# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:30:38 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N~5~-[(1E)-2-sulfanylethanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)CS)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
 VUR  VUR  N~5~-[(1E)-2-sulfanylethanimidoyl]-L-ornithine  ligand  27  13  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VUR
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
 VUR  C    C  C      0   0.383  -4.4763  -0.4219  -0.0550
 VUR  N    N  NH2    0  -0.786  -3.3187   1.8374   0.0312
 VUR  C1   C  C      0   0.418   2.9756  -0.0755   0.0947
 VUR  C2   C  CH2    0  -0.668   4.0831   0.9236  -0.2035
 VUR  S3   S  S2     0  -0.227   5.7470   0.2280  -0.3120
 VUR  CA   C  CH1    0  -0.211  -3.2457   0.4511  -0.4062
 VUR  CB   C  CH2    0  -0.419  -1.9841  -0.2083   0.1578
 VUR  CD   C  CH2    0  -0.228   0.5336  -0.2306   0.2867
 VUR  NE   N  NH1    0  -0.632   1.7430   0.4486  -0.1183
 VUR  CG   C  CH2    0  -0.450  -0.6919   0.4556  -0.2951
 VUR  NH   N  N      0  -0.664   3.1273  -1.2726   0.5057
 VUR  OA1  O  OC    -1  -0.624  -4.5528  -1.5212  -0.6432
 VUR  OA2  O  O      0  -0.609  -5.2764   0.0197   0.7939
 VUR  HN   H  HNH2   0   0.334  -4.0900   2.2879  -0.4465
 VUR  HNA  H  HNH2   0   0.322  -3.5966   1.8385   1.0065
 VUR  H2   H  HCH2   0   0.298   3.8562   1.4772  -1.1147
 VUR  H2A  H  HCH2   0   0.312   4.1231   1.6547   0.6069
 VUR  HS3  H  HSH1   0   0.236   5.5993  -0.3984  -1.4850
 VUR  HA   H  HCH1   0   0.207  -3.1497   0.4561  -1.4986
 VUR  HB   H  HCH2   0   0.207  -2.0356  -0.1983   1.2537
 VUR  HBA  H  HCH2   0   0.220  -1.9758  -1.2601  -0.1374
 VUR  HD   H  HCH2   0   0.224   0.5848  -1.2651  -0.0578
 VUR  HDA  H  HCH2   0   0.209   0.4531  -0.2737   1.3808
 VUR  HNE  H  HNH1   0   0.387   1.6766   1.4474  -0.2341
 VUR  HG   H  HCH2   0   0.216  -0.6328   0.4347  -1.3881
 VUR  HGA  H  HCH2   0   0.223  -0.7033   1.5093  -0.0039
 VUR  HNH  H  H      0   0.324   4.1171  -1.4915   0.5611

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
 VUR  OA2  C    deloc   1.247  0.020  1.247
 VUR  CA   C    single  1.549  0.020  1.549
 VUR  C    OA1  deloc   1.249  0.020  1.249
 VUR  N    CA   single  1.456  0.020  1.456
 VUR  N    HN   single  0.890  0.020  1.040
 VUR  N    HNA  single  0.890  0.020  1.040
 VUR  NH   C1   double  1.275  0.020  1.275
 VUR  C1   NE   single  1.356  0.020  1.356
 VUR  C1   C2   single  1.521  0.020  1.521
 VUR  C2   S3   single  1.807  0.020  1.807
 VUR  C2   H2   single  0.970  0.020  1.090
 VUR  C2   H2A  single  0.970  0.020  1.090
 VUR  S3   HS3  single  1.200  0.020  1.300
 VUR  CA   CB   single  1.531  0.020  1.531
 VUR  CA   HA   single  0.970  0.020  1.090
 VUR  CG   CB   single  1.522  0.020  1.522
 VUR  CB   HB   single  0.970  0.020  1.090
 VUR  CB   HBA  single  0.970  0.020  1.090
 VUR  CD   CG   single  1.520  0.020  1.520
 VUR  CD   NE   single  1.445  0.020  1.445
 VUR  CD   HD   single  0.970  0.020  1.090
 VUR  CD   HDA  single  0.970  0.020  1.090
 VUR  NE   HNE  single  0.890  0.020  1.040
 VUR  CG   HG   single  0.970  0.020  1.090
 VUR  CG   HGA  single  0.970  0.020  1.090
 VUR  NH   HNH  single  0.890  0.020  1.040

