# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 19:42:54 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])NCCC[C@@H]1NC(=O)[C@H]2CCCN2C1=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
 0HZ  0HZ  amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium  peptide  38  18  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0HZ
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
 0HZ  N     N  NT    0  -0.482  17.6240  44.7786  101.8189
 0HZ  CA    C  CH1   0  -0.192  18.2848  44.6460  103.1099
 0HZ  CB    C  CH2   0  -0.448  18.9597  46.0007  103.2817
 0HZ  CG    C  CH2   0  -0.502  17.9447  46.9479  102.6474
 0HZ  CD    C  CH2   0  -0.253  17.4137  46.1721  101.4422
 0HZ  C     C  C     0   0.549  19.2176  43.4563  103.1669
 0HZ  O     O  O     0  -0.472  20.1925  43.4429  103.8988
 0HZ  N1    N  NH1   0  -0.631  18.8661  42.4378  102.3676
 0HZ  CA1   C  CH1   0  -0.224  17.6426  42.3823  101.5919
 0HZ  C1    C  C     0   0.550  17.2823  43.7515  101.0390
 0HZ  O1    O  O     0  -0.487  16.6992  43.8760   99.9721
 0HZ  CB1   C  CH2   0  -0.425  16.4521  41.8097  102.3699
 0HZ  CG1   C  CH2   0  -0.480  16.6951  40.3861  102.8495
 0HZ  CD1   C  CH2   0  -0.272  15.4488  39.8227  103.5091
 0HZ  NE    N  NH1   0  -0.635  15.6848  38.4597  103.9535
 0HZ  CZ    C  C     0   0.826  14.7891  37.7139  104.5871
 0HZ  NH1   N  NH2   0  -0.821  15.1062  36.4832  104.9724
 0HZ  NH2   N  NC2   1  -0.815  13.5786  38.1918  104.8446
 0HZ  HA    H  HCH1  0   0.296  17.5371  44.5067  103.9039
 0HZ  HB2   H  HCH2  0   0.261  19.1676  46.2304  104.3245
 0HZ  HB3   H  HCH2  0   0.248  19.9030  46.0215  102.7319
 0HZ  HG2   H  HCH2  0   0.246  17.1357  47.1525  103.3507
 0HZ  HG3   H  HCH2  0   0.262  18.3807  47.9024  102.3578
 0HZ  HD2   H  HCH2  0   0.247  17.9741  46.4002  100.5326
 0HZ  HD3   H  HCH2  0   0.253  16.3601  46.3713  101.2443
 0HZ  H     H  HNH1  0   0.406  19.4452  41.6103  102.3866
 0HZ  HA1   H  HCH1  0   0.299  17.8390  41.7368  100.7340
 0HZ  HB21  H  HCH2  0   0.251  16.2158  42.4545  103.2221
 0HZ  HB31  H  HCH2  0   0.254  15.5808  41.8276  101.7098
 0HZ  HG21  H  HCH2  0   0.251  16.9758  39.7566  101.9994
 0HZ  HG31  H  HCH2  0   0.252  17.5262  40.3607  103.5589
 0HZ  HD21  H  HCH2  0   0.260  15.1702  40.4458  104.3639
 0HZ  HD31  H  HCH2  0   0.258  14.6191  39.8461  102.7960
 0HZ  HE    H  HNH1  0   0.428  16.5751  38.0394  103.7336
 0HZ  HH11  H  HNH2  0   0.432  14.4428  35.9027  105.4574
 0HZ  HH12  H  HNH2  0   0.431  16.0463  36.1337  104.8889
 0HZ  HH21  H  HNC2  0   0.445  13.2611  39.0681  104.4666
 0HZ  HH22  H  HNC2  0   0.435  12.8910  37.6262  105.3144

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
 0HZ  N    CA    single  1.458  0.019  1.458
 0HZ  N    CD    single  1.473  0.014  1.473
 0HZ  CA   CB    single  1.521  0.033  1.521
 0HZ  CA   C     single  1.525  0.021  1.525
 0HZ  CA   HA    single  0.970  0.020  0.970
 0HZ  CB   CG    single  1.526  0.020  1.526
 0HZ  CB   HB2   single  0.970  0.020  1.090
