# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:04:12 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (2E,4S)-2-{[(5S)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C(C[C@@H](O)CCC(O)=O)C(O)=O)C(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
 LYF  LYF  '(2E,4S)-2-{[(5S)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid'  L-peptide  41  22  .  2012-08-28  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_LYF
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
 LYF  C     C  C      0   0.384  -93.5451  14.1735  33.2444
 LYF  N     N  NH2    0  -0.806  -95.4616  15.7029  32.8248
 LYF  O     O  O      0  -0.605  -93.0626  14.9957  34.0473
 LYF  CA    C  CH1    0  -0.157  -94.5812  14.7032  32.2243
 LYF  CB    C  CH2    0  -0.422  -93.8686  15.3521  31.0345
 LYF  CD    C  CH2    0  -0.421  -92.4138  15.1042  28.9836
 LYF  CE    C  CH2    0  -0.305  -91.5141  14.1923  28.1557
 LYF  CG    C  CH2    0  -0.424  -92.9895  14.4167  30.2148
 LYF  NZ    N  N      0  -0.364  -90.9052  14.9448  27.0858
 LYF  C11   C  CH2    0  -0.554  -91.9757  13.5652  25.3240
 LYF  C12   C  CH1    0   0.074  -91.1875  12.2591  25.2007
 LYF  C13   C  CH2    0  -0.433  -89.9650  12.4013  24.2979
 LYF  C14   C  C      0   0.375  -90.4853  15.6406  24.8332
 LYF  O15   O  OC    -1  -0.592  -89.3614  16.0961  25.1026
 LYF  O16   O  O      0  -0.592  -91.1789  15.8756  23.8239
 LYF  O17   O  OH1    0  -0.676  -92.1037  11.2899  24.7220
 LYF  C18   C  CH2    0  -0.602  -89.1568  11.1208  24.1534
 LYF  C20   C  C      0   0.415  -87.8308  11.2484  23.3693
 LYF  O21   O  OC    -1  -0.601  -87.4647  12.3898  23.0290
 LYF  O22   O  O      0  -0.623  -87.2283  10.1768  23.1515
 LYF  C41   C  C      0   0.072  -91.1250  14.6907  25.8625
 LYF  OXT   O  OC    -1  -0.615  -93.2559  12.9614  33.1535
 LYF  HN    H  HNH2   0   0.328  -96.1957  15.9258  32.1626
 LYF  HNA   H  HNH2   0   0.331  -95.9348  15.3043  33.6264
 LYF  HA    H  HCH1   0   0.167  -95.1391  13.8348  31.8419
 LYF  HB    H  HCH2   0   0.207  -94.6288  15.7853  30.3728
 LYF  HBA   H  HCH2   0   0.203  -93.2728  16.1944  31.4015
 LYF  HD    H  HCH2   0   0.212  -91.8433  15.9875  29.2868
 LYF  HDA   H  HCH2   0   0.211  -93.2295  15.4674  28.3496
 LYF  HE    H  HCH2   0   0.221  -90.7076  13.8214  28.7976
 LYF  HEA   H  HCH2   0   0.199  -92.0846  13.3116  27.8376
 LYF  HG    H  HCH2   0   0.213  -92.1695  14.0349  30.8289
 LYF  HGA   H  HCH2   0   0.204  -93.5700  13.5406  29.9064
 LYF  H11   H  HCH2   0   0.246  -92.3480  13.8468  24.3391
 LYF  H11A  H  HCH2   0   0.246  -92.8473  13.3888  25.9589
 LYF  H12   H  HCH1   0   0.186  -90.8331  11.9746  26.2049
 LYF  H13   H  HCH2   0   0.204  -90.2854  12.7623  23.3152
 LYF  H13A  H  HCH2   0   0.214  -89.3201  13.1777  24.7149
 LYF  HO17  H  HOH1   0   0.446  -91.6557  10.4390  24.6923
