# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:20:39 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: (2S,3S)-2-amino-3-hydroxybutanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](N)C=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
 9VD  9VD  (2S,3S)-2-amino-3-hydroxybutanal  ligand  16  7  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9VD
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
 9VD  CDF  C  C1    0   0.180  -1.3574  -0.7468  -0.2011
 9VD  ODK  O  O     0  -0.379  -2.3804  -0.5778   0.4156
 9VD  CDE  C  CH1   0  -0.241  -0.2937   0.3200  -0.3730
 9VD  CDR  C  CH1   0   0.039   0.9787  -0.0867   0.4043
 9VD  CDS  C  CH3   0  -0.680   2.1570   0.8071   0.0612
 9VD  ODT  O  OH1   0  -0.664   1.2809  -1.4536   0.2176
 9VD  NDD  N  NH2   0  -0.780  -0.7013   1.6491   0.0157
 9VD  H1   H  H     0   0.191  -1.1505  -1.7109  -0.6938
 9VD  H2   H  HCH1  0   0.258  -0.0409   0.3253  -1.4421
 9VD  H3   H  HCH1  0   0.233   0.7538   0.0150   1.4719
 9VD  H4   H  HCH3  0   0.238   1.9282   1.8506   0.2671
 9VD  H5   H  HCH3  0   0.238   3.0320   0.5254   0.6483
 9VD  H6   H  HCH3  0   0.222   2.4148   0.7225  -0.9979
 9VD  H7   H  HOH1  0   0.446   1.5952  -1.5779  -0.6848
 9VD  H8   H  HNH2  0   0.356  -1.4611   1.9658  -0.5728
 9VD  H9   H  HNH2  0   0.344  -1.0692   1.6350   0.9596

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
 9VD  CDF  ODK  double  1.206  0.020  1.206
 9VD  CDF  CDE  single  1.516  0.020  1.516
 9VD  CDE  CDR  single  1.545  0.020  1.545
 9VD  CDE  NDD  single  1.443  0.020  1.443
 9VD  CDR  ODT  single  1.412  0.020  1.412
 9VD  CDR  CDS  single  1.518  0.020  1.518
 9VD  CDF  H1   single  0.930  0.020  1.080
 9VD  CDE  H2   single  0.970  0.020  1.090
 9VD  CDR  H3   single  0.970  0.020  1.090
 9VD  CDS  H4   single  0.970  0.020  1.090
 9VD  CDS  H5   single  0.970  0.020  1.090
 9VD  CDS  H6   single  0.970  0.020  1.090
 9VD  ODT  H7   single  0.850  0.020  0.980
 9VD  NDD  H8   single  0.890  0.020  1.040
 9VD  NDD  H9   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
 9VD  H1   CDF  CDE  115.66  3.000
 9VD  H1   CDF  ODK  120.67  3.000
 9VD  CDE  CDF  ODK  123.66  3.000
 9VD  H2   CDE  NDD  108.82  3.000
 9VD  H2   CDE  CDR  107.54  3.000
 9VD  NDD  CDE  CDR  109.84  3.000
 9VD  H2   CDE  CDF  105.97  3.000
 9VD  NDD  CDE  CDF  114.78  3.000
 9VD  CDR  CDE  CDF  109.60  3.000
 9VD  H3   CDR  ODT  105.22  3.000
 9VD  H3   CDR  CDS  108.96  3.000
 9VD  ODT  CDR  CDS  111.95  3.000
 9VD  H3   CDR  CDE  107.26  3.000
 9VD  CDS  CDR  CDE  111.74  3.000
 9VD  ODT  CDR  CDE  111.37  3.000
 9VD  H6   CDS  H5   108.20  3.000
 9VD  H6   CDS  H4   107.89  3.000
 9VD  H5   CDS  H4   108.34  3.000
 9VD  H6   CDS  CDR  110.88  3.000
 9VD  H5   CDS  CDR  110.42  3.000
 9VD  H4   CDS  CDR  111.02  3.000
 9VD  H7   ODT  CDR  108.57  3.000
 9VD  H9   NDD  H8   105.88  3.000
 9VD  H9   NDD  CDE  109.92  3.000
 9VD  H8   NDD  CDE  110.10  3.000

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
 9VD  chir_01  CDE  CDF  CDR  NDD  positiv
 9VD  chir_02  CDR  ODT  CDE  CDS  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
 9VD  plan-1  CDF  0.020
 9VD  plan-1  ODK  0.020
 9VD  plan-1  CDE  0.020
 9VD  plan-1  H1   0.020

