# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:26:33 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N~5~-[(1Z)-2-(propylsulfanyl)ethanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCSCC(=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
 JM5  JM5  N~5~-[(1Z)-2-(propylsulfanyl)ethanimidoyl]-L-ornithine  ligand  37  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JM5
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
 JM5  C     C  C     0   0.520  -5.9028  -0.1022   0.0727
 JM5  N     N  NH2   0  -0.776  -4.4052  -2.0017  -0.4826
 JM5  C1    C  C     0   0.444   1.5005   0.7453  -0.1092
 JM5  C2    C  CH2   0  -0.625   2.7245  -0.0283   0.3098
 JM5  S3    S  S2    0  -0.013   4.2251   0.7280  -0.3532
 JM5  C4    C  CH2   0  -0.540   5.4225  -0.4997   0.2472
 JM5  C5    C  CH2   0  -0.427   6.8288  -0.1108  -0.1858
 JM5  C6    C  CH3   0  -0.659   7.8629  -1.1185   0.2984
 JM5  CA    C  CH1   0  -0.207  -4.5522  -0.7788   0.2685
 JM5  CB    C  CH2   0  -0.432  -3.4369   0.2125  -0.0921
 JM5  CD    C  CH2   0  -0.258  -0.9616   0.6655  -0.1233
 JM5  NE    N  NH1   0  -0.644   0.3383   0.1252   0.1989
 JM5  CG    C  CH2   0  -0.464  -2.0556  -0.3162   0.2639
 JM5  NH    N  N     0  -0.689   1.6398   1.8771  -0.6868
 JM5  OA1   O  O     0  -0.440  -6.6549  -0.3281  -0.8422
 JM5  OA2   O  OH1   0  -0.593  -6.1609   0.7864   1.0259
 JM5  HN    H  HNH2  0   0.355  -5.0977  -2.6809  -0.1945
 JM5  HNA   H  HNH2  0   0.344  -4.5677  -1.8290  -1.4673
 JM5  H2    H  HCH2  0   0.290   2.7751  -0.0634   1.4015
 JM5  H2A   H  HCH2  0   0.282   2.6470  -1.0613  -0.0381
 JM5  H4    H  HCH2  0   0.253   5.3655  -0.5588   1.3369
 JM5  H4A   H  HCH2  0   0.253   5.1624  -1.4831  -0.1523
 JM5  H5    H  HCH2  0   0.228   6.8684  -0.0356  -1.2756
 JM5  H5A   H  HCH2  0   0.229   7.0702   0.8810   0.2047
 JM5  H6    H  HCH3  0   0.222   7.8744  -1.1795   1.3878
 JM5  H6A   H  HCH3  0   0.222   7.6533  -2.1173  -0.0881
 JM5  H6B   H  HCH3  0   0.234   8.8648  -0.8407  -0.0288
 JM5  HA    H  HCH1  0   0.267  -4.4611  -1.0170   1.3333
 JM5  HB    H  HCH2  0   0.235  -3.4900   0.4278  -1.1647
 JM5  HBA   H  HCH2  0   0.246  -3.6083   1.1599   0.4240
 JM5  HD    H  HCH2  0   0.229  -1.1177   1.6198   0.3935
 JM5  HG    H  HCH2  0   0.233  -2.0058  -0.5080   1.3403
 JM5  HGA   H  HCH2  0   0.241  -1.8826  -1.2702  -0.2385
 JM5  HNH   H  H     0   0.335   0.7469   2.3098  -0.9050
 JM5  HOA2  H  HOH1  0   0.481  -7.0143   1.2144   0.8601
 JM5  H20   H  HCH2  0   0.229  -1.0242   0.8759  -1.1976
 JM5  H21   H  HNH1  0   0.397   0.3769  -0.7759   0.6463

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
 JM5  C    OA2   single  1.328  0.020  1.328
 JM5  N    CA    single  1.443  0.020  1.443
 JM5  N    HN    single  0.890  0.020  1.040
 JM5  N    HNA   single  0.890  0.020  1.040
 JM5  C1   C2    single  1.507  0.020  1.507
 JM5  C2   H2    single  0.970  0.020  1.090
 JM5  C2   H2A   single  0.970  0.020  1.090
 JM5  S3   C2    single  1.806  0.020  1.806
 JM5  S3   C4    single  1.817  0.020  1.817
 JM5  C4   C5    single  1.522  0.020  1.522
 JM5  C4   H4    single  0.970  0.020  1.090
 JM5  C4   H4A   single  0.970  0.020  1.090
 JM5  C5   C6    single  1.523  0.020  1.523
 JM5  C5   H5    single  0.970  0.020  1.090
 JM5  C5   H5A   single  0.970  0.020  1.090
 JM5  C6   H6    single  0.970  0.020  1.090
 JM5  C6   H6A   single  0.970  0.020  1.090
 JM5  C6   H6B   single  0.970  0.020  1.090
 JM5  CA   C     single  1.523  0.020  1.523
 JM5  CA   CB    single  1.535  0.020  1.535
 JM5  CA   HA    single  0.970  0.020  1.090
 JM5  CB   HB    single  0.970  0.020  1.090
 JM5  CB   HBA   single  0.970  0.020  1.090
 JM5  CD   HD    single  0.970  0.020  1.090
 JM5  NE   C1    single  1.353  0.020  1.353
 JM5  NE   CD    single  1.444  0.020  1.444
 JM5  CG   CB    single  1.521  0.020  1.521
