# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:22:26 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: S-{(S)-amino[(4-aminobutyl)amino]methyl}-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCN[C@H](N)SC[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
 AGT  AGT  S-{(S)-amino[(4-aminobutyl)amino]methyl}-L-cysteine  L-peptide  34  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_AGT
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
 AGT  O     O  O      0  -0.589  25.1242  -3.6829  64.5369
 AGT  C     C  C      0   0.421  24.4651  -3.4104  65.5591
 AGT  CA    C  CH1    0  -0.194  24.4855  -1.9357  66.0276
 AGT  N     N  NH2    0  -0.809  24.3831  -1.8712  67.4788
 AGT  CB    C  CH2    0  -0.526  25.7459  -1.2022  65.5914
 AGT  SG    S  S2     0  -0.038  25.8309  -0.9716  63.7908
 AGT  CZ    C  CH1    0  -0.049  26.2374   0.8145  63.7015
 AGT  NH2   N  NH2    0  -0.791  25.1730   1.5968  64.2860
 AGT  NE    N  NH1    0  -0.576  27.4612   1.1019  64.4040
 AGT  CD    C  CH2    0  -0.287  28.6683   0.7414  63.6867
 AGT  CG    C  CH2    0  -0.450  29.8810   0.7059  64.6093
 AGT  CK    C  CH2    0  -0.421  29.7629  -0.2796  65.7680
 AGT  CJ    C  CH2    0  -0.279  29.6154  -1.7295  65.3294
 AGT  NB    N  NH2    0  -0.801  29.4717  -2.6069  66.4833
 AGT  OXT   O  OC    -1  -0.605  23.7620  -4.1946  66.2272
 AGT  HA    H  HCH1   0   0.197  23.6324  -1.4426  65.5282
 AGT  HN1   H  HNH2   0   0.331  24.0266  -0.9671  67.7601
 AGT  HN2   H  HNH2   0   0.334  23.7041  -2.5611  67.7739
 AGT  HB    H  HCH2   0   0.254  25.7647  -0.2032  66.0283
 AGT  HZ    H  HCH1   0   0.221  26.3408   0.9786  62.6127
 AGT  HH21  H  HNH2   0   0.350  25.3166   2.5795  64.0769
 AGT  HH22  H  HNH2   0   0.351  24.2940   1.3407  63.8564
 AGT  HE    H  HNH1   0   0.344  27.4903   2.0817  64.6615
 AGT  HDC1  H  HCH2   0   0.222  28.5131  -0.2458  63.2466
 AGT  HDC2  H  HCH2   0   0.208  28.8728   1.4185  62.8443
 AGT  HGC1  H  HCH2   0   0.216  30.7619   0.4644  64.0061
 AGT  HGC2  H  HCH2   0   0.222  30.0588   1.7097  65.0080
 AGT  HKC1  H  HCH2   0   0.213  30.6541  -0.1907  66.3987
 AGT  HKC2  H  HCH2   0   0.211  28.9124  -0.0120  66.3988
 AGT  HJC1  H  HCH2   0   0.215  28.7150  -1.8367  64.7194
 AGT  HJC2  H  HCH2   0   0.188  30.4629  -1.9927  64.6783
 AGT  HBN1  H  HNH2   0   0.342  29.3505  -3.5611  66.1690
 AGT  HBN2  H  HNH2   0   0.334  30.3319  -2.6033  67.0183
 AGT  HB2   H  HCH2   0   0.242  26.6349  -1.7313  65.9385

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
 AGT  O    C     deloc   1.231  0.020  1.231
 AGT  C    CA    single  1.525  0.021  1.525
 AGT  C    OXT   deloc   1.247  0.020  1.247
 AGT  CA   N     single  1.458  0.019  1.458
 AGT  CA   CB    single  1.530  0.020  1.530
 AGT  CA   HA    single  0.970  0.020  0.970
 AGT  N    HN1   single  0.890  0.020  1.040
 AGT  N    HN2   single  0.890  0.020  1.040
 AGT  CB   SG    single  1.817  0.020  1.817
 AGT  CB   HB    single  0.970  0.020  1.090
 AGT  CB   HB2   single  0.970  0.020  1.090
 AGT  SG   CZ    single  1.834  0.020  1.834
 AGT  CZ   NH2   single  1.444  0.020  1.444
 AGT  CZ   NE    single  1.440  0.020  1.440
 AGT  CZ   HZ    single  0.970  0.020  1.090
 AGT  NH2  HH21  single  0.890  0.020  1.040
 AGT  NH2  HH22  single  0.890  0.020  1.040
 AGT  NE   CD    single  1.450  0.020  1.450
 AGT  NE   HE    single  0.890  0.020  1.040
