# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:51:10 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N~5~-[(1E)-2-(methylsulfanyl)ethanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC(=N)NCCC[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
 JM2  JM2  N~5~-[(1E)-2-(methylsulfanyl)ethanimidoyl]-L-ornithine  ligand  30  14  .  2022-07-25  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_JM2
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
 JM2  C    C  C      0   0.384   4.9933  -0.1745   0.2740
 JM2  N    N  NH2    0  -0.787   3.7287   1.7997  -0.7049
 JM2  C1   C  C      0   0.424  -2.4552  -0.3370  -0.1106
 JM2  C2   C  CH2    0  -0.654  -3.6413   0.4199   0.4547
 JM2  S3   S  S2     0  -0.028  -5.0097   0.4369  -0.7341
 JM2  C4   C  CH3    0  -0.767  -6.3609   0.8883   0.3753
 JM2  CA   C  CH1    0  -0.212   3.7132   0.6979   0.2457
 JM2  CB   C  CH2    0  -0.418   2.5002  -0.2002  -0.0104
 JM2  CD   C  CH2    0  -0.226  -0.0075  -0.4150  -0.1199
 JM2  NE   N  NH1    0  -0.634  -1.2637   0.2545   0.1280
 JM2  CG   C  CH2    0  -0.456   1.1655   0.5141   0.1480
 JM2  NH   N  N      0  -0.662  -2.5269  -1.4506  -0.7353
 JM2  OA1  O  O      0  -0.608   5.7952  -0.0580  -0.6739
 JM2  OA2  O  OC    -1  -0.625   5.1037  -0.9494   1.2478
 JM2  HN   H  HNH2   0   0.334   4.4486   2.4572  -0.4294
 JM2  HNA  H  HNH2   0   0.322   4.0499   1.4358  -1.5955
 JM2  H2   H  HCH2   0   0.299  -3.9743  -0.0892   1.3626
 JM2  H2A  H  HCH2   0   0.282  -3.3703   1.4410   0.7265
 JM2  H4   H  HCH3   0   0.265  -6.1995   1.8687   0.8201
 JM2  H4A  H  HCH3   0   0.278  -7.2725   0.9209  -0.2184
 JM2  H4B  H  HCH3   0   0.266  -6.4820   0.1472   1.1641
 JM2  HA   H  HCH1   0   0.207   3.5928   1.1305   1.2464
 JM2  HB   H  HCH2   0   0.207   2.5727  -0.6219  -1.0208
 JM2  HBA  H  HCH2   0   0.220   2.5410  -1.0470   0.6789
 JM2  HD   H  HCH2   0   0.211   0.0736  -1.3150   0.5025
 JM2  HG   H  HCH2   0   0.214   1.0928   0.9121   1.1668
 JM2  HGA  H  HCH2   0   0.229   1.1217   1.3702  -0.5281
 JM2  HNH  H  H      0   0.321  -3.4964  -1.7310  -0.8361
 JM2  H16  H  HCH2   0   0.223   0.0171  -0.7562  -1.1577
 JM2  H17  H  HNH1   0   0.390  -1.2465   1.0479   0.7468

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
 JM2  C    CA   single  1.549  0.020  1.549
 JM2  C    OA2  deloc   1.249  0.020  1.249
 JM2  N    HN   single  0.890  0.020  1.040
 JM2  N    HNA  single  0.890  0.020  1.040
 JM2  C1   NH   double  1.279  0.020  1.279
 JM2  C1   NE   single  1.351  0.020  1.351
 JM2  C2   C1   single  1.516  0.020  1.516
 JM2  C2   H2   single  0.970  0.020  1.090
 JM2  C2   H2A  single  0.970  0.020  1.090
 JM2  S3   C2   single  1.813  0.020  1.813
 JM2  C4   S3   single  1.806  0.020  1.806
 JM2  C4   H4   single  0.970  0.020  1.090
 JM2  C4   H4A  single  0.970  0.020  1.090
 JM2  C4   H4B  single  0.970  0.020  1.090
 JM2  CA   N    single  1.455  0.020  1.455
 JM2  CA   HA   single  0.970  0.020  1.090
 JM2  CB   CA   single  1.531  0.020  1.531
 JM2  CB   CG   single  1.522  0.020  1.522
 JM2  CB   HB   single  0.970  0.020  1.090
