# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 05:46:42 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: amino{[(4S)-4,5-diamino-5-oxopentyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=[NH2+])C(N)=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
 AAR  AAR  amino{[(4S)-4,5-diamino-5-oxopentyl]amino}methaniminium  L-peptide  28  12  .  2022-09-22  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_AAR
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
 AAR  N     N  NH2   0  -0.788   2.5003   1.8084  -0.1302
 AAR  CA    C  CH1   0  -0.220   2.2828   0.4570   0.3475
 AAR  CB    C  CH2   0  -0.430   1.0350  -0.2519  -0.2044
 AAR  CG    C  CH2   0  -0.483  -0.2591   0.4198   0.2322
 AAR  CD    C  CH2   0  -0.270  -1.4728  -0.3537  -0.2533
 AAR  NE    N  NH1   0  -0.637  -2.6919   0.3113   0.1746
 AAR  CZ    C  C     0   0.829  -3.9146  -0.1561  -0.0358
 AAR  NH1   N  NH2   0  -0.817  -4.0929  -1.3083  -0.6670
 AAR  NH2   N  NC2   1  -0.823  -4.9667   0.5377   0.3805
 AAR  C     C  C     0   0.523   3.5028  -0.3833  -0.0088
 AAR  O     O  O     0  -0.494   4.0458  -0.2850  -1.1001
 AAR  NT    N  NH2   0  -0.798   3.8928  -1.2533   0.9317
 AAR  H     H  HNH2  0   0.343   2.5401   1.8122  -1.1423
 AAR  H2    H  HNH2  0   0.354   1.7199   2.3970   0.1294
 AAR  HA    H  HCH1  0   0.252   2.1875   0.5032   1.4373
 AAR  HB2   H  HCH2  0   0.237   1.0934  -0.2817  -1.2969
 AAR  HB3   H  HCH2  0   0.237   1.0306  -1.2916   0.1373
 AAR  HG2   H  HCH2  0   0.248  -0.2889   0.4851   1.3240
 AAR  HG3   H  HCH2  0   0.242  -0.3089   1.4416  -0.1540
 AAR  HD2   H  HCH2  0   0.259  -1.4533  -0.4329  -1.3441
 AAR  HD3   H  HCH2  0   0.257  -1.4422  -1.3676   0.1549
 AAR  HE    H  HNH1  0   0.427  -2.6059   1.1979   0.6464
 AAR  HH11  H  HNH2  0   0.447  -3.3195  -1.8771  -0.9672
 AAR  HH12  H  HNH2  0   0.434  -5.0139  -1.6912  -0.7965
 AAR  HH21  H  HNC2  0   0.431  -5.9034   0.1960   0.2515
 AAR  HH22  H  HNC2  0   0.433  -4.8562   1.4078   0.8726
 AAR  HNT1  H  HNH2  0   0.408   3.4542  -1.2924   1.8351
 AAR  HNT2  H  HNH2  0   0.401   4.6599  -1.8837   0.7628

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
 AAR  N    CA    single  1.458  0.019  1.458
 AAR  N    H     single  0.860  0.020  0.860
 AAR  N    H2    single  0.890  0.020  1.040
 AAR  CA   CB    single  1.530  0.020  1.530
 AAR  CA   C     single  1.525  0.021  1.525
 AAR  CA   HA    single  0.970  0.020  0.970
 AAR  CB   CG    single  1.522  0.020  1.522
 AAR  CB   HB2   single  0.970  0.020  1.090
 AAR  CB   HB3   single  0.970  0.020  1.090
 AAR  CG   CD    single  1.519  0.020  1.519
 AAR  CG   HG2   single  0.970  0.020  1.090
 AAR  CG   HG3   single  0.970  0.020  1.090
 AAR  CD   NE    single  1.453  0.020  1.453
 AAR  CD   HD2   single  0.970  0.020  1.090
 AAR  CD   HD3   single  0.970  0.020  1.090
 AAR  NE   CZ    single  1.326  0.020  1.326
 AAR  NE   HE    single  0.860  0.020  1.020
 AAR  CZ   NH1   single  1.326  0.020  1.326
 AAR  CZ   NH2   double  1.327  0.020  1.327
 AAR  NH1  HH11  single  0.860  0.020  1.020
 AAR  NH1  HH12  single  0.860  0.020  1.020
 AAR  NH2  HH21  single  0.860  0.020  1.020
