# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:31:52 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 3-(1H-imidazol-3-ium-4-yl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1c[nH]c[nH+]1)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
 DHI  DHI  3-(1H-imidazol-3-ium-4-yl)-D-alanine  D-peptide  20  11  .  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_DHI
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
 DHI  N    N  NH2    0  -0.804  19.0143  -5.2428  34.3453
 DHI  CA   C  CH1    0  -0.196  19.7365  -5.0444  35.5983
 DHI  C    C  C      0   0.402  21.1991  -4.6221  35.3008
 DHI  O    O  O      0  -0.601  21.3531  -3.5380  34.7070
 DHI  CB   C  CH2    0  -0.516  19.0359  -3.9550  36.4098
 DHI  CG   C  CR5    0   0.312  17.6854  -4.3705  36.8803
 DHI  ND1  N  NR15   1  -0.587  16.6346  -3.4960  37.0226
 DHI  CD2  C  CR15   0  -0.109  17.2039  -5.5802  37.2740
 DHI  CE1  C  CR15   0   0.236  15.5651  -4.1269  37.4793
 DHI  NE2  N  NR15   0  -0.541  15.8957  -5.3942  37.6363
 DHI  OXT  O  OC    -1  -0.597  22.0878  -5.4069  35.6830
 DHI  H    H  HNH2   0   0.341  18.1036  -5.6446  34.5353
 DHI  H2   H  HNH2   0   0.343  19.4951  -5.9363  33.7851
 DHI  HA   H  HCH1   0   0.191  19.7751  -5.9562  36.2115
 DHI  HB2  H  HCH2   0   0.272  19.6413  -3.6916  37.2822
 DHI  HB3  H  HCH2   0   0.259  18.9499  -3.0544  35.7995
 DHI  HD1  H  HNR5   0   0.456  16.6647  -2.5079  36.8078
 DHI  HD2  H  HCR5   0   0.327  17.6802  -6.5435  37.3238
 DHI  HE1  H  HCR5   0   0.355  14.6030  -3.6884  37.6811
 DHI  HE2  H  HNR5   0   0.459  15.2698  -6.1139  37.9715

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
 DHI  N    CA   single    1.458  0.019  1.458
 DHI  N    H    single    0.860  0.020  0.860
 DHI  N    H2   single    0.890  0.020  1.040
 DHI  CA   C    single    1.525  0.021  1.525
 DHI  CA   CB   single    1.521  0.033  1.521
 DHI  CA   HA   single    0.970  0.020  0.970
 DHI  C    O    deloc     1.231  0.020  1.231
 DHI  C    OXT  deloc     1.246  0.020  1.246
 DHI  CB   CG   single    1.489  0.020  1.489
 DHI  CB   HB2  single    0.970  0.020  1.090
 DHI  CB   HB3  single    0.970  0.020  1.090
 DHI  CG   ND1  aromatic  1.374  0.020  1.374
 DHI  CG   CD2  aromatic  1.360  0.020  1.360
 DHI  ND1  CE1  aromatic  1.323  0.020  1.323
 DHI  ND1  HD1  single    0.860  0.020  1.020
 DHI  CD2  NE2  aromatic  1.370  0.020  1.370
 DHI  CD2  HD2  single    0.930  0.020  1.080
 DHI  CE1  NE2  aromatic  1.319  0.020  1.319
 DHI  CE1  HE1  single    0.930  0.020  1.080
 DHI  NE2  HE2  single    0.860  0.020  1.020

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
 DHI  H2   N    H    105.00  3.000
 DHI  H2   N    CA   109.45  3.000
 DHI  H    N    CA   114.00  3.000
 DHI  HA   CA   CB   109.00  3.000
 DHI  HA   CA   C    110.00  3.000
 DHI  CB   CA   C    110.50  1.500
 DHI  HA   CA   N    110.00  3.000
 DHI  CB   CA   N    110.40  1.500
 DHI  C    CA   N    111.00  2.800
 DHI  OXT  C    O    127.32  3.000
 DHI  OXT  C    CA   120.80  1.700
 DHI  O    C    CA   120.80  1.700
 DHI  HB3  CB   HB2  106.91  3.000
 DHI  HB3  CB   CG   109.60  3.000
 DHI  HB2  CB   CG   108.48  3.000
 DHI  HB3  CB   CA   109.11  3.000
 DHI  HB2  CB   CA   109.95  3.000
 DHI  CG   CB   CA   112.61  3.000
 DHI  CD2  CG   ND1  105.38  3.000
 DHI  CD2  CG   CB   131.34  3.000
 DHI  ND1  CG   CB   123.26  3.000
 DHI  HD1  ND1  CE1  124.27  3.000
 DHI  HD1  ND1  CG   125.22  3.000
 DHI  CE1  ND1  CG   110.51  3.000
 DHI  HD2  CD2  NE2  122.14  3.000
 DHI  HD2  CD2  CG   130.77  3.000
 DHI  NE2  CD2  CG   107.08  3.000
 DHI  HE1  CE1  NE2  126.38  3.000
 DHI  HE1  CE1  ND1  126.37  3.000
 DHI  NE2  CE1  ND1  107.25  3.000
 DHI  HE2  NE2  CE1  124.63  3.000
 DHI  HE2  NE2  CD2  125.60  3.000
 DHI  CE1  NE2  CD2  109.77  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
 DHI  CONST_01  NE2  CE1  ND1  CG      0.00   0.0  0
 DHI  CONST_02  CE1  NE2  CD2  CG      0.00   0.0  0
 DHI  CONST_03  NE2  CD2  CG   ND1     0.00   0.0  0
 DHI  CONST_04  CD2  NE2  CE1  ND1     0.00   0.0  0
 DHI  CONST_05  CE1  ND1  CG   CD2     0.00   0.0  0
 DHI  CONST_06  CE1  ND1  CG   CB    180.00   0.0  0
 DHI  CONST_07  NE2  CD2  CG   CB    180.00   0.0  0
 DHI  CONST_08  HE1  CE1  ND1  CG    180.00   0.0  0
 DHI  CONST_09  HE2  NE2  CD2  CG    180.00   0.0  0
 DHI  CONST_10  HD2  CD2  CG   ND1   180.00   0.0  0
 DHI  CONST_11  HD1  ND1  CG   CD2   180.00   0.0  0
 DHI  Var_01    ND1  CG   CB   CA   -147.09  30.0  2

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
 DHI  chir_01  CA  N  C  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
 DHI  plan-1  CB   0.020
 DHI  plan-1  CG   0.020
 DHI  plan-1  ND1  0.020
 DHI  plan-1  CD2  0.020
 DHI  plan-1  CE1  0.020
 DHI  plan-1  NE2  0.020
 DHI  plan-1  HD1  0.020
 DHI  plan-1  HD2  0.020
 DHI  plan-1  HE1  0.020
 DHI  plan-1  HE2  0.020
 DHI  plan-2  CA   0.020
 DHI  plan-2  C    0.020
 DHI  plan-2  O    0.020
 DHI  plan-2  OXT  0.020

