# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:27:19 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  27  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  -0.171   0.3587  -0.6169   4.2945
 A5P  O1    O  OH1   0  -0.670  -0.3886  -0.3276   5.4530
 A5P  C2    C  CH1   0  -0.010  -0.2976   0.0633   3.1056
 A5P  O2    O  OH1   0  -0.670  -0.3438   1.4682   3.2435
 A5P  C3    C  CH1   0  -0.033   0.3887  -0.3520   1.7996
 A5P  O3    O  OH1   0  -0.663   1.7536   0.0080   1.7797
 A5P  C4    C  CH1   0  -0.030  -0.3390   0.1925   0.5578
 A5P  O4    O  OH1   0  -0.655  -1.7129  -0.1025   0.5805
 A5P  C5    C  CH2   0  -0.175   0.3213  -0.3342  -0.7056
 A5P  O5    O  O2    0  -0.588  -0.3262   0.2729  -1.8295
 A5P  P     P  P     0   1.456   0.1151  -0.1375  -3.3055
 A5P  O1P   O  O     0  -0.712   0.1608  -1.5799  -3.6093
 A5P  O2P   O  OH1   0  -0.732  -0.9593   0.7521  -4.0771
 A5P  O3P   O  OH1   0  -0.744   1.5566   0.5051  -3.5611
 A5P  H11   H  HCH2  0   0.200   1.3982  -0.2750   4.3915
 A5P  H12   H  HCH2  0   0.203   0.3986  -1.6964   4.0972
 A5P  HO1   H  HOH1  0   0.456   0.0777  -0.6983   6.2074
 A5P  HC2   H  HCH1  0   0.233  -1.3364  -0.2756   3.0571
 A5P  HO2   H  HOH1  0   0.447   0.4706   1.7759   3.6538
 A5P  HC3   H  HCH1  0   0.237   0.3704  -1.4483   1.7530
 A5P  HO3   H  HOH1  0   0.444   1.8236   0.9687   1.7412
 A5P  HC4   H  HCH1  0   0.244  -0.2682   1.2857   0.5624
 A5P  HO4   H  HOH1  0   0.448  -1.8295  -1.0594   0.5641
 A5P  H51   H  HCH2  0   0.247   1.3862  -0.0964  -0.7091
 A5P  H52   H  HCH2  0   0.236   0.2176  -1.4235  -0.7569
 A5P  HOP2  H  HOH1  0   0.504  -0.9930   0.5873  -5.0289
 A5P  HOP3  H  HOH1  0   0.495   1.6187   1.4618  -3.4373

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  1.409  0.020  1.409
 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  1.412  0.020  1.412
 A5P  C2   C3    single  1.533  0.020  1.533
 A5P  C2   HC2   single  0.970  0.020  1.090
 A5P  O2   HO2   single  0.850  0.020  0.980
 A5P  C3   O3    single  1.412  0.020  1.412
 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  1.405  0.020  1.405
 A5P  C4   C5    single  1.520  0.020  1.520
 A5P  C4   HC4   single  0.970  0.020  1.090
 A5P  O4   HO4   single  0.850  0.020  0.980
 A5P  C5   O5    single  1.432  0.020  1.432
 A5P  C5   H51   single  0.970  0.020  1.090
 A5P  C5   H52   single  0.970  0.020  1.090
 A5P  O5   P     single  1.594  0.020  1.594
 A5P  P    O1P   double  1.475  0.020  1.475
 A5P  P    O2P   single  1.594  0.020  1.594
 A5P  P    O3P   single  1.599  0.020  1.599
 A5P  O2P  HOP2  single  0.850  0.020  0.980
 A5P  O3P  HOP3  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
 A5P  H12   C1   H11  106.70  3.000
 A5P  H12   C1   C2   108.38  3.000
 A5P  H11   C1   C2   109.79  3.000
 A5P  H12   C1   O1   111.65  3.000
 A5P  H11   C1   O1   111.44  3.000
 A5P  C2    C1   O1   108.82  3.000
 A5P  HO1   O1   C1   108.00  3.000
 A5P  HC2   C2   C3   107.67  3.000
 A5P  HC2   C2   O2   106.35  3.000
 A5P  C3    C2   O2   111.56  3.000
 A5P  HC2   C2   C1   107.83  3.000
 A5P  C3    C2   C1   110.62  3.000
 A5P  O2    C2   C1   112.53  3.000
 A5P  HO2   O2   C2   109.39  3.000
 A5P  HC3   C3   C4   108.14  3.000
 A5P  HC3   C3   O3   105.68  3.000
 A5P  C4    C3   O3   110.83  3.000
 A5P  HC3   C3   C2   107.42  3.000
 A5P  C4    C3   C2   112.34  3.000
 A5P  O3    C3   C2   112.08  3.000
 A5P  HO3   O3   C3   108.96  3.000
 A5P  HC4   C4   C5   108.74  3.000
 A5P  HC4   C4   O4   105.81  3.000
 A5P  C5    C4   O4   111.44  3.000
 A5P  HC4   C4   C3   108.61  3.000
 A5P  C5    C4   C3   110.05  3.000
 A5P  O4    C4   C3   112.02  3.000
 A5P  HO4   O4   C4   109.04  3.000
 A5P  H52   C5   H51  108.00  3.000
 A5P  H52   C5   O5   110.00  3.000
 A5P  H51   C5   O5   110.26  3.000
 A5P  H52   C5   C4   110.02  3.000
 A5P  H51   C5   C4   110.56  3.000
 A5P  O5    C5   C4   108.00  3.000
 A5P  P     O5   C5   119.49  3.000
 A5P  O3P   P    O2P  107.82  3.000
 A5P  O3P   P    O1P  109.40  3.000
 A5P  O2P   P    O1P  117.84  3.000
 A5P  O3P   P    O5   107.10  3.000
 A5P  O2P   P    O5    96.77  3.000
 A5P  O1P   P    O5   116.81  3.000
 A5P  HOP2  O2P  P    113.89  3.000
 A5P  HOP3  O3P  P    115.80  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  50.99  30.0  3
 A5P  Var_02  H51  C5  O5  P   61.67  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

