# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:05:40 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 1,4-anhydro-2-deoxy-5-O-thiophosphono-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCO[C@@H]1CO[P](O)(S)=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
 DV3  DV3  1,4-anhydro-2-deoxy-5-O-thiophosphono-D-erythro-pentitol  ligand  22  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DV3
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
 DV3  O5'  O  O2     0  -0.601  -0.5869  -0.6069  -0.5315
 DV3  P    P  P      0   1.179  -2.0603  -0.0996  -0.0404
 DV3  SP3  S  S2     0  -0.501  -1.7036   1.9695   0.4072
 DV3  OP2  O  O      0  -0.779  -2.4078  -0.6772   1.2937
 DV3  OP3  O  OP    -1  -0.762  -2.9398  -0.2120  -1.2404
 DV3  C2'  C  CH2    0  -0.549   3.1948   0.8129   0.7197
 DV3  C5'  C  CH2    0  -0.148   0.4817  -0.6646   0.3907
 DV3  C4'  C  CH1    0  -0.029   1.7857  -0.7147  -0.3859
 DV3  O4'  O  O2     0  -0.499   1.9262   0.4163  -1.2273
 DV3  C1'  C  CH2    0  -0.145   2.8459   1.3443  -0.6651
 DV3  C3'  C  CH1    0   0.003   2.9881  -0.6886   0.5507
 DV3  O3'  O  OH1    0  -0.673   4.0676  -1.3063  -0.1142
 DV3  H1   H  HSH1   0   0.217  -1.4018   2.3815  -0.8297
 DV3  H5   H  HCH2   0   0.207   0.4739   0.2080   1.0547
 DV3  H6   H  HCH2   0   0.216   0.4041  -1.5583   1.0188
 DV3  H7   H  HCH1   0   0.243   1.7941  -1.6171  -1.0088
 DV3  H8   H  HCH2   0   0.220   2.3910   2.3370  -0.6266
 DV3  H9   H  HCH2   0   0.208   3.7357   1.4104  -1.2992
 DV3  H10  H  HCH1   0   0.233   2.7717  -1.1839   1.5058
 DV3  H11  H  HOH1   0   0.451   4.8590  -1.1818   0.4189
 DV3  H3   H  HCH2   0   0.263   4.2074   1.0715   1.0317
 DV3  H4   H  HCH2   0   0.245   2.5116   1.2007   1.4781

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
 DV3  C1'  C2'  single  1.524  0.020  1.524
 DV3  C1'  O4'  single  1.422  0.020  1.422
 DV3  C2'  C3'  single  1.525  0.020  1.525
 DV3  O4'  C4'  single  1.417  0.020  1.417
 DV3  O3'  C3'  single  1.410  0.020  1.410
 DV3  C3'  C4'  single  1.524  0.020  1.524
 DV3  C4'  C5'  single  1.519  0.020  1.519
 DV3  C5'  O5'  single  1.413  0.020  1.413
 DV3  O5'  P    single  1.634  0.020  1.634
 DV3  OP2  P    deloc   1.495  0.020  1.495
 DV3  P    SP3  single  2.147  0.020  2.147
 DV3  P    OP3  deloc   1.492  0.020  1.492
 DV3  SP3  H1   single  1.200  0.020  1.300
 DV3  C2'  H3   single  0.970  0.020  1.090
 DV3  C2'  H4   single  0.970  0.020  1.090
 DV3  C5'  H5   single  0.970  0.020  1.090
 DV3  C5'  H6   single  0.970  0.020  1.090
 DV3  C4'  H7   single  0.970  0.020  1.090
 DV3  C1'  H8   single  0.970  0.020  1.090
 DV3  C1'  H9   single  0.970  0.020  1.090
 DV3  C3'  H10  single  0.970  0.020  1.090
 DV3  O3'  H11  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
 DV3  C5'  O5'  P    119.91  3.000
 DV3  OP3  P    OP2  123.48  3.000
 DV3  OP3  P    SP3  109.77  3.000
 DV3  OP2  P    SP3  103.00  3.000
 DV3  OP3  P    O5'  105.45  3.000
 DV3  SP3  P    O5'  102.24  3.000
 DV3  OP2  P    O5'  110.98  3.000
 DV3  H1   SP3  P     98.13  3.000
 DV3  H4   C2'  H3   107.34  3.000
 DV3  H4   C2'  C3'  109.99  3.000
 DV3  H3   C2'  C3'  113.02  3.000
 DV3  H4   C2'  C1'  111.35  3.000
 DV3  H3   C2'  C1'  112.94  3.000
 DV3  C3'  C2'  C1'  102.22  3.000
 DV3  H6   C5'  H5   107.55  3.000
 DV3  H6   C5'  C4'  109.10  3.000
 DV3  H5   C5'  C4'  110.00  3.000
 DV3  H6   C5'  O5'  110.75  3.000
 DV3  H5   C5'  O5'  110.94  3.000
 DV3  C4'  C5'  O5'  108.49  3.000
 DV3  H7   C4'  C3'  110.92  3.000
 DV3  H7   C4'  O4'  108.59  3.000
 DV3  C3'  C4'  O4'  105.85  3.000
 DV3  H7   C4'  C5'  108.92  3.000
 DV3  C3'  C4'  C5'  111.26  3.000
 DV3  O4'  C4'  C5'  111.26  3.000
 DV3  C1'  O4'  C4'  110.50  3.000
 DV3  H9   C1'  H8   107.70  3.000
 DV3  H9   C1'  O4'  109.63  3.000
 DV3  H8   C1'  O4'  109.72  3.000
 DV3  H9   C1'  C2'  111.19  3.000
 DV3  H8   C1'  C2'  112.35  3.000
 DV3  O4'  C1'  C2'  106.24  3.000
 DV3  H10  C3'  O3'  111.32  3.000
 DV3  H10  C3'  C4'  111.81  3.000
 DV3  O3'  C3'  C4'  107.86  3.000
 DV3  H10  C3'  C2'  112.00  3.000
 DV3  C4'  C3'  C2'  101.06  3.000
 DV3  O3'  C3'  C2'  112.32  3.000
 DV3  H11  O3'  C3'  108.16  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
 DV3  Var_01  C3'  C2'  C1'  O4'    27.41  30.0  1
 DV3  Var_02  H8   C1'  O4'  C4'  -128.17  30.0  1
 DV3  Var_03  C4'  C5'  O5'  P    -161.64  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
 DV3  chir_02  C4'  O4'  C3'  C5'  negativ
 DV3  chir_03  C3'  O3'  C4'  C2'  positiv

