# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:09:40 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: 3-ammonio-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[NH3+])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
 DNP  DNP  '3-ammonio-L-alanine      '  L-peptide  15  7  .  2012-08-28  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DNP
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
 DNP  N    N  NH2    0  -0.791  3.7002  -3.1477  -4.2891
 DNP  CA   C  CH1    0  -0.250  2.4412  -3.2563  -5.0134
 DNP  CB   C  CH2    0  -0.333  2.1645  -4.6327  -5.6259
 DNP  NG   N  NT3    1  -0.813  1.9105  -5.6276  -4.5542
 DNP  C    C  C      0   0.476  1.2986  -2.7967  -4.0693
 DNP  O    O  O      0  -0.545  1.0554  -1.5940  -3.9951
 DNP  OXT  O  OC    -1  -0.612  0.7201  -3.7159  -3.4118
 DNP  H    H  HNH2   0   0.345  3.7035  -3.7259  -3.4577
 DNP  H2   H  HNH2   0   0.353  4.4679  -3.4660  -4.8679
 DNP  HA   H  HCH1   0   0.255  2.4835  -2.5585  -5.8530
 DNP  HB2  H  HCH2   0   0.282  2.9941  -4.9714  -6.2446
 DNP  HB3  H  HCH2   0   0.277  1.2679  -4.6021  -6.2438
 DNP  HG1  H  HNT3   0   0.461  1.2956  -5.0633  -3.8656
 DNP  HG2  H  HNT3   0   0.442  2.7643  -5.9301  -4.0906
 DNP  HG3  H  HNT3   0   0.452  1.4336  -6.4587  -4.8938

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
 DNP  N   CA   single  1.458  0.019  1.458
 DNP  N   H    single  0.860  0.020  0.860
 DNP  N   H2   single  0.890  0.020  1.040
 DNP  CA  CB   single  1.521  0.033  1.521
 DNP  CA  C    single  1.525  0.021  1.525
 DNP  CA  HA   single  0.970  0.020  0.970
 DNP  CB  NG   single  1.484  0.020  1.484
 DNP  CB  HB2  single  0.970  0.020  1.090
 DNP  CB  HB3  single  0.970  0.020  1.090
 DNP  NG  HG1  single  0.890  0.020  1.040
 DNP  NG  HG2  single  0.890  0.020  1.040
 DNP  NG  HG3  single  0.890  0.020  1.040
 DNP  C   O    deloc   1.231  0.020  1.231
 DNP  C   OXT  deloc   1.270  0.020  1.270

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
 DNP  H2   N   H    106.69  3.000
 DNP  H2   N   CA   110.34  3.000
 DNP  H    N   CA   114.00  3.000
 DNP  HA   CA  C    109.00  3.000
 DNP  HA   CA  CB   109.00  3.000
 DNP  C    CA  CB   110.50  1.500
 DNP  HA   CA  N    110.00  3.000
 DNP  C    CA  N    111.00  2.800
 DNP  CB   CA  N    110.40  1.500
 DNP  HB3  CB  HB2  108.27  3.000
 DNP  HB3  CB  NG   106.72  3.000
 DNP  HB2  CB  NG   109.40  3.000
 DNP  HB3  CB  CA   110.50  3.000
 DNP  HB2  CB  CA   111.65  3.000
 DNP  NG   CB  CA   110.15  3.000
 DNP  HG3  NG  HG2  107.62  3.000
 DNP  HG3  NG  HG1  111.86  3.000
 DNP  HG2  NG  HG1  110.00  3.000
 DNP  HG3  NG  CB   112.77  3.000
 DNP  HG2  NG  CB   112.62  3.000
 DNP  HG1  NG  CB   101.96  3.000
 DNP  OXT  C   O    125.94  3.000
 DNP  OXT  C   CA   115.86  3.000
 DNP  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
 DNP  Var_01  HG1  NG  CB  CA  41.12  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
 DNP  chir_01  CA  N  CB  C  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
 DNP  plan-1  CA   0.020
 DNP  plan-1  C    0.020
 DNP  plan-1  O    0.020
 DNP  plan-1  OXT  0.020

