  N15   C6   O27   121.17  3.000
 37U  O27   C6   C7    120.76  3.000
 37U  N15   C6   C7    118.04  3.000
 37U  H8A   C8   H8    106.33  3.000
 37U  H8A   C8   C9    110.56  3.000
 37U  H8    C8   C9    109.64  3.000
 37U  H8A   C8   C7    108.38  3.000
 37U  H8    C8   C7    109.52  3.000
 37U  C9    C8   C7    112.22  3.000
 37U  C14   C9   C10   118.45  3.000
 37U  C14   C9   C8    121.31  3.000
 37U  C10   C9   C8    120.22  3.000
 37U  H10   C10  C11   119.49  3.000
 37U  H10   C10  C9    119.52  3.000
 37U  C11   C10  C9    120.99  3.000
 37U  H14   C14  C13   119.65  3.000
 37U  H14   C14  C9    119.53  3.000
 37U  C13   C14  C9    120.82  3.000
 37U  H11   C11  C12   120.14  3.000
 37U  H11   C11  C10   119.84  3.000
 37U  C12   C11  C10   120.03  3.000
 37U  H13   C13  C12   120.01  3.000
 37U  H13   C13  C14   119.79  3.000
 37U  C12   C13  C14   120.21  3.000
 37U  H12   C12  C13   120.26  3.000
 37U  H12   C12  C11   120.23  3.000
 37U  C13   C12  C11   119.51  3.000
 37U  C15   N15  C5    112.46  3.000
 37U  C15   N15  C6    127.66  3.000
 37U  C5    N15  C6    119.87  3.000
 37U  H5    C5   C17   110.51  3.000
 37U  H5    C5   C4    110.42  3.000
 37U  C17   C5   C4    110.26  3.000
 37U  H5    C5   N15   110.23  3.000
 37U  C17   C5   N15   103.83  3.000
 37U  C4    C5   N15   111.41  3.000
 37U  N9    C4   O26   124.16  3.000
 37U  O26   C4   C5    121.62  3.000
 37U  N9    C4   C5    114.07  3.000
 37U  H17A  C17  H17   107.89  3.000
 37U  H17A  C17  C16   113.72  3.000
 37U  H17   C17  C16   109.34  3.000
 37U  H17A  C17  C5    111.78  3.000
 37U  H17   C17  C5    110.48  3.000
 37U  C16   C17  C5    103.61  3.000
 37U  H16A  C16  H16   108.06  3.000
 37U  H16A  C16  C15   112.35  3.000
 37U  H16   C16  C15   110.05  3.000
 37U  H16A  C16  C17   112.85  3.000
 37U  H16   C16  C17   110.73  3.000
 37U  C15   C16  C17   102.77  3.000
 37U  H15A  C15  H15   108.05  3.000
 37U  H15A  C15  C16   111.23  3.000
 37U  H15   C15  C16   112.04  3.000
 37U  H15A  C15  N15   110.96  3.000
 37U  H15   C15  N15   112.01  3.000
 37U  C16   C15  N15   102.54  3.000
 37U  H1    C1   C21   119.32  3.000
 37U  H1    C1   C2    120.30  3.000
 37U  C21   C1   C2    120.38  3.000
 37U  C18   C2   C3    119.38  3.000
 37U  C18   C2   C1    119.22  3.000
 37U  C3    C2   C1    121.38  3.000
 37U  H3A   C3   H3    106.68  3.000
 37U  H3A   C3   N9    108.02  3.000
 37U  H3    C3   N9    109.35  3.000
 37U  H3A   C3   C2    109.78  3.000
 37U  H3    C3   C2    109.63  3.000
 37U  N9    C3   C2    113.18  3.000
 37U  HN9   N9   C3    117.18  3.000
 37U  HN9   N9   C4    118.54  3.000
 37U  C3    N9   C4    124.25  3.000
 37U  H18   C18  C19   119.98  3.000
 37U  H18   C18  C2    120.79  3.000
 37U  C19   C18  C2    119.23  3.000
