# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:37:50 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 5,5-dihydroxy-6-oxo-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(O)(O)C=O)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
 DO2  DO2  5,5-dihydroxy-6-oxo-L-norleucine  L-peptide  22  12  .  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_DO2
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
 DO2  C    C  C      0   0.404  40.7589  127.2040  85.6201
 DO2  N    N  NH2    0  -0.809  38.4994  126.2895  85.1738
 DO2  OXT  O  OC     0  -0.599  41.1215  126.4225  84.7199
 DO2  CA   C  CH1    0  -0.186  39.2414  127.2954  85.9203
 DO2  CB   C  CH2    0  -0.429  38.9306  127.1165  87.4141
 DO2  CD   C  CT     0   0.394  38.7450  128.2500  89.7238
 DO2  CE   C  C1     0   0.136  39.6150  127.2024  90.4198
 DO2  CG   C  CH2    0  -0.524  39.1563  128.3688  88.2526
 DO2  OE1  O  O      0  -0.354  40.4525  127.4767  91.2367
 DO2  O    O  O     -1  -0.601  41.4998  127.9438  86.3006
 DO2  H    H  HNH2   0   0.327  37.5276  126.5655  85.1099
 DO2  H2   H  HNH2   0   0.331  38.8557  126.2484  84.2289
 DO2  HA   H  HCH1   0   0.190  38.9371  128.3212  85.6440
 DO2  HB   H  HCH2   0   0.215  37.8805  126.8233  87.4985
 DO2  HBA  H  HCH2   0   0.219  39.5098  126.2705  87.7966
 DO2  O4   O  OH1    0  -0.655  38.9255  129.5077  90.2860
 DO2  O5   O  OH1    0  -0.666  37.4434  127.7647  89.8932
 DO2  HE   H  H      0   0.205  39.4232  126.1590  90.1170
 DO2  HG   H  HCH2   0   0.258  40.2028  128.6664  88.1985
 DO2  HGA  H  HCH2   0   0.240  38.5765  129.1949  87.8219
 DO2  H10  H  HOH1   0   0.447  38.8369  129.4536  91.2455
 DO2  H11  H  HOH1   0   0.457  36.8510  128.2250  89.2856

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
 DO2  C   OXT  deloc   1.246  0.020  1.246
 DO2  C   CA   single  1.525  0.021  1.525
 DO2  N   CA   single  1.458  0.019  1.458
 DO2  N   H    single  0.860  0.020  0.860
 DO2  N   H2   single  0.890  0.020  1.040
 DO2  CA  CB   single  1.521  0.033  1.521
 DO2  CA  HA   single  0.970  0.020  0.970
 DO2  CB  CG   single  1.524  0.020  1.524
 DO2  CB  HB   single  0.970  0.020  1.090
 DO2  CB  HBA  single  0.970  0.020  1.090
 DO2  CD  CE   single  1.529  0.020  1.529
 DO2  CD  O4   single  1.389  0.020  1.389
 DO2  CD  O5   single  1.399  0.020  1.399
 DO2  CE  OE1  double  1.202  0.020  1.202
 DO2  CE  HE   single  0.930  0.020  1.080
 DO2  CG  CD   single  1.532  0.020  1.532
 DO2  CG  HG   single  0.970  0.020  1.090
 DO2  CG  HGA  single  0.970  0.020  1.090
 DO2  O   C    deloc   1.231  0.020  1.231
 DO2  O4  H10  single  0.850  0.020  0.980
 DO2  O5  H11  single  0.850  0.020  0.980

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
 DO2  O    C   CA   120.80  1.700
 DO2  O    C   OXT  126.35  3.000
 DO2  CA   C   OXT  120.80  1.700
 DO2  H2   N   H    106.89  3.000
 DO2  H2   N   CA   109.13  3.000
 DO2  H    N   CA   114.00  3.000
 DO2  HA   CA  CB   109.00  3.000
 DO2  HA   CA  N    110.00  3.000
 DO2  CB   CA  N    110.40  1.500
 DO2  HA   CA  C    110.00  3.000
 DO2  CB   CA  C    110.50  1.500
 DO2  N    CA  C    111.00  2.800
 DO2  HBA  CB  HB   105.90  3.000
 DO2  HBA  CB  CG   111.38  3.000
 DO2  HB   CB  CG   108.67  3.000
 DO2  HBA  CB  CA   108.83  3.000
 DO2  HB   CB  CA   107.49  3.000
 DO2  CG   CB  CA   114.17  3.000
 DO2  O5   CD  O4   112.69  3.000
 DO2  O5   CD  CG   113.13  3.000
 DO2  O4   CD  CG   106.47  3.000
 DO2  CG   CD  CE   109.72  3.000
 DO2  O5   CD  CE   103.68  3.000
 DO2  O4   CD  CE   111.22  3.000
 DO2  HE   CE  OE1  121.58  3.000
 DO2  HE   CE  CD   115.08  3.000
 DO2  OE1  CE  CD   123.34  3.000
 DO2  HGA  CG  HG   106.40  3.000
 DO2  HGA  CG  CD   107.06  3.000
 DO2  HG   CG  CD   109.07  3.000
 DO2  HGA  CG  CB   108.93  3.000
 DO2  HG   CG  CB   109.84  3.000
 DO2  CD   CG  CB   115.14  3.000
 DO2  H10  O4  CD   109.86  3.000
 DO2  H11  O5  CD   109.22  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
 DO2  Var_01  CD   CG  CB  CA  175.22  30.0  3
 DO2  Var_02  CE   CD  CG  CB   64.15  30.0  3
 DO2  Var_03  OE1  CE  CD  CG  109.50  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
 DO2  chir_01  CA  C  N  CB  negativ

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
 DO2  plan-1  C    0.020
 DO2  plan-1  OXT  0.020
 DO2  plan-1  CA   0.020
 DO2  plan-1  O    0.020
 DO2  plan-2  CD   0.020
 DO2  plan-2  CE   0.020
 DO2  plan-2  OE1  0.020
 DO2  plan-2  HE   0.020

