# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:56:34 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  37  16  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.521   6.0299  -0.0589   0.2549
 JM8  N     N  NH2   0  -0.776   4.7176   1.8718  -0.5854
 JM8  C1    C  C     0   0.428  -1.3711  -0.5886  -0.2925
 JM8  C2    C  CH2   0  -0.538  -2.5940   0.1099   0.2695
 JM8  C3    C  CH2   0  -0.576  -3.9110  -0.3849  -0.3018
 JM8  S4    S  S2    0  -0.032  -5.2791   0.5214   0.4707
 JM8  C5    C  CH2   0  -0.535  -6.6863  -0.3238  -0.3064
 JM8  C6    C  CH3   0  -0.663  -7.9893   0.2178   0.2544
 JM8  CA    C  CH1   0  -0.207   4.7187   0.7170   0.2790
 JM8  CB    C  CH2   0  -0.433   3.5632  -0.2297  -0.0736
 JM8  CD    C  CH2   0  -0.226   1.0769  -0.5458  -0.2460
 JM8  NE    N  NH1   0  -0.640  -0.2124   0.0692  -0.0319
 JM8  CG    C  CH2   0  -0.457   2.1986   0.4273   0.0807
 JM8  NH    N  N     0  -0.678  -1.3543  -1.6898  -0.9417
 JM8  OA1   O  O     0  -0.440   6.8877   0.0700  -0.5826
 JM8  OA2   O  OH1   0  -0.594   6.1227  -0.9151   1.2663
 JM8  HN    H  HNH2  0   0.354   5.4338   2.5278  -0.3014
 JM8  HNA   H  HNH2  0   0.343   4.9411   1.5986  -1.5346
 JM8  H2    H  HCH2  0   0.276  -2.5896  -0.0304   1.3549
 JM8  H2A   H  HCH2  0   0.265  -2.4949   1.1849   0.0997
 JM8  H3    H  HCH2  0   0.273  -3.9458  -0.2397  -1.3832
 JM8  H3A   H  HCH2  0   0.264  -4.0506  -1.4484  -0.0968
 JM8  H5    H  HCH2  0   0.261  -6.6394  -0.1728  -1.3861
 JM8  H5A   H  HCH2  0   0.260  -6.6006  -1.3949  -0.1159
 JM8  H6    H  HCH3  0   0.246  -8.8337  -0.2860  -0.2159
 JM8  H6A   H  HCH3  0   0.234  -8.0591   0.0542   1.3298
 JM8  H6B   H  HCH3  0   0.234  -8.0921   1.2866   0.0665
 JM8  HA    H  HCH1  0   0.267   4.5676   1.0603   1.3082
 JM8  HB    H  HCH2  0   0.233   3.6922  -0.5845  -1.1022
 JM8  HBA   H  HCH2  0   0.243   3.6095  -1.1127   0.5679
 JM8  HD    H  HCH2  0   0.210   1.1792  -1.4535   0.3627
 JM8  HG    H  HCH2  0   0.223   2.0869   0.7818   1.1113
 JM8  HGA   H  HCH2  0   0.238   2.1302   1.3035  -0.5660
 JM8  HNH   H  H     0   0.330  -2.2917  -2.0457  -1.0825
 JM8  HOA2  H  HOH1  0   0.481   6.9549  -1.4088   1.2134
 JM8  H20   H  HCH2  0   0.224   1.1530  -0.8642  -1.2881
 JM8  H21   H  HNH1  0   0.387  -0.2506   0.8096   0.6498

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  1.524  0.020  1.524
 JM8  C    OA2   single  1.328  0.020  1.328
 JM8  N    HN    single  0.890  0.020  1.040
 JM8  N    HNA   single  0.890  0.020  1.040
 JM8  C1   NE    single  1.358  0.020  1.358
 JM8  C1   NH    double  1.278  0.020  1.278
 JM8  C2   C1    single  1.516  0.020  1.516
 JM8  C2   C3    single  1.518  0.020  1.518
 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  1.518  0.020  1.518
 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  1.443  0.020  1.443
 JM8  CA   HA    single  0.970  0.020  1.090
 JM8  CB   CA    single  1.535  0.020  1.535
 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  1.445  0.020  1.445
 JM8  CD   CG    single  1.520  0.020  1.520