 JM5  CG   CD    single  1.520  0.020  1.520
 JM5  CG   HG    single  0.970  0.020  1.090
 JM5  CG   HGA   single  0.970  0.020  1.090
 JM5  NH   C1    double  1.278  0.020  1.278
 JM5  NH   HNH   single  0.890  0.020  1.040
 JM5  OA1  C     double  1.206  0.020  1.206
 JM5  OA2  HOA2  single  0.850  0.020  0.980
 JM5  CD   H20   single  0.970  0.020  1.090
 JM5  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
 JM5  OA2   C    OA1  123.27  3.000
 JM5  OA1   C    CA   124.57  3.000
 JM5  OA2   C    CA   112.16  3.000
 JM5  HNA   N    HN   106.35  3.000
 JM5  HNA   N    CA   110.20  3.000
 JM5  HN    N    CA   110.55  3.000
 JM5  NH    C1   NE   127.04  3.000
 JM5  NH    C1   C2   119.43  3.000
 JM5  NE    C1   C2   113.52  3.000
 JM5  H2A   C2   H2   106.90  3.000
 JM5  H2A   C2   S3   109.75  3.000
 JM5  H2    C2   S3   109.97  3.000
 JM5  S3    C2   C1   110.96  3.000
 JM5  H2A   C2   C1   109.81  3.000
 JM5  H2    C2   C1   109.36  3.000
 JM5  C4    S3   C2    98.24  3.000
 JM5  H4A   C4   H4   107.67  3.000
 JM5  H4A   C4   C5   110.23  3.000
 JM5  H4    C4   C5   110.22  3.000
 JM5  H4A   C4   S3   109.29  3.000
 JM5  H4    C4   S3   109.37  3.000
 JM5  C5    C4   S3   110.01  3.000
 JM5  H5A   C5   H5   106.60  3.000
 JM5  H5A   C5   C6   109.69  3.000
 JM5  H5    C5   C6   109.75  3.000
 JM5  H5A   C5   C4   109.53  3.000
 JM5  H5    C5   C4   109.55  3.000
 JM5  C6    C5   C4   111.59  3.000
 JM5  H6B   C6   H6A  107.67  3.000
 JM5  H6B   C6   H6   107.72  3.000
 JM5  H6A   C6   H6   107.72  3.000
 JM5  H6B   C6   C5   111.10  3.000
 JM5  H6A   C6   C5   111.25  3.000
 JM5  H6    C6   C5   111.20  3.000
 JM5  HA    CA   CB   107.97  3.000
 JM5  HA    CA   N    108.27  3.000
 JM5  CB    CA   N    110.55  3.000
 JM5  HA    CA   C    107.18  3.000
 JM5  CB    CA   C    109.09  3.000
 JM5  N     CA   C    113.57  3.000
 JM5  HBA   CB   HB   106.53  3.000
 JM5  HBA   CB   CG   109.46  3.000
 JM5  HB    CB   CG   109.97  3.000
 JM5  CG    CB   CA   112.35  3.000
 JM5  HBA   CB   CA   109.58  3.000
 JM5  HB    CB   CA   108.77  3.000
 JM5  H20   CD   HD   106.66  3.000
 JM5  H20   CD   CG   109.42  3.000
 JM5  HD    CD   CG   109.86  3.000
 JM5  H20   CD   NE   109.98  3.000
 JM5  CG    CD   NE   110.45  3.000
 JM5  HD    CD   NE   110.40  3.000
 JM5  H21   NE   CD   117.94  3.000
 JM5  H21   NE   C1   118.59  3.000
 JM5  CD    NE   C1   123.44  3.000
 JM5  HGA   CG   HG   106.99  3.000
 JM5  HGA   CG   CD   109.45  3.000
 JM5  HG    CG   CD   109.33  3.000
 JM5  HGA   CG   CB   109.86  3.000
 JM5  HG    CG   CB   109.41  3.000
 JM5  CD    CG   CB   111.68  3.000
 JM5  HNH   NH   C1   112.23  3.000
 JM5  HOA2  OA2  C    110.11  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
 JM5  CONST_01  CD    NE   C1  C2   180.00   0.0  0
 JM5  CONST_02  NH    C1   NE  CD     0.00   0.0  0
 JM5  CONST_03  H21   NE   C1  C2     0.00   0.0  0
 JM5  CONST_04  HNH   NH   C1  C2   180.00   0.0  0
 JM5  CONST_05  HOA2  OA2  C   CA   180.00   0.0  0
 JM5  Var_01    CG    CD   NE  C1   175.83  30.0  3
 JM5  Var_02    C5    C4   S3  C2   179.70  30.0  3
 JM5  Var_03    NE    C1   C2  S3   171.28  30.0  1
 JM5  Var_04    C6    C5   C4  S3  -179.95  30.0  3
 JM5  Var_05    CD    CG   CB  CA   178.92  30.0  1
 JM5  Var_06    NE    CD   CG  CB  -178.73  30.0  3
 JM5  Var_07    H2    C2   S3  C4    62.40  30.0  3
 JM5  Var_08    H6    C6   C5  C4   -60.90  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
 JM5  chir_01  CA  N  C  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
 JM5  plan-1  C1    0.020
 JM5  plan-1  C2    0.020
 JM5  plan-1  CD    0.020
 JM5  plan-1  NE    0.020
 JM5  plan-1  NH    0.020
 JM5  plan-1  HNH   0.020
 JM5  plan-1  H21   0.020
 JM5  plan-2  C     0.020
 JM5  plan-2  CA    0.020
 JM5  plan-2  OA1   0.020
 JM5  plan-2  OA2   0.020
 JM5  plan-2  HOA2  0.020

