# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:02:13 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 1-{[(4S)-4-amino-4-carboxybutyl]amino}butan-1-iminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=[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
 VIO  VIO  1-{[(4S)-4-amino-4-carboxybutyl]amino}butan-1-iminium  ligand  33  14  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VIO
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
 VIO  N     N  NH2    0  -0.786  -3.1353  -1.5534  -1.0487
 VIO  CA    C  CH1    0  -0.217  -3.1219  -0.6758   0.1116
 VIO  C     C  C      0   0.387  -4.4298   0.1195   0.3561
 VIO  O     O  O      0  -0.606  -5.2752   0.1357  -0.5603
 VIO  OXT   O  OC    -1  -0.623  -4.5178   0.7018   1.4575
 VIO  CB    C  CH2    0  -0.421  -1.9497   0.3052   0.0214
 VIO  CG    C  CH2    0  -0.464  -0.5967  -0.3817  -0.0964
 VIO  CD    C  CH2    0  -0.288   0.5280   0.6358  -0.1668
 VIO  NE    N  NH1    0  -0.594   1.8178  -0.0287  -0.2874
 VIO  CZ    C  C      0   0.629   2.9600   0.5720  -0.5027
 VIO  CH1   C  CH2    0  -0.544   4.2176  -0.2336  -0.5351
 VIO  NH2   N  NC2    1  -0.774   3.0387   1.8747  -0.6424
 VIO  C1    C  CH2    0  -0.429   4.8792  -0.2779   0.8482
 VIO  C2    C  CH3    0  -0.666   6.1488  -1.1143   0.8262
 VIO  H     H  HNH2   0   0.336  -3.7975  -2.3009  -0.8796
 VIO  HN2   H  HNH2   0   0.323  -3.5377  -1.0354  -1.8222
 VIO  HA    H  HCH1   0   0.212  -2.9514  -1.3047   0.9937
 VIO  HB1   H  HCH2   0   0.226  -1.9619   0.9439   0.9076
 VIO  HB2   H  HCH2   0   0.214  -2.0969   0.9687  -0.8398
 VIO  HG1   H  HCH2   0   0.244  -0.5781  -1.0139  -0.9859
 VIO  HG2   H  HCH2   0   0.233  -0.4436  -1.0378   0.7669
 VIO  HD1   H  HCH2   0   0.264   0.5290   1.2671   0.7264
 VIO  HD2   H  HCH2   0   0.260   0.3835   1.2875  -1.0328
 VIO  HE    H  HNH1   0   0.434   1.8408  -1.0320  -0.1800
 VIO  HH11  H  HCH2   0   0.289   4.9011   0.2061  -1.2634
 VIO  HH12  H  HCH2   0   0.288   3.9897  -1.2449  -0.8750
 VIO  HH21  H  HNC2   0   0.447   2.2435   2.4901  -0.5675
 VIO  HH22  H  HNC2   0   0.442   3.9271   2.3095  -0.8312
 VIO  H11   H  HCH2   0   0.244   4.1747  -0.6907   1.5735
 VIO  H12   H  HCH2   0   0.244   5.1104   0.7381   1.1751
 VIO  H21   H  HCH3   0   0.228   6.8820  -0.7034   0.1309
 VIO  H22   H  HCH3   0   0.240   6.6082  -1.1432   1.8139
 VIO  H23   H  HCH3   0   0.228   5.9422  -2.1425   0.5256

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
 VIO  N    CA    single  1.455  0.020  1.455
 VIO  N    H     single  0.860  0.020  1.020
 VIO  N    HN2   single  0.890  0.020  1.040
 VIO  CA   C     single  1.550  0.020  1.550
 VIO  CA   CB    single  1.531  0.020  1.531
 VIO  CA   HA    single  0.970  0.020  1.090
 VIO  C    O     deloc   1.247  0.020  1.247
 VIO  C    OXT   deloc   1.249  0.020  1.249
 VIO  CB   CG    single  1.522  0.020  1.522
 VIO  CB   HB1   single  0.970  0.020  1.090
 VIO  CB   HB2   single  0.970  0.020  1.090
 VIO  CG   CD    single  1.518  0.020  1.518
 VIO  CG   HG1   single  0.970  0.020  1.090
 VIO  CG   HG2   single  0.970  0.020  1.090
 VIO  CD   NE    single  1.456  0.020  1.456
 VIO  CD   HD1   single  0.970  0.020  1.090
 VIO  CD   HD2   single  0.970  0.020  1.090
 VIO  NE   CZ    single  1.308  0.020  1.308
 VIO  NE   HE    single  0.860  0.020  1.020
 VIO  CZ   CH1   single  1.494  0.020  1.494
 VIO  CZ   NH2   double  1.312  0.020  1.312
 VIO  CH1  C1    single  1.534  0.020  1.534
 VIO  CH1  HH11  single  0.970  0.020  1.090
 VIO  CH1  HH12  single  0.970  0.020  1.090