 0HZ  CB   HB3   single  0.970  0.020  1.090
 0HZ  CG   CD    single  1.528  0.020  1.528
 0HZ  CG   HG2   single  0.970  0.020  1.090
 0HZ  CG   HG3   single  0.970  0.020  1.090
 0HZ  CD   HD2   single  0.970  0.020  1.090
 0HZ  CD   HD3   single  0.970  0.020  1.090
 0HZ  C    O     double  1.231  0.020  1.231
 0HZ  N1   CA1   single  1.450  0.020  1.450
 0HZ  N1   H     single  0.860  0.020  1.020
 0HZ  CA1  C1    single  1.520  0.020  1.520
 0HZ  CA1  CB1   single  1.533  0.020  1.533
 0HZ  CA1  HA1   single  0.970  0.020  1.090
 0HZ  C1   O1    double  1.222  0.020  1.222
 0HZ  CB1  CG1   single  1.522  0.020  1.522
 0HZ  CB1  HB21  single  0.970  0.020  1.090
 0HZ  CB1  HB31  single  0.970  0.020  1.090
 0HZ  CG1  CD1   single  1.519  0.020  1.519
 0HZ  CG1  HG21  single  0.970  0.020  1.090
 0HZ  CG1  HG31  single  0.970  0.020  1.090
 0HZ  CD1  NE    single  1.453  0.020  1.453
 0HZ  CD1  HD21  single  0.970  0.020  1.090
 0HZ  CD1  HD31  single  0.970  0.020  1.090
 0HZ  NE   CZ    single  1.327  0.020  1.327
 0HZ  NE   HE    single  0.860  0.020  1.020
 0HZ  CZ   NH1   single  1.328  0.020  1.328
 0HZ  CZ   NH2   double  1.327  0.020  1.327
 0HZ  NH1  HH11  single  0.860  0.020  1.020
 0HZ  NH1  HH12  single  0.860  0.020  1.020
 0HZ  NH2  HH21  single  0.860  0.020  1.020
 0HZ  NH2  HH22  single  0.860  0.020  1.020
 0HZ  N    C1    single  1.334  0.020  1.334
 0HZ  N1   C     single  1.342  0.020  1.342

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
 0HZ  C1    N    CD    123.20  3.000
 0HZ  C1    N    CA    124.36  3.000
 0HZ  CD    N    CA    112.41  3.000
 0HZ  HA    CA   C     110.00  3.000
 0HZ  HA    CA   CB    109.00  3.000
 0HZ  C     CA   CB    110.50  1.500
 0HZ  HA    CA   N     110.00  3.000
 0HZ  C     CA   N     111.00  2.800
 0HZ  CB    CA   N     110.40  1.500
 0HZ  HB3   CB   HB2   108.27  3.000
 0HZ  HB3   CB   CG    110.69  3.000
 0HZ  HB2   CB   CG    113.23  3.000
 0HZ  HB3   CB   CA    110.05  3.000
 0HZ  HB2   CB   CA    112.37  3.000
 0HZ  CG    CB   CA    102.14  3.000
 0HZ  HG3   CG   HG2   107.69  3.000
 0HZ  HG3   CG   CD    111.99  3.000
 0HZ  HG2   CG   CD    110.23  3.000
 0HZ  HG3   CG   CB    112.85  3.000
 0HZ  HG2   CG   CB    109.96  3.000
 0HZ  CD    CG   CB    104.11  3.000
 0HZ  HD3   CD   HD2   107.84  3.000
 0HZ  HD3   CD   CG    112.71  3.000
 0HZ  HD2   CD   CG    111.86  3.000
 0HZ  HD3   CD   N     111.14  3.000
 0HZ  HD2   CD   N     109.91  3.000
 0HZ  CG    CD   N     103.20  1.500
 0HZ  N1    C    O     123.97  3.000
 0HZ  N1    C    CA    114.40  3.000
 0HZ  O     C    CA    120.80  1.700
 0HZ  H     N1   CA1   117.54  3.000
 0HZ  H     N1   C     117.42  3.000
 0HZ  CA1   N1   C     124.68  3.000
 0HZ  HA1   CA1  CB1   108.53  3.000
 0HZ  HA1   CA1  C1    106.83  3.000
 0HZ  CB1   CA1  C1    109.69  3.000
 0HZ  HA1   CA1  N1    106.94  3.000
 0HZ  CB1   CA1  N1    113.46  3.000
 0HZ  C1    CA1  N1    111.11  3.000
 0HZ  O1    C1   CA1   121.49  3.000
 0HZ  O1    C1   N     123.65  3.000
