# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:44:13 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: amino{[(3S)-3-amino-3-carboxypropyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCNC(N)=[NH2+])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
 4J5  4J5  amino{[(3S)-3-amino-3-carboxypropyl]amino}methaniminium  L-peptide  23  11  .  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 (side chain)
;

data_comp_4J5
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
 4J5  OXT   O  OC    -1  -0.597  2.7732  -7.1525  -0.9476
 4J5  C     C  C      0   0.413  3.0565  -5.9467  -1.0667
 4J5  N     N  NH2    0  -0.826  4.6927  -4.2391  -1.8536
 4J5  O     O  O      0  -0.592  2.4842  -4.9786  -0.5280
 4J5  CA    C  CH1    0  -0.226  4.2433  -5.6224  -2.0149
 4J5  CB    C  CH2    0  -0.438  5.4159  -6.5728  -1.7886
 4J5  ND    N  NH1    0  -0.621  7.3525  -6.3359  -0.2018
 4J5  CE    C  C      0   0.782  7.9633  -5.1719  -0.4064
 4J5  CG    C  CH2    0  -0.326  5.9214  -6.5277  -0.3352
 4J5  NH1   N  NH2    0  -0.825  9.2901  -5.1095  -0.2787
 4J5  NH2   N  NC2    1  -0.851  7.2616  -4.0943  -0.7156
 4J5  H     H  HNH2   0   0.360  4.8672  -3.8106  -2.7535
 4J5  HA    H  HCH1   0   0.237  3.8720  -5.7890  -3.0352
 4J5  HD    H  HNH1   0   0.417  7.9274  -7.1513  -0.0654
 4J5  HB2   H  HCH2   0   0.240  5.1233  -7.5887  -2.0505
 4J5  HB3   H  HCH2   0   0.235  6.2270  -6.3035  -2.4705
 4J5  HG2   H  HCH2   0   0.278  5.6882  -7.4569   0.1789
 4J5  HG3   H  HCH2   0   0.252  5.4180  -5.7375   0.2283
 4J5  HH11  H  HNH2   0   0.424  9.7811  -4.2395  -0.3953
 4J5  HH12  H  HNH2   0   0.423  9.8111  -5.8782   0.1084
 4J5  HH21  H  HNC2   0   0.470  6.2709  -4.1393  -1.0659
 4J5  HH22  H  HNC2   0   0.410  7.7493  -3.2247  -0.8582
 4J5  HNA   H  HNH2   0   0.360  3.9445  -3.7187  -1.4083

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
 4J5  O     C     deloc   1.231  0.020  1.231
 4J5  CA    C     single  1.525  0.021  1.525
 4J5  C     OXT   deloc   1.244  0.020  1.244
 4J5  CA    N     single  1.458  0.019  1.458
 4J5  N     H     single  0.860  0.020  0.860
 4J5  N     HNA   single  0.890  0.020  1.040
 4J5  HA    CA    single  0.970  0.020  0.970
 4J5  CA    CB    single  1.530  0.020  1.530
 4J5  HB2   CB    single  0.970  0.020  1.090
 4J5  CB    HB3   single  0.970  0.020  1.090
 4J5  CB    CG    single  1.539  0.020  1.539
 4J5  HD    ND    single  0.860  0.020  1.020
 4J5  CE    ND    single  1.330  0.020  1.330
 4J5  ND    CG    single  1.450  0.020  1.450
 4J5  NH1   CE    single  1.334  0.020  1.334
 4J5  CE    NH2   double  1.323  0.020  1.323
 4J5  CG    HG3   single  0.970  0.020  1.090
 4J5  CG    HG2   single  0.970  0.020  1.090
 4J5  HH11  NH1   single  0.860  0.020  1.020
 4J5  HH12  NH1   single  0.860  0.020  1.020
 4J5  HH22  NH2   single  0.860  0.020  1.020
 4J5  NH2   HH21  single  0.860  0.020  1.020

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
 4J5  CA    C    O     120.80  1.700
 4J5  CA    C    OXT   115.77  3.000
 4J5  O     C    OXT   127.33  3.000
 4J5  HNA   N    H     107.48  3.000
 4J5  HNA   N    CA    107.87  3.000
 4J5  H     N    CA    114.00  3.000
 4J5  HA    CA   CB    109.00  3.000
 4J5  CB    CA   N     110.50  1.700
 4J5  HA    CA   N     110.00  3.000
 4J5  CB    CA   C     110.10  1.900
 4J5  HA    CA   C     109.00  3.000
 4J5  N     CA   C     111.00  2.800
 4J5  HB3   CB   HB2   106.20  3.000
 4J5  HB3   CB   CG    109.76  3.000
 4J5  HB2   CB   CG    110.04  3.000
 4J5  CG    CB   CA    111.96  3.000
 4J5  HB3   CB   CA    108.91  3.000
 4J5  HB2   CB   CA    109.80  3.000
 4J5  HD    ND   CG    117.95  3.000
 4J5  CG    ND   CE    123.69  3.000
 4J5  HD    ND   CE    117.86  3.000
 4J5  NH2   CE   NH1   120.79  3.000
 4J5  NH2   CE   ND    120.35  3.000
 4J5  NH1   CE   ND    118.86  3.000
 4J5  HG3   CG   HG2   105.98  3.000
 4J5  HG2   CG   ND    106.33  3.000
 4J5  HG3   CG   ND    108.14  3.000
 4J5  HG2   CG   CB    110.55  3.000
 4J5  HG3   CG   CB    110.89  3.000
 4J5  ND    CG   CB    114.51  3.000
 4J5  HH12  NH1  HH11  116.91  3.000
 4J5  HH12  NH1  CE    121.07  3.000
 4J5  HH11  NH1  CE    120.98  3.000
 4J5  HH22  NH2  HH21  116.48  3.000
 4J5  HH21  NH2  CE    122.87  3.000
 4J5  HH22  NH2  CE    118.66  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
 4J5  CONST_01  NH1   CE   ND  CG    180.00   0.0  0
 4J5  CONST_02  NH2   CE   ND  CG      0.00   0.0  0
 4J5  CONST_03  HH11  NH1  CE  ND    180.00   0.0  0
 4J5  CONST_04  HH12  NH1  CE  ND      0.00   0.0  0
 4J5  CONST_05  HH22  NH2  CE  ND    180.00   0.0  0
 4J5  CONST_07  HD    ND   CE  NH1     0.00   0.0  0
 4J5  Var_01    ND    CG   CB  CA   -129.29  30.0  3
 4J5  Var_02    CE    ND   CG  CB     74.77  30.0  1

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
 4J5  chir_01  CA  C  N  CB  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
 4J5  plan-1  ND    0.020
 4J5  plan-1  CE    0.020
 4J5  plan-1  CG    0.020
 4J5  plan-1  NH1   0.020
 4J5  plan-1  NH2   0.020
 4J5  plan-1  HD    0.020
 4J5  plan-1  HH11  0.020
 4J5  plan-1  HH12  0.020
 4J5  plan-1  HH21  0.020
 4J5  plan-1  HH22  0.020
 4J5  plan-2  OXT   0.020
 4J5  plan-2  C     0.020
 4J5  plan-2  O     0.020
 4J5  plan-2  CA    0.020

