# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:08:37 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: (4R)-N~6~-[(1Z)-ethanimidoyl]-4-fluoro-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=N)NCC[C@@H](F)C[C@H](N)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
 I58  I58  (4R)-N~6~-[(1Z)-ethanimidoyl]-4-fluoro-L-lysine  L-peptide  29  14  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_I58
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
 I58  N    N  NH2    0  -0.790  129.7540  117.6664  91.8317
 I58  C    C  C      0   0.408  128.0994  119.1636  90.7761
 I58  O    O  O      0  -0.614  127.5139  119.4679  89.7170
 I58  OXT  O  OC    -1  -0.599  128.2080  119.8618  91.8017
 I58  CA   C  CH1    0  -0.221  128.7067  117.7371  90.8275
 I58  CB   C  CH2    0  -0.518  127.5293  116.7518  90.9814
 I58  CG   C  CH1    0   0.213  127.8869  115.2800  90.8212
 I58  F    F  F      0  -0.394  126.7386  114.5906  90.3799
 I58  CD   C  CH2    0  -0.512  128.4171  114.5424  92.0447
 I58  CE   C  CH2    0  -0.310  127.3667  114.0390  93.0392
 I58  NZ   N  NH1    0  -0.619  126.4358  115.0172  93.5547
 I58  CX   C  C      0   0.394  126.7279  115.9815  94.4742
 I58  NX   N  N      0  -0.676  126.0080  117.0157  94.7067
 I58  CT   C  CH3    0  -0.748  127.9709  115.7750  95.2900
 I58  H    H  HNH2   0   0.328  129.3639  117.8516  92.7473
 I58  H2   H  HNH2   0   0.337  130.1696  116.7456  91.8636
 I58  HA   H  HCH1   0   0.206  129.1742  117.5371  89.8564
 I58  HB2  H  HCH2   0   0.236  126.8115  116.9886  90.1924
 I58  HB3  H  HCH2   0   0.232  127.0315  116.9442  91.9345
 I58  HG   H  HCH1   0   0.212  128.6177  115.1920  90.0096
 I58  HD2  H  HCH2   0   0.228  129.1335  115.1857  92.5561
 I58  HD3  H  HCH2   0   0.246  128.9834  113.6651  91.7195
 I58  HE2  H  HCH2   0   0.253  127.8905  113.5640  93.8696
 I58  HE3  H  HCH2   0   0.257  126.7752  113.2502  92.5760
 I58  HZ   H  HNH1   0   0.380  125.6406  115.2046  92.9629
 I58  HNX  H  H      0   0.306  125.2044  117.0500  94.0829
 I58  HT1  H  HCH3   0   0.254  128.8695  115.8314  94.6737
 I58  HT2  H  HCH3   0   0.258  128.0335  116.5477  96.0511
 I58  HT3  H  HCH3   0   0.253  127.9730  114.8011  95.7810

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
 I58  N   CA   single  1.458  0.019  1.458
 I58  N   H    single  0.860  0.020  0.860
 I58  N   H2   single  0.890  0.020  1.040
 I58  C   O    deloc   1.231  0.020  1.231
 I58  C   OXT  deloc   1.246  0.020  1.246
 I58  C   CA   single  1.525  0.021  1.525
 I58  CA  CB   single  1.530  0.020  1.530
 I58  CA  HA   single  0.970  0.020  0.970
 I58  CB  CG   single  1.523  0.020  1.523
 I58  CB  HB2  single  0.970  0.020  1.090
 I58  CB  HB3  single  0.970  0.020  1.090
 I58  CG  F    single  1.410  0.020  1.410
 I58  CG  CD   single  1.524  0.020  1.524
 I58  CG  HG   single  0.970  0.020  1.090
 I58  CD  CE   single  1.532  0.020  1.532
 I58  CD  HD2  single  0.970  0.020  1.090