 0HZ  CA1   C1   N     114.84  3.000
 0HZ  HB31  CB1  HB21  106.77  3.000
 0HZ  HB31  CB1  CG1   109.44  3.000
 0HZ  HB21  CB1  CG1   109.89  3.000
 0HZ  HB31  CB1  CA1   107.84  3.000
 0HZ  HB21  CB1  CA1   110.04  3.000
 0HZ  CG1   CB1  CA1   112.66  3.000
 0HZ  HG31  CG1  HG21  107.21  3.000
 0HZ  HG31  CG1  CD1   109.48  3.000
 0HZ  HG21  CG1  CD1   109.54  3.000
 0HZ  HG31  CG1  CB1   110.35  3.000
 0HZ  HG21  CG1  CB1   109.52  3.000
 0HZ  CD1   CG1  CB1   110.67  3.000
 0HZ  HD31  CD1  HD21  107.69  3.000
 0HZ  HD31  CD1  NE    110.04  3.000
 0HZ  HD21  CD1  NE    109.68  3.000
 0HZ  HD31  CD1  CG1   109.35  3.000
 0HZ  HD21  CD1  CG1   109.70  3.000
 0HZ  NE    CD1  CG1   110.34  3.000
 0HZ  HE    NE   CZ    117.76  3.000
 0HZ  HE    NE   CD1   117.87  3.000
 0HZ  CZ    NE   CD1   124.32  3.000
 0HZ  NH2   CZ   NH1   119.69  3.000
 0HZ  NH2   CZ   NE    120.41  3.000
 0HZ  NH1   CZ   NE    119.89  3.000
 0HZ  HH12  NH1  HH11  117.10  3.000
 0HZ  HH12  NH1  CZ    121.39  3.000
 0HZ  HH11  NH1  CZ    121.14  3.000
 0HZ  HH22  NH2  HH21  116.70  3.000
 0HZ  HH22  NH2  CZ    120.75  3.000
 0HZ  HH21  NH2  CZ    121.94  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
 0HZ  CONST_01  CA1   C1   N    CA      0.00   0.0  0
 0HZ  CONST_02  CA1   N1   C    CA      0.00   0.0  0
 0HZ  CONST_03  CA1   C1   N    CD    180.00   0.0  0
 0HZ  CONST_04  O1    C1   N    CA    180.00   0.0  0
 0HZ  CONST_05  O1    C1   N    CD      0.00   0.0  0
 0HZ  CONST_06  CA1   N1   C    O     180.00   0.0  0
 0HZ  CONST_07  H     N1   C    CA    180.00   0.0  0
 0HZ  CONST_08  NH1   CZ   NE   CD1   180.00   0.0  0
 0HZ  CONST_09  NH2   CZ   NE   CD1     0.00   0.0  0
 0HZ  CONST_10  HH11  NH1  CZ   NE    180.00   0.0  0
 0HZ  CONST_11  HH12  NH1  CZ   NE      0.00   0.0  0
 0HZ  CONST_12  HH21  NH2  CZ   NE      0.00   0.0  0
 0HZ  CONST_13  HH22  NH2  CZ   NE    180.00   0.0  0
 0HZ  CONST_14  HE    NE   CZ   NH1     0.00   0.0  0
 0HZ  Var_01    CB    CG   CD   N      25.41  30.0  1
 0HZ  Var_02    CG    CD   N    CA     -2.55  30.0  1
 0HZ  Var_03    CD    CG   CB   CA    -38.15  30.0  1
 0HZ  Var_04    CD1   CG1  CB1  CA1  -175.19  30.0  3
 0HZ  Var_05    NE    CD1  CG1  CB1   179.49  30.0  3
 0HZ  Var_06    CZ    NE   CD1  CG1   178.72  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
 0HZ  chir_01  CA   N   CB  C    positiv
 0HZ  chir_02  CA1  N1  C1  CB1  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
 0HZ  plan-1  CD1   0.020
 0HZ  plan-1  NE    0.020
 0HZ  plan-1  CZ    0.020
 0HZ  plan-1  NH1   0.020
 0HZ  plan-1  NH2   0.020
 0HZ  plan-1  HE    0.020
 0HZ  plan-1  HH11  0.020
 0HZ  plan-1  HH12  0.020
 0HZ  plan-1  HH21  0.020
 0HZ  plan-1  HH22  0.020
 0HZ  plan-2  N     0.020
 0HZ  plan-2  CA    0.020
 0HZ  plan-2  CD    0.020
 0HZ  plan-2  CA1   0.020
 0HZ  plan-2  C1    0.020
 0HZ  plan-2  O1    0.020
 0HZ  plan-3  CA    0.020
 0HZ  plan-3  C     0.020
 0HZ  plan-3  O     0.020
 0HZ  plan-3  N1    0.020
 0HZ  plan-3  CA1   0.020
 0HZ  plan-3  H     0.020

