# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:56:29 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 3-[(2S,5S)-5-(hydroxymethyl)-6-oxo-1,2,5,6-tetrahydropyrazin-2-yl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CC[C@@H]1NC(=O)[C@H](CO)N=C1
#
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
 9VA  9VA  3-[(2S,5S)-5-(hydroxymethyl)-6-oxo-1,2,5,6-tetrahydropyrazin-2-yl]propanamide  ligand  27  14  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9VA
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
 9VA  CAC  C  C1    0  -0.050  -0.9690  -0.0439  -1.8171
 9VA  NFB  N  N     0  -0.317  -2.1119  -0.3436  -1.3799
 9VA  CFA  C  CH1   0  -0.283  -2.4832   0.0766  -0.0470
 9VA  CFD  C  CH2   0  -0.126  -2.4363  -1.1134   0.9143
 9VA  OFE  O  OH1   0  -0.662  -3.3037  -2.1089   0.4396
 9VA  CEZ  C  C     0   0.508  -1.6821   1.2181   0.5568
 9VA  OFC  O  O     0  -0.492  -2.1246   1.8585   1.4999
 9VA  NAA  N  NH1   0  -0.625  -0.4904   1.4678   0.0004
 9VA  CAB  C  CH1   0  -0.149   0.0891   0.7351  -1.1007
 9VA  CAH  C  CH2   0  -0.416   1.2134  -0.2175  -0.6732
 9VA  CAJ  C  CH2   0  -0.589   2.3633   0.5122   0.0020
 9VA  CAK  C  C     0   0.533   3.5055  -0.4118   0.3720
 9VA  OAL  O  O     0  -0.495   3.3320  -1.5969   0.6192
 9VA  NAM  N  NH2   0  -0.804   4.7096   0.1757   0.4295
 9VA  H76  H  HCH1  0   0.283  -3.5209   0.4231  -0.0856
 9VA  H77  H  HCH2  0   0.201  -1.4005  -1.4737   0.9858
 9VA  H78  H  HCH2  0   0.218  -2.7263  -0.7595   1.9100
 9VA  H79  H  HOH1  0   0.459  -3.2764  -2.8439   1.0592
 9VA  H80  H  HNH1  0   0.406   0.0342   2.2456   0.3759
 9VA  H81  H  HCH1  0   0.285   0.5066   1.4590  -1.8080
 9VA  H82  H  HCH2  0   0.245   0.8046  -0.9820  -0.0098
 9VA  H83  H  HCH2  0   0.255   1.5754  -0.7315  -1.5673
 9VA  H84  H  HCH2  0   0.263   2.7257   1.3238  -0.6343
 9VA  H85  H  HCH2  0   0.279   2.0216   0.9837   0.9294
 9VA  H86  H  HNH2  0   0.406   4.8364   1.1522   0.2273
 9VA  H87  H  HNH2  0   0.399   5.5195  -0.3464   0.7215
 9VA  H2   H  H     0   0.271  -0.6908  -0.4007  -2.8074

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
 9VA  CAC  NFB  double  1.260  0.020  1.260
 9VA  CAC  CAB  single  1.497  0.020  1.497
 9VA  NFB  CFA  single  1.446  0.020  1.446
 9VA  CFA  CFD  single  1.530  0.020  1.530
 9VA  CFA  CEZ  single  1.520  0.020  1.520
 9VA  CFD  OFE  single  1.403  0.020  1.403
 9VA  CEZ  NAA  single  1.339  0.020  1.339
 9VA  CEZ  OFC  double  1.223  0.020  1.223
 9VA  NAA  CAB  single  1.444  0.020  1.444
 9VA  CAB  CAH  single  1.534  0.020  1.534
 9VA  CAH  CAJ  single  1.520  0.020  1.520
 9VA  CAJ  CAK  single  1.515  0.020  1.515
 9VA  CAK  OAL  double  1.223  0.020  1.223
 9VA  CAK  NAM  single  1.341  0.020  1.341
 9VA  CFA  H76  single  0.970  0.020  1.090
 9VA  CFD  H77  single  0.970  0.020  1.090
 9VA  CFD  H78  single  0.970  0.020  1.090
 9VA  OFE  H79  single  0.850  0.020  0.980
 9VA  NAA  H80  single  0.860  0.020  1.020
