# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:18:52 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2S,5R)-1-formyl-3-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C[C@H](CN(C=O)[C@@H]1C(N)=O)NO[S](O)(=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
 JXG  JXG  (2S,5R)-1-formyl-3-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide  ligand  31  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JXG
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
 JXG  OAG  O  OS    0  -0.697  -3.2457  -1.3533   1.1828
 JXG  SAR  S  S     0   1.664  -3.8281  -0.0224   0.5603
 JXG  OAE  O  OS    0  -0.623  -4.5769  -0.3135  -0.6320
 JXG  OAF  O  OS    0  -0.619  -4.3955   0.7190   1.6481
 JXG  OAL  O  OC2   0  -0.472  -2.4992   0.8031   0.1766
 JXG  NAK  N  NH1   0  -0.373  -1.7167   0.0479  -0.7411
 JXG  CAO  C  CH1   0  -0.138  -0.3504  -0.0045  -0.2345
 JXG  CAJ  C  CH2   0  -0.291   0.4094  -0.9386  -1.1657
 JXG  CAI  C  C1    0  -0.289   0.3416   1.3267  -0.2209
 JXG  CAN  C  C     0   0.088   1.6492   1.4541  -0.4266
 JXG  CAD  C  CH3   0  -0.710   2.3335   2.7835  -0.5002
 JXG  CAP  C  CH1   0  -0.205   2.5437   0.2451  -0.5482
 JXG  CAM  C  C     0   0.515   3.2878   0.1230   0.7959
 JXG  O2   O  O     0  -0.469   2.7276  -0.3255   1.7791
 JXG  N    N  NH2   0  -0.789   4.5257   0.6275   0.7953
 JXG  NAQ  N  NT    0  -0.454   1.8053  -0.9756  -0.7946
 JXG  CAH  C  C1    0   0.271   2.4807  -2.1369  -0.8024
 JXG  O    O  O     0  -0.482   3.6775  -2.2340  -0.6002
 JXG  H1   H  HNH1  0   0.399  -1.7543   0.5918  -1.5997
 JXG  H2   H  HCH1  0   0.286  -0.3894  -0.4505   0.7630
 JXG  H3   H  HCH2  0   0.279   0.0076  -1.9492  -1.1054
 JXG  H4   H  HCH2  0   0.254   0.2938  -0.5954  -2.1994
 JXG  H5   H  H     0   0.265  -0.2620   2.2173  -0.0801
 JXG  H6   H  HCH3  0   0.253   1.6132   3.5972  -0.4399
 JXG  H7   H  HCH3  0   0.249   3.0596   2.9174   0.3039
 JXG  H8   H  HCH3  0   0.247   2.8827   2.8812  -1.4393
 JXG  H9   H  HCH1  0   0.296   3.2639   0.4122  -1.3583
 JXG  H10  H  HNH2  0   0.405   5.0766   0.6221   1.6386
 JXG  H11  H  HNH2  0   0.409   4.9933   0.8856  -0.0568
 JXG  H13  H  H     0   0.215   1.8410  -3.0072  -1.0097
 JXG  H14  H  H     0   0.514  -3.0403  -2.0246   0.5092

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
 JXG  N    CAM  single  1.337  0.020  1.337
 JXG  CAM  O2   double  1.217  0.020  1.217
 JXG  CAM  CAP  single  1.541  0.020  1.541
 JXG  CAD  CAN  single  1.497  0.020  1.497
 JXG  CAP  CAN  single  1.509  0.020  1.509
 JXG  CAP  NAQ  single  1.448  0.020  1.448
 JXG  O    CAH  double  1.218  0.020  1.218
 JXG  CAN  CAI  double  1.330  0.020  1.330
 JXG  NAQ  CAH  single  1.343  0.020  1.343
 JXG  NAQ  CAJ  single  1.445  0.020  1.445
 JXG  CAI  CAO  single  1.500  0.020  1.500
 JXG  CAJ  CAO  single  1.522  0.020  1.522
 JXG  CAO  NAK  single  1.458  0.020  1.458
 JXG  OAF  SAR  double  1.434  0.020  1.434
 JXG  OAL  SAR  single  1.611  0.020  1.611
 JXG  OAL  NAK  single  1.423  0.020  1.423
 JXG  SAR  OAE  double  1.438  0.020  1.438
 JXG  SAR  OAG  single  1.580  0.020  1.580
 JXG  NAK  H1   single  0.890  0.020  1.040
 JXG  CAO  H2   single  0.970  0.020  1.090
 JXG  CAJ  H3   single  0.970  0.020  1.090
 JXG  CAJ  H4   single  0.970  0.020  1.090
