# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:52:11 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: amino{[(1S,4S)-4-amino-4-carboxy-1-methylbutyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC[C@H](N)C(O)=O)NC(N)=[NH2+]
#
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
 AGM  AGM  amino{[(1S,4S)-4-amino-4-carboxy-1-methylbutyl]amino}methaniminium  L-peptide  29  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_AGM
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
 AGM  N     N  NH2    0  -0.806  50.2378  80.5120  57.8387
 AGM  CA    C  CH1    0  -0.220  50.1822  79.6817  59.0330
 AGM  CB    C  CH2    0  -0.411  48.7679  79.1289  59.2265
 AGM  CG    C  CH2    0  -0.408  48.3391  78.1760  58.1185
 AGM  CD    C  CH1    0  -0.117  46.8418  77.8695  58.1240
 AGM  CE2   C  CH3    0  -0.672  46.3877  77.1352  59.3758
 AGM  NE1   N  NH1    0  -0.620  46.4706  77.0592  56.9643
 AGM  CZ    C  C      0   0.817  46.2548  77.5117  55.7364
 AGM  NH1   N  NH2    0  -0.821  45.9879  76.6508  54.7587
 AGM  NH2   N  NC2    1  -0.813  46.2930  78.8105  55.4660
 AGM  C     C  C      0   0.406  51.2455  78.5540  58.9919
 AGM  O     O  O      0  -0.609  51.1493  77.6792  59.8757
 AGM  OXT   O  OC    -1  -0.599  52.1259  78.6295  58.1120
 AGM  H     H  HNH2   0   0.329  49.9095  81.4448  58.0513
 AGM  H2    H  HNH2   0   0.333  51.2028  80.5908  57.5471
 AGM  HA    H  HCH1   0   0.205  50.4139  80.2642  59.9411
 AGM  HB2   H  HCH2   0   0.215  48.7146  78.6354  60.1975
 AGM  HB3   H  HCH2   0   0.208  48.0663  79.9704  59.2713
 AGM  HG2   H  HCH2   0   0.225  48.6120  78.6202  57.1574
 AGM  HG3   H  HCH2   0   0.223  48.8885  77.2334  58.1975
 AGM  HD    H  HCH1   0   0.249  46.2778  78.8067  58.0705
 AGM  HE21  H  HCH3   0   0.233  46.9219  76.1893  59.4884
 AGM  HE22  H  HCH3   0   0.252  46.5852  77.7364  60.2609
 AGM  HE23  H  HCH3   0   0.247  45.3185  76.9269  59.3437
 AGM  HE1   H  HNH1   0   0.421  46.5122  76.0568  57.0807
 AGM  HH11  H  HNH2   0   0.430  45.7718  76.9690  53.8289
 AGM  HH12  H  HNH2   0   0.430  45.8437  75.6739  54.9532
 AGM  HH21  H  HNC2   0   0.441  46.5766  79.4925  56.1478
 AGM  HH22  H  HNC2   0   0.433  46.1002  79.1516  54.5393

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
 AGM  N    CA    single  1.458  0.019  1.458
 AGM  N    H     single  0.860  0.020  0.860
 AGM  N    H2    single  0.890  0.020  1.040
 AGM  CA   CB    single  1.530  0.020  1.530
 AGM  CA   C     single  1.525  0.021  1.525
 AGM  CA   HA    single  0.970  0.020  0.970
 AGM  CB   CG    single  1.523  0.020  1.523
 AGM  CB   HB2   single  0.970  0.020  1.090
 AGM  CB   HB3   single  0.970  0.020  1.090
 AGM  CG   CD    single  1.528  0.020  1.528
 AGM  CG   HG2   single  0.970  0.020  1.090
 AGM  CG   HG3   single  0.970  0.020  1.090
 AGM  CD   CE2   single  1.521  0.020  1.521
 AGM  CD   NE1   single  1.463  0.020  1.463
 AGM  CD   HD    single  0.970  0.020  1.090
 AGM  CE2  HE21  single  0.970  0.020  1.090
 AGM  CE2  HE22  single  0.970  0.020  1.090
 AGM  CE2  HE23  single  0.970  0.020  1.090
 AGM  NE1  CZ    single  1.326  0.020  1.326
 AGM  NE1  HE1   single  0.860  0.020  1.020
 AGM  CZ   NH1   single  1.330  0.020  1.330
 AGM  CZ   NH2   double  1.327  0.020  1.327
 AGM  NH1  HH11  single  0.860  0.020  1.020
 AGM  NH1  HH12  single  0.860  0.020  1.020
 AGM  NH2  HH21  single  0.860  0.020  1.020
 AGM  NH2  HH22  single  0.860  0.020  1.020
 AGM  C    O     deloc   1.231  0.020  1.231
 AGM  C    OXT   deloc   1.247  0.020  1.247

