# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 00:23:18 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (2S,3S)-2-amino-5-carbamimidamido-3-hydroxypentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H](O)CCNC(N)=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
 ZZU  ZZU  '(2S,3S)-2-amino-5-carbamimidamido-3-hydroxypentanoic acid (non-preferred name)'  L-peptide  26  13  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_ZZU
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
 ZZU  O     O  O     -1  -0.599  12.2723   7.7804  21.1633
 ZZU  C     C  C      0   0.406  12.2232   6.9153  20.2670
 ZZU  OXT   O  OC     0  -0.597  12.7093   5.7689  20.3104
 ZZU  CA    C  CH1    0  -0.245  11.5006   7.3372  18.9630
 ZZU  N     N  NH2    0  -0.818  11.6781   6.3292  17.9192
 ZZU  CB    C  CH1    0   0.077   9.9741   7.4786  19.1301
 ZZU  OB    O  OH1    0  -0.688   9.4351   6.2038  19.4018
 ZZU  CG    C  CH2    0  -0.446   9.4556   8.4598  20.1689
 ZZU  CD    C  CH2    0  -0.279   9.9175   9.8925  19.9194
 ZZU  NE    N  NH1    0  -0.640   9.1752  10.8935  20.6502
 ZZU  CZ    C  C      0   0.550   9.3832  11.1451  21.9760
 ZZU  NH2   N  N      0  -0.720  10.3944  10.6490  22.5927
 ZZU  NH1   N  NH2    0  -0.839   8.4809  12.0374  22.5238
 ZZU  HA    H  HCH1   0   0.211  11.9080   8.3145  18.6693
 ZZU  HN1   H  HNH2   0   0.341  11.6563   6.7582  17.0034
 ZZU  HN2   H  HNH2   0   0.345  12.5725   5.8733  18.0294
 ZZU  HB    H  HCH1   0   0.172   9.6051   7.8390  18.1514
 ZZU  HC    H  HOH1   0   0.429   9.9646   5.6169  18.8364
 ZZU  HG1C  H  HCH2   0   0.211   8.3614   8.4366  20.1221
 ZZU  HG2C  H  HCH2   0   0.220   9.7425   8.1490  21.1733
 ZZU  HD1C  H  HCH2   0   0.233  10.9733   9.9897  20.1650
 ZZU  HD2C  H  HCH2   0   0.226   9.8145  10.1356  18.8584
 ZZU  HE    H  HNH1   0   0.377   8.2659  11.1132  20.2784
 ZZU  HH2   H  H      0   0.311  10.4260  10.9865  23.5473
 ZZU  HH11  H  HNH2   0   0.379   7.5660  12.0878  22.1023
 ZZU  HH12  H  HNH2   0   0.382   8.4252  12.0169  23.5292

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
 ZZU  O    C     deloc   1.231  0.020  1.231
 ZZU  C    OXT   deloc   1.246  0.020  1.246
 ZZU  C    CA    single  1.525  0.021  1.525
 ZZU  CA   N     single  1.458  0.019  1.458
 ZZU  CA   CB    single  1.521  0.033  1.521
 ZZU  CB   OB    single  1.410  0.020  1.410
 ZZU  CB   CG    single  1.520  0.020  1.520
 ZZU  CG   CD    single  1.526  0.020  1.526
 ZZU  CD   NE    single  1.445  0.020  1.445
 ZZU  NE   CZ    single  1.365  0.020  1.365
 ZZU  CZ   NH2   double  1.284  0.020  1.284
 ZZU  CZ   NH1   single  1.382  0.020  1.382
 ZZU  CA   HA    single  0.970  0.020  0.970
 ZZU  N    HN1   single  0.890  0.020  1.040
 ZZU  N    HN2   single  0.890  0.020  1.040
 ZZU  CB   HB    single  0.970  0.020  1.090