 37U  C20   C19  F7    118.98  3.000
 37U  C20   C19  C18   122.50  3.000
 37U  F7    C19  C18   118.52  3.000
 37U  H20   C20  C21   121.30  3.000
 37U  H20   C20  C19   120.84  3.000
 37U  C21   C20  C19   117.86  3.000
 37U  H21   C21  C20   119.35  3.000
 37U  H21   C21  C1    119.84  3.000
 37U  C20   C21  C1    120.81  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
 37U  CONST_01  C12   C11  C10  C9      0.00   0.0  0
 37U  CONST_02  C12   C13  C14  C9      0.00   0.0  0
 37U  CONST_03  C13   C14  C9   C10     0.00   0.0  0
 37U  CONST_04  C13   C12  C11  C10     0.00   0.0  0
 37U  CONST_05  C11   C10  C9   C14     0.00   0.0  0
 37U  CONST_06  C11   C12  C13  C14     0.00   0.0  0
 37U  CONST_07  C19   C18  C2   C1      0.00   0.0  0
 37U  CONST_08  C19   C20  C21  C1      0.00   0.0  0
 37U  CONST_09  C20   C21  C1   C2      0.00   0.0  0
 37U  CONST_10  C20   C19  C18  C2      0.00   0.0  0
 37U  CONST_11  C21   C1   C2   C18     0.00   0.0  0
 37U  CONST_12  C21   C20  C19  C18     0.00   0.0  0
 37U  CONST_13  C11   C10  C9   C8    180.00   0.0  0
 37U  CONST_14  C13   C14  C9   C8    180.00   0.0  0
 37U  CONST_15  F7    C19  C18  C2    180.00   0.0  0
 37U  CONST_16  C21   C1   C2   C3    180.00   0.0  0
 37U  CONST_17  C19   C18  C2   C3    180.00   0.0  0
 37U  CONST_18  C21   C20  C19  F7    180.00   0.0  0
 37U  CONST_19  H11   C11  C10  C9    180.00   0.0  0
 37U  CONST_20  H13   C13  C14  C9    180.00   0.0  0
 37U  CONST_21  H14   C14  C9   C10   180.00   0.0  0
 37U  CONST_22  H12   C12  C11  C10   180.00   0.0  0
 37U  CONST_23  H10   C10  C9   C14   180.00   0.0  0
 37U  CONST_24  H12   C12  C13  C14   180.00   0.0  0
 37U  CONST_25  H13   C13  C12  C11   180.00   0.0  0
 37U  CONST_26  H11   C11  C12  C13   180.00   0.0  0
 37U  CONST_27  H10   C10  C11  C12   180.00   0.0  0
 37U  CONST_28  H14   C14  C13  C12   180.00   0.0  0
 37U  CONST_29  H18   C18  C2   C1    180.00   0.0  0
 37U  CONST_30  H20   C20  C21  C1    180.00   0.0  0
 37U  CONST_31  H21   C21  C1   C2    180.00   0.0  0
 37U  CONST_32  H1    C1   C2   C18   180.00   0.0  0
 37U  CONST_33  H20   C20  C19  C18   180.00   0.0  0
 37U  CONST_34  H21   C21  C20  C19   180.00   0.0  0
 37U  CONST_35  H18   C18  C19  C20   180.00   0.0  0
 37U  CONST_36  H1    C1   C21  C20   180.00   0.0  0
 37U  CONST_37  C5    N15  C6   C7    180.00   0.0  0
 37U  CONST_38  C15   N15  C6   C7      0.00   0.0  0
 37U  CONST_39  C5    N15  C6   O27     0.00   0.0  0
 37U  CONST_40  C15   N15  C6   O27   180.00   0.0  0
 37U  CONST_41  C3    N9   C4   C5    180.00   0.0  0
 37U  CONST_42  HN9   N9   C4   C5      0.00   0.0  0
 37U  CONST_43  C3    N9   C4   O26     0.00   0.0  0
 37U  CONST_44  HN9   N9   C4   O26   180.00   0.0  0
 37U  Var_01    C17   C16  C15  N15   -35.87  30.0  1