 AAR  NH2  HH22  single  0.860  0.020  1.020
 AAR  C    O     double  1.231  0.020  1.231
 AAR  C    NT    single  1.339  0.020  1.339
 AAR  NT   HNT1  single  0.860  0.020  1.020
 AAR  NT   HNT2  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
 AAR  H2    N    H     106.53  3.000
 AAR  H2    N    CA    110.01  3.000
 AAR  H     N    CA    114.00  3.000
 AAR  HA    CA   C     109.00  3.000
 AAR  HA    CA   CB    109.00  3.000
 AAR  C     CA   CB    110.10  1.900
 AAR  HA    CA   N     110.00  3.000
 AAR  C     CA   N     111.00  2.800
 AAR  CB    CA   N     110.50  1.700
 AAR  HB3   CB   HB2   106.62  3.000
 AAR  HB3   CB   CG    109.04  3.000
 AAR  HB2   CB   CG    110.10  3.000
 AAR  HB3   CB   CA    109.22  3.000
 AAR  HB2   CB   CA    109.12  3.000
 AAR  CG    CB   CA    112.55  3.000
 AAR  HG3   CG   HG2   107.19  3.000
 AAR  HG3   CG   CD    109.06  3.000
 AAR  HG2   CG   CD    109.12  3.000
 AAR  HG3   CG   CB    110.48  3.000
 AAR  HG2   CG   CB    109.62  3.000
 AAR  CD    CG   CB    111.28  3.000
 AAR  HD3   CD   HD2   107.74  3.000
 AAR  HD3   CD   NE    109.75  3.000
 AAR  HD2   CD   NE    109.98  3.000
 AAR  HD3   CD   CG    109.30  3.000
 AAR  HD2   CD   CG    109.96  3.000
 AAR  NE    CD   CG    110.07  3.000
 AAR  HE    NE   CZ    117.58  3.000
 AAR  HE    NE   CD    117.95  3.000
 AAR  CZ    NE   CD    124.45  3.000
 AAR  NH2   CZ   NH1   119.81  3.000
 AAR  NH2   CZ   NE    119.80  3.000
 AAR  NH1   CZ   NE    120.39  3.000
 AAR  HH12  NH1  HH11  116.76  3.000
 AAR  HH12  NH1  CZ    121.02  3.000
 AAR  HH11  NH1  CZ    122.02  3.000
 AAR  HH22  NH2  HH21  117.33  3.000
 AAR  HH22  NH2  CZ    121.24  3.000
 AAR  HH21  NH2  CZ    121.37  3.000
 AAR  NT    C    O     123.34  3.000
 AAR  NT    C    CA    115.29  3.000
 AAR  O     C    CA    120.80  1.700
 AAR  HNT2  NT   HNT1  117.31  3.000
 AAR  HNT2  NT   C     120.71  3.000
 AAR  HNT1  NT   C     121.96  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
 AAR  CONST_01  NH1   CZ   NE  CD      0.00   0.0  0
 AAR  CONST_02  NH2   CZ   NE  CD    180.00   0.0  0
 AAR  CONST_03  HNT1  NT   C   CA      0.00   0.0  0
 AAR  CONST_04  HNT2  NT   C   CA    180.00   0.0  0
 AAR  CONST_05  HH11  NH1  CZ  NE      0.00   0.0  0
 AAR  CONST_06  HH12  NH1  CZ  NE    180.00   0.0  0
 AAR  CONST_07  HH21  NH2  CZ  NE    180.00   0.0  0
 AAR  CONST_08  HH22  NH2  CZ  NE      0.00   0.0  0
 AAR  CONST_09  HE    NE   CZ  NH1   180.00   0.0  0
 AAR  Var_01    CD    CG   CB  CA   -176.33  30.0  3
 AAR  Var_02    NE    CD   CG  CB   -179.86  30.0  3
 AAR  Var_03    CZ    NE   CD  CG   -176.43  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
 AAR  chir_01  CA  N  CB  C  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
 AAR  plan-1  CA    0.020
 AAR  plan-1  C     0.020
 AAR  plan-1  O     0.020
 AAR  plan-1  NT    0.020
 AAR  plan-1  HNT1  0.020
 AAR  plan-1  HNT2  0.020
 AAR  plan-2  CD    0.020
 AAR  plan-2  NE    0.020
 AAR  plan-2  CZ    0.020
 AAR  plan-2  NH1   0.020
 AAR  plan-2  NH2   0.020
 AAR  plan-2  HE    0.020
 AAR  plan-2  HH11  0.020
 AAR  plan-2  HH12  0.020
 AAR  plan-2  HH21  0.020
 AAR  plan-2  HH22  0.020