 9VA  CAB  H81  single  0.970  0.020  1.090
 9VA  CAH  H82  single  0.970  0.020  1.090
 9VA  CAH  H83  single  0.970  0.020  1.090
 9VA  CAJ  H84  single  0.970  0.020  1.090
 9VA  CAJ  H85  single  0.970  0.020  1.090
 9VA  NAM  H86  single  0.860  0.020  1.020
 9VA  NAM  H87  single  0.860  0.020  1.020
 9VA  CAC  H2   single  0.930  0.020  1.080

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
 9VA  H2   CAC  CAB  115.17  3.000
 9VA  H2   CAC  NFB  118.01  3.000
 9VA  CAB  CAC  NFB  126.80  3.000
 9VA  CFA  NFB  CAC  118.93  3.000
 9VA  H76  CFA  CEZ  106.02  3.000
 9VA  H76  CFA  CFD  107.30  3.000
 9VA  CEZ  CFA  CFD  108.56  3.000
 9VA  H76  CFA  NFB  107.63  3.000
 9VA  CEZ  CFA  NFB  116.68  3.000
 9VA  CFD  CFA  NFB  110.19  3.000
 9VA  H78  CFD  H77  107.23  3.000
 9VA  H78  CFD  OFE  111.90  3.000
 9VA  H77  CFD  OFE  111.84  3.000
 9VA  H78  CFD  CFA  108.15  3.000
 9VA  H77  CFD  CFA  108.95  3.000
 9VA  OFE  CFD  CFA  108.68  3.000
 9VA  H79  OFE  CFD  107.86  3.000
 9VA  NAA  CEZ  OFC  123.02  3.000
 9VA  OFC  CEZ  CFA  120.60  3.000
 9VA  NAA  CEZ  CFA  116.38  3.000
 9VA  H80  NAA  CAB  117.75  3.000
 9VA  H80  NAA  CEZ  116.83  3.000
 9VA  CAB  NAA  CEZ  125.41  3.000
 9VA  H81  CAB  CAH  108.12  3.000
 9VA  H81  CAB  NAA  108.07  3.000
 9VA  CAH  CAB  NAA  113.37  3.000
 9VA  H81  CAB  CAC  107.72  3.000
 9VA  CAH  CAB  CAC  109.17  3.000
 9VA  NAA  CAB  CAC  110.21  3.000
 9VA  H83  CAH  H82  106.97  3.000
 9VA  H83  CAH  CAJ  109.79  3.000
 9VA  H82  CAH  CAJ  110.46  3.000
 9VA  H83  CAH  CAB  107.86  3.000
 9VA  H82  CAH  CAB  109.25  3.000
 9VA  CAJ  CAH  CAB  112.34  3.000
 9VA  H85  CAJ  H84  106.07  3.000
 9VA  H85  CAJ  CAK  106.92  3.000
 9VA  H84  CAJ  CAK  110.18  3.000
 9VA  H85  CAJ  CAH  110.29  3.000
 9VA  H84  CAJ  CAH  110.40  3.000
 9VA  CAK  CAJ  CAH  112.71  3.000
 9VA  NAM  CAK  OAL  122.90  3.000
 9VA  NAM  CAK  CAJ  114.85  3.000
 9VA  OAL  CAK  CAJ  122.24  3.000
 9VA  H87  NAM  H86  117.43  3.000
 9VA  H87  NAM  CAK  120.50  3.000
 9VA  H86  NAM  CAK  122.02  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
 9VA  CONST_01  CAB  NAA  CEZ  CFA     0.00   0.0  0
 9VA  CONST_02  CAB  NAA  CEZ  OFC   180.00   0.0  0
 9VA  CONST_03  H80  NAA  CEZ  CFA   180.00   0.0  0
 9VA  CONST_04  H86  NAM  CAK  CAJ     0.00   0.0  0
 9VA  CONST_05  H87  NAM  CAK  CAJ   180.00   0.0  0
 9VA  Var_01    CAB  CAC  NFB  CFA    -0.58  30.0  1
 9VA  Var_02    CAK  CAJ  CAH  CAB  -177.43  30.0  3
 9VA  Var_03    OAL  CAK  CAJ  CAH   -28.05  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
 9VA  chir_01  CFA  NFB  CFD  CEZ  negativ
 9VA  chir_02  CAB  NAA  CAH  CAC  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
 9VA  plan-1  CAJ  0.020
 9VA  plan-1  CAK  0.020
 9VA  plan-1  OAL  0.020
 9VA  plan-1  NAM  0.020
 9VA  plan-1  H86  0.020
 9VA  plan-1  H87  0.020
 9VA  plan-2  CFA  0.020
 9VA  plan-2  CEZ  0.020
 9VA  plan-2  OFC  0.020
 9VA  plan-2  NAA  0.020
 9VA  plan-2  CAB  0.020
 9VA  plan-2  H80  0.020