 LYF  H18   H  HCH2   0   0.219  -88.9174  10.7255  25.1489
 LYF  H18A  H  HCH2   0   0.211  -89.7482  10.3375  23.6673

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
 LYF  CA   C     single  1.525  0.021  1.525
 LYF  C    O     deloc   1.231  0.020  1.231
 LYF  C    OXT   deloc   1.249  0.020  1.249
 LYF  CA   N     single  1.458  0.019  1.458
 LYF  N    HN    single  0.890  0.020  1.040
 LYF  N    HNA   single  0.890  0.020  1.040
 LYF  CB   CA    single  1.530  0.020  1.530
 LYF  CA   HA    single  0.970  0.020  0.970
 LYF  CG   CB    single  1.523  0.020  1.523
 LYF  CB   HB    single  0.970  0.020  1.090
 LYF  CB   HBA   single  0.970  0.020  1.090
 LYF  CE   CD    single  1.525  0.020  1.525
 LYF  CD   CG    single  1.523  0.020  1.523
 LYF  CD   HD    single  0.970  0.020  1.090
 LYF  CD   HDA   single  0.970  0.020  1.090
 LYF  NZ   CE    single  1.443  0.020  1.443
 LYF  CE   HE    single  0.970  0.020  1.090
 LYF  CE   HEA   single  0.970  0.020  1.090
 LYF  CG   HG    single  0.970  0.020  1.090
 LYF  CG   HGA   single  0.970  0.020  1.090
 LYF  C41  NZ    double  1.269  0.020  1.269
 LYF  C11  C12   single  1.530  0.020  1.530
 LYF  C11  C41   single  1.510  0.020  1.510
 LYF  C11  H11   single  0.970  0.020  1.090
 LYF  C11  H11A  single  0.970  0.020  1.090
 LYF  O17  C12   single  1.417  0.020  1.417
 LYF  C13  C12   single  1.526  0.020  1.526
 LYF  C12  H12   single  0.970  0.020  1.090
 LYF  C18  C13   single  1.521  0.020  1.521
 LYF  C13  H13   single  0.970  0.020  1.090
 LYF  C13  H13A  single  0.970  0.020  1.090
 LYF  O16  C14   deloc   1.247  0.020  1.247
 LYF  C14  O15   deloc   1.242  0.020  1.242
 LYF  C14  C41   single  1.540  0.020  1.540
 LYF  O17  HO17  single  0.850  0.020  0.980
 LYF  C18  C20   single  1.546  0.020  1.546
 LYF  C18  H18   single  0.970  0.020  1.090
 LYF  C18  H18A  single  0.970  0.020  1.090
 LYF  O22  C20   deloc   1.249  0.020  1.249
 LYF  C20  O21   deloc   1.246  0.020  1.246

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
 LYF  OXT   C    CA   116.05  3.000
 LYF  OXT   C    O    126.67  3.000
 LYF  CA    C    O    120.80  1.700
 LYF  HNA   N    HN   105.38  3.000
 LYF  HNA   N    CA   109.73  3.000
 LYF  HN    N    CA   108.57  3.000
 LYF  HA    CA   CB   109.00  3.000
 LYF  HA    CA   N    110.00  3.000
 LYF  CB    CA   N    110.50  1.700
 LYF  HA    CA   C    109.00  3.000
 LYF  CB    CA   C    110.10  1.900
 LYF  N     CA   C    111.00  2.800
 LYF  HBA   CB   HB   105.98  3.000
 LYF  HBA   CB   CG   109.80  3.000
 LYF  HB    CB   CG   108.53  3.000
 LYF  HBA   CB   CA   108.59  3.000
 LYF  HB    CB   CA   108.28  3.000
 LYF  CG    CB   CA   115.25  3.000
 LYF  HDA   CD   HD   106.32  3.000
 LYF  HDA   CD   CG   109.64  3.000
 LYF  HD    CD   CG   109.72  3.000
 LYF  HDA   CD   CE   108.87  3.000
