# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:11:25 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N~2~-[(1S)-1-carboxy-3-phenylpropyl]-L-lysyl-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@H](N[C@@H](CCc1ccccc1)C(O)=O)C(=O)N2CCC[C@H]2C(O)=O
#
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
 LPR  LPR  N~2~-[(1S)-1-carboxy-3-phenylpropyl]-L-lysyl-L-proline  ligand  58  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LPR
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
 LPR  O2    O  OC    -1  -0.589   2.2874   2.4822  -0.0441
 LPR  O3    O  O      0  -0.625   1.0338   3.4924   1.4930
 LPR  C3    C  C      0   0.406   1.3940   2.5016   0.8205
 LPR  C4    C  CH1    0  -0.178   0.6305   1.1905   1.1373
 LPR  C14   C  CH2    0  -0.436   0.9368   0.7611   2.5735
 LPR  C15   C  CH2    0  -0.526   0.1012  -0.4311   3.0562
 LPR  C16   C  CR6    0   0.148   0.2491  -0.6519   4.5348
 LPR  C17   C  CR16   0  -0.318  -0.6586  -0.0985   5.4356
 LPR  C18   C  CR16   0  -0.240  -0.5014  -0.2687   6.8052
 LPR  C19   C  CR16   0  -0.276   0.5735  -0.9965   7.2987
 LPR  C20   C  CR16   0  -0.240   1.4861  -1.5531   6.4113
 LPR  C21   C  CR16   0  -0.312   1.3223  -1.3818   5.0431
 LPR  HB    H  HCH1   0   0.185  -0.4429   1.4497   1.1202
 LPR  H141  H  HCH2   0   0.219   2.0018   0.5250   2.6758
 LPR  H142  H  HCH2   0   0.231   0.7407   1.6131   3.2261
 LPR  H151  H  HCH2   0   0.240  -0.9484  -0.2544   2.8053
 LPR  H152  H  HCH2   0   0.235   0.3986  -1.3424   2.5305
 LPR  H17   H  HCR6   0   0.244  -1.5044   0.4668   5.0607
 LPR  H18   H  HCR6   0   0.251  -1.2222   0.1653   7.4868
 LPR  H19   H  HCR6   0   0.251   0.6977  -1.1324   8.3653
 LPR  H20   H  HCR6   0   0.251   2.3263  -2.1245   6.7851
 LPR  H21   H  HCR6   0   0.244   2.0370  -1.8265   4.3598
 LPR  N1    N  NH1    0  -0.597   0.9365   0.1167   0.2097
 LPR  N3    N  NH2    0  -0.801   4.8071  -2.1809  -4.8219
 LPR  C1    C  C      0   0.553  -1.1885   0.1123  -1.0599
 LPR  C2    C  CH1    0  -0.216   0.3335   0.2821  -1.0908
 LPR  O1    O  O      0  -0.520  -1.7145  -0.6444  -0.2467
 LPR  C10   C  CH2    0  -0.421   0.8942  -0.7416  -2.0848
 LPR  C11   C  CH2    0  -0.407   2.3419  -0.4657  -2.4632
 LPR  C12   C  CH2    0  -0.428   2.8959  -1.4902  -3.4442
 LPR  C13   C  CH2    0  -0.271   4.3229  -1.1867  -3.8732
 LPR  H1    H  HNH1   0   0.337   0.5893  -0.7567   0.5888
 LPR  H3N1  H  HNH2   0   0.344   5.7428  -1.9360  -5.1202
 LPR  H3N2  H  HNH2   0   0.336   4.9003  -3.0713  -4.3482
 LPR  HA    H  HCH1   0   0.243   0.5997   1.2760  -1.4530
 LPR  H101  H  HCH2   0   0.231   0.2737  -0.7546  -2.9864
 LPR  H102  H  HCH2   0   0.216   0.8036  -1.7436  -1.6503
 LPR  H111  H  HCH2   0   0.216   2.9533  -0.4391  -1.5582
 LPR  H112  H  HCH2   0   0.205   2.4084   0.5350  -2.9038
 LPR  H121  H  HCH2   0   0.208   2.2594  -1.5336  -4.3339
 LPR  H122  H  HCH2   0   0.208   2.8599  -2.4877  -2.9908
 LPR  H131  H  HCH2   0   0.185   4.9531  -1.0960  -2.9763
 LPR  H132  H  HCH2   0   0.209   4.3458  -0.2082  -4.3618
 LPR  O4    O  OC    -1  -0.620  -4.7239  -1.4354  -2.1275
 LPR  O5    O  O      0  -0.599  -2.7167  -1.6259  -3.0885
 LPR  N2    N  NT     0  -0.466  -1.9134   0.7734  -1.9721
 LPR  C5    C  CH1    0  -0.140  -3.3277   0.4706  -2.1407
