# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:23:07 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: {[(4S)-4-amino-4-carboxybutyl]amino}(propylamino)methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=[NH2+])NCCC[C@H](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
 3AR  3AR  {[(4S)-4-amino-4-carboxybutyl]amino}(propylamino)methaniminium  L-peptide  35  15  .  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_3AR
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
 3AR  N     N  NH2    0  -0.793   8.9055  -0.8000  25.9622
 3AR  CA    C  CH1    0  -0.208   8.9345  -1.2678  24.5859
 3AR  C     C  C      0   0.401   8.7309  -2.7991  24.5143
 3AR  O     O  O      0  -0.602   9.0037  -3.4593  25.5357
 3AR  CB    C  CH2    0  -0.433  10.2059  -0.9249  23.7888
 3AR  CG    C  CH2    0  -0.478  10.5507   0.5671  23.7291
 3AR  CD    C  CH2    0  -0.339  11.5545   1.0400  24.7777
 3AR  NE    N  NH1    0  -0.642  12.8485   0.3798  24.6888
 3AR  CZ    C  C      0   0.853  13.7338   0.5335  23.7075
 3AR  NH1   N  NH1    0  -0.635  13.6002   1.5132  22.8221
 3AR  NH2   N  NC2    1  -0.830  14.7488  -0.3214  23.6085
 3AR  C1    C  CH2    0  -0.294  14.4614   1.7209  21.6677
 3AR  C2    C  CH2    0  -0.472  13.7565   2.5578  20.6124
 3AR  C3    C  CH3    0  -0.668  12.5406   1.8752  20.0045
 3AR  OXT   O  OC    -1  -0.616   8.3529  -3.2467  23.4118
 3AR  H     H  HNH2   0   0.336   9.0670   0.1983  26.0044
 3AR  H2    H  HNH2   0   0.325   9.6477  -1.2445  26.4878
 3AR  HA    H  HCH1   0   0.202   8.0945  -0.7911  24.0670
 3AR  HB2   H  HCH2   0   0.226  10.0692  -1.2985  22.7724
 3AR  HB3   H  HCH2   0   0.212  11.0511  -1.4891  24.2002
 3AR  HG2   H  HCH2   0   0.242   9.6462   1.1733  23.8412
 3AR  HG3   H  HCH2   0   0.251  10.9392   0.8136  22.7383
 3AR  HD2   H  HCH2   0   0.268  11.1927   0.8331  25.7823
 3AR  HD3   H  HCH2   0   0.265  11.6829   2.1243  24.7255
 3AR  HE    H  HNH1   0   0.425  13.0458  -0.3331  25.3729
 3AR  HH1   H  HNH1   0   0.431  12.9340   2.2436  23.0245
 3AR  HH21  H  HNC2   0   0.439  15.5717  -0.1023  23.0727
 3AR  HH22  H  HNC2   0   0.431  14.8254  -1.1006  24.2413
 3AR  H11   H  HCH2   0   0.254  14.7171   0.7498  21.2387
 3AR  H12   H  HCH2   0   0.266  15.3923   2.2066  21.9728
 3AR  H21   H  HCH2   0   0.250  14.4904   2.7711  19.8332
 3AR  H22   H  HCH2   0   0.239  13.4780   3.5256  21.0392
 3AR  H31   H  HCH3   0   0.225  12.8122   0.9198  19.5528
 3AR  H32   H  HCH3   0   0.238  12.0979   2.4967  19.2267
 3AR  H33   H  HCH3   0   0.234  11.7659   1.6826  20.7474

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
 3AR  N    CA    single  1.458  0.019  1.458
 3AR  N    H     single  0.860  0.020  0.860
 3AR  N    H2    single  0.890  0.020  1.040
 3AR  CA   C     single  1.525  0.021  1.525
 3AR  CA   CB    single  1.521  0.033  1.521
 3AR  CA   HA    single  0.970  0.020  0.970
 3AR  C    O     deloc   1.231  0.020  1.231
 3AR  C    OXT   deloc   1.248  0.020  1.248
 3AR  CB   CG    single  1.533  0.020  1.533
 3AR  CB   HB2   single  0.970  0.020  1.090
 3AR  CB   HB3   single  0.970  0.020  1.090
 3AR  CG   CD    single  1.527  0.020  1.527
 3AR  CG   HG2   single  0.970  0.020  1.090
 3AR  CG   HG3   single  0.970  0.020  1.090
 3AR  CD   NE    single  1.455  0.020  1.455
 3AR  CD   HD2   single  0.970  0.020  1.090
 3AR  CD   HD3   single  0.970  0.020  1.090
 3AR  NE   CZ    single  1.331  0.020  1.331
 3AR  NE   HE    single  0.860  0.020  1.020
 3AR  CZ   NH1   single  1.327  0.020  1.327
 3AR  CZ   NH2   double  1.331  0.020  1.331
 3AR  NH1  C1    single  1.455  0.020  1.455
 3AR  NH1  HH1   single  0.860  0.020  1.020
 3AR  NH2  HH21  single  0.860  0.020  1.020
 3AR  NH2  HH22  single  0.860  0.020  1.020
 3AR  C1   C2    single  1.520  0.020  1.520
 3AR  C1   H11   single  0.970  0.020  1.090