 JXG  CAI  H5   single  0.930  0.020  1.080
 JXG  CAD  H6   single  0.970  0.020  1.090
 JXG  CAD  H7   single  0.970  0.020  1.090
 JXG  CAD  H8   single  0.970  0.020  1.090
 JXG  CAP  H9   single  0.970  0.020  1.090
 JXG  N    H10  single  0.860  0.020  1.020
 JXG  N    H11  single  0.860  0.020  1.020
 JXG  CAH  H13  single  0.930  0.020  1.080
 JXG  OAG  H14  single  0.850  0.020  0.980

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
 JXG  H14  OAG  SAR  112.71  3.000
 JXG  OAL  SAR  OAF  104.02  3.000
 JXG  OAL  SAR  OAE  109.63  3.000
 JXG  OAF  SAR  OAE  121.86  3.000
 JXG  OAE  SAR  OAG  110.37  3.000
 JXG  OAL  SAR  OAG  102.79  3.000
 JXG  OAF  SAR  OAG  106.40  3.000
 JXG  NAK  OAL  SAR  109.59  3.000
 JXG  H1   NAK  CAO  110.31  3.000
 JXG  H1   NAK  OAL  103.90  3.000
 JXG  CAO  NAK  OAL  108.08  3.000
 JXG  H2   CAO  CAI  111.72  3.000
 JXG  H2   CAO  CAJ  109.00  3.000
 JXG  CAI  CAO  CAJ  108.65  3.000
 JXG  H2   CAO  NAK  107.35  3.000
 JXG  CAJ  CAO  NAK  106.10  3.000
 JXG  CAI  CAO  NAK  113.79  3.000
 JXG  H4   CAJ  H3   107.70  3.000
 JXG  H4   CAJ  NAQ  110.63  3.000
 JXG  H3   CAJ  NAQ  108.57  3.000
 JXG  H4   CAJ  CAO  109.41  3.000
 JXG  H3   CAJ  CAO  110.57  3.000
 JXG  NAQ  CAJ  CAO  109.93  3.000
 JXG  H5   CAI  CAN  119.24  3.000
 JXG  H5   CAI  CAO  118.22  3.000
 JXG  CAN  CAI  CAO  122.49  3.000
 JXG  CAP  CAN  CAD  115.89  3.000
 JXG  CAP  CAN  CAI  121.24  3.000
 JXG  CAD  CAN  CAI  122.83  3.000
 JXG  H8   CAD  H7   106.73  3.000
 JXG  H8   CAD  H6   108.27  3.000
 JXG  H7   CAD  H6   107.92  3.000
 JXG  H8   CAD  CAN  110.58  3.000
 JXG  H7   CAD  CAN  112.13  3.000
 JXG  H6   CAD  CAN  111.02  3.000
 JXG  H9   CAP  NAQ  109.73  3.000
 JXG  H9   CAP  CAM  109.83  3.000
 JXG  NAQ  CAP  CAM  109.14  3.000
 JXG  H9   CAP  CAN  109.07  3.000
 JXG  NAQ  CAP  CAN  112.76  3.000
 JXG  CAM  CAP  CAN  106.23  3.000
 JXG  N    CAM  O2   124.44  3.000
 JXG  O2   CAM  CAP  120.76  3.000
 JXG  N    CAM  CAP  114.63  3.000
 JXG  H11  N    H10  117.16  3.000
 JXG  H11  N    CAM  121.86  3.000
 JXG  H10  N    CAM  120.27  3.000
 JXG  CAH  NAQ  CAP  118.25  3.000
 JXG  CAH  NAQ  CAJ  120.42  3.000
 JXG  CAP  NAQ  CAJ  120.99  3.000
 JXG  H13  CAH  O    122.68  3.000
 JXG  H13  CAH  NAQ  113.12  3.000
 JXG  O    CAH  NAQ  124.20  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
 JXG  CONST_01  O    CAH  NAQ  CAJ   180.00   0.0  0
 JXG  CONST_02  O    CAH  NAQ  CAP     0.00   0.0  0
 JXG  CONST_03  H10  N    CAM  CAP   180.00   0.0  0
 JXG  CONST_04  H11  N    CAM  CAP     0.00   0.0  0
 JXG  Var_01    CAP  CAN  CAI  CAO    -6.32  30.0  1
 JXG  Var_02    CAP  NAQ  CAJ  CAO   -47.70  30.0  1
 JXG  Var_03    H6   CAD  CAN  CAI    -4.28  30.0  3
 JXG  Var_04    CAO  NAK  OAL  SAR  -129.35  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
 JXG  chir_01  CAO  CAI  CAJ  NAK  positiv
 JXG  chir_02  CAP  NAQ  CAN  CAM  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
 JXG  plan-1  CAP  0.020
 JXG  plan-1  CAM  0.020
 JXG  plan-1  O2   0.020
 JXG  plan-1  N    0.020
 JXG  plan-1  H10  0.020
 JXG  plan-1  H11  0.020
 JXG  plan-2  CAJ  0.020
 JXG  plan-2  CAP  0.020
 JXG  plan-2  NAQ  0.020
 JXG  plan-2  CAH  0.020
 JXG  plan-2  O    0.020
 JXG  plan-2  H13  0.020

