# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:05:08 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (2R,3R,4S,5S)-4-fluoro-3,5-dihydroxytetrahydrofuran-2-yl 2-phenylethyl hydrogen (S)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@H](O[P](O)(=O)OCCc2ccccc2)[C@@H](O)[C@@H]1F
#
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
 46Z  46Z  '(2R,3R,4S,5S)-4-fluoro-3,5-dihydroxytetrahydrofuran-2-yl 2-phenylethyl hydrogen (S)-phosphate'  D-saccharide  37  21  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_46Z
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
 46Z  O1    O  OH1   0  -0.646  -4.9952   2.3370   0.1206
 46Z  P     P  P     0   1.465  -0.2009  -0.3435   1.0384
 46Z  C1    C  CH1   0   0.228  -4.1918   1.3560  -0.4009
 46Z  C2    C  CH1   0   0.124  -4.9053   0.0157  -0.4398
 46Z  F2    F  F     0  -0.360  -5.6893  -0.1125  -1.5706
 46Z  C3    C  CH1   0  -0.097  -3.7511  -0.9673  -0.4141
 46Z  O3    O  OH1   0  -0.656  -4.0321  -2.2396   0.0827
 46Z  C4    C  CH1   0   0.293  -2.7727  -0.2479   0.5129
 46Z  O4    O  O2    0  -0.494  -3.0885   1.1064   0.4693
 46Z  O5    O  O2    0  -0.594  -1.4536  -0.4598   0.0421
 46Z  CAE   C  CR16  0  -0.269   7.2502   0.5560  -0.0749
 46Z  CAF   C  CR16  0  -0.240   6.7621  -0.7195   0.1776
 46Z  CAG   C  CR16  0  -0.240   6.4101   1.5152  -0.6254
 46Z  CAH   C  CR16  0  -0.300   5.4416  -1.0313  -0.1185
 46Z  CAI   C  CR16  0  -0.300   5.0905   1.1988  -0.9201
 46Z  CAJ   C  CH2   0  -0.152   2.2982  -0.1165   0.2638
 46Z  CAK   C  CH2   0  -0.547   3.1510  -0.4048  -0.9585
 46Z  CAP   C  CR6   0   0.102   4.5910  -0.0776  -0.6726
 46Z  OP1   O  O     0  -0.701  -0.1927   0.7886   1.9800
 46Z  OP2   O  OH1   0  -0.735  -0.1343  -1.7167   1.8498
 46Z  OP3   O  O2    0  -0.581   0.9279  -0.3877  -0.0795
 46Z  HO1   H  HOH1  0   0.473  -4.6786   3.2021  -0.1600
 46Z  H1    H  HCH1  0   0.227  -3.8164   1.6267  -1.3967
 46Z  H2    H  HCH1  0   0.242  -5.5448  -0.1010   0.4412
 46Z  H3    H  HCH1  0   0.262  -3.3147  -1.0067  -1.4220
 46Z  HO3   H  HOH1  0   0.467  -4.3925  -2.7791  -0.6272
 46Z  H4    H  HCH1  0   0.249  -2.8689  -0.6140   1.5417
 46Z  HAF   H  HCR6  0   0.255   7.4107  -1.4751   0.6024
 46Z  HAG   H  HCR6  0   0.255   6.7821   2.5111  -0.8295
 46Z  HAH   H  HCR6  0   0.251   5.0695  -2.0303   0.0782
 46Z  HAI   H  HCR6  0   0.251   4.4434   1.9522  -1.3547
 46Z  HAJ   H  HCH2  0   0.243   2.6136  -0.7449   1.1014
 46Z  HAJA  H  HCH2  0   0.248   2.4001   0.9285   0.5638
 46Z  HAK   H  HCH2  0   0.261   3.0476  -1.4566  -1.2332
 46Z  HAKA  H  HCH2  0   0.262   2.7895   0.1917  -1.7992
 46Z  HOP2  H  HOH1  0   0.498  -0.1185  -2.5251   1.3196
 46Z  HAE   H  HCR6  0   0.256   8.2797   0.7995   0.1534

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
 46Z  O1   C1    single    1.371  0.020  1.371