 3AR  C1   H12   single  0.970  0.020  1.090
 3AR  C2   C3    single  1.521  0.020  1.521
 3AR  C2   H21   single  0.970  0.020  1.090
 3AR  C2   H22   single  0.970  0.020  1.090
 3AR  C3   H31   single  0.970  0.020  1.090
 3AR  C3   H32   single  0.970  0.020  1.090
 3AR  C3   H33   single  0.970  0.020  1.090

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
 3AR  H2    N    H     107.12  3.000
 3AR  H2    N    CA    109.61  3.000
 3AR  H     N    CA    114.00  3.000
 3AR  HA    CA   CB    109.00  3.000
 3AR  HA    CA   C     110.00  3.000
 3AR  CB    CA   C     110.50  1.500
 3AR  HA    CA   N     110.00  3.000
 3AR  CB    CA   N     110.40  1.500
 3AR  C     CA   N     111.00  2.800
 3AR  OXT   C    O     126.87  3.000
 3AR  OXT   C    CA    120.80  1.700
 3AR  O     C    CA    120.80  1.700
 3AR  HB3   CB   HB2   105.66  3.000
 3AR  HB3   CB   CG    110.01  3.000
 3AR  HB2   CB   CG    108.97  3.000
 3AR  HB3   CB   CA    109.13  3.000
 3AR  HB2   CB   CA    107.61  3.000
 3AR  CG    CB   CA    115.02  3.000
 3AR  HG3   CG   HG2   105.18  3.000
 3AR  HG3   CG   CD    108.62  3.000
 3AR  HG2   CG   CD    107.54  3.000
 3AR  HG3   CG   CB    109.57  3.000
 3AR  HG2   CG   CB    110.44  3.000
 3AR  CD    CG   CB    115.01  3.000
 3AR  HD3   CD   HD2   105.78  3.000
 3AR  HD3   CD   NE    110.04  3.000
 3AR  HD2   CD   NE    105.42  3.000
 3AR  HD3   CD   CG    110.59  3.000
 3AR  HD2   CD   CG    110.90  3.000
 3AR  NE    CD   CG    113.71  3.000
 3AR  HE    NE   CZ    116.88  3.000
 3AR  HE    NE   CD    116.98  3.000
 3AR  CZ    NE   CD    125.75  3.000
 3AR  NH2   CZ   NH1   120.09  3.000
 3AR  NH2   CZ   NE    119.22  3.000
 3AR  NH1   CZ   NE    120.68  3.000
 3AR  HH1   NH1  C1    116.53  3.000
 3AR  HH1   NH1  CZ    117.84  3.000
 3AR  C1    NH1  CZ    125.10  3.000
 3AR  HH22  NH2  HH21  116.17  3.000
 3AR  HH22  NH2  CZ    120.57  3.000
 3AR  HH21  NH2  CZ    121.57  3.000
 3AR  H12   C1   H11   107.78  3.000
 3AR  H12   C1   C2    110.11  3.000
 3AR  H11   C1   C2    108.99  3.000
 3AR  H12   C1   NH1   110.24  3.000
 3AR  H11   C1   NH1   108.87  3.000
 3AR  C2    C1   NH1   110.78  3.000
 3AR  H22   C2   H21   106.08  3.000
 3AR  H22   C2   C3    110.45  3.000
 3AR  H21   C2   C3    109.87  3.000
 3AR  H22   C2   C1    109.53  3.000
 3AR  H21   C2   C1    106.94  3.000
 3AR  C3    C2   C1    113.64  3.000
 3AR  H33   C3   H32   107.36  3.000
 3AR  H33   C3   H31   107.71  3.000
 3AR  H32   C3   H31   107.76  3.000
 3AR  H33   C3   C2    112.02  3.000
 3AR  H32   C3   C2    110.73  3.000
 3AR  H31   C3   C2    111.07  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
 3AR  CONST_01  NH1   CZ   NE   CD     0.00   0.0  0
 3AR  CONST_02  NH2   CZ   NE   CD   180.00   0.0  0
 3AR  CONST_03  C1    NH1  CZ   NE   180.00   0.0  0
 3AR  CONST_04  C1    NH1  CZ   NH2    0.00   0.0  0
 3AR  CONST_05  HH1   NH1  CZ   NE     0.00   0.0  0
 3AR  CONST_07  HH22  NH2  CZ   NE     0.00   0.0  0
 3AR  CONST_08  HE    NE   CZ   NH1  180.00   0.0  0
 3AR  Var_01    CD    CG   CB   CA    95.42  30.0  3
 3AR  Var_02    NE    CD   CG   CB    60.45  30.0  3
 3AR  Var_03    CZ    NE   CD   CG    68.84  30.0  3
 3AR  Var_04    C2    C1   NH1  CZ   158.59  30.0  3
 3AR  Var_05    C3    C2   C1   NH1  -64.97  30.0  3
 3AR  Var_06    H31   C3   C2   C1   -57.90  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
 3AR  chir_01  CA  N  C  CB  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
 3AR  plan-1  CD    0.020
 3AR  plan-1  NE    0.020
 3AR  plan-1  CZ    0.020
 3AR  plan-1  NH1   0.020
 3AR  plan-1  NH2   0.020
 3AR  plan-1  C1    0.020
 3AR  plan-1  HE    0.020
 3AR  plan-1  HH1   0.020
 3AR  plan-1  HH21  0.020
 3AR  plan-1  HH22  0.020
 3AR  plan-2  CA    0.020
 3AR  plan-2  C     0.020
 3AR  plan-2  O     0.020
 3AR  plan-2  OXT   0.020

