# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:19:01 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 5-O-[(S)-butoxy(hydroxy)phosphoryl]-2-deoxy-2-fluoro-alpha-D-arabinofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCO[P](O)(=O)OC[C@H]1O[C@H](O)[C@@H](F)[C@@H]1O
#
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
 27C  27C  5-O-[(S)-butoxy(hydroxy)phosphoryl]-2-deoxy-2-fluoro-alpha-D-arabinofuranose  D-saccharide  35  18  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_27C
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
 27C  O1    O  OH1    0  -0.664  -5.5445   9.6557  52.1717
 27C  P     P  P      0   1.372  -6.5303   9.7906  57.7194
 27C  C1    C  CH1    0   0.191  -6.5474   8.7774  52.5693
 27C  C2    C  CH1    0   0.172  -7.8745   9.3975  52.1586
 27C  F2    F  F      0  -0.374  -8.8352   8.3938  52.1333
 27C  C3    C  CH1    0  -0.069  -8.1827  10.3548  53.3054
 27C  O3    O  OH1    0  -0.661  -7.8254  11.6537  52.9135
 27C  C4    C  CH1    0  -0.013  -7.3273   9.7993  54.4709
 27C  O4    O  O2     0  -0.503  -6.6496   8.6566  53.9572
 27C  C5    C  CH2    0  -0.185  -8.1761   9.3957  55.6594
 27C  O5    O  O2     0  -0.622  -7.4492   8.8385  56.7312
 27C  C1C   C  CH2    0  -0.154  -4.2605   8.8457  56.7112
 27C  C2C   C  CH2    0  -0.452  -3.1758   9.2016  55.7137
 27C  C3C   C  CH2    0  -0.416  -2.3002  10.3768  56.1325
 27C  C4C   C  CH3    0  -0.659  -1.1873  10.6579  55.1324
 27C  OP1   O  OP    -1  -0.787  -6.2812   8.9636  58.9393
 27C  OP2   O  O      0  -0.791  -7.1122  11.1673  57.7738
 27C  OP3   O  O2     0  -0.621  -5.1400   9.9465  56.8609
 27C  HO1   H  HOH1   0   0.464  -4.6871   9.2637  52.3717
 27C  H1    H  HCH1   0   0.243  -6.3967   7.7706  52.1637
 27C  H2    H  HCH1   0   0.242  -7.8554   9.8831  51.1821
 27C  H3    H  HCH1   0   0.242  -9.2532  10.2952  53.5452
 27C  HO3   H  HOH1   0   0.456  -8.0048  12.2539  53.6441
 27C  H4    H  HCH1   0   0.239  -6.6018  10.5642  54.7667
 27C  H51   H  HCH2   0   0.212  -8.7439  10.2749  55.9804
 27C  H52   H  HCH2   0   0.224  -8.9006   8.6406  55.3394
 27C  H1C   H  HCH2   0   0.198  -3.8057   8.5859  57.6740
 27C  H1CA  H  HCH2   0   0.205  -4.7985   7.9591  56.3584
 27C  H2C   H  HCH2   0   0.216  -2.5489   8.3139  55.5803
 27C  H2CA  H  HCH2   0   0.216  -3.6290   9.4029  54.7370
 27C  H3C   H  HCH2   0   0.216  -2.9137  11.2722  56.2534
 27C  H3CA  H  HCH2   0   0.209  -1.8658  10.1684  57.1153
 27C  H4C   H  HCH3   0   0.225  -0.5707  11.5002  55.4474
 27C  H4CA  H  HCH3   0   0.215  -0.5318   9.7927  55.0161
 27C  H4CB  H  HCH3   0   0.215  -1.5927  10.8966  54.1472

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
 27C  O1   C1    single  1.391  0.020  1.391
 27C  O1   HO1   single  0.850  0.020  0.980
 27C  O5   P     single  1.652  0.020  1.652
 27C  OP2  P     deloc   1.496  0.020  1.496
 27C  OP3  P     single  1.641  0.020  1.641
 27C  P    OP1   deloc   1.495  0.020  1.495
 27C  C1   C2    single  1.521  0.020  1.521
 27C  C1   O4    single  1.397  0.020  1.397
 27C  C1   H1    single  0.970  0.020  1.090
 27C  C2   F2    single  1.390  0.020  1.390
 27C  C2   C3    single  1.525  0.020  1.525
 27C  C2   H2    single  0.970  0.020  1.090
 27C  O3   C3    single  1.403  0.020  1.403
 27C  C3   C4    single  1.549  0.020  1.549
 27C  C3   H3    single  0.970  0.020  1.090
 27C  O3   HO3   single  0.850  0.020  0.980
 27C  O4   C4    single  1.424  0.020  1.424
 27C  C4   C5    single  1.515  0.020  1.515
 27C  C4   H4    single  0.970  0.020  1.090
 27C  C5   O5    single  1.410  0.020  1.410
 27C  C5   H51   single  0.970  0.020  1.090