 ZZU  OB   HC    single  0.850  0.020  0.980
 ZZU  CG   HG1C  single  0.970  0.020  1.090
 ZZU  CG   HG2C  single  0.970  0.020  1.090
 ZZU  CD   HD1C  single  0.970  0.020  1.090
 ZZU  CD   HD2C  single  0.970  0.020  1.090
 ZZU  NE   HE    single  0.890  0.020  1.040
 ZZU  NH2  HH2   single  0.890  0.020  1.040
 ZZU  NH1  HH11  single  0.890  0.020  1.040
 ZZU  NH1  HH12  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
 ZZU  CA    C    OXT   120.80  1.700
 ZZU  CA    C    O     120.80  1.700
 ZZU  OXT   C    O     126.72  3.000
 ZZU  HA    CA   CB    109.00  3.000
 ZZU  HA    CA   N     110.00  3.000
 ZZU  CB    CA   N     110.40  1.500
 ZZU  HA    CA   C     110.00  3.000
 ZZU  CB    CA   C     110.50  1.500
 ZZU  N     CA   C     111.00  2.800
 ZZU  HN2   N    HN1   108.02  3.000
 ZZU  HN2   N    CA    109.93  3.000
 ZZU  HN1   N    CA    110.57  3.000
 ZZU  HB    CB   CG    106.29  3.000
 ZZU  HB    CB   OB    109.72  3.000
 ZZU  CG    CB   OB    108.75  3.000
 ZZU  HB    CB   CA    105.32  3.000
 ZZU  CG    CB   CA    118.09  3.000
 ZZU  OB    CB   CA    108.44  3.000
 ZZU  HC    OB   CB    103.03  3.000
 ZZU  HG2C  CG   HG1C  107.23  3.000
 ZZU  HG2C  CG   CD    109.80  3.000
 ZZU  HG1C  CG   CD    108.38  3.000
 ZZU  HG2C  CG   CB    110.85  3.000
 ZZU  HG1C  CG   CB    107.33  3.000
 ZZU  CD    CG   CB    113.02  3.000
 ZZU  HD2C  CD   HD1C  106.89  3.000
 ZZU  HD2C  CD   NE    106.77  3.000
 ZZU  HD1C  CD   NE    108.81  3.000
 ZZU  HD2C  CD   CG    109.81  3.000
 ZZU  HD1C  CD   CG    109.92  3.000
 ZZU  NE    CD   CG    114.35  3.000
 ZZU  HE    NE   CZ    117.13  3.000
 ZZU  HE    NE   CD    115.37  3.000
 ZZU  CZ    NE   CD    122.72  3.000
 ZZU  NH1   CZ   NH2   124.97  3.000
 ZZU  NH1   CZ   NE    113.85  3.000
 ZZU  NH2   CZ   NE    121.01  3.000
 ZZU  HH2   NH2  CZ    110.39  3.000
 ZZU  HH12  NH1  HH11  111.60  3.000
 ZZU  HH12  NH1  CZ    114.75  3.000
 ZZU  HH11  NH1  CZ    117.31  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
 ZZU  CONST_01  NH2  CZ   NE  CD     0.00   0.0  0
 ZZU  CONST_02  NH1  CZ   NE  CD   180.00   0.0  0
 ZZU  CONST_03  HH2  NH2  CZ  NE   180.00   0.0  0
 ZZU  CONST_06  HE   NE   CZ  NH2  180.00   0.0  0
 ZZU  Var_01    NE   CD   CG  CB   164.24  30.0  3
 ZZU  Var_02    CZ   NE   CD  CG    77.76  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
 ZZU  chir_01  CA  C   N   CB  negativ
 ZZU  chir_02  CB  OB  CA  CG  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
 ZZU  plan-1  CD    0.020
 ZZU  plan-1  NE    0.020
 ZZU  plan-1  CZ    0.020
 ZZU  plan-1  NH2   0.020
 ZZU  plan-1  NH1   0.020
 ZZU  plan-1  HE    0.020
 ZZU  plan-1  HH2   0.020
 ZZU  plan-1  HH11  0.020
 ZZU  plan-1  HH12  0.020
 ZZU  plan-2  O     0.020
 ZZU  plan-2  C     0.020
 ZZU  plan-2  OXT   0.020
 ZZU  plan-2  CA    0.020

