# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 12:35:14 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: D-phenylalanyl-N-(3-methylbenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(CNC(=O)[C@@H]2CCCN2C(=O)[C@H](N)Cc3ccccc3)c1
#
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
 51U  51U  D-phenylalanyl-N-(3-methylbenzyl)-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_51U
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
 51U  N1    N  NH2   0  -0.780   3.0126   1.7032   0.9514
 51U  C2    C  CH1   0  -0.226   2.8145   0.3658   0.4372
 51U  C3    C  C     0   0.572   1.3236   0.1395   0.2281
 51U  O1    O  O     0  -0.501   0.5957   1.0550  -0.1375
 51U  C1    C  CH2   0  -0.542   3.5274   0.0682  -0.9047
 51U  C17   C  CR6   0   0.135   5.0159   0.2159  -0.7900
 51U  C18   C  CR16  0  -0.303   5.7883  -0.8253  -0.2768
 51U  C23   C  CR16  0  -0.319   5.6539   1.4019  -1.1456
 51U  C19   C  CR16  0  -0.240   7.1607  -0.6889  -0.1268
 51U  C22   C  CR16  0  -0.241   7.0285   1.5430  -0.9984
 51U  C20   C  CR16  0  -0.270   7.7864   0.4985  -0.4875
 51U  N2    N  NT    0  -0.478   0.8477  -1.1022   0.3994
 51U  C7    C  CH1   0  -0.163  -0.5604  -1.3722   0.1666
 51U  C8    C  C     0   0.567  -1.4399  -0.4876   1.0416
 51U  O2    O  O     0  -0.498  -1.1694  -0.2780   2.2139
 51U  C6    C  CH2   0  -0.480  -0.7141  -2.8526   0.5460
 51U  C5    C  CH2   0  -0.470   0.6860  -3.4219   0.3477
 51U  C4    C  CH2   0  -0.283   1.5847  -2.2886   0.8191
 51U  N3    N  NH1   0  -0.633  -2.5543  -0.0388   0.4515
 51U  C9    C  CH2   0  -0.320  -3.5188   0.7949   1.1432
 51U  C10   C  CR6   0   0.074  -4.7775   0.9190   0.3296
 51U  C11   C  CR16  0  -0.331  -5.6403  -0.1676   0.2091
 51U  C12   C  CR6   0   0.115  -6.8034  -0.0931  -0.5509
 51U  C13   C  CH3   0  -0.723  -7.7406  -1.2629  -0.6375
 51U  C14   C  CR16  0  -0.310  -7.0904   1.1051  -1.2045
 51U  C15   C  CR16  0  -0.226  -6.2398   2.1947  -1.0939
 51U  C16   C  CR16  0  -0.320  -5.0841   2.1040  -0.3289
 51U  HN1   H  HNH2  0   0.355   4.0000   1.8603   1.1096
 51U  HN1A  H  HNH2  0   0.343   2.7202   2.3875   0.2642
 51U  H2    H  HCH1  0   0.268   3.1973  -0.3272   1.1911
 51U  H1    H  HCH2  0   0.256   3.2854  -0.9448  -1.2392
 51U  H1A   H  HCH2  0   0.263   3.1344   0.7492  -1.6644
 51U  H18   H  HCR6  0   0.247   5.3103  -1.7573   0.0043
 51U  H23   H  HCR6  0   0.251   5.0745   2.2208  -1.5554
 51U  H19   H  HCR6  0   0.255   7.7426  -1.5119   0.2681
 51U  H22   H  HCR6  0   0.255   7.5063   2.4705  -1.2870
 51U  H20   H  HCR6  0   0.255   8.8573   0.6066  -0.3744
 51U  H7    H  HCH1  0   0.275  -0.8010  -1.2232  -0.8915
 51U  H6    H  HCH2  0   0.266  -1.4726  -3.3443  -0.0601
 51U  H6A   H  HCH2  0   0.252  -1.0067  -2.9480   1.5935
 51U  H5    H  HCH2  0   0.246   0.8709  -3.6280  -0.7083
 51U  H5A   H  HCH2  0   0.259   0.8550  -4.3410   0.9067
 51U  H4    H  HCH2  0   0.253   2.5731  -2.3330   0.3636
 51U  H4A   H  HCH2  0   0.251   1.7101  -2.3071   1.9056
 51U  HN3   H  HNH1  0   0.402  -2.6585  -0.1520  -0.5441
 51U  H9    H  HCH2  0   0.257  -3.7399   0.3463   2.1135
 51U  H9A   H  HCH2  0   0.253  -3.0991   1.7859   1.3376
 51U  H11   H  HCR6  0   0.245  -5.3996  -1.0929   0.7232
 51U  H13   H  HCH3  0   0.249  -8.4480  -1.2563   0.1942