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
 VUR  OA2  C   OA1  126.35  3.000
 VUR  OA1  C   CA   115.96  3.000
 VUR  OA2  C   CA   117.67  3.000
 VUR  HNA  N   HN   104.15  3.000
 VUR  HNA  N   CA   107.68  3.000
 VUR  HN   N   CA   108.67  3.000
 VUR  NH   C1  NE   121.45  3.000
 VUR  NE   C1  C2   112.15  3.000
 VUR  NH   C1  C2   126.39  3.000
 VUR  H2A  C2  H2   106.73  3.000
 VUR  H2A  C2  S3   105.58  3.000
 VUR  H2   C2  S3   109.70  3.000
 VUR  H2A  C2  C1   108.71  3.000
 VUR  H2   C2  C1   110.24  3.000
 VUR  S3   C2  C1   115.43  3.000
 VUR  HS3  S3  C2    97.54  3.000
 VUR  HA   CA  CB   107.27  3.000
 VUR  HA   CA  N    107.42  3.000
 VUR  CB   CA  N    109.93  3.000
 VUR  HA   CA  C    107.33  3.000
 VUR  CB   CA  C    109.17  3.000
 VUR  N    CA  C    115.39  3.000
 VUR  HBA  CB  HB   106.20  3.000
 VUR  HBA  CB  CG   109.46  3.000
 VUR  HB   CB  CG   109.46  3.000
 VUR  HBA  CB  CA   108.74  3.000
 VUR  HB   CB  CA   108.99  3.000
 VUR  CG   CB  CA   113.71  3.000
 VUR  HDA  CD  HD   106.30  3.000
 VUR  HDA  CD  CG   109.88  3.000
 VUR  HD   CD  CG   110.18  3.000
 VUR  HDA  CD  NE   111.04  3.000
 VUR  HD   CD  NE   108.53  3.000
 VUR  CG   CD  NE   110.81  3.000
 VUR  HNE  NE  CD   116.30  3.000
 VUR  HNE  NE  C1   117.45  3.000
 VUR  CD   NE  C1   122.34  3.000
 VUR  HGA  CG  HG   106.56  3.000
 VUR  HGA  CG  CD   109.97  3.000
 VUR  HG   CG  CD   109.26  3.000
 VUR  HGA  CG  CB   109.41  3.000
 VUR  HG   CG  CB   109.55  3.000
 VUR  CD   CG  CB   111.94  3.000
 VUR  HNH  NH  C1   109.64  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
 VUR  CONST_01  CD   NE  C1  C2   180.00   0.0  0
 VUR  CONST_02  NH   C1  NE  CD     0.00   0.0  0
 VUR  CONST_03  HNH  NH  C1  C2     0.00   0.0  0
 VUR  CONST_04  HNE  NE  C1  C2     0.00   0.0  0
 VUR  Var_01    CG   CD  NE  C1  -169.73  30.0  1
 VUR  Var_02    NH   C1  C2  S3    13.57  30.0  2
 VUR  Var_03    CD   CG  CB  CA  -179.96  30.0  1
 VUR  Var_04    NE   CD  CG  CB  -177.87  30.0  1

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
 VUR  chir_01  CA  C  N  CB  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
 VUR  plan-1  C1   0.020
 VUR  plan-1  C2   0.020
 VUR  plan-1  CD   0.020
 VUR  plan-1  NE   0.020
 VUR  plan-1  NH   0.020
 VUR  plan-1  HNE  0.020
 VUR  plan-1  HNH  0.020
 VUR  plan-2  C    0.020
 VUR  plan-2  CA   0.020
 VUR  plan-2  OA1  0.020
 VUR  plan-2  OA2  0.020