 37U  Var_02    C16   C15  N15  C5     21.86  30.0  1
 37U  Var_03    C15   C16  C17  C5     37.24  30.0  1
 37U  Var_04    C16   C15  N15  C6   -159.42  30.0  1
 37U  Var_05    H16   C16  C15  N15    82.10  30.0  1
 37U  Var_06    H16A  C16  C15  N15  -157.45  30.0  1
 37U  Var_07    H15   C15  N15  C5    142.17  30.0  1
 37U  Var_08    H15A  C15  N15  C5    -96.98  30.0  1
 37U  Var_09    H16   C16  C17  C5    -80.25  30.0  1
 37U  Var_10    H16A  C16  C17  C5    158.48  30.0  1
 37U  Var_11    H15   C15  C16  C17  -156.16  30.0  1
 37U  Var_12    H15A  C15  C16  C17    82.78  30.0  1
 37U  Var_13    H17   C17  C16  C15   -80.56  30.0  1
 37U  Var_14    H17A  C17  C16  C15   158.79  30.0  1
 37U  Var_15    C10   C9   C8   C7     88.51  30.0  2
 37U  Var_16    C14   C9   C8   C7    -89.91  30.0  2
 37U  Var_17    N9    C3   C2   C1     40.52  30.0  2
 37U  Var_18    C18   C2   C3   N9   -140.90  30.0  2
 37U  Var_19    H15   C15  N15  C6    -39.11  30.0  1
 37U  Var_20    H15A  C15  N15  C6     81.74  30.0  1
 37U  Var_21    H8    C8   C9   C10   -33.44  30.0  2
 37U  Var_22    H8A   C8   C9   C10  -150.35  30.0  2
 37U  Var_23    H8    C8   C9   C14   148.14  30.0  2
 37U  Var_24    H8A   C8   C9   C14    31.22  30.0  2
 37U  Var_25    H3    C3   C2   C1    162.88  30.0  2
 37U  Var_26    H3A   C3   C2   C1    -80.25  30.0  2
 37U  Var_27    H3    C3   C2   C18   -18.53  30.0  2
 37U  Var_28    H3A   C3   C2   C18    98.34  30.0  2
 37U  Var_29    C2    C3   N9   C4   -108.22  30.0  2
 37U  Var_30    HN9   N9   C3   C2     69.48  30.0  3
 37U  Var_31    H3    C3   N9   C4    129.25  30.0  2
 37U  Var_32    H3A   C3   N9   C4     13.53  30.0  2

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
 37U  chir_01  C7  C6   N25  C8  positiv
 37U  chir_02  C5  N15  C17  C4  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
 37U  plan-1  C8   0.020
 37U  plan-1  C9   0.020
 37U  plan-1  C10  0.020
 37U  plan-1  C14  0.020
 37U  plan-1  C11  0.020
 37U  plan-1  C13  0.020
 37U  plan-1  C12  0.020
 37U  plan-1  H10  0.020
 37U  plan-1  H14  0.020
 37U  plan-1  H11  0.020
 37U  plan-1  H13  0.020
 37U  plan-1  H12  0.020
 37U  plan-2  C1   0.020
 37U  plan-2  C2   0.020
 37U  plan-2  C3   0.020
 37U  plan-2  C18  0.020
 37U  plan-2  C19  0.020
 37U  plan-2  F7   0.020
 37U  plan-2  C20  0.020
 37U  plan-2  C21  0.020
 37U  plan-2  H18  0.020
 37U  plan-2  H20  0.020
 37U  plan-2  H21  0.020
 37U  plan-2  H1   0.020
 37U  plan-3  C5   0.020
 37U  plan-3  C4   0.020
 37U  plan-3  O26  0.020
 37U  plan-3  C3   0.020
 37U  plan-3  N9   0.020
 37U  plan-3  HN9  0.020
 37U  plan-4  C7   0.020
 37U  plan-4  C6   0.020
 37U  plan-4  O27  0.020
 37U  plan-4  N15  0.020
 37U  plan-4  C5   0.020
 37U  plan-4  C15  0.020