 JM2  CB   HBA  single  0.970  0.020  1.090
 JM2  CD   NE   single  1.445  0.020  1.445
 JM2  CD   CG   single  1.520  0.020  1.520
 JM2  CD   HD   single  0.970  0.020  1.090
 JM2  CG   HG   single  0.970  0.020  1.090
 JM2  CG   HGA  single  0.970  0.020  1.090
 JM2  NH   HNH  single  0.890  0.020  1.040
 JM2  OA1  C    deloc   1.247  0.020  1.247
 JM2  CD   H16  single  0.970  0.020  1.090
 JM2  NE   H17  single  0.860  0.020  1.020

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
 JM2  OA2  C   OA1  126.41  3.000
 JM2  OA1  C   CA   117.69  3.000
 JM2  OA2  C   CA   115.88  3.000
 JM2  HNA  N   HN   104.28  3.000
 JM2  HNA  N   CA   107.78  3.000
 JM2  HN   N   CA   108.74  3.000
 JM2  NH   C1  NE   121.12  3.000
 JM2  NE   C1  C2   113.91  3.000
 JM2  NH   C1  C2   124.95  3.000
 JM2  H2A  C2  H2   107.75  3.000
 JM2  H2A  C2  S3   110.01  3.000
 JM2  H2   C2  S3   108.61  3.000
 JM2  S3   C2  C1   110.53  3.000
 JM2  H2A  C2  C1   111.45  3.000
 JM2  H2   C2  C1   108.39  3.000
 JM2  C4   S3  C2    99.46  3.000
 JM2  H4B  C4  H4A  108.80  3.000
 JM2  H4B  C4  H4   109.48  3.000
 JM2  H4A  C4  H4   108.67  3.000
 JM2  H4B  C4  S3   110.98  3.000
 JM2  H4A  C4  S3   107.40  3.000
 JM2  H4   C4  S3   111.42  3.000
 JM2  HA   CA  CB   107.27  3.000
 JM2  CB   CA  N    110.08  3.000
 JM2  HA   CA  N    107.38  3.000
 JM2  CB   CA  C    109.11  3.000
 JM2  HA   CA  C    107.23  3.000
 JM2  N    CA  C    115.43  3.000
 JM2  HBA  CB  HB   106.30  3.000
 JM2  HBA  CB  CG   109.32  3.000
 JM2  HB   CB  CG   109.52  3.000
 JM2  HBA  CB  CA   108.64  3.000
 JM2  HB   CB  CA   109.09  3.000
 JM2  CG   CB  CA   113.71  3.000
 JM2  H16  CD  HD   106.32  3.000
 JM2  H16  CD  CG   109.93  3.000
 JM2  HD   CD  CG   110.14  3.000
 JM2  H16  CD  NE   109.10  3.000
 JM2  HD   CD  NE   110.30  3.000
 JM2  CG   CD  NE   110.94  3.000
 JM2  H17  NE  CD   117.12  3.000
 JM2  H17  NE  C1   117.96  3.000
 JM2  CD   NE  C1   122.23  3.000
 JM2  HGA  CG  HG   106.75  3.000
 JM2  HGA  CG  CD   109.83  3.000
 JM2  HG   CG  CD   109.55  3.000
 JM2  HGA  CG  CB   109.80  3.000
 JM2  HG   CG  CB   108.98  3.000
 JM2  CD   CG  CB   111.80  3.000
 JM2  HNH  NH  C1   110.06  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
 JM2  CONST_01  CD   NE  C1  C2  180.00   0.0  0
 JM2  CONST_02  NH   C1  NE  CD    0.00   0.0  0
 JM2  CONST_03  HNH  NH  C1  C2    0.00   0.0  0
 JM2  CONST_04  H17  NE  C1  C2    0.00   0.0  0
 JM2  Var_01    CG   CD  NE  C1  176.20  30.0  2
 JM2  Var_02    NH   C1  C2  S3  -43.65  30.0  3
 JM2  Var_03    CD   CG  CB  CA  179.82  30.0  3
 JM2  Var_04    NE   CD  CG  CB  175.91  30.0  1
 JM2  Var_05    H4   C4  S3  C2   61.97  30.0  3
 JM2  Var_06    H2   C2  S3  C4   43.83  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
 JM2  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
 JM2  plan-1  C1   0.020
 JM2  plan-1  C2   0.020
 JM2  plan-1  CD   0.020
 JM2  plan-1  NE   0.020
 JM2  plan-1  NH   0.020
 JM2  plan-1  HNH  0.020
 JM2  plan-1  H17  0.020
 JM2  plan-2  C    0.020
 JM2  plan-2  CA   0.020
 JM2  plan-2  OA1  0.020
 JM2  plan-2  OA2  0.020