 LYF  HD    CD   CE   109.00  3.000
 LYF  CG    CD   CE   113.07  3.000
 LYF  HEA   CE   HE   106.33  3.000
 LYF  HEA   CE   NZ   115.05  3.000
 LYF  HE    CE   NZ   107.49  3.000
 LYF  HEA   CE   CD   109.31  3.000
 LYF  HE    CE   CD   108.58  3.000
 LYF  NZ    CE   CD   109.85  3.000
 LYF  HGA   CG   HG   106.04  3.000
 LYF  HGA   CG   CD   109.50  3.000
 LYF  HG    CG   CD   109.16  3.000
 LYF  HGA   CG   CB   109.68  3.000
 LYF  HG    CG   CB   110.18  3.000
 LYF  CD    CG   CB   112.09  3.000
 LYF  C41   NZ   CE   122.51  3.000
 LYF  H11A  C11  H11  107.11  3.000
 LYF  H11A  C11  C41  111.25  3.000
 LYF  H11   C11  C41  108.79  3.000
 LYF  H11A  C11  C12  108.65  3.000
 LYF  H11   C11  C12  108.89  3.000
 LYF  C41   C11  C12  112.00  3.000
 LYF  H12   C12  O17  109.82  3.000
 LYF  H12   C12  C13  107.78  3.000
 LYF  O17   C12  C13  112.44  3.000
 LYF  H12   C12  C11  108.21  3.000
 LYF  C13   C12  C11  112.37  3.000
 LYF  O17   C12  C11  106.13  3.000
 LYF  H13A  C13  H13  106.32  3.000
 LYF  H13A  C13  C18  108.73  3.000
 LYF  H13   C13  C18  110.36  3.000
 LYF  H13A  C13  C12  108.26  3.000
 LYF  H13   C13  C12  109.10  3.000
 LYF  C18   C13  C12  113.79  3.000
 LYF  C41   C14  O16  115.23  3.000
 LYF  C41   C14  O15  117.20  3.000
 LYF  O16   C14  O15  127.57  3.000
 LYF  HO17  O17  C12  108.32  3.000
 LYF  H18A  C18  H18  105.23  3.000
 LYF  H18A  C18  C20  107.28  3.000
 LYF  H18   C18  C20  107.62  3.000
 LYF  H18A  C18  C13  110.93  3.000
 LYF  H18   C18  C13  109.45  3.000
 LYF  C20   C18  C13  115.75  3.000
 LYF  O22   C20  O21  126.64  3.000
 LYF  O21   C20  C18  117.79  3.000
 LYF  O22   C20  C18  115.57  3.000
 LYF  C14   C41  C11  117.09  3.000
 LYF  C14   C41  NZ   116.68  3.000
 LYF  C11   C41  NZ   126.21  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
 LYF  Var_01  C11  C41  NZ   CE     -2.87   0.0  2
 LYF  Var_02  CD   CG   CB   CA    175.02  30.0  2
 LYF  Var_03  CE   CD   CG   CB    179.23  30.0  1
 LYF  Var_04  NZ   CE   CD   CG   -174.43  30.0  2
 LYF  Var_05  C12  C11  C41  NZ    -85.25  30.0  1
 LYF  Var_06  O16  C14  C41  NZ   -143.26  30.0  2
 LYF  Var_07  C20  C18  C13  C12  -173.92  30.0  1
 LYF  Var_08  O22  C20  C18  C13  -173.98  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
 LYF  chir_01  CA   C    N    CB   negativ
 LYF  chir_02  C12  C11  O17  C13  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
 LYF  plan-1  C    0.020
 LYF  plan-1  O    0.020
 LYF  plan-1  CA   0.020
 LYF  plan-1  OXT  0.020
 LYF  plan-2  C14  0.020
 LYF  plan-2  O15  0.020
 LYF  plan-2  O16  0.020
 LYF  plan-2  C41  0.020
 LYF  plan-3  C18  0.020
 LYF  plan-3  C20  0.020
 LYF  plan-3  O21  0.020
 LYF  plan-3  O22  0.020
 LYF  plan-4  CE   0.020
 LYF  plan-4  NZ   0.020
 LYF  plan-4  C11  0.020
 LYF  plan-4  C14  0.020
 LYF  plan-4  C41  0.020