 I58  CD  HD3  single  0.970  0.020  1.090
 I58  CE  NZ   single  1.445  0.020  1.445
 I58  CE  HE2  single  0.970  0.020  1.090
 I58  CE  HE3  single  0.970  0.020  1.090
 I58  NZ  CX   single  1.364  0.020  1.364
 I58  NZ  HZ   single  0.890  0.020  1.040
 I58  CX  NX   double  1.281  0.020  1.281
 I58  CX  CT   single  1.501  0.020  1.501
 I58  NX  HNX  single  0.890  0.020  1.040
 I58  CT  HT1  single  0.970  0.020  1.090
 I58  CT  HT2  single  0.970  0.020  1.090
 I58  CT  HT3  single  0.970  0.020  1.090

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
 I58  H2   N   H    107.25  3.000
 I58  H2   N   CA   111.26  3.000
 I58  H    N   CA   114.00  3.000
 I58  CA   C   OXT  117.00  3.000
 I58  CA   C   O    120.80  1.700
 I58  OXT  C   O    127.09  3.000
 I58  HA   CA  CB   109.00  3.000
 I58  HA   CA  C    109.00  3.000
 I58  CB   CA  C    110.10  1.900
 I58  HA   CA  N    110.00  3.000
 I58  CB   CA  N    110.50  1.700
 I58  C    CA  N    111.00  2.800
 I58  HB3  CB  HB2  107.00  3.000
 I58  HB3  CB  CG   111.65  3.000
 I58  HB2  CB  CG   106.72  3.000
 I58  HB3  CB  CA   108.80  3.000
 I58  HB2  CB  CA   106.91  3.000
 I58  CG   CB  CA   115.31  3.000
 I58  HG   CG  CD   108.89  3.000
 I58  HG   CG  F    105.78  3.000
 I58  CD   CG  F    107.33  3.000
 I58  HG   CG  CB   108.19  3.000
 I58  CD   CG  CB   117.71  3.000
 I58  F    CG  CB   108.32  3.000
 I58  HD3  CD  HD2  105.82  3.000
 I58  HD3  CD  CE   106.53  3.000
 I58  HD2  CD  CE   109.88  3.000
 I58  HD3  CD  CG   109.26  3.000
 I58  HD2  CD  CG   108.64  3.000
 I58  CE   CD  CG   116.22  3.000
 I58  HE3  CE  HE2  105.62  3.000
 I58  HE3  CE  NZ   106.97  3.000
 I58  HE2  CE  NZ   109.42  3.000
 I58  HE3  CE  CD   109.53  3.000
 I58  HE2  CE  CD   107.95  3.000
 I58  NZ   CE  CD   116.80  3.000
 I58  HZ   NZ  CX   115.65  3.000
 I58  HZ   NZ  CE   115.10  3.000
 I58  CX   NZ  CE   125.51  3.000
 I58  CT   CX  NX   118.52  3.000
 I58  CT   CX  NZ   116.52  3.000
 I58  NX   CX  NZ   124.93  3.000
 I58  HNX  NX  CX   111.07  3.000
 I58  HT3  CT  HT2  108.64  3.000
 I58  HT3  CT  HT1  107.39  3.000
 I58  HT2  CT  HT1  108.15  3.000
 I58  HT3  CT  CX   111.66  3.000
 I58  HT2  CT  CX   109.31  3.000
 I58  HT1  CT  CX   111.59  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
 I58  CONST_03  HNX  NX  CX  NZ    0.00   0.0  0
 I58  CONST_04  HZ   NZ  CX  NX    0.00   0.0  0
 I58  Var_01    NZ   CE  CD  CG  -54.54  30.0  3
 I58  Var_02    CX   NZ  CE  CD  -73.74  30.0  3
 I58  Var_03    HT1  CT  CX  NZ   66.48  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
 I58  chir_01  CA  N  C   CB  positiv
 I58  chir_02  CG  F  CD  CB  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
 I58  plan-1  CE   0.020
 I58  plan-1  NZ   0.020
 I58  plan-1  CX   0.020
 I58  plan-1  NX   0.020
 I58  plan-1  CT   0.020
 I58  plan-1  HZ   0.020
 I58  plan-1  HNX  0.020
 I58  plan-2  C    0.020
 I58  plan-2  O    0.020
 I58  plan-2  OXT  0.020
 I58  plan-2  CA   0.020