 51U  H13A  H  HCH3  0   0.244  -8.3223  -1.2425  -1.5585
 51U  H13B  H  HCH3  0   0.244  -7.2043  -2.2107  -0.5976
 51U  H14   H  HCR6  0   0.248  -7.9885   1.1844  -1.8059
 51U  H15   H  HCR6  0   0.254  -6.4754   3.1173  -1.6089
 51U  H16   H  HCR6  0   0.251  -4.4195   2.9555  -0.2465

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
 51U  C1   C2    single    1.548  0.020  1.548
 51U  C1   C17   single    1.500  0.020  1.500
 51U  N1   C2    single    1.446  0.020  1.446
 51U  C2   C3    single    1.522  0.020  1.522
 51U  C3   O1    double    1.225  0.020  1.225
 51U  C3   N2    single    1.341  0.020  1.341
 51U  N2   C4    single    1.458  0.020  1.458
 51U  N2   C7    single    1.453  0.020  1.453
 51U  C4   C5    single    1.521  0.020  1.521
 51U  C5   C6    single    1.524  0.020  1.524
 51U  C6   C7    single    1.536  0.020  1.536
 51U  C7   C8    single    1.524  0.020  1.524
 51U  C8   N3    single    1.339  0.020  1.339
 51U  C8   O2    double    1.221  0.020  1.221
 51U  N3   C9    single    1.450  0.020  1.450
 51U  C9   C10   single    1.504  0.020  1.504
 51U  C10  C11   aromatic  1.393  0.020  1.393
 51U  C10  C16   aromatic  1.390  0.020  1.390
 51U  C11  C12   aromatic  1.391  0.020  1.391
 51U  C12  C13   single    1.501  0.020  1.501
 51U  C12  C14   aromatic  1.395  0.020  1.395
 51U  C14  C15   aromatic  1.387  0.020  1.387
 51U  C15  C16   aromatic  1.389  0.020  1.389
 51U  C17  C18   aromatic  1.394  0.020  1.394
 51U  C17  C23   aromatic  1.393  0.020  1.393
 51U  C18  C19   aromatic  1.387  0.020  1.387
 51U  C19  C20   aromatic  1.390  0.020  1.390
 51U  C20  C22   aromatic  1.388  0.020  1.388
 51U  C22  C23   aromatic  1.390  0.020  1.390
 51U  C1   H1    single    0.970  0.020  1.090
 51U  C1   H1A   single    0.970  0.020  1.090
 51U  N1   HN1   single    0.890  0.020  1.040
 51U  N1   HN1A  single    0.890  0.020  1.040
 51U  C2   H2    single    0.970  0.020  1.090
 51U  C4   H4    single    0.970  0.020  1.090
 51U  C4   H4A   single    0.970  0.020  1.090
 51U  C5   H5    single    0.970  0.020  1.090
 51U  C5   H5A   single    0.970  0.020  1.090
 51U  C6   H6    single    0.970  0.020  1.090
 51U  C6   H6A   single    0.970  0.020  1.090
 51U  C7   H7    single    0.970  0.020  1.090
 51U  N3   HN3   single    0.860  0.020  1.020
 51U  C9   H9    single    0.970  0.020  1.090
 51U  C9   H9A   single    0.970  0.020  1.090
 51U  C11  H11   single    0.930  0.020  1.080
 51U  C13  H13   single    0.970  0.020  1.090
 51U  C13  H13A  single    0.970  0.020  1.090
 51U  C13  H13B  single    0.970  0.020  1.090
 51U  C14  H14   single    0.930  0.020  1.080
 51U  C15  H15   single    0.930  0.020  1.080
 51U  C16  H16   single    0.930  0.020  1.080
 51U  C18  H18   single    0.930  0.020  1.080
 51U  C19  H19   single    0.930  0.020  1.080
 51U  C20  H20   single    0.930  0.020  1.080
 51U  C22  H22   single    0.930  0.020  1.080
 51U  C23  H23   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
 51U  HN1A  N1   HN1   106.42  3.000
 51U  HN1A  N1   C2    110.12  3.000
 51U  HN1   N1   C2    109.43  3.000
 51U  H2    C2   C1    108.34  3.000
 51U  H2    C2   C3    110.09  3.000
 51U  C1    C2   C3    107.66  3.000
 51U  H2    C2   N1    107.03  3.000
 51U  C3    C2   N1    108.68  3.000