 27C  C5   H52   single  0.970  0.020  1.090
 27C  OP3  C1C   single  1.417  0.020  1.417
 27C  C1C  C2C   single  1.516  0.020  1.516
 27C  C1C  H1C   single  0.970  0.020  1.090
 27C  C1C  H1CA  single  0.970  0.020  1.090
 27C  C2C  C3C   single  1.524  0.020  1.524
 27C  C2C  H2C   single  0.970  0.020  1.090
 27C  C2C  H2CA  single  0.970  0.020  1.090
 27C  C4C  C3C   single  1.522  0.020  1.522
 27C  C3C  H3C   single  0.970  0.020  1.090
 27C  C3C  H3CA  single  0.970  0.020  1.090
 27C  C4C  H4C   single  0.970  0.020  1.090
 27C  C4C  H4CA  single  0.970  0.020  1.090
 27C  C4C  H4CB  single  0.970  0.020  1.090

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
 27C  HO1   O1   C1    108.98  3.000
 27C  OP3   P    OP2   105.14  3.000
 27C  OP3   P    OP1   109.77  3.000
 27C  OP2   P    OP1   122.98  3.000
 27C  OP1   P    O5    105.20  3.000
 27C  OP3   P    O5    102.31  3.000
 27C  OP2   P    O5    109.63  3.000
 27C  H1    C1   O4    107.36  3.000
 27C  H1    C1   C2    113.24  3.000
 27C  O4    C1   C2    103.87  3.000
 27C  H1    C1   O1    112.03  3.000
 27C  O4    C1   O1    113.03  3.000
 27C  C2    C1   O1    107.12  3.000
 27C  H2    C2   C3    113.41  3.000
 27C  H2    C2   F2    108.51  3.000
 27C  C3    C2   F2    109.11  3.000
 27C  H2    C2   C1    114.07  3.000
 27C  C3    C2   C1    103.24  3.000
 27C  F2    C2   C1    108.28  3.000
 27C  H3    C3   C4    110.76  3.000
 27C  H3    C3   O3    111.06  3.000
 27C  C4    C3   O3    113.67  3.000
 27C  H3    C3   C2    109.09  3.000
 27C  C4    C3   C2    103.25  3.000
 27C  O3    C3   C2    108.64  3.000
 27C  HO3   O3   C3    108.53  3.000
 27C  H4    C4   C5    110.20  3.000
 27C  H4    C4   O4    110.03  3.000
 27C  C5    C4   O4    109.62  3.000
 27C  H4    C4   C3    108.59  3.000
 27C  C5    C4   C3    112.11  3.000
 27C  O4    C4   C3    106.21  3.000
 27C  C4    O4   C1    108.89  3.000
 27C  H52   C5   H51   107.25  3.000
 27C  H52   C5   O5    106.91  3.000
 27C  H51   C5   O5    111.22  3.000
 27C  H52   C5   C4    108.98  3.000
 27C  H51   C5   C4    107.86  3.000
 27C  O5    C5   C4    114.38  3.000
 27C  C5    O5   P     120.92  3.000
 27C  H1CA  C1C  H1C   107.15  3.000
 27C  H1CA  C1C  OP3   110.98  3.000
 27C  H1C   C1C  OP3   110.42  3.000
 27C  H1CA  C1C  C2C   109.24  3.000
 27C  H1C   C1C  C2C   109.68  3.000
 27C  OP3   C1C  C2C   109.34  3.000
 27C  H2CA  C2C  H2C   106.09  3.000
 27C  H2CA  C2C  C3C   109.94  3.000
 27C  H2C   C2C  C3C   109.25  3.000
 27C  H2CA  C2C  C1C   109.50  3.000
 27C  H2C   C2C  C1C   107.43  3.000
 27C  C3C   C2C  C1C   114.28  3.000
 27C  H3CA  C3C  H3C   106.24  3.000
 27C  H3CA  C3C  C4C   109.57  3.000
 27C  H3C   C3C  C4C   109.39  3.000
 27C  H3CA  C3C  C2C   109.14  3.000
 27C  H3C   C3C  C2C   109.87  3.000
 27C  C4C   C3C  C2C   112.44  3.000
 27C  H4CB  C4C  H4CA  107.47  3.000
 27C  H4CB  C4C  H4C   107.56  3.000
 27C  H4CA  C4C  H4C   107.66  3.000
 27C  H4CB  C4C  C3C   111.21  3.000
 27C  H4CA  C4C  C3C   111.26  3.000
 27C  H4C   C4C  C3C   111.48  3.000
 27C  C1C   OP3  P     120.48  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
 27C  Var_01  C4   C5   O5   P      74.56  30.0  1
 27C  Var_02  C2C  C1C  OP3  P     171.61  30.0  3
 27C  Var_03  OP2  P    O5   C5     28.60  30.0  3
 27C  Var_04  C4C  C3C  C2C  C1C   177.41  30.0  3
 27C  Var_05  OP3  C1C  C2C  C3C    61.70  30.0  1
 27C  Var_06  H4C  C4C  C3C  C2C  -179.96  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
 27C  chir_02  C1  O1  C2  O4  positiv
 27C  chir_03  C2  F2  C3  C1  negativ
 27C  chir_04  C3  O3  C2  C4  negativ
 27C  chir_05  C4  O4  C3  C5  negativ

