# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:00:05 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  31  14  .  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_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   0.521   4.9697  -0.1714   0.1554
 JM2  N     N  NH2   0  -0.776   3.7152   1.7941  -0.6924
 JM2  C1    C  C     0   0.425  -2.4614  -0.3168  -0.1318
 JM2  C2    C  CH2   0  -0.655  -3.6426   0.4373   0.4473
 JM2  S3    S  S2    0  -0.027  -5.0121   0.4852  -0.7391
 JM2  C4    C  CH3   0  -0.767  -6.3622   0.9117   0.3812
 JM2  CA    C  CH1   0  -0.207   3.7006   0.6699   0.2113
 JM2  CB    C  CH2   0  -0.433   2.4867  -0.2303  -0.0559
 JM2  CD    C  CH2   0  -0.230  -0.0168  -0.4288  -0.1107
 JM2  NE    N  NH1   0  -0.635  -1.2646   0.2556   0.1362
 JM2  CG    C  CH2   0  -0.456   1.1635   0.4991   0.1288
 JM2  NH    N  N     0  -0.660  -2.5393  -1.4076  -0.7929
 JM2  OA1   O  O     0  -0.440   5.7873  -0.1216  -0.7293
 JM2  OA2   O  OH1   0  -0.594   5.0743  -0.9884   1.1979
 JM2  HN    H  HNH2  0   0.354   4.4760   2.4212  -0.4649
 JM2  HNA   H  HNH2  0   0.343   3.8799   1.4792  -1.6407
 JM2  H2    H  HCH2  0   0.300  -3.9777  -0.0855   1.3468
 JM2  H2A   H  HCH2  0   0.283  -3.3636   1.4513   0.7368
 JM2  H4    H  HCH3  0   0.266  -6.2018   1.8832   0.8453
 JM2  H4A   H  HCH3  0   0.278  -7.2743   0.9549  -0.2112
 JM2  H4B   H  HCH3  0   0.266  -6.4817   0.1546   1.1548
 JM2  HA    H  HCH1  0   0.267   3.6149   1.0548   1.2332
 JM2  HB    H  HCH2  0   0.233   2.5526  -0.6288  -1.0744
 JM2  HBA   H  HCH2  0   0.244   2.5188  -1.0910   0.6161
 JM2  HD    H  HCH2  0   0.215   0.0669  -1.3195   0.5249
 JM2  HG    H  HCH2  0   0.225   1.1162   0.9017   1.1465
 JM2  HGA   H  HCH2  0   0.239   1.1083   1.3503  -0.5514
 JM2  HNH   H  H     0   0.322  -3.5109  -1.6719  -0.9158
 JM2  HOA2  H  HOH1  0   0.481   5.8772  -1.5258   1.1234
 JM2  H16   H  HCH2  0   0.229  -0.0073  -0.7848  -1.1429
 JM2  H17   H  HNH1  0   0.390  -1.2467   1.0037   0.8094

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  1.524  0.020  1.524
 JM2  C    OA2   single  1.329  0.020  1.329
 JM2  N    HN    single  0.890  0.020  1.040
 JM2  N    HNA   single  0.890  0.020  1.040
 JM2  C1   NH    double  1.278  0.020  1.278
 JM2  C1   NE    single  1.353  0.020  1.353
 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  1.812  0.020  1.812
 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  1.442  0.020  1.442
 JM2  CA   HA    single  0.970  0.020  1.090
 JM2  CB   CA    single  1.535  0.020  1.535
 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  1.444  0.020  1.444
 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     double  1.206  0.020  1.206
 JM2  OA2  HOA2  single  0.850  0.020  0.980
 JM2  CD   H16   single  0.970  0.020  1.090
 JM2  NE   H17   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
 JM2  OA2   C    OA1  123.22  3.000
 JM2  OA1   C    CA   124.67  3.000
 JM2  OA2   C    CA   112.10  3.000
 JM2  HNA   N    HN   106.31  3.000
 JM2  HNA   N    CA   110.24  3.000
 JM2  HN    N    CA   110.47  3.000
 JM2  NH    C1   NE   121.16  3.000
 JM2  NE    C1   C2   113.76  3.000
 JM2  NH    C1   C2   125.07  3.000
 JM2  H2A   C2   H2   107.74  3.000
 JM2  H2A   C2   S3   110.02  3.000
 JM2  H2    C2   S3   108.64  3.000
 JM2  S3    C2   C1   110.60  3.000
 JM2  H2A   C2   C1   111.37  3.000
 JM2  H2    C2   C1   108.38  3.000
 JM2  C4    S3   C2    99.50  3.000
 JM2  H4B   C4   H4A  108.80  3.000
 JM2  H4B   C4   H4   109.50  3.000
 JM2  H4A   C4   H4   108.67  3.000
 JM2  H4B   C4   S3   111.01  3.000
 JM2  H4A   C4   S3   107.36  3.000
 JM2  H4    C4   S3   111.41  3.000
 JM2  HA    CA   CB   107.86  3.000
 JM2  CB    CA   N    110.86  3.000
 JM2  HA    CA   N    108.15  3.000
 JM2  CB    CA   C    109.18  3.000
 JM2  HA    CA   C    107.06  3.000
 JM2  N     CA   C    113.51  3.000
 JM2  HBA   CB   HB   106.47  3.000
 JM2  HBA   CB   CG   109.17  3.000
 JM2  HB    CB   CG   109.84  3.000
 JM2  HBA   CB   CA   109.38  3.000
 JM2  HB    CB   CA   109.12  3.000
 JM2  CG    CB   CA   112.67  3.000
 JM2  H16   CD   HD   106.39  3.000
 JM2  H16   CD   CG   109.95  3.000
 JM2  HD    CD   CG   110.17  3.000
 JM2  H16   CD   NE   108.88  3.000
 JM2  HD    CD   NE   110.58  3.000
 JM2  CG    CD   NE   110.76  3.000
 JM2  H17   NE   CD   116.82  3.000
 JM2  H17   NE   C1   117.54  3.000
 JM2  CD    NE   C1   121.98  3.000
 JM2  HGA   CG   HG   106.87  3.000
 JM2  HGA   CG   CD   109.80  3.000
 JM2  HG    CG   CD   109.71  3.000
 JM2  HGA   CG   CB   110.01  3.000
 JM2  HG    CG   CB   109.05  3.000
 JM2  CD    CG   CB   111.30  3.000
 JM2  HNH   NH   C1   110.09  3.000
 JM2  HOA2  OA2  C    110.24  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  CONST_05  HOA2  OA2  C   CA   180.00   0.0  0
 JM2  Var_01    CG    CD   NE  C1   173.50  30.0  1
 JM2  Var_02    NH    C1   C2  S3   -42.57  30.0  3
 JM2  Var_03    CD    CG   CB  CA  -178.64  30.0  3
 JM2  Var_04    NE    CD   CG  CB   176.97  30.0  2
 JM2  Var_05    H4    C4   S3  C2    62.28  30.0  3
 JM2  Var_06    H2    C2   S3  C4    43.34  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
 JM2  plan-2  HOA2  0.020

