# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:31:03 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  23  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  -0.567  -0.6063  -0.4321  -0.4978
 DV3  P    P  P     0   1.247  -2.0952  -0.1806   0.0097
 DV3  SP3  S  S2    0  -0.379  -2.1800   1.7732   0.7277
 DV3  OP2  O  O     0  -0.684  -2.6157  -1.0780   1.0599
 DV3  OP3  O  OH1   0  -0.712  -2.7838  -0.2104  -1.4254
 DV3  C2'  C  CH2   0  -0.543   3.3022   0.8137   0.6633
 DV3  C5'  C  CH2   0  -0.174   0.4627  -0.5008   0.4520
 DV3  C4'  C  CH1   0  -0.021   1.7578  -0.6744  -0.3167
 DV3  O4'  O  O2    0  -0.499   1.9554   0.3976  -1.2183
 DV3  C1'  C  CH2   0  -0.150   3.0085   1.2431  -0.7659
 DV3  C3'  C  CH1   0  -0.005   2.9565  -0.6709   0.6300
 DV3  O3'  O  OH1   0  -0.671   3.9715  -1.4476   0.0377
 DV3  H1   H  HSH1  0   0.263  -1.7012   2.3782  -0.3681
 DV3  H2   H  HOH1  0   0.507  -3.7493  -0.1604  -1.3997
 DV3  H4   H  HCH2  0   0.247   2.6526   1.3302   1.3731
 DV3  H5   H  HCH2  0   0.236   0.4826   0.4130   1.0557
 DV3  H6   H  HCH2  0   0.250   0.3163  -1.3510   1.1222
 DV3  H7   H  HCH1  0   0.256   1.7100  -1.6148  -0.8783
 DV3  H8   H  HCH2  0   0.228   2.6907   2.2852  -0.8357
 DV3  H9   H  HCH2  0   0.212   3.8867   1.1184  -1.4072
 DV3  H10  H  HCH1  0   0.240   2.6918  -1.0525   1.6240
 DV3  H11  H  HOH1  0   0.453   4.7687  -1.3527   0.5684
 DV3  H3   H  HCH2  0   0.266   4.3327   1.0067   0.9637

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  1.521  0.020  1.521
 DV3  C1'  O4'  single  1.424  0.020  1.424
 DV3  C2'  C3'  single  1.525  0.020  1.525
 DV3  O4'  C4'  single  1.415  0.020  1.415
 DV3  O3'  C3'  single  1.409  0.020  1.409
 DV3  C3'  C4'  single  1.528  0.020  1.528
 DV3  C4'  C5'  single  1.516  0.020  1.516
 DV3  C5'  O5'  single  1.432  0.020  1.432
 DV3  O5'  P    single  1.593  0.020  1.593
 DV3  OP2  P    double  1.476  0.020  1.476
 DV3  P    SP3  single  2.083  0.020  2.083
 DV3  P    OP3  single  1.592  0.020  1.592
 DV3  SP3  H1   single  1.200  0.020  1.300
 DV3  OP3  H2   single  0.850  0.020  0.980
 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    119.62  3.000
 DV3  OP3  P    OP2  118.52  3.000
 DV3  OP3  P    SP3  108.10  3.000
 DV3  OP2  P    SP3  108.09  3.000
 DV3  OP3  P    O5'   96.56  3.000
 DV3  SP3  P    O5'  107.21  3.000
 DV3  OP2  P    O5'  117.40  3.000
 DV3  H1   SP3  P     97.30  3.000
 DV3  H2   OP3  P    114.00  3.000
 DV3  H4   C2'  H3   107.42  3.000
 DV3  H4   C2'  C3'  109.87  3.000
 DV3  H3   C2'  C3'  113.11  3.000
 DV3  H4   C2'  C1'  111.24  3.000
 DV3  H3   C2'  C1'  113.03  3.000
 DV3  C3'  C2'  C1'  102.16  3.000
 DV3  H6   C5'  H5   108.28  3.000
 DV3  H6   C5'  C4'  109.66  3.000
 DV3  H5   C5'  C4'  111.07  3.000
 DV3  H6   C5'  O5'  110.14  3.000
 DV3  H5   C5'  O5'  109.82  3.000
 DV3  C4'  C5'  O5'  107.88  3.000
 DV3  H7   C4'  C3'  110.71  3.000
 DV3  H7   C4'  O4'  109.25  3.000
 DV3  C3'  C4'  O4'  106.48  3.000
 DV3  H7   C4'  C5'  108.71  3.000
 DV3  C3'  C4'  C5'  110.84  3.000
 DV3  O4'  C4'  C5'  110.84  3.000
 DV3  C1'  O4'  C4'  110.53  3.000
 DV3  H9   C1'  H8   107.75  3.000
 DV3  H9   C1'  O4'  109.84  3.000
 DV3  H8   C1'  O4'  109.33  3.000
 DV3  H9   C1'  C2'  111.31  3.000
 DV3  H8   C1'  C2'  112.69  3.000
 DV3  O4'  C1'  C2'  105.88  3.000
 DV3  H10  C3'  O3'  111.28  3.000
 DV3  H10  C3'  C4'  111.80  3.000
 DV3  O3'  C3'  C4'  107.67  3.000
 DV3  H10  C3'  C2'  111.94  3.000
 DV3  C4'  C3'  C2'  101.17  3.000
 DV3  O3'  C3'  C2'  112.50  3.000
 DV3  H11  O3'  C3'  108.10  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'    30.49  30.0  1
 DV3  Var_02  H8   C1'  O4'  C4'  -133.42  30.0  1
 DV3  Var_03  C4'  C5'  O5'  P    -177.14  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
 DV3  chir_04  P    OP2  SP3  OP3  both

