# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:32:09 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: (2S)-2-aminohex-5-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC#C)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
 IZO  IZO  '(2S)-2-aminohex-5-ynoic acid'  L-peptide  17  9  .  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_IZO
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
 IZO  N     N  NH2    0  -0.798  -19.3388  41.4618  4.8619
 IZO  CA    C  CH1    0  -0.203  -18.6142  40.7867  3.7987
 IZO  C     C  C      0   0.401  -19.1682  39.3574  3.5765
 IZO  O     O  O      0  -0.611  -18.9593  38.8592  2.4524
 IZO  CB    C  CH2    0  -0.431  -17.0960  40.6717  4.0161
 IZO  CG    C  CH2    0  -0.586  -16.3942  42.0305  4.1038
 IZO  CD    C  CSP    0   0.293  -14.9515  41.9030  4.2611
 IZO  CE    C  CSP1   0  -0.571  -13.7608  41.7794  4.3828
 IZO  OXT   O  OC    -1  -0.599  -19.7292  38.8110  4.5464
 IZO  HN1   H  HNH2   0   0.326  -19.3398  40.8693  5.6825
 IZO  HN2   H  HNH2   0   0.334  -18.8833  42.3277  5.1211
 IZO  HA    H  HCH1   0   0.202  -18.7677  41.3544  2.8732
 IZO  HB1C  H  HCH2   0   0.222  -16.9002  40.1049  4.9320
 IZO  HB2C  H  HCH2   0   0.227  -16.6597  40.1050  3.1910
 IZO  HG1C  H  HCH2   0   0.264  -16.6059  42.6137  3.2026
 IZO  HG2C  H  HCH2   0   0.257  -16.7837  42.6101  4.9451
 IZO  HE    H  H      0   0.274  -12.7073  41.6670  4.4978

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
 IZO  N   CA    single  1.458  0.019  1.458
 IZO  CA  C     single  1.525  0.021  1.525
 IZO  CA  CB    single  1.530  0.020  1.530
 IZO  C   O     deloc   1.231  0.020  1.231
 IZO  C   OXT   deloc   1.247  0.020  1.247
 IZO  CB  CG    single  1.532  0.020  1.532
 IZO  CG  CD    single  1.457  0.020  1.457
 IZO  CD  CE    triple  1.203  0.020  1.203
 IZO  N   HN1   single  0.868  0.020  1.013
 IZO  N   HN2   single  0.868  0.020  1.013
 IZO  CA  HA    single  0.970  0.020  0.970
 IZO  CB  HB1C  single  0.939  0.020  1.096
 IZO  CB  HB2C  single  0.939  0.020  1.096
 IZO  CG  HG1C  single  0.939  0.020  1.096
 IZO  CG  HG2C  single  0.939  0.020  1.096
 IZO  CE  HE    single  0.913  0.020  1.066

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
 IZO  HN2   N   HN1   107.07  3.000
 IZO  HN2   N   CA    111.13  3.000
 IZO  HN1   N   CA    108.77  3.000
 IZO  HA    CA  CB    109.00  3.000
 IZO  HA    CA  C     110.00  3.000
 IZO  CB    CA  C     110.10  1.900
 IZO  HA    CA  N     110.00  3.000
 IZO  CB    CA  N     110.50  1.700
 IZO  C     CA  N     111.00  2.800
 IZO  OXT   C   O     126.99  3.000
 IZO  OXT   C   CA    116.99  3.000
 IZO  O     C   CA    120.80  1.700
 IZO  HB2C  CB  HB1C  106.98  3.000
 IZO  HB2C  CB  CG    108.69  3.000
 IZO  HB1C  CB  CG    109.24  3.000
 IZO  HB2C  CB  CA    109.05  3.000
 IZO  HB1C  CB  CA    109.49  3.000
 IZO  CG    CB  CA    113.20  3.000
 IZO  HG2C  CG  HG1C  106.40  3.000
 IZO  HG2C  CG  CD    108.43  3.000
 IZO  HG1C  CG  CD    109.10  3.000
 IZO  HG2C  CG  CB    110.55  3.000
 IZO  HG1C  CG  CB    109.70  3.000
 IZO  CD    CG  CB    112.47  3.000
 IZO  CE    CD  CG    180.00  3.000
 IZO  HE    CE  CD    180.00  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
 IZO  Var_01  CD  CG  CB  CA  -177.91  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
 IZO  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
 IZO  plan-1  CA   0.020
 IZO  plan-1  C    0.020
 IZO  plan-1  O    0.020
 IZO  plan-1  OXT  0.020

