# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:26:29 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N~5~-[(1E)-3-(ethylsulfanyl)propanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCSCCC(=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
 JM8  JM8  N~5~-[(1E)-3-(ethylsulfanyl)propanimidoyl]-L-ornithine  ligand  36  16  .  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_JM8
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
 JM8  C    C  C      0   0.383   6.0058  -0.2116   0.4238
 JM8  N    N  NH2    0  -0.786   4.6998   1.8759  -0.1977
 JM8  C1   C  C      0   0.432  -1.3911  -0.4432  -0.6035
 JM8  C2   C  CH2    0  -0.537  -2.6212   0.4015  -0.3311
 JM8  C3   C  CH2    0  -0.570  -3.9047  -0.4082  -0.2410
 JM8  S4   S  S2     0  -0.033  -5.2838   0.6982   0.1628
 JM8  C5   C  CH2    0  -0.534  -6.6595  -0.4865   0.1198
 JM8  C6   C  CH3    0  -0.663  -7.9635   0.2295   0.4255
 JM8  CA   C  CH1    0  -0.211   4.6893   0.6014   0.5037
 JM8  CB   C  CH2    0  -0.420   3.5308  -0.2663   0.0042
 JM8  CD   C  CH2    0  -0.222   1.0434  -0.5290  -0.3053
 JM8  NE   N  NH1    0  -0.641  -0.2371   0.1284  -0.1885
 JM8  CG   C  CH2    0  -0.454   2.1670   0.3977   0.1312
 JM8  NH   N  N      0  -0.680  -1.3719  -1.5726  -1.2060
 JM8  OA1  O  O      0  -0.608   6.8617   0.1533  -0.4065
 JM8  OA2  O  OC    -1  -0.625   6.0921  -1.1891   1.1971
 JM8  HN   H  HNH2   0   0.334   5.4184   2.4629   0.2089
 JM8  HNA  H  HNH2   0   0.322   5.0218   1.7090  -1.1450
 JM8  H2   H  HCH2   0   0.257  -2.4770   0.9600   0.5973
 JM8  H2A  H  HCH2   0   0.278  -2.7094   1.1466  -1.1271
 JM8  H3   H  HCH2   0   0.262  -4.1269  -0.8975  -1.1917
 JM8  H3A  H  HCH2   0   0.272  -3.8201  -1.1808   0.5254
 JM8  H5   H  HCH2   0   0.260  -6.6964  -0.9498  -0.8676
 JM8  H5A  H  HCH2   0   0.260  -6.4742  -1.2735   0.8522
 JM8  H6   H  HCH3   0   0.246  -8.7922  -0.4778   0.3959
 JM8  H6A  H  HCH3   0   0.234  -7.9468   0.6822   1.4169
 JM8  H6B  H  HCH3   0   0.234  -8.1689   1.0142  -0.3027
 JM8  HA   H  HCH1   0   0.207   4.5009   0.8136   1.5634
 JM8  HB   H  HCH2   0   0.207   3.7079  -0.5328  -1.0454
 JM8  HBA  H  HCH2   0   0.219   3.5367  -1.2034   0.5653
 JM8  HD   H  HCH2   0   0.208   1.0620  -1.4482   0.2936
 JM8  HG   H  HCH2   0   0.213   2.0062   0.6993   1.1727
 JM8  HGA  H  HCH2   0   0.226   2.1433   1.3106  -0.4671
 JM8  HNH  H  H      0   0.324  -2.3044  -1.8465  -1.4901
 JM8  H20  H  HCH2   0   0.218   1.1948  -0.8354  -1.3438
 JM8  H21  H  HNH1   0   0.386  -0.2980   0.9092   0.4430

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
 JM8  C    CA   single  1.549  0.020  1.549
 JM8  C    OA2  deloc   1.249  0.020  1.249
 JM8  N    HN   single  0.890  0.020  1.040
 JM8  N    HNA  single  0.890  0.020  1.040
 JM8  C1   NE   single  1.353  0.020  1.353
 JM8  C1   NH   double  1.280  0.020  1.280
 JM8  C2   C1   single  1.517  0.020  1.517
 JM8  C2   C3   single  1.520  0.020  1.520
 JM8  C2   H2   single  0.970  0.020  1.090
 JM8  C2   H2A  single  0.970  0.020  1.090
 JM8  C3   S4   single  1.814  0.020  1.814
 JM8  C3   H3   single  0.970  0.020  1.090
 JM8  C3   H3A  single  0.970  0.020  1.090
 JM8  C5   S4   single  1.816  0.020  1.816
 JM8  C5   H5   single  0.970  0.020  1.090
 JM8  C5   H5A  single  0.970  0.020  1.090
 JM8  C6   C5   single  1.519  0.020  1.519
 JM8  C6   H6   single  0.970  0.020  1.090
 JM8  C6   H6A  single  0.970  0.020  1.090
 JM8  C6   H6B  single  0.970  0.020  1.090
 JM8  CA   N    single  1.455  0.020  1.455
 JM8  CA   HA   single  0.970  0.020  1.090
 JM8  CB   CA   single  1.531  0.020  1.531
