# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:06:05 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: [(2S)-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
 5DL  5DL  '[(2S)-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_5DL
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
 5DL  N1   N  N      0  -0.269  -3.0840  -0.9711  -0.6494
 5DL  C3   C  CR15   0   0.112  -3.3421   0.9802   0.2908
 5DL  N2   N  NR5    0  -0.248  -2.5805   0.2605  -0.5323
 5DL  C8   C  CH2    0  -0.769   1.1882   0.5815  -0.9249
 5DL  C7   C  CH1    0   0.064  -0.1330   0.1753  -0.2739
 5DL  C6   C  CH2    0  -0.293  -1.3127   0.6220  -1.1283
 5DL  C5   C  CR15   0  -0.007  -4.1529  -0.9266   0.1111
 5DL  O10  O  OP    -1  -0.880   3.8647   0.8353  -0.4300
 5DL  O11  O  O      0  -0.894   2.1955   0.7399   1.5283
 5DL  O12  O  OP    -1  -0.886   2.7091  -1.3859   0.1786
 5DL  O13  O  OH1    0  -0.732  -0.2814   0.7365   1.0025
 5DL  N4   N  N      0  -0.470  -4.3601   0.2614   0.7150
 5DL  H1   H  HCR5   0   0.293  -3.1297   2.0076   0.5416
 5DL  H2   H  HCH2   0   0.206   1.2834   0.1031  -1.9045
 5DL  H3   H  HCH2   0   0.200   1.1834   1.6636  -1.1040
 5DL  H4   H  HCH1   0   0.169  -0.1581  -0.9271  -0.2272
 5DL  H5   H  HCH2   0   0.260  -1.2648   0.1750  -2.1208
 5DL  H6   H  HCH2   0   0.251  -1.3014   1.7066  -1.2454
 5DL  H7   H  HCR5   0   0.266  -4.8062  -1.7779   0.2299
 5DL  H10  H  HOH1   0   0.432   0.6650   0.7921   1.3648
 5DL  P9   P  P      0   1.195   2.6397   0.1399   0.1564

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
 5DL  O11  P9   deloc     1.562  0.020  1.562
 5DL  O10  P9   deloc     1.526  0.020  1.526
 5DL  P9   O12  deloc     1.528  0.020  1.528
 5DL  P9   C8   single    1.863  0.020  1.863
 5DL  C8   C7   single    1.528  0.020  1.528
 5DL  C7   C6   single    1.524  0.020  1.524
 5DL  C7   O13  single    1.402  0.020  1.402
 5DL  C6   N2   single    1.447  0.020  1.447
 5DL  C3   N2   aromatic  1.332  0.020  1.332
 5DL  C3   N4   aromatic  1.316  0.020  1.316
 5DL  N2   N1   aromatic  1.336  0.020  1.336
 5DL  N4   C5   aromatic  1.349  0.020  1.349
 5DL  N1   C5   aromatic  1.313  0.020  1.313
 5DL  C3   H1   single    0.930  0.020  1.080
 5DL  C8   H2   single    0.970  0.020  1.090
 5DL  C8   H3   single    0.970  0.020  1.090
 5DL  C7   H4   single    0.970  0.020  1.090
 5DL  C6   H5   single    0.970  0.020  1.090
 5DL  C6   H6   single    0.970  0.020  1.090
 5DL  C5   H7   single    0.930  0.020  1.080
 5DL  O13  H10  single    0.850  0.020  0.980

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
 5DL  C5   N1   N2   103.00  3.000
 5DL  H1   C3   N4   126.69  3.000
 5DL  H1   C3   N2   123.06  3.000
 5DL  N4   C3   N2   110.25  3.000
 5DL  C6   N2   C3   128.34  3.000
 5DL  C3   N2   N1   109.68  3.000
 5DL  C6   N2   N1   121.64  3.000
 5DL  H3   C8   H2   106.59  3.000
 5DL  H3   C8   P9   109.39  3.000
 5DL  H2   C8   P9   110.37  3.000
 5DL  H3   C8   C7   109.15  3.000
 5DL  H2   C8   C7   109.91  3.000
 5DL  P9   C8   C7   111.31  3.000
 5DL  H4   C7   O13  111.03  3.000
 5DL  H4   C7   C6   107.39  3.000
 5DL  O13  C7   C6   108.13  3.000
 5DL  H4   C7   C8   107.65  3.000
 5DL  O13  C7   C8   111.90  3.000
 5DL  C6   C7   C8   110.65  3.000
 5DL  H6   C6   H5   108.04  3.000
 5DL  H6   C6   C7   110.10  3.000
 5DL  H5   C6   C7   110.89  3.000
 5DL  H6   C6   N2   107.57  3.000
 5DL  H5   C6   N2   108.13  3.000
 5DL  C7   C6   N2   111.97  3.000
 5DL  H7   C5   N4   123.53  3.000
 5DL  H7   C5   N1   121.99  3.000
 5DL  N4   C5   N1   114.48  3.000
 5DL  H10  O13  C7   104.37  3.000
 5DL  C5   N4   C3   102.59  3.000
 5DL  O12  P9   O11  112.57  3.000
 5DL  O12  P9   O10  115.11  3.000
 5DL  O11  P9   O10  113.00  3.000
 5DL  O12  P9   C8   106.30  3.000
 5DL  O10  P9   C8   107.12  3.000
 5DL  O11  P9   C8   101.37  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
 5DL  CONST_01  N4   C3  N2  N1    0.00   0.0  0
 5DL  CONST_02  C3   N4  C5  N1    0.00   0.0  0
 5DL  CONST_03  C5   N1  N2  C3    0.00   0.0  0
 5DL  CONST_04  C5   N4  C3  N2    0.00   0.0  0
 5DL  CONST_05  N4   C5  N1  N2    0.00   0.0  0
 5DL  CONST_06  N4   C3  N2  C6  180.00   0.0  0
 5DL  CONST_07  C5   N1  N2  C6  180.00   0.0  0
 5DL  CONST_08  H1   C3  N2  N1  180.00   0.0  0
 5DL  CONST_09  H7   C5  N4  C3  180.00   0.0  0
 5DL  Var_01    C7   C6  N2  N1  -80.85  30.0  2
 5DL  Var_02    O11  P9  C8  C7  -49.78  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
 5DL  chir_01  C7  C8  C6  O13  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
 5DL  plan-1  N1  0.020
 5DL  plan-1  C3  0.020
 5DL  plan-1  N2  0.020
 5DL  plan-1  C6  0.020
 5DL  plan-1  C5  0.020
 5DL  plan-1  N4  0.020
 5DL  plan-1  H1  0.020
 5DL  plan-1  H7  0.020