 51U  C1    C2   N1    115.01  3.000
 51U  N2    C3   O1    121.28  3.000
 51U  N2    C3   C2    117.88  3.000
 51U  O1    C3   C2    120.77  3.000
 51U  H1A   C1   H1    106.54  3.000
 51U  H1A   C1   C17   110.39  3.000
 51U  H1    C1   C17   109.51  3.000
 51U  H1A   C1   C2    108.48  3.000
 51U  H1    C1   C2    109.95  3.000
 51U  C17   C1   C2    111.82  3.000
 51U  C23   C17  C18   118.43  3.000
 51U  C23   C17  C1    121.25  3.000
 51U  C18   C17  C1    120.28  3.000
 51U  H18   C18  C19   119.50  3.000
 51U  H18   C18  C17   119.54  3.000
 51U  C19   C18  C17   120.96  3.000
 51U  H23   C23  C22   119.49  3.000
 51U  H23   C23  C17   119.68  3.000
 51U  C22   C23  C17   120.83  3.000
 51U  H19   C19  C20   120.15  3.000
 51U  H19   C19  C18   119.77  3.000
 51U  C20   C19  C18   120.08  3.000
 51U  H22   C22  C20   120.12  3.000
 51U  H22   C22  C23   119.70  3.000
 51U  C20   C22  C23   120.18  3.000
 51U  H20   C20  C22   120.24  3.000
 51U  H20   C20  C19   120.24  3.000
 51U  C22   C20  C19   119.51  3.000
 51U  C4    N2   C7    112.63  3.000
 51U  C7    N2   C3    119.72  3.000
 51U  C4    N2   C3    127.65  3.000
 51U  H7    C7   C6    110.35  3.000
 51U  H7    C7   C8    110.42  3.000
 51U  C6    C7   C8    111.10  3.000
 51U  H7    C7   N2    110.02  3.000
 51U  C8    C7   N2    111.08  3.000
 51U  C6    C7   N2    103.68  3.000
 51U  N3    C8   O2    123.37  3.000
 51U  O2    C8   C7    121.54  3.000
 51U  N3    C8   C7    114.97  3.000
 51U  H6A   C6   H6    107.94  3.000
 51U  H6A   C6   C5    109.78  3.000
 51U  H6    C6   C5    113.51  3.000
 51U  H6A   C6   C7    110.37  3.000
 51U  H6    C6   C7    111.57  3.000
 51U  C5    C6   C7    103.65  3.000
 51U  H5A   C5   H5    108.12  3.000
 51U  H5A   C5   C4    112.21  3.000
 51U  H5    C5   C4    109.90  3.000
 51U  H5A   C5   C6    113.02  3.000
 51U  H5    C5   C6    110.61  3.000
 51U  C4    C5   C6    102.94  3.000
 51U  H4A   C4   H4    108.09  3.000
 51U  H4A   C4   C5    111.28  3.000
 51U  H4    C4   C5    112.10  3.000
 51U  H4A   C4   N2    110.95  3.000
 51U  H4    C4   N2    111.80  3.000
 51U  C5    C4   N2    102.62  3.000
 51U  HN3   N3   C9    117.85  3.000
 51U  HN3   N3   C8    118.95  3.000
 51U  C9    N3   C8    122.42  3.000
 51U  H9A   C9   H9    106.98  3.000
 51U  H9A   C9   C10   110.04  3.000
 51U  H9    C9   C10   110.20  3.000
 51U  H9A   C9   N3    110.51  3.000
 51U  H9    C9   N3    108.81  3.000
 51U  C10   C9   N3    110.24  3.000
 51U  C16   C10  C11   119.17  3.000
 51U  C16   C10  C9    120.75  3.000
 51U  C11   C10  C9    120.06  3.000
 51U  H11   C11  C12   119.32  3.000
 51U  H11   C11  C10   119.12  3.000
 51U  C12   C11  C10   121.56  3.000
 51U  C14   C12  C13   120.92  3.000
 51U  C14   C12  C11   118.30  3.000
 51U  C13   C12  C11   120.77  3.000
 51U  H13B  C13  H13A  108.07  3.000
 51U  H13B  C13  H13   107.23  3.000
 51U  H13A  C13  H13   107.32  3.000
 51U  H13B  C13  C12   111.62  3.000
 51U  H13A  C13  C12   111.56  3.000
 51U  H13   C13  C12   110.84  3.000
 51U  H14   C14  C15   119.67  3.000
 51U  H14   C14  C12   119.57  3.000
 51U  C15   C14  C12   120.76  3.000
 51U  H15   C15  C16   119.92  3.000
 51U  H15   C15  C14   119.88  3.000
 51U  C16   C15  C14   120.20  3.000
 51U  H16   C16  C15   120.07  3.000
 51U  H16   C16  C10   119.91  3.000
