# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 02:29:06 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: [(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-5-fluoro-7-hydroxy-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H]2[C@H](F)C[C@]1(CO[P](O)(O)=O)O[C@H]2N3C=CC(=O)NC3=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
 ULF  ULF  '[(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-5-fluoro-7-hydroxy-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate'  ligand  37  23  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ULF
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
 ULF  F7'  F  F     0  -0.375   0.6837   3.3654   1.3060
 ULF  C6'  C  CH1   0   0.240   0.2777   2.9091   0.0558
 ULF  C8'  C  CH2   0  -0.501  -1.1016   2.2241   0.1128
 ULF  C2'  C  CH1   0  -0.450   1.2082   1.8048  -0.4630
 ULF  C3'  C  CH1   0   0.035   0.2890   1.1032  -1.4726
 ULF  O3'  O  OH1   0  -0.653  -0.2258   1.9118  -2.4837
 ULF  C1'  C  CH1   0   0.239   1.2725   0.7209   0.6140
 ULF  O4'  O  O2    0  -0.503  -0.0121   0.1583   0.6090
 ULF  C4'  C  CT    0   0.143  -0.7773   0.8215  -0.4077
 ULF  C5'  C  CH2   0  -0.175  -1.9280  -0.0433  -0.8291
 ULF  O5'  O  O2    0  -0.588  -2.8207  -0.1643   0.2777
 ULF  P    P  P     0   1.463  -4.1059  -1.1075   0.1536
 ULF  OP2  O  OH1   0  -0.729  -4.7385  -0.7362   1.5662
 ULF  OP1  O  O     0  -0.709  -4.9339  -0.9284  -1.0528
 ULF  N1   N  NR6   0  -0.572   2.2731  -0.3268   0.3192
 ULF  C6   C  CR16  0   0.085   1.9366  -1.5662  -0.1385
 ULF  C5   C  CR16  0  -0.508   2.8448  -2.5222  -0.4006
 ULF  C4   C  CR6   0   0.566   4.2451  -2.2589  -0.1879
 ULF  O4   O  O     0  -0.465   5.1616  -3.0338  -0.3904
 ULF  N3   N  NR16  0  -0.732   4.4952  -0.9838   0.2981
 ULF  C2   C  CR6   0   0.740   3.5884   0.0040   0.5692
 ULF  O2   O  O     0  -0.479   3.9149   1.0937   0.9937
 ULF  H1   H  HCH1  0   0.250   0.2836   3.7709  -0.6106
 ULF  H2   H  HCH2  0   0.278  -1.4981   2.1950   1.1280
 ULF  H3   H  HCH2  0   0.269  -1.8309   2.7321  -0.5172
 ULF  H4   H  HCH1  0   0.293   2.1763   2.1496  -0.8203
 ULF  H5   H  HCH1  0   0.259   0.7289   0.1837  -1.8801
 ULF  H6   H  HOH1  0   0.468   0.4748   2.1016  -3.1160
 ULF  H7   H  HCH1  0   0.291   1.5156   1.1062   1.6039
 ULF  H8   H  HCH2  0   0.261  -2.4322   0.4229  -1.6787
 ULF  H9   H  HCH2  0   0.254  -1.5622  -1.0254  -1.1453
 ULF  H12  H  HCR6  0   0.325   0.8831  -1.7554  -0.2718
 ULF  H13  H  HCR6  0   0.293   2.5298  -3.4892  -0.7603
 ULF  H14  H  HNR6  0   0.427   5.4628  -0.7400   0.4714
 ULF  OP3  O  OH1   0  -0.740  -3.5806  -2.6144   0.2256
 ULF  H10  H  HOH1  0   0.497  -3.0607  -2.8408   1.0084
 ULF  H11  H  HOH1  0   0.505  -5.6059  -1.1308   1.7294

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