 AGT  CD   CG    single  1.524  0.020  1.524
 AGT  CD   HDC1  single  0.970  0.020  1.090
 AGT  CD   HDC2  single  0.970  0.020  1.090
 AGT  CG   CK    single  1.526  0.020  1.526
 AGT  CG   HGC1  single  0.970  0.020  1.090
 AGT  CG   HGC2  single  0.970  0.020  1.090
 AGT  CK   CJ    single  1.522  0.020  1.522
 AGT  CK   HKC1  single  0.970  0.020  1.090
 AGT  CK   HKC2  single  0.970  0.020  1.090
 AGT  CJ   NB    single  1.457  0.020  1.457
 AGT  CJ   HJC1  single  0.970  0.020  1.090
 AGT  CJ   HJC2  single  0.970  0.020  1.090
 AGT  NB   HBN1  single  0.890  0.020  1.040
 AGT  NB   HBN2  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
 AGT  OXT   C    CA    116.39  3.000
 AGT  OXT   C    O     126.86  3.000
 AGT  CA    C    O     120.80  1.700
 AGT  HA    CA   CB    109.00  3.000
 AGT  HA    CA   N     110.00  3.000
 AGT  CB    CA   N     110.50  1.700
 AGT  HA    CA   C     109.00  3.000
 AGT  CB    CA   C     110.10  1.900
 AGT  N     CA   C     111.00  2.800
 AGT  HN2   N    HN1   106.96  3.000
 AGT  HN2   N    CA    107.91  3.000
 AGT  HN1   N    CA    109.96  3.000
 AGT  HB2   CB   HB    107.62  3.000
 AGT  HB2   CB   SG    109.79  3.000
 AGT  HB    CB   SG    106.26  3.000
 AGT  HB2   CB   CA    110.47  3.000
 AGT  HB    CB   CA    109.93  3.000
 AGT  SG    CB   CA    112.57  3.000
 AGT  CZ    SG   CB    100.50  3.000
 AGT  HZ    CZ   NE    111.79  3.000
 AGT  HZ    CZ   NH2   112.77  3.000
 AGT  NE    CZ   NH2   108.71  3.000
 AGT  HZ    CZ   SG    102.31  3.000
 AGT  NE    CZ   SG    111.03  3.000
 AGT  NH2   CZ   SG    110.14  3.000
 AGT  HH22  NH2  HH21  106.30  3.000
 AGT  HH22  NH2  CZ    109.36  3.000
 AGT  HH21  NH2  CZ    109.68  3.000
 AGT  HE    NE   CD    110.01  3.000
 AGT  HE    NE   CZ    109.96  3.000
 AGT  CD    NE   CZ    114.62  3.000
 AGT  HDC2  CD   HDC1  105.91  3.000
 AGT  HDC2  CD   CG    109.27  3.000
 AGT  HDC1  CD   CG    109.63  3.000
 AGT  HDC2  CD   NE    112.38  3.000
 AGT  HDC1  CD   NE    107.81  3.000
 AGT  CG    CD   NE    111.64  3.000
 AGT  HGC2  CG   HGC1  105.81  3.000
 AGT  HGC2  CG   CK    109.17  3.000
 AGT  HGC1  CG   CK    109.78  3.000
 AGT  HGC2  CG   CD    109.16  3.000
 AGT  HGC1  CG   CD    108.17  3.000
 AGT  CK    CG   CD    114.40  3.000
 AGT  HKC2  CK   HKC1  106.33  3.000
 AGT  HKC2  CK   CJ    108.93  3.000
 AGT  HKC1  CK   CJ    108.79  3.000
 AGT  HKC2  CK   CG    109.91  3.000
 AGT  HKC1  CK   CG    108.77  3.000
 AGT  CJ    CK   CG    113.83  3.000
 AGT  HJC2  CJ   HJC1  106.31  3.000
 AGT  HJC2  CJ   NB    113.61  3.000
 AGT  HJC1  CJ   NB    107.57  3.000
 AGT  HJC2  CJ   CK    108.89  3.000
 AGT  HJC1  CJ   CK    109.52  3.000
 AGT  NB    CJ   CK    110.80  3.000
 AGT  HBN2  NB   HBN1  105.61  3.000
 AGT  HBN2  NB   CJ    109.42  3.000
 AGT  HBN1  NB   CJ    109.50  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
 AGT  Var_01  CG    CD  NE  CZ  -164.22  30.0  3
 AGT  Var_02  CK    CG  CD  NE    59.31  30.0  3
 AGT  Var_03  CJ    CK  CG  CD    61.60  30.0  3
 AGT  Var_04  NB    CJ  CK  CG  -178.45  30.0  3
 AGT  Var_05  HB    CB  SG  CZ    10.72  30.0  1
 AGT  Var_06  HBN1  NB  CJ  CK   178.50  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
 AGT  chir_01  CA  C   N   CB   negativ
 AGT  chir_02  CZ  SG  NE  NH2  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
 AGT  plan-1  O    0.020
 AGT  plan-1  C    0.020
 AGT  plan-1  CA   0.020
 AGT  plan-1  OXT  0.020

