# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 23:57:29 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-(2,6-dideoxy-2-fluoro-5-O-phosphono-beta-D-allofuranosyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[P](O)(O)=O)[C@H]1O[C@H]([C@H](F)[C@@H]1O)N2C=CC(=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
 U5R  U5R  1-(2,6-dideoxy-2-fluoro-5-O-phosphono-beta-D-allofuranosyl)pyrimidine-2,4(1H,3H)-dione  ligand  36  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U5R
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
 U5R  O2   O  O     0  -0.467  -1.7215   0.7519  -1.4284
 U5R  C2   C  CR6   0   0.752  -2.6831   0.5542  -0.7182
 U5R  N3   N  NR16  0  -0.735  -3.8796   1.1874  -0.9059
 U5R  C4   C  CR6   0   0.572  -5.0450   1.0510  -0.1640
 U5R  O4   O  O     0  -0.456  -6.0383   1.6900  -0.4503
 U5R  C5   C  CR16  0  -0.511  -4.9254   0.1110   0.9248
 U5R  C6   C  CR16  0   0.107  -3.7619  -0.5226   1.1285
 U5R  N1   N  NR6   0  -0.576  -2.6582  -0.3378   0.3384
 U5R  C1'  C  CR15  0   0.179  -1.4211  -1.0047   0.6749
 U5R  O4'  O  O     0  -0.486  -0.5082  -0.0615   1.1641
 U5R  C2'  C  CR15  0   0.091  -0.7122  -1.7730  -0.4560
 U5R  F2'  F  F     0  -0.366  -0.5157  -3.0765  -0.0217
 U5R  C3'  C  CR15  0  -0.005   0.6374  -1.0651  -0.5706
 U5R  O3'  O  OH1   0  -0.678   1.7127  -1.9110  -0.9040
 U5R  C4'  C  CR15  0   0.046   0.8037  -0.4699   0.8325
 U5R  C5'  C  CH1   0  -0.025   1.7331   0.7332   0.9496
 U5R  C5M  C  CH3   0  -0.663   1.5797   1.4884   2.2527
 U5R  O5'  O  O2    0  -0.600   3.0682   0.2033   0.8910
 U5R  P    P  P     0   1.431   4.0858   0.6116  -0.2741
 U5R  OP1  O  O     0  -0.710   4.3306   2.0518  -0.4844
 U5R  OP2  O  OH1   0  -0.734   5.3255  -0.2476   0.2501
 U5R  OP3  O  OH1   0  -0.774   3.5312  -0.0847  -1.5909
 U5R  H1   H  HNR6  0   0.430  -3.9058   1.8355  -1.6843
 U5R  H2   H  HCR6  0   0.298  -5.7708  -0.0717   1.5696
 U5R  H3   H  HCR6  0   0.333  -3.6408  -1.2279   1.9380
 U5R  H4   H  HCR5  0   0.283  -1.6772  -1.7359   1.4483
 U5R  H5   H  HCR5  0   0.276  -1.2707  -1.8211  -1.3897
 U5R  H6   H  HCR5  0   0.266   0.5300  -0.2552  -1.2983
 U5R  H7   H  HOH1  0   0.484   1.5001  -2.4024  -1.7075
 U5R  H8   H  HCR5  0   0.254   1.1536  -1.2509   1.5247
 U5R  H9   H  HCH1  0   0.252   1.5502   1.4186   0.1137
 U5R  H10  H  HCH3  0   0.245   0.6006   1.9595   2.3119
 U5R  H11  H  HCH3  0   0.237   1.6990   0.8286   3.1131
 U5R  H12  H  HCH3  0   0.250   2.3300   2.2763   2.3144
 U5R  H13  H  HOH1  0   0.501   6.1802   0.0682  -0.0712