 LPR  C6    C  CH2    0  -0.493  -3.7446   1.3574  -3.3258
 LPR  C7    C  CH2    0  -0.460  -2.6980   2.4652  -3.3552
 LPR  C8    C  CH2    0  -0.275  -1.4268   1.7335  -2.9512
 LPR  C9    C  C      0   0.400  -3.5993  -1.0125  -2.4643
 LPR  H5    H  HCH1   0   0.223  -3.8781   0.7607  -1.2404
 LPR  H6    H  HCH2   0   0.247  -4.7630   1.7293  -3.2207
 LPR  H62   H  HCH2   0   0.233  -3.6959   0.7877  -4.2577
 LPR  H7    H  HCH2   0   0.234  -2.9311   3.2358  -2.6169
 LPR  H72   H  HCH2   0   0.244  -2.6078   2.9480  -4.3280
 LPR  H8C1  H  HCH2   0   0.247  -0.6826   2.4055  -2.5261
 LPR  H8C2  H  HCH2   0   0.228  -0.9758   1.2307  -3.8131

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
 LPR  O1   C1    double    1.229  0.020  1.229
 LPR  O2   C3    deloc     1.243  0.020  1.243
 LPR  O3   C3    deloc     1.250  0.020  1.250
 LPR  O4   C9    deloc     1.248  0.020  1.248
 LPR  O5   C9    deloc     1.243  0.020  1.243
 LPR  N1   C2    single    1.443  0.020  1.443
 LPR  N1   C4    single    1.452  0.020  1.452
 LPR  N1   H1    single    0.890  0.020  1.040
 LPR  N2   C1    single    1.340  0.020  1.340
 LPR  N2   C5    single    1.456  0.020  1.456
 LPR  N2   C8    single    1.455  0.020  1.455
 LPR  N3   C13   single    1.457  0.020  1.457
 LPR  N3   H3N1  single    0.890  0.020  1.040
 LPR  N3   H3N2  single    0.890  0.020  1.040
 LPR  C1   C2    single    1.532  0.020  1.532
 LPR  C2   C10   single    1.533  0.020  1.533
 LPR  C2   HA    single    0.970  0.020  1.090
 LPR  C3   C4    single    1.550  0.020  1.550
 LPR  C4   C14   single    1.530  0.020  1.530
 LPR  C4   HB    single    0.970  0.020  1.090
 LPR  C5   C6    single    1.538  0.020  1.538
 LPR  C5   C9    single    1.542  0.020  1.542
 LPR  C5   H5    single    0.970  0.020  1.090
 LPR  C6   C7    single    1.524  0.020  1.524
 LPR  C6   H6    single    0.970  0.020  1.090
 LPR  C6   H62   single    0.970  0.020  1.090
 LPR  C7   C8    single    1.521  0.020  1.521
 LPR  C7   H7    single    0.970  0.020  1.090
 LPR  C7   H72   single    0.970  0.020  1.090
 LPR  C8   H8C1  single    0.970  0.020  1.090
 LPR  C8   H8C2  single    0.970  0.020  1.090
 LPR  C10  C11   single    1.522  0.020  1.522
 LPR  C10  H101  single    0.970  0.020  1.090
 LPR  C10  H102  single    0.970  0.020  1.090
 LPR  C11  C12   single    1.523  0.020  1.523
 LPR  C11  H111  single    0.970  0.020  1.090
 LPR  C11  H112  single    0.970  0.020  1.090
 LPR  C12  C13   single    1.521  0.020  1.521
 LPR  C12  H121  single    0.970  0.020  1.090
 LPR  C12  H122  single    0.970  0.020  1.090
 LPR  C13  H131  single    0.970  0.020  1.090
 LPR  C13  H132  single    0.970  0.020  1.090
 LPR  C14  C15   single    1.534  0.020  1.534
 LPR  C14  H141  single    0.970  0.020  1.090
 LPR  C14  H142  single    0.970  0.020  1.090
 LPR  C15  C16   single    1.502  0.020  1.502
 LPR  C15  H151  single    0.970  0.020  1.090
 LPR  C15  H152  single    0.970  0.020  1.090
 LPR  C16  C17   aromatic  1.393  0.020  1.393
 LPR  C16  C21   aromatic  1.394  0.020  1.394
 LPR  C17  C18   aromatic  1.389  0.020  1.389
 LPR  C17  H17   single    0.930  0.020  1.080
 LPR  C18  C19   aromatic  1.389  0.020  1.389
 LPR  C18  H18   single    0.930  0.020  1.080
