# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:43:11 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: 5-phosphono-D-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC[P](O)(O)=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
 2JJ  2JJ  '5-phosphono-D-norvaline  '  D-peptide  21  12  .  2016-04-22  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_2JJ
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
 2JJ  OAC  O  OP    -1  -0.909  19.3613  -20.2649  52.4918
 2JJ  PAL  P  P      0   1.164  20.6985  -20.9197  52.1003
 2JJ  OAE  O  O      0  -0.913  20.6033  -22.4496  51.9742
 2JJ  OAF  O  OP    -1  -0.912  21.8913  -20.4426  52.9458
 2JJ  CAI  C  CH2    0  -0.707  21.0871  -20.3506  50.3528
 2JJ  CAG  C  CH2    0  -0.403  21.6013  -18.9214  50.1743
 2JJ  CB   C  CH2    0  -0.386  20.6015  -17.8255  50.5226
 2JJ  CA   C  CH1    0  -0.214  21.1597  -16.4119  50.3648
 2JJ  N    N  NH2    0  -0.815  21.5491  -16.1652  48.9810
 2JJ  C    C  C      0   0.406  20.1608  -15.3319  50.8584
 2JJ  OXT  O  OC     0  -0.609  19.5988  -15.5541  51.9495
 2JJ  O    O  O     -1  -0.606  20.0212  -14.3113  50.1519
 2JJ  H3   H  HCH2   0   0.168  20.2028  -20.4972  49.7187
 2JJ  H4   H  HCH2   0   0.175  21.8472  -21.0309  49.9492
 2JJ  H5   H  HCH2   0   0.180  21.9329  -18.7834  49.1382
 2JJ  H6   H  HCH2   0   0.172  19.7157  -17.9276  49.8828
 2JJ  H7   H  HCH1   0   0.178  22.0263  -16.3353  51.0479
 2JJ  H8   H  HNH2   0   0.328  21.6139  -15.1652  48.8444
 2JJ  H9   H  HNH2   0   0.327  22.4696  -16.5454  48.8059
 2JJ  H12  H  HCH2   0   0.176  22.4968  -18.7920  50.7925
 2JJ  H13  H  HCH2   0   0.202  20.2613  -17.9698  51.5461

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
 2JJ  N    CA   single  1.458  0.019  1.458
 2JJ  CAG  CB   single  1.524  0.020  1.524
 2JJ  CAG  CAI  single  1.529  0.020  1.529
 2JJ  CA   CB   single  1.521  0.033  1.521
 2JJ  CA   C    single  1.525  0.021  1.525
 2JJ  O    C    deloc   1.231  0.020  1.231
 2JJ  CAI  PAL  single  1.878  0.020  1.878
 2JJ  C    OXT  deloc   1.247  0.020  1.247
 2JJ  OAE  PAL  deloc   1.538  0.020  1.538
 2JJ  PAL  OAC  deloc   1.540  0.020  1.540
 2JJ  PAL  OAF  deloc   1.538  0.020  1.538
 2JJ  CAI  H3   single  0.970  0.020  1.090
 2JJ  CAI  H4   single  0.970  0.020  1.090
 2JJ  CAG  H5   single  0.970  0.020  1.090
 2JJ  CB   H6   single  0.970  0.020  1.090
 2JJ  CA   H7   single  0.970  0.020  1.090
 2JJ  N    H8   single  0.890  0.020  1.040
 2JJ  N    H9   single  0.890  0.020  1.040
 2JJ  CAG  H12  single  0.970  0.020  1.090
 2JJ  CB   H13  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
 2JJ  CAI  PAL  OAF  104.89  3.000
 2JJ  OAF  PAL  OAE  113.68  3.000
 2JJ  CAI  PAL  OAE  103.76  3.000
 2JJ  OAF  PAL  OAC  113.70  3.000
 2JJ  OAE  PAL  OAC  112.96  3.000
 2JJ  CAI  PAL  OAC  106.70  3.000
 2JJ  H4   CAI  H3   105.23  3.000
 2JJ  H4   CAI  CAG  107.67  3.000
 2JJ  H3   CAI  CAG  109.15  3.000
 2JJ  H4   CAI  PAL  107.32  3.000
 2JJ  H3   CAI  PAL  109.28  3.000
 2JJ  CAG  CAI  PAL  117.47  3.000
 2JJ  H12  CAG  H5   105.73  3.000
 2JJ  H12  CAG  CB   108.80  3.000
 2JJ  H5   CAG  CB   108.90  3.000
 2JJ  H12  CAG  CAI  108.62  3.000
 2JJ  H5   CAG  CAI  109.25  3.000
 2JJ  CB   CAG  CAI  115.14  3.000
 2JJ  H13  CB   H6   106.48  3.000
 2JJ  H13  CB   CA   109.51  3.000
 2JJ  H6   CB   CA   108.71  3.000
 2JJ  H13  CB   CAG  108.95  3.000
 2JJ  H6   CB   CAG  109.23  3.000
 2JJ  CA   CB   CAG  113.71  3.000
 2JJ  H7   CA   C    105.06  3.000
 2JJ  H7   CA   N    111.40  3.000
 2JJ  C    CA   N    111.00  2.800
 2JJ  H7   CA   CB   106.65  3.000
 2JJ  C    CA   CB   110.50  1.500
 2JJ  N    CA   CB   110.40  1.500
 2JJ  H9   N    H8   106.86  3.000
 2JJ  H9   N    CA   110.10  3.000
 2JJ  H8   N    CA   108.21  3.000
 2JJ  O    C    OXT  126.15  3.000
 2JJ  OXT  C    CA   120.80  1.700
 2JJ  O    C    CA   120.80  1.700

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
 2JJ  Var_01  CAG  CAI  PAL  OAC   75.81  30.0  3
 2JJ  Var_02  CB   CAG  CAI  PAL  -66.02  30.0  1
 2JJ  Var_03  CA   CB   CAG  CAI  178.60  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
 2JJ  chir_01  CA  N  CB  C  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
 2JJ  plan-1  CA   0.020
 2JJ  plan-1  C    0.020
 2JJ  plan-1  OXT  0.020
 2JJ  plan-1  O    0.020