 U5R  H14  H  HOH1  0   0.498   2.9724  -0.8839  -1.4197

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
 U5R  O3'  C3'  single  1.408  0.020  1.408
 U5R  C5M  C5'  single  1.514  0.020  1.514
 U5R  OP1  P    double  1.476  0.020  1.476
 U5R  C3'  C2'  single  1.528  0.020  1.528
 U5R  C3'  C4'  single  1.533  0.020  1.533
 U5R  O5'  P    single  1.600  0.020  1.600
 U5R  O5'  C5'  single  1.438  0.020  1.438
 U5R  P    OP2  single  1.597  0.020  1.597
 U5R  C5'  C4'  single  1.525  0.020  1.525
 U5R  C2'  F2'  single  1.388  0.020  1.388
 U5R  C2'  C1'  single  1.540  0.020  1.540
 U5R  C4'  O4'  single  1.413  0.020  1.413
 U5R  C6   C5   double  1.340  0.020  1.340
 U5R  C6   N1   single  1.370  0.020  1.370
 U5R  O4'  C1'  single  1.401  0.020  1.401
 U5R  C5   C4   single  1.443  0.020  1.443
 U5R  C1'  N1   single  1.445  0.020  1.445
 U5R  N1   C2   single  1.383  0.020  1.383
 U5R  C4   O4   double  1.215  0.020  1.215
 U5R  C4   N3   single  1.388  0.020  1.388
 U5R  C2   N3   single  1.367  0.020  1.367
 U5R  C2   O2   double  1.212  0.020  1.212
 U5R  P    OP3  single  1.589  0.020  1.589
 U5R  N3   H1   single  0.860  0.020  1.020
 U5R  C5   H2   single  0.930  0.020  1.080
 U5R  C6   H3   single  0.930  0.020  1.080
 U5R  C1'  H4   single  0.970  0.020  1.090
 U5R  C2'  H5   single  0.970  0.020  1.090
 U5R  C3'  H6   single  0.970  0.020  1.090
 U5R  O3'  H7   single  0.850  0.020  0.980
 U5R  C4'  H8   single  0.970  0.020  1.090
 U5R  C5'  H9   single  0.970  0.020  1.090
 U5R  C5M  H10  single  0.970  0.020  1.090
 U5R  C5M  H11  single  0.970  0.020  1.090
 U5R  C5M  H12  single  0.970  0.020  1.090
 U5R  OP2  H13  single  0.850  0.020  0.980
 U5R  OP3  H14  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
 U5R  N1   C2   N3   114.81  3.000
 U5R  N3   C2   O2   122.59  3.000
 U5R  N1   C2   O2   122.60  3.000
 U5R  H1   N3   C4   116.85  3.000
 U5R  H1   N3   C2   115.12  3.000
 U5R  C4   N3   C2   128.02  3.000
 U5R  C5   C4   O4   126.00  3.000
 U5R  O4   C4   N3   120.57  3.000
 U5R  C5   C4   N3   113.43  3.000
 U5R  H2   C5   C6   120.61  3.000
 U5R  H2   C5   C4   119.75  3.000
 U5R  C6   C5   C4   119.63  3.000
 U5R  H3   C6   N1   115.46  3.000
 U5R  H3   C6   C5   121.32  3.000
 U5R  N1   C6   C5   123.22  3.000
 U5R  C1'  N1   C6   119.55  3.000
 U5R  C1'  N1   C2   119.40  3.000
 U5R  C6   N1   C2   120.88  3.000
 U5R  H4   C1'  C2'  107.05  3.000
 U5R  H4   C1'  O4'  110.82  3.000
 U5R  C2'  C1'  O4'  107.00  3.000
 U5R  H4   C1'  N1   105.81  3.000
 U5R  O4'  C1'  N1   109.18  3.000