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
 AGM  H2    N    H     107.37  3.000
 AGM  H2    N    CA    108.51  3.000
 AGM  H     N    CA    114.00  3.000
 AGM  HA    CA   C     109.00  3.000
 AGM  HA    CA   CB    109.00  3.000
 AGM  C     CA   CB    110.10  1.900
 AGM  HA    CA   N     110.00  3.000
 AGM  C     CA   N     111.00  2.800
 AGM  CB    CA   N     110.50  1.700
 AGM  HB3   CB   HB2   106.24  3.000
 AGM  HB3   CB   CG    109.25  3.000
 AGM  HB2   CB   CG    110.54  3.000
 AGM  HB3   CB   CA    108.62  3.000
 AGM  HB2   CB   CA    108.73  3.000
 AGM  CG    CB   CA    113.21  3.000
 AGM  HG3   CG   HG2   106.75  3.000
 AGM  HG3   CG   CD    108.60  3.000
 AGM  HG2   CG   CD    109.22  3.000
 AGM  HG3   CG   CB    110.19  3.000
 AGM  HG2   CG   CB    108.36  3.000
 AGM  CD    CG   CB    113.50  3.000
 AGM  HD    CD   NE1   107.74  3.000
 AGM  HD    CD   CE2   107.44  3.000
 AGM  NE1   CD   CE2   108.02  3.000
 AGM  HD    CD   CG    109.44  3.000
 AGM  NE1   CD   CG    110.91  3.000
 AGM  CE2   CD   CG    113.10  3.000
 AGM  HE23  CE2  HE22  107.92  3.000
 AGM  HE23  CE2  HE21  108.50  3.000
 AGM  HE22  CE2  HE21  107.81  3.000
 AGM  HE23  CE2  CD    111.16  3.000
 AGM  HE22  CE2  CD    110.41  3.000
 AGM  HE21  CE2  CD    110.92  3.000
 AGM  HE1   NE1  CZ    116.87  3.000
 AGM  HE1   NE1  CD    116.62  3.000
 AGM  CZ    NE1  CD    125.89  3.000
 AGM  NH2   CZ   NH1   119.31  3.000
 AGM  NH2   CZ   NE1   121.19  3.000
 AGM  NH1   CZ   NE1   119.50  3.000
 AGM  HH12  NH1  HH11  117.05  3.000
 AGM  HH12  NH1  CZ    121.00  3.000
 AGM  HH11  NH1  CZ    121.18  3.000
 AGM  HH22  NH2  HH21  116.66  3.000
 AGM  HH22  NH2  CZ    120.92  3.000
 AGM  HH21  NH2  CZ    122.27  3.000
 AGM  OXT   C    O     126.65  3.000
 AGM  OXT   C    CA    117.31  3.000
 AGM  O     C    CA    120.80  1.700

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
 AGM  CONST_01  NH1   CZ   NE1  CD    180.00   0.0  0
 AGM  CONST_02  NH2   CZ   NE1  CD      0.00   0.0  0
 AGM  CONST_03  HH11  NH1  CZ   NE1   180.00   0.0  0
 AGM  CONST_04  HH12  NH1  CZ   NE1     0.00   0.0  0
 AGM  CONST_05  HH21  NH2  CZ   NE1     0.00   0.0  0
 AGM  CONST_06  HH22  NH2  CZ   NE1   180.00   0.0  0
 AGM  CONST_07  HE1   NE1  CZ   NH1     0.00   0.0  0
 AGM  Var_01    CD    CG   CB   CA   -166.89  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
 AGM  chir_01  CA  N    CB  C    negativ
 AGM  chir_02  CD  NE1  CG  CE2  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
 AGM  plan-1  CD    0.020
 AGM  plan-1  NE1   0.020
 AGM  plan-1  CZ    0.020
 AGM  plan-1  NH1   0.020
 AGM  plan-1  NH2   0.020
 AGM  plan-1  HE1   0.020
 AGM  plan-1  HH11  0.020
 AGM  plan-1  HH12  0.020
 AGM  plan-1  HH21  0.020
 AGM  plan-1  HH22  0.020
 AGM  plan-2  CA    0.020
 AGM  plan-2  C     0.020
 AGM  plan-2  O     0.020
 AGM  plan-2  OXT   0.020