 ULF  OP1  P    double  1.474  0.020  1.474
 ULF  C8'  C4'  single  1.531  0.020  1.531
 ULF  C8'  C6'  single  1.541  0.020  1.541
 ULF  C5'  C4'  single  1.500  0.020  1.500
 ULF  C5'  O5'  single  1.427  0.020  1.427
 ULF  P    O5'  single  1.599  0.020  1.599
 ULF  P    OP2  single  1.592  0.020  1.592
 ULF  C4'  O4'  single  1.435  0.020  1.435
 ULF  C4'  C3'  single  1.533  0.020  1.533
 ULF  F7'  C6'  single  1.391  0.020  1.391
 ULF  O4'  C1'  single  1.402  0.020  1.402
 ULF  C6'  C2'  single  1.534  0.020  1.534
 ULF  O3'  C3'  single  1.393  0.020  1.393
 ULF  C3'  C2'  single  1.535  0.020  1.535
 ULF  C1'  C2'  single  1.529  0.020  1.529
 ULF  C1'  N1   single  1.478  0.020  1.478
 ULF  N1   C6   single  1.363  0.020  1.363
 ULF  N1   C2   single  1.379  0.020  1.379
 ULF  C6   C5   double  1.344  0.020  1.344
 ULF  O2   C2   double  1.214  0.020  1.214
 ULF  C2   N3   single  1.368  0.020  1.368
 ULF  C5   C4   single  1.441  0.020  1.441
 ULF  N3   C4   single  1.387  0.020  1.387
 ULF  C4   O4   double  1.217  0.020  1.217
 ULF  C6'  H1   single  0.970  0.020  1.090
 ULF  C8'  H2   single  0.970  0.020  1.090
 ULF  C8'  H3   single  0.970  0.020  1.090
 ULF  C2'  H4   single  0.970  0.020  1.090
 ULF  C3'  H5   single  0.970  0.020  1.090
 ULF  O3'  H6   single  0.850  0.020  0.980
 ULF  C1'  H7   single  0.970  0.020  1.090
 ULF  C5'  H8   single  0.970  0.020  1.090
 ULF  C5'  H9   single  0.970  0.020  1.090
 ULF  C6   H12  single  0.930  0.020  1.080
 ULF  C5   H13  single  0.930  0.020  1.080
 ULF  N3   H14  single  0.860  0.020  1.020
 ULF  P    OP3  single  1.597  0.020  1.597
 ULF  OP3  H10  single  0.850  0.020  0.980
 ULF  OP2  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
 ULF  H1   C6'  C2'  111.06  3.000
 ULF  H1   C6'  C8'  112.28  3.000
 ULF  C2'  C6'  C8'  103.61  3.000
 ULF  H1   C6'  F7'  106.78  3.000
 ULF  C2'  C6'  F7'  111.27  3.000
 ULF  C8'  C6'  F7'  111.94  3.000
 ULF  H3   C8'  H2   107.91  3.000
 ULF  H3   C8'  C4'  111.87  3.000
 ULF  H2   C8'  C4'  111.67  3.000
 ULF  H3   C8'  C6'  111.74  3.000
 ULF  H2   C8'  C6'  111.83  3.000
 ULF  C4'  C8'  C6'  101.83  3.000
 ULF  H4   C2'  C1'  114.74  3.000
 ULF  H4   C2'  C3'  117.49  3.000
 ULF  C1'  C2'  C3'   99.47  3.000
 ULF  H4   C2'  C6'  114.99  3.000
 ULF  C1'  C2'  C6'  107.31  3.000
 ULF  C3'  C2'  C6'  100.84  3.000
 ULF  H5   C3'  C4'  112.50  3.000
 ULF  H5   C3'  O3'  111.40  3.000
 ULF  C4'  C3'  O3'  110.72  3.000
 ULF  H5   C3'  C2'  112.77  3.000
 ULF  O3'  C3'  C2'  115.68  3.000
 ULF  C4'  C3'  C2'   92.50  3.000
 ULF  H6   O3'  C3'  108.79  3.000
 ULF  H7   C1'  N1   106.30  3.000
 ULF  H7   C1'  O4'  110.45  3.000
 ULF  N1   C1'  O4'  109.57  3.000
 ULF  H7   C1'  C2'  113.49  3.000
