# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:53:53 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-O-phosphono-D-arabinitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@H](O)[C@H](O)CO[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
 A5P  A5P  5-O-phosphono-D-arabinitol  ligand  25  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A5P
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
 A5P  C1   C  CH2    0  -0.166   0.4259  -0.6412   4.2739
 A5P  O1   O  OH1    0  -0.672  -0.2871  -0.4161   5.4688
 A5P  C2   C  CH1    0  -0.004  -0.3147   0.0232   3.1258
 A5P  O2   O  OH1    0  -0.671  -0.4386   1.4191   3.3062
 A5P  C3   C  CH1    0  -0.029   0.3371  -0.3232   1.7833
 A5P  O3   O  OH1    0  -0.668   1.6815   0.1161   1.7321
 A5P  C4   C  CH1    0  -0.030  -0.4610   0.2036   0.5781
 A5P  O4   O  OH1    0  -0.664  -1.8320  -0.1115   0.6947
 A5P  C5   C  CH2    0  -0.128   0.1209  -0.3065  -0.7329
 A5P  O5   O  O2     0  -0.657  -0.5355   0.2914  -1.8075
 A5P  P    P  P      0   1.221   0.0518  -0.0682  -3.3698
 A5P  O1P  O  O      0  -0.908  -0.0895  -1.5809  -3.5053
 A5P  O2P  O  OP    -1  -0.899  -0.9063   0.7496  -4.2258
 A5P  O3P  O  OP    -1  -0.907   1.4955   0.4249  -3.3681
 A5P  H11  H  HCH2   0   0.197   1.4483  -0.2444   4.3372
 A5P  H12  H  HCH2   0   0.199   0.5168  -1.7135   4.0536
 A5P  HO1  H  HOH1   0   0.454   0.2217  -0.7929   6.1918
 A5P  HC2  H  HCH1   0   0.229  -1.3341  -0.3713   3.1118
 A5P  HO2  H  HOH1   0   0.441   0.4122   1.7767   3.5797
 A5P  HC3  H  HCH1   0   0.222   0.3798  -1.4180   1.7118
 A5P  HO3  H  HOH1   0   0.442   1.6926   1.0671   1.5782
 A5P  HC4  H  HCH1   0   0.214  -0.4101   1.2994   0.5853
 A5P  HO4  H  HOH1   0   0.442  -1.9390  -1.0580   0.5496
 A5P  H51  H  HCH2   0   0.180   1.1983  -0.1023  -0.7539
 A5P  H52  H  HCH2   0   0.164   0.0180  -1.4049  -0.7522

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
 A5P  C1  O1   single  1.410  0.020  1.410
 A5P  C1  C2   single  1.519  0.020  1.519
 A5P  C1  H11  single  0.970  0.020  1.090
 A5P  C1  H12  single  0.970  0.020  1.090
 A5P  O1  HO1  single  0.850  0.020  0.980
 A5P  C2  O2   single  1.413  0.020  1.413
 A5P  C2  C3   single  1.532  0.020  1.532
 A5P  C2  HC2  single  0.970  0.020  1.090
 A5P  O2  HO2  single  0.850  0.020  0.980
 A5P  C3  O3   single  1.415  0.020  1.415
 A5P  C3  C4   single  1.539  0.020  1.539
 A5P  C3  HC3  single  0.970  0.020  1.090
 A5P  O3  HO3  single  0.850  0.020  0.980
 A5P  C4  O4   single  1.412  0.020  1.412
 A5P  C4  C5   single  1.522  0.020  1.522
 A5P  C4  HC4  single  0.970  0.020  1.090
 A5P  O4  HO4  single  0.850  0.020  0.980
 A5P  C5  O5   single  1.394  0.020  1.394
 A5P  C5  H51  single  0.970  0.020  1.090
 A5P  C5  H52  single  0.970  0.020  1.090
 A5P  O5  P    single  1.707  0.020  1.707
 A5P  P   O1P  deloc   1.525  0.020  1.525
 A5P  P   O2P  deloc   1.523  0.020  1.523
 A5P  P   O3P  deloc   1.526  0.020  1.526

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
 A5P  H12  C1  H11  106.69  3.000
 A5P  H12  C1  C2   108.41  3.000
 A5P  H11  C1  C2   109.84  3.000
 A5P  H12  C1  O1   111.58  3.000
 A5P  H11  C1  O1   111.36  3.000
 A5P  C2   C1  O1   108.91  3.000
 A5P  HO1  O1  C1   107.90  3.000
 A5P  HC2  C2  C3   107.70  3.000
 A5P  HC2  C2  O2   106.04  3.000
 A5P  C3   C2  O2   111.87  3.000
 A5P  HC2  C2  C1   107.85  3.000
 A5P  C3   C2  C1   110.85  3.000
 A5P  O2   C2  C1   112.23  3.000
 A5P  HO2  O2  C2   109.01  3.000
 A5P  HC3  C3  C4   108.09  3.000
 A5P  HC3  C3  O3   105.68  3.000
 A5P  C4   C3  O3   110.99  3.000
 A5P  HC3  C3  C2   107.40  3.000
 A5P  C4   C3  C2   112.85  3.000
 A5P  O3   C3  C2   111.45  3.000
 A5P  HO3  O3  C3   108.85  3.000
 A5P  HC4  C4  C5   108.82  3.000
 A5P  HC4  C4  O4   105.52  3.000
 A5P  C5   C4  O4   111.57  3.000
 A5P  HC4  C4  C3   108.23  3.000
 A5P  C5   C4  C3   111.20  3.000
 A5P  O4   C4  C3   111.27  3.000
 A5P  HO4  O4  C4   108.35  3.000
 A5P  H52  C5  H51  106.06  3.000
 A5P  H52  C5  O5   111.69  3.000
 A5P  H51  C5  O5   111.58  3.000
 A5P  H52  C5  C4   108.24  3.000
 A5P  H51  C5  C4   109.25  3.000
 A5P  O5   C5  C4   109.89  3.000
 A5P  P    O5  C5   116.94  3.000
 A5P  O3P  P   O2P  114.99  3.000
 A5P  O3P  P   O1P  114.10  3.000
 A5P  O2P  P   O1P  115.11  3.000
 A5P  O3P  P   O5   104.86  3.000
 A5P  O2P  P   O5   100.65  3.000
 A5P  O1P  P   O5   104.97  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
 A5P  Var_01  O1P  P   O5  C5  60.02  30.0  3
 A5P  Var_02  H51  C5  O5  P   54.37  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
 A5P  chir_01  C2  C1  O2  C3  negativ
 A5P  chir_02  C3  O3  C2  C4  negativ
 A5P  chir_03  C4  O4  C3  C5  negativ

