# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:14:21 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: [(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](Cn1cncn1)C[P](O)(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
 5LD  5LD  '[(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid'  ligand  21  13  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5LD
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
 5LD  O10  O  OP    -1  -0.887   2.6736   0.7681   1.3839
 5LD  P9   P  P      0   1.195   2.6735   0.0590   0.0305
 5LD  O11  O  OP    -1  -0.881   3.8958   0.3297  -0.8418
 5LD  O12  O  O      0  -0.894   2.3340  -1.4602   0.1492
 5LD  C8   C  CH2    0  -0.771   1.1871   0.7017  -0.8895
 5LD  C7   C  CH1    0   0.061  -0.1114   0.2252  -0.2405
 5LD  O13  O  OH1    0  -0.728  -0.1689  -1.1717  -0.1525
 5LD  C6   C  CH2    0  -0.290  -1.3168   0.7253  -1.0264
 5LD  N2   N  NR5    0  -0.254  -2.5772   0.3532  -0.4156
 5LD  N1   N  N      0  -0.256  -3.2196  -0.7725  -0.7332
 5LD  C5   C  CR15   0  -0.011  -4.2498  -0.7659   0.0800
 5LD  N4   N  N      0  -0.467  -4.3034   0.2997   0.9057
 5LD  C3   C  CR15   0   0.102  -3.2304   0.9805   0.5644
 5LD  H3   H  HCH2   0   0.206   1.2065   1.7954  -0.9219
 5LD  H4   H  HCH2   0   0.201   1.2179   0.3578  -1.9308
 5LD  H5   H  HCH1   0   0.165  -0.1675   0.6870   0.7615
 5LD  H6   H  HOH1   0   0.431   0.7935  -1.4502  -0.0004
 5LD  H7   H  HCH2   0   0.259  -1.2883   1.8133  -1.0906
 5LD  H8   H  HCH2   0   0.256  -1.3118   0.3280  -2.0415
 5LD  H9   H  HCR5   0   0.266  -4.9889  -1.5528   0.0736
 5LD  H10  H  HCR5   0   0.296  -2.9006   1.9178   0.9865

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
 5LD  O12  P9   deloc     1.561  0.020  1.561
 5LD  O10  P9   deloc     1.528  0.020  1.528
 5LD  P9   O11  deloc     1.526  0.020  1.526
 5LD  P9   C8   single    1.862  0.020  1.862
 5LD  C8   C7   single    1.528  0.020  1.528
 5LD  C6   C7   single    1.523  0.020  1.523
 5LD  C6   N2   single    1.449  0.020  1.449
 5LD  C7   O13  single    1.401  0.020  1.401
 5LD  C3   N2   aromatic  1.334  0.020  1.334
 5LD  C3   N4   aromatic  1.316  0.020  1.316
 5LD  N2   N1   aromatic  1.334  0.020  1.334
 5LD  N4   C5   aromatic  1.349  0.020  1.349
 5LD  N1   C5   aromatic  1.312  0.020  1.312
 5LD  C8   H3   single    0.970  0.020  1.090
 5LD  C8   H4   single    0.970  0.020  1.090
 5LD  C7   H5   single    0.970  0.020  1.090
 5LD  O13  H6   single    0.850  0.020  0.980
 5LD  C6   H7   single    0.970  0.020  1.090
 5LD  C6   H8   single    0.970  0.020  1.090
 5LD  C5   H9   single    0.930  0.020  1.080
 5LD  C3   H10  single    0.930  0.020  1.080

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
 5LD  C8   P9   O12  101.52  3.000
 5LD  C8   P9   O11  107.20  3.000
 5LD  O12  P9   O11  112.97  3.000
 5LD  C8   P9   O10  106.11  3.000
 5LD  O11  P9   O10  115.09  3.000
 5LD  O12  P9   O10  112.60  3.000
 5LD  H4   C8   H3   106.54  3.000
 5LD  H4   C8   C7   109.23  3.000
 5LD  H3   C8   C7   109.83  3.000
 5LD  H4   C8   P9   109.77  3.000
 5LD  H3   C8   P9   110.20  3.000
 5LD  C7   C8   P9   111.15  3.000
 5LD  H5   C7   C6   106.88  3.000
 5LD  H5   C7   O13  110.97  3.000
 5LD  C6   C7   O13  109.10  3.000
 5LD  H5   C7   C8   107.34  3.000
 5LD  O13  C7   C8   111.88  3.000
 5LD  C6   C7   C8   110.54  3.000
 5LD  H6   O13  C7   104.15  3.000
 5LD  H8   C6   H7   107.99  3.000
 5LD  H8   C6   N2   107.63  3.000
 5LD  H7   C6   N2   107.68  3.000
 5LD  H8   C6   C7   110.93  3.000
 5LD  H7   C6   C7   109.71  3.000
 5LD  N2   C6   C7   112.73  3.000
 5LD  C3   N2   N1   109.61  3.000
 5LD  N1   N2   C6   122.34  3.000
 5LD  C3   N2   C6   127.92  3.000
 5LD  C5   N1   N2   103.07  3.000
 5LD  H9   C5   N4   123.51  3.000
 5LD  H9   C5   N1   122.01  3.000
 5LD  N4   C5   N1   114.48  3.000
 5LD  C3   N4   C5   102.56  3.000
 5LD  H10  C3   N4   126.65  3.000
 5LD  H10  C3   N2   123.08  3.000
 5LD  N4   C3   N2   110.27  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
 5LD  CONST_01  C5   N4  C3  N2     0.00   0.0  0
 5LD  CONST_02  N4   C5  N1  N2     0.00   0.0  0
 5LD  CONST_03  N4   C3  N2  N1     0.00   0.0  0
 5LD  CONST_04  C3   N4  C5  N1     0.00   0.0  0
 5LD  CONST_05  C3   N2  N1  C5     0.00   0.0  0
 5LD  CONST_06  N4   C3  N2  C6   180.00   0.0  0
 5LD  CONST_07  C5   N1  N2  C6   180.00   0.0  0
 5LD  CONST_08  H9   C5  N1  N2   180.00   0.0  0
 5LD  CONST_09  H10  C3  N2  N1   180.00   0.0  0
 5LD  Var_01    C3   N2  C6  C7    84.10  30.0  2
 5LD  Var_02    C7   C8  P9  O10  -68.28  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
 5LD  chir_01  C7  C8  C6  O13  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
 5LD  plan-1  C6   0.020
 5LD  plan-1  N2   0.020
 5LD  plan-1  N1   0.020
 5LD  plan-1  C5   0.020
 5LD  plan-1  N4   0.020
 5LD  plan-1  C3   0.020
 5LD  plan-1  H9   0.020
 5LD  plan-1  H10  0.020