 ULF  N1   C1'  C2'  112.97  3.000
 ULF  O4'  C1'  C2'  104.08  3.000
 ULF  C4'  O4'  C1'  107.79  3.000
 ULF  C5'  C4'  O4'  109.98  3.000
 ULF  O4'  C4'  C3'  101.90  3.000
 ULF  C5'  C4'  C3'  116.38  3.000
 ULF  C3'  C4'  C8'  102.43  3.000
 ULF  O4'  C4'  C8'  107.19  3.000
 ULF  C5'  C4'  C8'  117.47  3.000
 ULF  H9   C5'  H8   108.21  3.000
 ULF  H9   C5'  O5'  110.91  3.000
 ULF  H8   C5'  O5'  110.52  3.000
 ULF  H9   C5'  C4'  110.01  3.000
 ULF  H8   C5'  C4'  109.06  3.000
 ULF  O5'  C5'  C4'  108.11  3.000
 ULF  P    O5'  C5'  119.51  3.000
 ULF  OP3  P    OP1  109.65  3.000
 ULF  OP3  P    OP2  108.10  3.000
 ULF  OP1  P    OP2  118.34  3.000
 ULF  OP3  P    O5'  106.77  3.000
 ULF  OP2  P    O5'   96.48  3.000
 ULF  OP1  P    O5'  116.32  3.000
 ULF  H11  OP2  P    114.27  3.000
 ULF  C2   N1   C6   120.95  3.000
 ULF  C2   N1   C1'  116.06  3.000
 ULF  C6   N1   C1'  122.96  3.000
 ULF  H12  C6   C5   120.73  3.000
 ULF  H12  C6   N1   116.23  3.000
 ULF  C5   C6   N1   123.03  3.000
 ULF  H13  C5   C4   119.79  3.000
 ULF  H13  C5   C6   120.35  3.000
 ULF  C4   C5   C6   119.86  3.000
 ULF  N3   C4   O4   120.51  3.000
 ULF  O4   C4   C5   126.22  3.000
 ULF  N3   C4   C5   113.26  3.000
 ULF  H14  N3   C2   115.19  3.000
 ULF  H14  N3   C4   116.96  3.000
 ULF  C2   N3   C4   127.85  3.000
 ULF  O2   C2   N3   122.62  3.000
 ULF  N3   C2   N1   115.02  3.000
 ULF  O2   C2   N1   122.35  3.000
 ULF  H10  OP3  P    115.74  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
 ULF  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 ULF  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 ULF  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 ULF  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 ULF  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 ULF  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 ULF  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 ULF  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 ULF  CONST_09  H14  N3   C2   N1   180.00   0.0  0
 ULF  Var_01    OP1  P    O5'  C5'  -48.98  30.0  1
 ULF  Var_02    H8   C5'  O5'  P     64.39  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
 ULF  chir_01  C6'  C8'  F7'  C2'  negativ
 ULF  chir_02  C2'  C6'  C3'  C1'  positiv
 ULF  chir_03  C3'  O3'  C2'  C4'  negativ
 ULF  chir_04  C1'  O4'  N1   C2'  negativ
 ULF  chir_05  C4'  O4'  C5'  C8'  negativ

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
 ULF  plan-1  C1'  0.020
 ULF  plan-1  N1   0.020
 ULF  plan-1  C6   0.020
 ULF  plan-1  C5   0.020
 ULF  plan-1  C4   0.020
 ULF  plan-1  O4   0.020
 ULF  plan-1  N3   0.020
 ULF  plan-1  C2   0.020
 ULF  plan-1  O2   0.020
 ULF  plan-1  H12  0.020
 ULF  plan-1  H13  0.020
 ULF  plan-1  H14  0.020