 46Z  O1   HO1   single    0.850  0.020  0.980
 46Z  OP1  P     double    1.473  0.020  1.473
 46Z  O5   P     single    1.605  0.020  1.605
 46Z  P    OP2   single    1.596  0.020  1.596
 46Z  P    OP3   single    1.589  0.020  1.589
 46Z  C2   C1    single    1.519  0.020  1.519
 46Z  C1   O4    single    1.427  0.020  1.427
 46Z  C1   H1    single    0.970  0.020  1.090
 46Z  C2   C3    single    1.516  0.020  1.516
 46Z  C2   F2    single    1.382  0.020  1.382
 46Z  C2   H2    single    0.970  0.020  1.090
 46Z  O3   C3    single    1.395  0.020  1.395
 46Z  C3   C4    single    1.528  0.020  1.528
 46Z  C3   H3    single    0.970  0.020  1.090
 46Z  O3   HO3   single    0.850  0.020  0.980
 46Z  C4   O4    single    1.391  0.020  1.391
 46Z  C4   O5    single    1.417  0.020  1.417
 46Z  C4   H4    single    0.970  0.020  1.090
 46Z  CAF  CAE   aromatic  1.389  0.020  1.389
 46Z  CAE  CAG   aromatic  1.389  0.020  1.389
 46Z  CAE  HAE   single    0.930  0.020  1.080
 46Z  CAH  CAF   aromatic  1.389  0.020  1.389
 46Z  CAF  HAF   single    0.930  0.020  1.080
 46Z  CAI  CAG   aromatic  1.389  0.020  1.389
 46Z  CAG  HAG   single    0.930  0.020  1.080
 46Z  CAH  CAP   aromatic  1.393  0.020  1.393
 46Z  CAH  HAH   single    0.930  0.020  1.080
 46Z  CAP  CAI   aromatic  1.393  0.020  1.393
 46Z  CAI  HAI   single    0.930  0.020  1.080
 46Z  OP3  CAJ   single    1.438  0.020  1.438
 46Z  CAJ  CAK   single    1.518  0.020  1.518
 46Z  CAJ  HAJ   single    0.970  0.020  1.090
 46Z  CAJ  HAJA  single    0.970  0.020  1.090
 46Z  CAK  CAP   single    1.504  0.020  1.504
 46Z  CAK  HAK   single    0.970  0.020  1.090
 46Z  CAK  HAKA  single    0.970  0.020  1.090
 46Z  OP2  HOP2  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
 46Z  HO1   O1   C1   109.84  3.000
 46Z  OP3   P    OP2  107.70  3.000
 46Z  OP3   P    OP1  117.85  3.000
 46Z  OP2   P    OP1  109.64  3.000
 46Z  OP3   P    O5    96.64  3.000
 46Z  OP2   P    O5   106.61  3.000
 46Z  OP1   P    O5   117.20  3.000
 46Z  H1    C1   O4   109.37  3.000
 46Z  H1    C1   C2   110.79  3.000
 46Z  O4    C1   C2   102.97  3.000
 46Z  H1    C1   O1   111.64  3.000
 46Z  O4    C1   O1   110.26  3.000
 46Z  C2    C1   O1   111.47  3.000
 46Z  H2    C2   C3   111.21  3.000
 46Z  H2    C2   F2   108.49  3.000
 46Z  C3    C2   F2   112.68  3.000
 46Z  H2    C2   C1   110.35  3.000
 46Z  F2    C2   C1   111.68  3.000
 46Z  C3    C2   C1   102.36  3.000
 46Z  H3    C3   C4   108.60  3.000
 46Z  H3    C3   O3   111.96  3.000
 46Z  C4    C3   O3   110.03  3.000
 46Z  H3    C3   C2   108.06  3.000
 46Z  C4    C3   C2   101.10  3.000
 46Z  O3    C3   C2   116.37  3.000
 46Z  HO3   O3   C3   108.92  3.000
 46Z  H4    C4   O5   110.11  3.000
 46Z  H4    C4   O4   109.55  3.000
 46Z  O5    C4   O4   110.28  3.000
 46Z  H4    C4   C3   110.85  3.000