 51U  C15   C16  C10   120.01  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
 51U  CONST_01  C20  C19  C18  C17     0.00   0.0  0
 51U  CONST_02  C20  C22  C23  C17     0.00   0.0  0
 51U  CONST_03  C22  C23  C17  C18     0.00   0.0  0
 51U  CONST_04  C22  C20  C19  C18     0.00   0.0  0
 51U  CONST_05  C19  C18  C17  C23     0.00   0.0  0
 51U  CONST_06  C19  C20  C22  C23     0.00   0.0  0
 51U  CONST_07  C14  C12  C11  C10     0.00   0.0  0
 51U  CONST_08  C14  C15  C16  C10     0.00   0.0  0
 51U  CONST_09  C15  C16  C10  C11     0.00   0.0  0
 51U  CONST_10  C15  C14  C12  C11     0.00   0.0  0
 51U  CONST_11  C16  C10  C11  C12     0.00   0.0  0
 51U  CONST_12  C16  C15  C14  C12     0.00   0.0  0
 51U  CONST_13  C19  C18  C17  C1    180.00   0.0  0
 51U  CONST_14  C22  C23  C17  C1    180.00   0.0  0
 51U  CONST_15  C12  C11  C10  C9    180.00   0.0  0
 51U  CONST_16  C15  C16  C10  C9    180.00   0.0  0
 51U  CONST_17  C13  C12  C11  C10   180.00   0.0  0
 51U  CONST_18  C15  C14  C12  C13   180.00   0.0  0
 51U  CONST_19  H19  C19  C18  C17   180.00   0.0  0
 51U  CONST_20  H22  C22  C23  C17   180.00   0.0  0
 51U  CONST_21  H23  C23  C17  C18   180.00   0.0  0
 51U  CONST_22  H20  C20  C19  C18   180.00   0.0  0
 51U  CONST_23  H18  C18  C17  C23   180.00   0.0  0
 51U  CONST_24  H15  C15  C16  C10   180.00   0.0  0
 51U  CONST_25  H16  C16  C10  C11   180.00   0.0  0
 51U  CONST_26  H14  C14  C12  C11   180.00   0.0  0
 51U  CONST_27  H11  C11  C12  C14   180.00   0.0  0
 51U  CONST_28  C4   N2   C3   C2      0.00   0.0  0
 51U  CONST_29  C7   N2   C3   C2    180.00   0.0  0
 51U  CONST_30  C4   N2   C3   O1    180.00   0.0  0
 51U  CONST_31  C7   N2   C3   O1      0.00   0.0  0
 51U  CONST_32  C9   N3   C8   C7    180.00   0.0  0
 51U  CONST_33  HN3  N3   C8   C7      0.00   0.0  0
 51U  CONST_34  C9   N3   C8   O2      0.00   0.0  0
 51U  Var_01    C6   C5   C4   N2    -34.96  30.0  1
 51U  Var_02    C5   C4   N2   C7     20.29  30.0  1
 51U  Var_03    C4   C5   C6   C7     37.29  30.0  1
 51U  Var_04    C18  C17  C1   C2     82.27  30.0  2
 51U  Var_05    C11  C10  C9   N3     71.99  30.0  2
 51U  Var_06    H13  C13  C12  C11    85.99  30.0  2
 51U  Var_07    C10  C9   N3   C8   -169.03  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
 51U  chir_01  C2  C1  N1  C3  negativ
 51U  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
 51U  plan-1  C1   0.020
 51U  plan-1  C17  0.020
 51U  plan-1  C18  0.020
 51U  plan-1  C23  0.020
 51U  plan-1  C19  0.020
 51U  plan-1  C22  0.020
 51U  plan-1  C20  0.020
 51U  plan-1  H18  0.020
 51U  plan-1  H23  0.020
 51U  plan-1  H19  0.020
 51U  plan-1  H22  0.020
 51U  plan-1  H20  0.020
 51U  plan-2  C9   0.020
 51U  plan-2  C10  0.020
 51U  plan-2  C11  0.020
 51U  plan-2  C12  0.020
 51U  plan-2  C13  0.020
 51U  plan-2  C14  0.020
 51U  plan-2  C15  0.020
 51U  plan-2  C16  0.020
 51U  plan-2  H11  0.020
 51U  plan-2  H14  0.020
 51U  plan-2  H15  0.020
 51U  plan-2  H16  0.020
 51U  plan-3  C7   0.020
 51U  plan-3  C8   0.020
 51U  plan-3  O2   0.020
 51U  plan-3  N3   0.020
 51U  plan-3  C9   0.020
 51U  plan-3  HN3  0.020
 51U  plan-4  C2   0.020
 51U  plan-4  C3   0.020
 51U  plan-4  O1   0.020
 51U  plan-4  N2   0.020
 51U  plan-4  C7   0.020
 51U  plan-4  C4   0.020

