# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:17:52 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 5-fluorouridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=C(F)C(=O)NC2=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
 5UD  5UD  '5-fluorouridine          '  ligand  29  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5UD
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
 5UD  F5    F  F     0  -0.294  -1.0380   1.2255  -3.9381
 5UD  C5    C  CR6   0   0.287  -0.4055   0.6241  -2.9279
 5UD  C4    C  CR6   0   0.471   0.7315  -0.2016  -3.2640
 5UD  O4    O  O     0  -0.445   1.1601  -0.3929  -4.3821
 5UD  N3    N  NR16  0  -0.740   1.3026  -0.7686  -2.1439
 5UD  C2    C  CR6   0   0.757   0.9261  -0.6459  -0.8256
 5UD  O2    O  O     0  -0.459   1.5213  -1.2223   0.0562
 5UD  C6    C  CR16  0  -0.080  -0.7997   0.7859  -1.6627
 5UD  N1    N  NR6   0  -0.574  -0.1653   0.1716  -0.6124
 5UD  C1'   C  CH1   0   0.234  -0.6558   0.4381   0.7360
 5UD  C2'   C  CH1   0  -0.022  -1.1404  -0.7756   1.5265
 5UD  O2'   O  OH1   0  -0.656  -2.4115  -1.1341   1.0834
 5UD  C3'   C  CH1   0  -0.048  -1.0405  -0.2279   2.9528
 5UD  O3'   O  OH1   0  -0.669  -2.1704   0.5718   3.1872
 5UD  C4'   C  CH1   0  -0.034   0.2528   0.5898   2.8616
 5UD  O4'   O  O2    0  -0.486   0.3297   1.0488   1.5071
 5UD  C5'   C  CH2   0  -0.150   1.4750  -0.2194   3.2443
 5UD  O5'   O  OH1   0  -0.671   2.6193   0.5778   3.0636
 5UD  HN3   H  HNR6  0   0.435   2.1083  -1.3625  -2.3017
 5UD  H6    H  HCR6  0   0.344  -1.6440   1.4149  -1.4166
 5UD  H1'   H  HCH1  0   0.254  -1.5059   1.1141   0.5884
 5UD  H2'   H  HCH1  0   0.260  -0.4287  -1.6010   1.4329
 5UD  HO2'  H  HOH1  0   0.463  -2.6321  -1.9973   1.4459
 5UD  H3'   H  HCH1  0   0.250  -0.9547  -1.0308   3.6959
 5UD  HO3'  H  HOH1  0   0.456  -2.0790   0.9799   4.0539
 5UD  H4'   H  HCH1  0   0.252   0.1999   1.4697   3.5130
 5UD  H5'1  H  HCH2  0   0.210   1.5187  -1.1360   2.6478
 5UD  H5'2  H  HCH2  0   0.199   1.3498  -0.5200   4.2934
 5UD  HO5'  H  HOH1  0   0.456   3.3920   0.0242   3.2049

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
 5UD  F5   C5    single  1.335  0.020  1.335
 5UD  C5   C4    single  1.445  0.020  1.445
 5UD  C5   C6    double  1.335  0.020  1.335
 5UD  C4   O4    double  1.213  0.020  1.213
 5UD  C4   N3    single  1.379  0.020  1.379
 5UD  N3   C2    single  1.376  0.020  1.376
 5UD  N3   HN3   single  0.860  0.020  1.020
 5UD  C2   O2    double  1.210  0.020  1.210
 5UD  C2   N1    single  1.380  0.020  1.380
 5UD  C6   N1    single  1.372  0.020  1.372
 5UD  C6   H6    single  0.930  0.020  1.080
 5UD  N1   C1'   single  1.459  0.020  1.459
 5UD  C1'  C2'   single  1.527  0.020  1.527
 5UD  C1'  O4'   single  1.392  0.020  1.392
 5UD  C1'  H1'   single  0.970  0.020  1.090
 5UD  C2'  O2'   single  1.393  0.020  1.393
 5UD  C2'  C3'   single  1.531  0.020  1.531
 5UD  C2'  H2'   single  0.970  0.020  1.090
 5UD  O2'  HO2'  single  0.850  0.020  0.980
 5UD  C3'  O3'   single  1.404  0.020  1.404
 5UD  C3'  C4'   single  1.533  0.020  1.533
 5UD  C3'  H3'   single  0.970  0.020  1.090
 5UD  O3'  HO3'  single  0.850  0.020  0.980
 5UD  C4'  O4'   single  1.432  0.020  1.432
 5UD  C4'  C5'   single  1.515  0.020  1.515