 JM8  CB   CG   single  1.522  0.020  1.522
 JM8  CB   HB   single  0.970  0.020  1.090
 JM8  CB   HBA  single  0.970  0.020  1.090
 JM8  CD   NE   single  1.444  0.020  1.444
 JM8  CD   CG   single  1.521  0.020  1.521
 JM8  CD   HD   single  0.970  0.020  1.090
 JM8  CG   HG   single  0.970  0.020  1.090
 JM8  CG   HGA  single  0.970  0.020  1.090
 JM8  NH   HNH  single  0.890  0.020  1.040
 JM8  OA1  C    deloc   1.247  0.020  1.247
 JM8  CD   H20  single  0.970  0.020  1.090
 JM8  NE   H21  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
 JM8  OA2  C   OA1  126.41  3.000
 JM8  OA1  C   CA   117.65  3.000
 JM8  OA2  C   CA   115.93  3.000
 JM8  HNA  N   HN   104.18  3.000
 JM8  HNA  N   CA   107.97  3.000
 JM8  HN   N   CA   108.62  3.000
 JM8  NH   C1  NE   120.28  3.000
 JM8  NH   C1  C2   126.01  3.000
 JM8  NE   C1  C2   113.66  3.000
 JM8  H2A  C2  H2   106.30  3.000
 JM8  H2A  C2  C3   109.74  3.000
 JM8  H2   C2  C3   109.46  3.000
 JM8  H2A  C2  C1   108.31  3.000
 JM8  H2   C2  C1   109.28  3.000
 JM8  C3   C2  C1   113.50  3.000
 JM8  H3A  C3  H3   108.05  3.000
 JM8  H3A  C3  S4   109.54  3.000
 JM8  H3   C3  S4   108.21  3.000
 JM8  H3A  C3  C2   110.68  3.000
 JM8  H3   C3  C2   111.03  3.000
 JM8  S4   C3  C2   109.29  3.000
 JM8  C5   S4  C3    99.95  3.000
 JM8  H5A  C5  H5   107.87  3.000
 JM8  H5A  C5  C6   110.54  3.000
 JM8  H5   C5  C6   110.68  3.000
 JM8  C6   C5  S4   109.77  3.000
 JM8  H5A  C5  S4   109.03  3.000
 JM8  H5   C5  S4   108.91  3.000
 JM8  H6B  C6  H6A  108.15  3.000
 JM8  H6B  C6  H6   107.81  3.000
 JM8  H6A  C6  H6   107.81  3.000
 JM8  H6B  C6  C5   111.51  3.000
 JM8  H6A  C6  C5   111.45  3.000
 JM8  H6   C6  C5   109.96  3.000
 JM8  HA   CA  CB   107.15  3.000
 JM8  CB   CA  N    110.16  3.000
 JM8  HA   CA  N    107.31  3.000
 JM8  CB   CA  C    109.19  3.000
 JM8  HA   CA  C    107.29  3.000
 JM8  N    CA  C    115.38  3.000
 JM8  HBA  CB  HB   106.39  3.000
 JM8  HBA  CB  CG   109.65  3.000
 JM8  HB   CB  CG   109.29  3.000
 JM8  HBA  CB  CA   108.33  3.000
 JM8  HB   CB  CA   109.12  3.000
 JM8  CG   CB  CA   113.79  3.000
 JM8  H20  CD  HD   106.34  3.000
 JM8  H20  CD  CG   109.95  3.000
 JM8  HD   CD  CG   109.96  3.000
 JM8  H20  CD  NE   109.10  3.000
 JM8  HD   CD  NE   110.62  3.000
 JM8  CG   CD  NE   110.77  3.000
 JM8  H21  NE  CD   117.24  3.000
 JM8  H21  NE  C1   117.95  3.000
 JM8  CD   NE  C1   122.63  3.000
 JM8  HGA  CG  HG   106.71  3.000
 JM8  HGA  CG  CD   109.65  3.000
 JM8  HG   CG  CD   109.39  3.000
 JM8  HGA  CG  CB   109.79  3.000
 JM8  HG   CG  CB   109.31  3.000
 JM8  CD   CG  CB   111.85  3.000
 JM8  HNH  NH  C1   110.91  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
 JM8  CONST_01  CD   NE  C1  C2   180.00   0.0  0
 JM8  CONST_02  NH   C1  NE  CD     0.00   0.0  0
 JM8  CONST_03  H21  NE  C1  C2     0.00   0.0  0
 JM8  CONST_04  HNH  NH  C1  C2     0.00   0.0  0
 JM8  Var_01    CG   CD  NE  C1   175.14  30.0  1
 JM8  Var_02    S4   C3  C2  C1   177.36  30.0  3
 JM8  Var_03    NE   C1  C2  C3  -155.93  30.0  3
 JM8  Var_04    C6   C5  S4  C3  -179.54  30.0  1
 JM8  Var_05    CD   CG  CB  CA  -176.87  30.0  3
 JM8  Var_06    NE   CD  CG  CB  -179.41  30.0  2
 JM8  Var_07    H6   C6  C5  S4   179.74  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
 JM8  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
 JM8  plan-1  C1   0.020
 JM8  plan-1  C2   0.020
 JM8  plan-1  CD   0.020
 JM8  plan-1  NE   0.020
 JM8  plan-1  NH   0.020
 JM8  plan-1  HNH  0.020
 JM8  plan-1  H21  0.020
 JM8  plan-2  C    0.020
 JM8  plan-2  CA   0.020
 JM8  plan-2  OA1  0.020
 JM8  plan-2  OA2  0.020