 46Z  O5    C4   C3   108.92  3.000
 46Z  O4    C4   C3   107.09  3.000
 46Z  C4    O4   C1   111.40  3.000
 46Z  C4    O5   P    120.64  3.000
 46Z  HAE   CAE  CAG  120.24  3.000
 46Z  HAE   CAE  CAF  120.17  3.000
 46Z  CAG   CAE  CAF  119.58  3.000
 46Z  HAF   CAF  CAH  119.77  3.000
 46Z  HAF   CAF  CAE  120.12  3.000
 46Z  CAH   CAF  CAE  120.11  3.000
 46Z  HAG   CAG  CAI  119.75  3.000
 46Z  HAG   CAG  CAE  120.14  3.000
 46Z  CAI   CAG  CAE  120.11  3.000
 46Z  HAH   CAH  CAP  119.57  3.000
 46Z  HAH   CAH  CAF  119.65  3.000
 46Z  CAP   CAH  CAF  120.78  3.000
 46Z  HAI   CAI  CAP  119.61  3.000
 46Z  HAI   CAI  CAG  119.60  3.000
 46Z  CAP   CAI  CAG  120.79  3.000
 46Z  HAJA  CAJ  HAJ  108.21  3.000
 46Z  HAJA  CAJ  OP3  109.56  3.000
 46Z  HAJ   CAJ  OP3  110.44  3.000
 46Z  HAJA  CAJ  CAK  110.52  3.000
 46Z  HAJ   CAJ  CAK  110.22  3.000
 46Z  OP3   CAJ  CAK  107.89  3.000
 46Z  HAKA  CAK  HAK  107.52  3.000
 46Z  HAKA  CAK  CAP  110.14  3.000
 46Z  HAK   CAK  CAP  110.36  3.000
 46Z  HAKA  CAK  CAJ  109.27  3.000
 46Z  HAK   CAK  CAJ  109.41  3.000
 46Z  CAP   CAK  CAJ  110.09  3.000
 46Z  CAK   CAP  CAI  120.59  3.000
 46Z  CAK   CAP  CAH  120.75  3.000
 46Z  CAI   CAP  CAH  118.63  3.000
 46Z  HOP2  OP2  P    116.17  3.000
 46Z  CAJ   OP3  P    120.23  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
 46Z  CONST_01  CAP  CAH  CAF  CAE    0.00   0.0  0
 46Z  CONST_02  CAP  CAI  CAG  CAE    0.00   0.0  0
 46Z  CONST_03  CAI  CAG  CAE  CAF    0.00   0.0  0
 46Z  CONST_04  CAI  CAP  CAH  CAF    0.00   0.0  0
 46Z  CONST_05  CAH  CAF  CAE  CAG    0.00   0.0  0
 46Z  CONST_06  CAH  CAP  CAI  CAG    0.00   0.0  0
 46Z  CONST_07  CAK  CAP  CAH  CAF  180.00   0.0  0
 46Z  CONST_08  CAK  CAP  CAI  CAG  180.00   0.0  0
 46Z  CONST_09  HAH  CAH  CAF  CAE  180.00   0.0  0
 46Z  CONST_10  HAI  CAI  CAG  CAE  180.00   0.0  0
 46Z  CONST_11  HAG  CAG  CAE  CAF  180.00   0.0  0
 46Z  CONST_12  HAF  CAF  CAE  CAG  180.00   0.0  0
 46Z  CONST_13  HAE  CAE  CAF  CAH  180.00   0.0  0
 46Z  Var_01    CAJ  CAK  CAP  CAH   88.37  30.0  2
 46Z  Var_02    OP1  P    O5   C4   -43.48  30.0  3
 46Z  Var_03    OP3  CAJ  CAK  CAP  177.46  30.0  1
 46Z  Var_04    CAK  CAJ  OP3  P    172.94  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
 46Z  chir_02  C1  O1  C2   O4   positiv
 46Z  chir_03  C2  F2  C3   C1   negativ
 46Z  chir_04  C3  O3  C2   C4   negativ
 46Z  chir_05  C4  O4  O5   C3   positiv
 46Z  chir_06  P   O5  OP2  OP3  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 46Z  plan-1  CAE  0.020
 46Z  plan-1  CAF  0.020
 46Z  plan-1  CAG  0.020
 46Z  plan-1  CAH  0.020
 46Z  plan-1  CAI  0.020
 46Z  plan-1  CAK  0.020
 46Z  plan-1  CAP  0.020
 46Z  plan-1  HAF  0.020
 46Z  plan-1  HAG  0.020
 46Z  plan-1  HAH  0.020
 46Z  plan-1  HAI  0.020
 46Z  plan-1  HAE  0.020