 U5R  C2'  C1'  N1   116.96  3.000
 U5R  C4'  O4'  C1'  109.17  3.000
 U5R  H5   C2'  C3'  114.15  3.000
 U5R  H5   C2'  F2'  107.42  3.000
 U5R  C3'  C2'  F2'  109.48  3.000
 U5R  H5   C2'  C1'  114.55  3.000
 U5R  F2'  C2'  C1'  107.69  3.000
 U5R  C3'  C2'  C1'  103.32  3.000
 U5R  H6   C3'  C4'  109.39  3.000
 U5R  H6   C3'  O3'  111.24  3.000
 U5R  C4'  C3'  O3'  111.53  3.000
 U5R  H6   C3'  C2'  107.82  3.000
 U5R  C4'  C3'  C2'  101.95  3.000
 U5R  O3'  C3'  C2'  114.45  3.000
 U5R  H7   O3'  C3'  109.54  3.000
 U5R  H8   C4'  C5'  108.53  3.000
 U5R  H8   C4'  C3'  109.55  3.000
 U5R  C5'  C4'  C3'  116.28  3.000
 U5R  H8   C4'  O4'  110.64  3.000
 U5R  C5'  C4'  O4'  108.65  3.000
 U5R  C3'  C4'  O4'  103.07  3.000
 U5R  H9   C5'  O5'  110.75  3.000
 U5R  H9   C5'  C5M  109.12  3.000
 U5R  O5'  C5'  C5M  108.25  3.000
 U5R  H9   C5'  C4'  109.45  3.000
 U5R  O5'  C5'  C4'  105.79  3.000
 U5R  C5M  C5'  C4'  113.45  3.000
 U5R  H12  C5M  H11  108.50  3.000
 U5R  H12  C5M  H10  107.66  3.000
 U5R  H11  C5M  H10  108.50  3.000
 U5R  H12  C5M  C5'  109.86  3.000
 U5R  H11  C5M  C5'  111.48  3.000
 U5R  H10  C5M  C5'  110.74  3.000
 U5R  P    O5'  C5'  121.76  3.000
 U5R  OP3  P    OP2  107.89  3.000
 U5R  OP3  P    OP1  111.55  3.000
 U5R  OP2  P    OP1  116.30  3.000
 U5R  OP3  P    O5'  105.64  3.000
 U5R  OP2  P    O5'   96.75  3.000
 U5R  OP1  P    O5'  117.28  3.000
 U5R  H13  OP2  P    113.69  3.000
 U5R  H14  OP3  P    114.03  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
 U5R  CONST_01  C6   N1  C2   N3     0.00   0.0  0
 U5R  CONST_02  C1'  N1  C2   N3   180.00   0.0  0
 U5R  CONST_03  N1   C2  N3   C4     0.00   0.0  0
 U5R  CONST_04  C6   N1  C2   O2   180.00   0.0  0
 U5R  CONST_05  C1'  N1  C2   O2     0.00   0.0  0
 U5R  CONST_06  C4   N3  C2   O2   180.00   0.0  0
 U5R  CONST_07  H1   N3  C2   N1   180.00   0.0  0
 U5R  Var_01    OP1  P   O5'  C5'   54.30  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
 U5R  chir_01  C1'  C2'  O4'  N1   negativ
 U5R  chir_02  C2'  F2'  C3'  C1'  positiv
 U5R  chir_03  C3'  O3'  C4'  C2'  positiv
 U5R  chir_04  C4'  O4'  C3'  C5'  negativ
 U5R  chir_05  C5'  O5'  C4'  C5M  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
 U5R  plan-1  O2   0.020
 U5R  plan-1  C2   0.020
 U5R  plan-1  N3   0.020
 U5R  plan-1  C4   0.020
 U5R  plan-1  O4   0.020
 U5R  plan-1  C5   0.020
 U5R  plan-1  C6   0.020
 U5R  plan-1  N1   0.020
 U5R  plan-1  C1'  0.020
 U5R  plan-1  H1   0.020
 U5R  plan-1  H2   0.020
 U5R  plan-1  H3   0.020