 5UD  C4'  H4'   single  0.970  0.020  1.090
 5UD  C5'  O5'   single  1.406  0.020  1.406
 5UD  C5'  H5'1  single  0.970  0.020  1.090
 5UD  C5'  H5'2  single  0.970  0.020  1.090
 5UD  O5'  HO5'  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
 5UD  C6    C5   C4    121.47  3.000
 5UD  C6    C5   F5    121.51  3.000
 5UD  C4    C5   F5    117.01  3.000
 5UD  N3    C4   O4    122.52  3.000
 5UD  N3    C4   C5    111.83  3.000
 5UD  O4    C4   C5    125.65  3.000
 5UD  HN3   N3   C2    114.76  3.000
 5UD  HN3   N3   C4    116.34  3.000
 5UD  C2    N3   C4    128.90  3.000
 5UD  N1    C2   O2    123.96  3.000
 5UD  N1    C2   N3    114.64  3.000
 5UD  O2    C2   N3    121.40  3.000
 5UD  H6    C6   N1    116.56  3.000
 5UD  H6    C6   C5    121.11  3.000
 5UD  N1    C6   C5    122.32  3.000
 5UD  C1'   N1   C6    118.04  3.000
 5UD  C1'   N1   C2    121.11  3.000
 5UD  C6    N1   C2    120.83  3.000
 5UD  H1'   C1'  O4'   110.67  3.000
 5UD  H1'   C1'  C2'   108.28  3.000
 5UD  O4'   C1'  C2'   106.65  3.000
 5UD  H1'   C1'  N1    104.41  3.000
 5UD  O4'   C1'  N1    110.73  3.000
 5UD  C2'   C1'  N1    116.09  3.000
 5UD  H2'   C2'  C3'   107.90  3.000
 5UD  H2'   C2'  O2'   111.85  3.000
 5UD  C3'   C2'  O2'   116.61  3.000
 5UD  H2'   C2'  C1'   110.42  3.000
 5UD  C3'   C2'  C1'   100.21  3.000
 5UD  O2'   C2'  C1'   109.23  3.000
 5UD  HO2'  O2'  C2'   108.68  3.000
 5UD  H3'   C3'  C4'   111.38  3.000
 5UD  H3'   C3'  O3'   111.51  3.000
 5UD  C4'   C3'  O3'   112.65  3.000
 5UD  H3'   C3'  C2'   111.97  3.000
 5UD  C4'   C3'  C2'   100.98  3.000
 5UD  O3'   C3'  C2'   107.87  3.000
 5UD  HO3'  O3'  C3'   108.39  3.000
 5UD  H4'   C4'  C5'   108.52  3.000
 5UD  H4'   C4'  O4'   107.90  3.000
 5UD  C5'   C4'  O4'   111.51  3.000
 5UD  H4'   C4'  C3'   110.62  3.000
 5UD  C5'   C4'  C3'   112.38  3.000
 5UD  O4'   C4'  C3'   105.82  3.000
 5UD  C4'   O4'  C1'   110.19  3.000
 5UD  H5'2  C5'  H5'1  107.21  3.000
 5UD  H5'2  C5'  O5'   111.75  3.000
 5UD  H5'1  C5'  O5'   111.86  3.000
 5UD  H5'2  C5'  C4'   107.19  3.000
 5UD  H5'1  C5'  C4'   109.99  3.000
 5UD  O5'   C5'  C4'   108.74  3.000
 5UD  HO5'  O5'  C5'   107.99  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
 5UD  CONST_01  C2   N3  C4  C5    0.00  0.0  0
 5UD  CONST_02  N1   C2  N3  C4    0.00  0.0  0
 5UD  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 5UD  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 5UD  CONST_05  O2   C2  N3  C4  180.00  0.0  0
 5UD  CONST_06  C2   N3  C4  O4  180.00  0.0  0
 5UD  CONST_07  C6   N1  C2  O2  180.00  0.0  0
 5UD  CONST_08  C1'  N1  C2  O2    0.00  0.0  0
 5UD  CONST_09  HN3  N3  C4  C5  180.00  0.0  0

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
 5UD  chir_01  C1'  N1   C2'  O4'  negativ
 5UD  chir_02  C2'  O2'  C3'  C1'  positiv
 5UD  chir_03  C3'  O3'  C4'  C2'  positiv
 5UD  chir_04  C4'  O4'  C3'  C5'  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
 5UD  plan-1  F5   0.020
 5UD  plan-1  C5   0.020
 5UD  plan-1  C4   0.020
 5UD  plan-1  O4   0.020
 5UD  plan-1  N3   0.020
 5UD  plan-1  C2   0.020
 5UD  plan-1  O2   0.020
 5UD  plan-1  C6   0.020
 5UD  plan-1  N1   0.020
 5UD  plan-1  C1'  0.020
 5UD  plan-1  HN3  0.020
 5UD  plan-1  H6   0.020