 LPR  C19  C20   aromatic  1.389  0.020  1.389
 LPR  C19  H19   single    0.930  0.020  1.080
 LPR  C20  C21   aromatic  1.388  0.020  1.388
 LPR  C20  H20   single    0.930  0.020  1.080
 LPR  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
 LPR  C4    C3   O3    114.74  3.000
 LPR  C4    C3   O2    118.87  3.000
 LPR  O3    C3   O2    126.39  3.000
 LPR  N1    C4   HB    111.63  3.000
 LPR  HB    C4   C14   105.96  3.000
 LPR  N1    C4   C14   110.49  3.000
 LPR  HB    C4   C3    106.08  3.000
 LPR  C14   C4   C3    109.31  3.000
 LPR  N1    C4   C3    113.03  3.000
 LPR  H142  C14  H141  106.68  3.000
 LPR  H142  C14  C15   108.71  3.000
 LPR  H141  C14  C15   109.43  3.000
 LPR  H142  C14  C4    107.84  3.000
 LPR  H141  C14  C4    110.05  3.000
 LPR  C15   C14  C4    113.86  3.000
 LPR  H152  C15  H151  106.59  3.000
 LPR  H152  C15  C16   108.90  3.000
 LPR  H151  C15  C16   110.13  3.000
 LPR  H152  C15  C14   110.39  3.000
 LPR  H151  C15  C14   108.97  3.000
 LPR  C16   C15  C14   111.74  3.000
 LPR  C21   C16  C17   118.28  3.000
 LPR  C21   C16  C15   120.78  3.000
 LPR  C17   C16  C15   120.92  3.000
 LPR  H17   C17  C18   119.54  3.000
 LPR  H17   C17  C16   119.45  3.000
 LPR  C18   C17  C16   121.00  3.000
 LPR  H18   C18  C19   120.11  3.000
 LPR  H18   C18  C17   119.75  3.000
 LPR  C19   C18  C17   120.14  3.000
 LPR  H19   C19  C20   120.25  3.000
 LPR  H19   C19  C18   120.32  3.000
 LPR  C20   C19  C18   119.43  3.000
 LPR  H20   C20  C21   119.79  3.000
 LPR  H20   C20  C19   120.04  3.000
 LPR  C21   C20  C19   120.17  3.000
 LPR  H21   C21  C20   119.52  3.000
 LPR  H21   C21  C16   119.50  3.000
 LPR  C20   C21  C16   120.98  3.000
 LPR  H1    N1   C2    107.02  3.000
 LPR  H1    N1   C4    109.04  3.000
 LPR  C2    N1   C4    113.77  3.000
 LPR  H3N2  N3   H3N1  105.39  3.000
 LPR  H3N2  N3   C13   109.02  3.000
 LPR  H3N1  N3   C13   109.51  3.000
 LPR  N2    C1   O1    121.52  3.000
 LPR  N2    C1   C2    117.99  3.000
 LPR  O1    C1   C2    120.45  3.000
 LPR  HA    C2   C10   107.69  3.000
 LPR  HA    C2   C1    110.50  3.000
 LPR  C10   C2   C1    107.61  3.000
 LPR  HA    C2   N1    107.56  3.000
 LPR  C10   C2   N1    110.79  3.000
 LPR  C1    C2   N1    112.60  3.000
 LPR  H102  C10  H101  105.60  3.000
 LPR  H102  C10  C11   110.07  3.000
 LPR  H101  C10  C11   109.67  3.000
 LPR  H102  C10  C2    108.85  3.000
 LPR  H101  C10  C2    109.55  3.000
 LPR  C11   C10  C2    112.84  3.000
 LPR  H112  C11  H111  106.08  3.000
 LPR  H112  C11  C12   109.47  3.000
 LPR  H111  C11  C12   110.27  3.000
 LPR  H112  C11  C10   108.87  3.000
 LPR  H111  C11  C10   109.32  3.000
 LPR  C12   C11  C10   112.60  3.000
 LPR  H122  C12  H121  106.32  3.000
 LPR  H122  C12  C13   109.22  3.000
 LPR  H121  C12  C13   108.92  3.000
 LPR  H122  C12  C11   109.49  3.000
 LPR  H121  C12  C11   109.80  3.000
 LPR  C13   C12  C11   112.88  3.000
 LPR  H132  C13  H131  106.17  3.000
 LPR  H132  C13  C12   108.92  3.000
 LPR  H131  C13  C12   108.91  3.000
 LPR  H132  C13  N3    108.21  3.000
 LPR  H131  C13  N3    113.38  3.000
 LPR  C12   C13  N3    111.06  3.000
 LPR  C8    N2   C5    112.59  3.000
 LPR  C8    N2   C1    127.08  3.000
 LPR  C5    N2   C1    120.12  3.000
 LPR  H5    C5   C9    109.82  3.000