 VIO  NH2  HH21  single  0.860  0.020  1.020
 VIO  NH2  HH22  single  0.860  0.020  1.020
 VIO  C1   C2    single  1.520  0.020  1.520
 VIO  C1   H11   single  0.970  0.020  1.090
 VIO  C1   H12   single  0.970  0.020  1.090
 VIO  C2   H21   single  0.970  0.020  1.090
 VIO  C2   H22   single  0.970  0.020  1.090
 VIO  C2   H23   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
 VIO  HN2   N    H     104.17  3.000
 VIO  HN2   N    CA    107.69  3.000
 VIO  H     N    CA    108.55  3.000
 VIO  HA    CA   CB    107.20  3.000
 VIO  HA    CA   C     107.37  3.000
 VIO  CB    CA   C     109.05  3.000
 VIO  HA    CA   N     107.28  3.000
 VIO  CB    CA   N     110.28  3.000
 VIO  C     CA   N     115.31  3.000
 VIO  OXT   C    O     126.47  3.000
 VIO  OXT   C    CA    115.96  3.000
 VIO  O     C    CA    117.57  3.000
 VIO  HB2   CB   HB1   106.36  3.000
 VIO  HB2   CB   CG    109.35  3.000
 VIO  HB1   CB   CG    109.67  3.000
 VIO  HB2   CB   CA    109.33  3.000
 VIO  HB1   CB   CA    108.56  3.000
 VIO  CG    CB   CA    113.33  3.000
 VIO  HG2   CG   HG1   107.04  3.000
 VIO  HG2   CG   CD    109.54  3.000
 VIO  HG1   CG   CD    109.75  3.000
 VIO  HG2   CG   CB    109.49  3.000
 VIO  HG1   CG   CB    109.85  3.000
 VIO  CD    CG   CB    111.08  3.000
 VIO  HD2   CD   HD1   107.63  3.000
 VIO  HD2   CD   NE    108.87  3.000
 VIO  HD1   CD   NE    109.29  3.000
 VIO  HD2   CD   CG    109.77  3.000
 VIO  HD1   CD   CG    110.47  3.000
 VIO  NE    CD   CG    110.74  3.000
 VIO  HE    NE   CZ    117.00  3.000
 VIO  HE    NE   CD    117.72  3.000
 VIO  CZ    NE   CD    125.27  3.000
 VIO  NH2   CZ   CH1   118.85  3.000
 VIO  NH2   CZ   NE    121.71  3.000
 VIO  CH1   CZ   NE    119.40  3.000
 VIO  HH12  CH1  HH11  107.24  3.000
 VIO  HH12  CH1  C1    110.13  3.000
 VIO  HH11  CH1  C1    110.08  3.000
 VIO  HH12  CH1  CZ    109.32  3.000
 VIO  HH11  CH1  CZ    108.93  3.000
 VIO  C1    CH1  CZ    111.04  3.000
 VIO  HH22  NH2  HH21  116.50  3.000
 VIO  HH22  NH2  CZ    120.09  3.000
 VIO  HH21  NH2  CZ    123.41  3.000
 VIO  H12   C1   H11   106.82  3.000
 VIO  H12   C1   C2    109.84  3.000
 VIO  H11   C1   C2    109.90  3.000
 VIO  H12   C1   CH1   109.53  3.000
 VIO  H11   C1   CH1   109.37  3.000
 VIO  C2    C1   CH1   111.28  3.000
 VIO  H23   C2   H22   107.74  3.000
 VIO  H23   C2   H21   107.86  3.000
 VIO  H22   C2   H21   107.72  3.000
 VIO  H23   C2   C1    111.37  3.000
 VIO  H22   C2   C1    110.70  3.000
 VIO  H21   C2   C1    111.30  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
 VIO  CONST_01  CH1   CZ   NE   CD    180.00   0.0  0
 VIO  CONST_02  NH2   CZ   NE   CD      0.00   0.0  0
 VIO  CONST_03  HH21  NH2  CZ   NE      0.00   0.0  0
 VIO  CONST_04  HH22  NH2  CZ   NE    180.00   0.0  0
 VIO  CONST_05  HE    NE   CZ   CH1     0.00   0.0  0
 VIO  Var_01    CD    CG   CB   CA   -179.37  30.0  3
 VIO  Var_02    NE    CD   CG   CB   -179.66  30.0  3
 VIO  Var_03    CZ    NE   CD   CG    172.80  30.0  3
 VIO  Var_04    C1    CH1  CZ   NE    -92.73  30.0  3
 VIO  Var_05    C2    C1   CH1  CZ    179.13  30.0  3
 VIO  Var_06    H21   C2   C1   CH1    60.50  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
 VIO  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
 VIO  plan-1  CD    0.020
 VIO  plan-1  NE    0.020
 VIO  plan-1  CZ    0.020
 VIO  plan-1  CH1   0.020
 VIO  plan-1  NH2   0.020
 VIO  plan-1  HE    0.020
 VIO  plan-1  HH21  0.020
 VIO  plan-1  HH22  0.020
 VIO  plan-2  CA    0.020
 VIO  plan-2  C     0.020
 VIO  plan-2  O     0.020
 VIO  plan-2  OXT   0.020