 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     double  1.206  0.020  1.206
 JM8  OA2  HOA2  single  0.850  0.020  0.980
 JM8  CD   H20   single  0.970  0.020  1.090
 JM8  NE   H21   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
 JM8  OA2   C    OA1  123.23  3.000
 JM8  OA1   C    CA   124.67  3.000
 JM8  OA2   C    CA   112.10  3.000
 JM8  HNA   N    HN   106.36  3.000
 JM8  HNA   N    CA   110.21  3.000
 JM8  HN    N    CA   110.50  3.000
 JM8  NH    C1   NE   120.24  3.000
 JM8  NH    C1   C2   126.56  3.000
 JM8  NE    C1   C2   113.20  3.000
 JM8  H2A   C2   H2   106.25  3.000
 JM8  H2A   C2   C3   109.92  3.000
 JM8  H2    C2   C3   109.56  3.000
 JM8  H2A   C2   C1   108.81  3.000
 JM8  H2    C2   C1   107.77  3.000
 JM8  C3    C2   C1   114.20  3.000
 JM8  H3A   C3   H3   108.15  3.000
 JM8  H3A   C3   S4   108.07  3.000
 JM8  H3    C3   S4   109.36  3.000
 JM8  H3A   C3   C2   110.95  3.000
 JM8  H3    C3   C2   110.91  3.000
 JM8  S4    C3   C2   109.34  3.000
 JM8  C5    S4   C3    99.76  3.000
 JM8  H5A   C5   H5   107.77  3.000
 JM8  H5A   C5   C6   110.67  3.000
 JM8  H5    C5   C6   110.67  3.000
 JM8  C6    C5   S4   109.93  3.000
 JM8  H5A   C5   S4   108.74  3.000
 JM8  H5    C5   S4   109.01  3.000
 JM8  H6B   C6   H6A  108.14  3.000
 JM8  H6B   C6   H6   107.80  3.000
 JM8  H6A   C6   H6   107.86  3.000
 JM8  H6B   C6   C5   111.53  3.000
 JM8  H6A   C6   C5   111.46  3.000
 JM8  H6    C6   C5   109.91  3.000
 JM8  HA    CA   CB   107.78  3.000
 JM8  CB    CA   N    110.82  3.000
 JM8  HA    CA   N    108.18  3.000
 JM8  CB    CA   C    109.28  3.000
 JM8  HA    CA   C    107.05  3.000
 JM8  N     CA   C    113.50  3.000
 JM8  HBA   CB   HB   106.53  3.000
 JM8  HBA   CB   CG   109.11  3.000
 JM8  HB    CB   CG   109.90  3.000
 JM8  HBA   CB   CA   109.37  3.000
 JM8  HB    CB   CA   109.07  3.000
 JM8  CG    CB   CA   112.66  3.000
 JM8  H20   CD   HD   106.35  3.000
 JM8  H20   CD   CG   109.88  3.000
 JM8  HD    CD   CG   109.96  3.000
 JM8  H20   CD   NE   109.13  3.000
 JM8  HD    CD   NE   110.68  3.000
 JM8  CG    CD   NE   110.74  3.000
 JM8  H21   NE   CD   116.56  3.000
 JM8  H21   NE   C1   116.99  3.000
 JM8  CD    NE   C1   121.80  3.000
 JM8  HGA   CG   HG   106.94  3.000
 JM8  HGA   CG   CD   109.91  3.000
 JM8  HG    CG   CD   109.51  3.000
 JM8  HGA   CG   CB   110.04  3.000
 JM8  HG    CG   CB   109.05  3.000
 JM8  CD    CG   CB   111.30  3.000
 JM8  HNH   NH   C1   111.17  3.000
 JM8  HOA2  OA2  C    110.29  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  CONST_05  HOA2  OA2  C   CA   180.00   0.0  0
 JM8  Var_01    CG    CD   NE  C1   178.05  30.0  2
 JM8  Var_02    S4    C3   C2  C1   179.37  30.0  3
 JM8  Var_03    NE    C1   C2  C3   164.76  30.0  3
 JM8  Var_04    C6    C5   S4  C3   176.70  30.0  1
 JM8  Var_05    CD    CG   CB  CA  -178.73  30.0  3
 JM8  Var_06    NE    CD   CG  CB   177.15  30.0  1
 JM8  Var_07    H6    C6   C5  S4   179.71  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
 JM8  plan-2  HOA2  0.020