 LPR  H5    C5   C6    110.17  3.000
 LPR  C9    C5   C6    110.19  3.000
 LPR  H5    C5   N2    109.76  3.000
 LPR  C9    C5   N2    113.29  3.000
 LPR  C6    C5   N2    103.45  3.000
 LPR  H62   C6   H6    107.57  3.000
 LPR  H62   C6   C7    109.38  3.000
 LPR  H6    C6   C7    113.30  3.000
 LPR  H62   C6   C5    110.14  3.000
 LPR  H6    C6   C5    112.08  3.000
 LPR  C7    C6   C5    104.35  3.000
 LPR  H72   C7   H7    107.97  3.000
 LPR  H72   C7   C8    112.39  3.000
 LPR  H7    C7   C8    109.76  3.000
 LPR  H72   C7   C6    113.33  3.000
 LPR  H7    C7   C6    110.68  3.000
 LPR  C8    C7   C6    102.65  3.000
 LPR  H8C2  C8   H8C1  108.01  3.000
 LPR  H8C2  C8   C7    110.85  3.000
 LPR  H8C1  C8   C7    112.20  3.000
 LPR  H8C2  C8   N2    111.37  3.000
 LPR  H8C1  C8   N2    111.91  3.000
 LPR  C7    C8   N2    102.51  3.000
 LPR  C5    C9   O5    117.06  3.000
 LPR  C5    C9   O4    115.34  3.000
 LPR  O5    C9   O4    127.47  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
 LPR  CONST_01  C19   C18  C17  C16     0.00   0.0  0
 LPR  CONST_02  C19   C20  C21  C16     0.00   0.0  0
 LPR  CONST_03  C20   C21  C16  C17     0.00   0.0  0
 LPR  CONST_04  C20   C19  C18  C17     0.00   0.0  0
 LPR  CONST_05  C21   C16  C17  C18     0.00   0.0  0
 LPR  CONST_06  C21   C20  C19  C18     0.00   0.0  0
 LPR  CONST_07  C18   C17  C16  C15   180.00   0.0  0
 LPR  CONST_08  C20   C21  C16  C15   180.00   0.0  0
 LPR  CONST_09  H18   C18  C17  C16   180.00   0.0  0
 LPR  CONST_10  H20   C20  C21  C16   180.00   0.0  0
 LPR  CONST_11  H21   C21  C16  C17   180.00   0.0  0
 LPR  CONST_12  H19   C19  C18  C17   180.00   0.0  0
 LPR  CONST_13  H17   C17  C18  C19   180.00   0.0  0
 LPR  CONST_14  C5    N2   C1   C2    180.00   0.0  0
 LPR  CONST_15  C8    N2   C1   C2      0.00   0.0  0
 LPR  CONST_16  C5    N2   C1   O1      0.00   0.0  0
 LPR  CONST_17  C8    N2   C1   O1    180.00   0.0  0
 LPR  Var_01    C6    C7   C8   N2    -36.11  30.0  1
 LPR  Var_02    C7    C8   N2   C5     23.68  30.0  1
 LPR  Var_03    C8    C7   C6   C5     36.20  30.0  1
 LPR  Var_04    C17   C16  C15  C14    94.27  30.0  2
 LPR  Var_05    C16   C15  C14  C4   -169.41  30.0  3
 LPR  Var_06    C11   C12  C13  N3   -179.33  30.0  1
 LPR  Var_07    C12   C11  C10  C2    179.66  30.0  3
 LPR  Var_08    C13   C12  C11  C10   177.52  30.0  3
 LPR  Var_09    H3N1  N3   C13  C12   177.70  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
 LPR  chir_01  C4  N1  C3  C14  positiv
 LPR  chir_02  C2  N1  C1  C10  positiv
 LPR  chir_03  C5  N2  C9  C6   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
 LPR  plan-1  C15  0.020
 LPR  plan-1  C16  0.020
 LPR  plan-1  C17  0.020
 LPR  plan-1  C18  0.020
 LPR  plan-1  C19  0.020
 LPR  plan-1  C20  0.020
 LPR  plan-1  C21  0.020
 LPR  plan-1  H17  0.020
 LPR  plan-1  H18  0.020
 LPR  plan-1  H19  0.020
 LPR  plan-1  H20  0.020
 LPR  plan-1  H21  0.020
 LPR  plan-2  C1   0.020
 LPR  plan-2  C2   0.020
 LPR  plan-2  O1   0.020
 LPR  plan-2  N2   0.020
 LPR  plan-2  C5   0.020
 LPR  plan-2  C8   0.020
 LPR  plan-3  O2   0.020
 LPR  plan-3  O3   0.020
 LPR  plan-3  C3   0.020
 LPR  plan-3  C4   0.020
 LPR  plan-4  O4   0.020
 LPR  plan-4  O5   0.020
 LPR  plan-4  C5   0.020
 LPR  plan-4  C9   0.020

