# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 09:52:51 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-(5-phosphono-1H-1,2,3-triazol-1-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cn1nncc1[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
 UKY  UKY  3-(5-phosphono-1H-1,2,3-triazol-1-yl)-L-alanine  L-peptide  21  15  .  2022-08-11  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_UKY
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
 UKY  C    C  C      0   0.384  63.8550  12.0779  203.2623
 UKY  O2   O  O      0  -0.866  59.1023  12.3555  203.1098
 UKY  O3   O  OP    -1  -0.865  57.8728  14.5732  203.5629
 UKY  O4   O  OP    -1  -0.862  60.0847  14.0605  204.7693
 UKY  N    N  NH2    0  -0.781  63.8595  14.5654  202.6902
 UKY  CA   C  CH1    0  -0.249  63.0639  13.3864  202.9806
 UKY  O    O  O      0  -0.614  63.1624  11.0819  203.5606
 UKY  CB   C  CH2    0  -0.293  62.0804  13.1149  201.8401
 UKY  NG   N  NR5    0  -0.276  61.2387  14.2490  201.5226
 UKY  CD1  C  CR5    0  -0.040  60.0996  14.6430  202.1335
 UKY  ND2  N  N      0  -0.139  61.5826  15.0598  200.5297
 UKY  CE1  C  CR15   0  -0.259  59.7735  15.7779  201.4206
 UKY  NE2  N  N      0  -0.321  60.6957  15.9931  200.4589
 UKY  P    P  P      0   1.154  59.1979  13.8162  203.5484
 UKY  H5   H  HNH2   0   0.333  64.4309  14.7728  203.4999
 UKY  H6   H  HNH2   0   0.321  64.5283  14.3342  201.9638
 UKY  H7   H  HCH1   0   0.232  62.4546  13.6055  203.8639
 UKY  H8   H  HCH2   0   0.253  61.4257  12.2897  202.1047
 UKY  H9   H  HCH2   0   0.241  62.6168  12.8521  200.9259
 UKY  H10  H  HCR5   0   0.241  58.9239  16.4293  201.5490
 UKY  OXT  O  OC    -1  -0.596  65.0960  12.1244  203.1663

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
 UKY  NE2  ND2  aromatic  1.289  0.020  1.289
 UKY  NE2  CE1  aromatic  1.350  0.020  1.350
 UKY  ND2  NG   aromatic  1.327  0.020  1.327
 UKY  CE1  CD1  aromatic  1.379  0.020  1.379
 UKY  NG   CB   single    1.448  0.020  1.448
 UKY  NG   CD1  aromatic  1.351  0.020  1.351
 UKY  CB   CA   single    1.521  0.033  1.521
 UKY  CD1  P    single    1.870  0.020  1.870
 UKY  O    C    deloc     1.231  0.020  1.231
 UKY  N    CA   single    1.458  0.019  1.458
 UKY  CA   C    single    1.525  0.021  1.525
 UKY  O2   P    deloc     1.528  0.020  1.528
 UKY  P    O3   deloc     1.526  0.020  1.526
 UKY  P    O4   deloc     1.529  0.020  1.529
 UKY  N    H5   single    0.890  0.020  1.040
 UKY  N    H6   single    0.890  0.020  1.040
 UKY  CA   H7   single    0.970  0.020  1.090
 UKY  CB   H8   single    0.970  0.020  1.090
 UKY  CB   H9   single    0.970  0.020  1.090
 UKY  CE1  H10  single    0.930  0.020  1.080
 UKY  C    OXT  deloc     1.246  0.020  1.246

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
 UKY  OXT  C    O    126.91  3.000
 UKY  OXT  C    CA   120.80  1.700
 UKY  O    C    CA   120.80  1.700
 UKY  H6   N    H5   104.32  3.000
 UKY  H6   N    CA   108.64  3.000
 UKY  H5   N    CA   108.41  3.000
 UKY  H7   CA   CB   106.20  3.000
 UKY  H7   CA   N    107.68  3.000
 UKY  CB   CA   N    110.40  1.500
 UKY  H7   CA   C    107.78  3.000
 UKY  N    CA   C    111.00  2.800
 UKY  CB   CA   C    110.50  1.500
 UKY  H9   CB   H8   108.50  3.000
 UKY  H9   CB   NG   106.89  3.000
 UKY  H8   CB   NG   107.35  3.000
 UKY  H9   CB   CA   110.54  3.000
 UKY  H8   CB   CA   109.92  3.000
 UKY  NG   CB   CA   113.46  3.000
 UKY  ND2  NG   CD1  112.24  3.000
 UKY  CD1  NG   CB   128.28  3.000
 UKY  ND2  NG   CB   119.47  3.000
 UKY  P    CD1  CE1  129.84  3.000
 UKY  P    CD1  NG   128.27  3.000
 UKY  CE1  CD1  NG   101.86  3.000
 UKY  NE2  ND2  NG   107.76  3.000
 UKY  H10  CE1  NE2  121.80  3.000
 UKY  H10  CE1  CD1  128.45  3.000
 UKY  NE2  CE1  CD1  109.75  3.000
 UKY  CE1  NE2  ND2  108.39  3.000
 UKY  CD1  P    O4   104.71  3.000
 UKY  O4   P    O3   114.63  3.000
 UKY  CD1  P    O3   101.92  3.000
 UKY  O4   P    O2   114.73  3.000
 UKY  O3   P    O2   114.99  3.000
 UKY  CD1  P    O2   103.62  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
 UKY  CONST_01  CE1  NE2  ND2  NG     0.00   0.0  0
 UKY  CONST_02  NE2  CE1  CD1  NG     0.00   0.0  0
 UKY  CONST_03  ND2  NE2  CE1  CD1    0.00   0.0  0
 UKY  CONST_04  NE2  ND2  NG   CD1    0.00   0.0  0
 UKY  CONST_05  CE1  CD1  NG   ND2    0.00   0.0  0
 UKY  CONST_06  NE2  ND2  NG   CB   180.00   0.0  0
 UKY  CONST_07  CE1  CD1  NG   CB   180.00   0.0  0
 UKY  CONST_08  P    CD1  NG   ND2  180.00   0.0  0
 UKY  CONST_09  P    CD1  CE1  NE2  180.00   0.0  0
 UKY  CONST_10  H10  CE1  CD1  NG   180.00   0.0  0
 UKY  Var_01    CE1  CD1  P    O2   129.28  30.0  2
 UKY  Var_02    ND2  NG   CB   CA    96.24  30.0  1

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
 UKY  chir_01  CA  CB  N  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
 UKY  plan-1  CB   0.020
 UKY  plan-1  NG   0.020
 UKY  plan-1  CD1  0.020
 UKY  plan-1  ND2  0.020
 UKY  plan-1  CE1  0.020
 UKY  plan-1  NE2  0.020
 UKY  plan-1  P    0.020
 UKY  plan-1  H10  0.020
 UKY  plan-2  C    0.020
 UKY  plan-2  CA   0.020
 UKY  plan-2  O    0.020
 UKY  plan-2  OXT  0.020

