# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  1 06:40:52 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2R)-1-{3-deoxy-5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-2-hydroxy-2,3-dihydropyrimidin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O[C@H]1N2C=CC(=O)N[C@H]2O
#
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
 U3H  U3H  (2R)-1-{3-deoxy-5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-2-hydroxy-2,3-dihydropyrimidin-4(1H)-one  ligand  41  28  .  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_U3H
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
 U3H  N1    N  NT     0  -0.518  -3.8491  2.0862  -0.5562
 U3H  C6    C  C1     0   0.041  -3.9264  3.4124  -0.8121
 U3H  C2    C  CH1    0   0.326  -4.9674  1.2266  -0.8449
 U3H  O2    O  OH1    0  -0.641  -4.8186  0.5728  -2.0743
 U3H  N3    N  NH1    0  -0.698  -6.1844  1.9745  -0.7383
 U3H  C4    C  C      0   0.532  -6.3326  3.2968  -1.0609
 U3H  O4    O  O      0  -0.521  -7.4487  3.7902  -1.2094
 U3H  C5    C  C1     0  -0.577  -5.0905  4.0277  -1.1238
 U3H  C1'   C  CH1    0   0.207  -2.5916  1.4663  -0.2236
 U3H  C2'   C  CH1    0  -0.076  -1.4351  1.7364  -1.1933
 U3H  O2'   O  OH1    0  -0.662  -1.4904  0.9443  -2.3506
 U3H  C3'   C  CH2    0  -0.557  -0.2296  1.5184  -0.2909
 U3H  C4'   C  CH1    0   0.004  -0.7263  2.0099   1.0672
 U3H  O4'   O  O2     0  -0.508  -2.1566  1.9232   1.0312
 U3H  C5'   C  CH2    0  -0.206  -0.3583  3.4517   1.3766
 U3H  O5'   O  O2     0  -0.625   1.0480  3.5111   1.5157
 U3H  PA    P  P      0   1.361   1.7888  4.9689   1.6120
 U3H  O1A   O  O      0  -0.815   3.2541  4.6706   1.5335
 U3H  O2A   O  OP    -1  -0.820   1.2239  5.7349   2.7725
 U3H  O3A   O  O2     0  -0.755   1.2668  5.7524   0.2851
 U3H  PB    P  P      0   1.341   1.6810  5.4757  -1.2995
 U3H  O1B   O  O      0  -0.803   1.7566  3.9993  -1.5450
 U3H  O2B   O  OP    -1  -0.831   2.8881  6.3224  -1.6000
 U3H  O3B   O  O2     0  -0.769   0.4383  6.1867  -2.0212
 U3H  PG    P  P      0   1.274  -1.2141  5.7426  -2.2334
 U3H  O1G   O  O      0  -0.841  -1.7660  5.5887  -0.8172
 U3H  O2G   O  OP    -1  -0.893  -1.7279  6.9770  -2.9640
 U3H  O3G   O  OP    -1  -0.866  -1.1900  4.4752  -3.0698
 U3H  H6    H  H      0   0.365  -3.0094  4.0035  -0.7544
 U3H  H2'   H  HCH1   0   0.263  -5.0013  0.4195  -0.1121
 U3H  H3    H  HNH1   0   0.397  -7.0295  1.4243  -0.6867
 U3H  H5    H  H      0   0.249  -5.1006  5.0884  -1.3240
 U3H  H1'   H  HCH1   0   0.225  -2.7824  0.3832  -0.1896
 U3H  H2''  H  HCH1   0   0.323  -1.4479  2.7707  -1.5496
 U3H  HA    H  HOH1   0   0.435  -1.4353  0.0176  -2.0938
 U3H  H3'   H  HCH2   0   0.228   0.0242  0.4537  -0.2453
 U3H  H3'2  H  HCH2   0   0.292   0.6396  2.0770  -0.6350
 U3H  H4'   H  HCH1   0   0.218  -0.3612  1.3670   1.8759
 U3H  H5'1  H  HCH2   0   0.191  -0.8519  3.7536   2.3101
 U3H  H5'2  H  HCH2   0   0.264  -0.7161  4.1086   0.5772
 U3H  HO5   H  HOH1   0   0.449  -4.6356  1.2216  -2.7650

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
 U3H  N1   C6    single  1.353  0.020  1.353
 U3H  N1   C2    single  1.440  0.020  1.440
 U3H  N1   C1'   single  1.441  0.020  1.441
 U3H  C6   C5    double  1.353  0.020  1.353
 U3H  C6   H6    single  0.930  0.020  1.080
 U3H  C2   O2    single  1.400  0.020  1.400
 U3H  C2   N3    single  1.432  0.020  1.432
 U3H  C2   H2'   single  0.970  0.020  1.090
 U3H  N3   C4    single  1.369  0.020  1.369
 U3H  N3   H3    single  0.860  0.020  1.020
 U3H  C4   O4    double  1.229  0.020  1.229
 U3H  C4   C5    single  1.443  0.020  1.443
 U3H  C5   H5    single  0.930  0.020  1.080
 U3H  C1'  C2'   single  1.533  0.020  1.533
 U3H  C1'  O4'   single  1.404  0.020  1.404
 U3H  C1'  H1'   single  0.970  0.020  1.090
 U3H  C2'  O2'   single  1.403  0.020  1.403
 U3H  C2'  C3'   single  1.522  0.020  1.522
 U3H  C2'  H2''  single  0.970  0.020  1.090
 U3H  O2'  HA    single  0.850  0.020  0.980
 U3H  C3'  C4'   single  1.527  0.020  1.527
 U3H  C3'  H3'   single  0.970  0.020  1.090
 U3H  C3'  H3'2  single  0.970  0.020  1.090
 U3H  C4'  O4'   single  1.433  0.020  1.433
 U3H  C4'  C5'   single  1.520  0.020  1.520
 U3H  C4'  H4'   single  0.970  0.020  1.090
 U3H  C5'  O5'   single  1.414  0.020  1.414
 U3H  C5'  H5'1  single  0.970  0.020  1.090
 U3H  C5'  H5'2  single  0.970  0.020  1.090
 U3H  O5'  PA    single  1.638  0.020  1.638
 U3H  PA   O1A   deloc   1.497  0.020  1.497
 U3H  PA   O2A   deloc   1.501  0.020  1.501
 U3H  PA   O3A   single  1.627  0.020  1.627
 U3H  O3A  PB    single  1.661  0.020  1.661
 U3H  PB   O1B   deloc   1.499  0.020  1.499
 U3H  PB   O2B   deloc   1.505  0.020  1.505
 U3H  PB   O3B   single  1.603  0.020  1.603
 U3H  O3B  PG    single  1.724  0.020  1.724
 U3H  PG   O1G   deloc   1.528  0.020  1.528
 U3H  PG   O2G   deloc   1.524  0.020  1.524
 U3H  PG   O3G   deloc   1.519  0.020  1.519
 U3H  HO5  O2    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
 U3H  C1'   N1   C2    117.86  3.000
 U3H  C1'   N1   C6    121.01  3.000
 U3H  C2    N1   C6    120.20  3.000
 U3H  H6    C6   C5    119.22  3.000
 U3H  H6    C6   N1    118.20  3.000
 U3H  C5    C6   N1    122.58  3.000
 U3H  H2'   C2   N3    108.06  3.000
 U3H  H2'   C2   O2    104.34  3.000
 U3H  N3    C2   O2    113.54  3.000
 U3H  H2'   C2   N1    109.34  3.000
 U3H  N3    C2   N1    109.46  3.000
 U3H  O2    C2   N1    111.86  3.000
 U3H  HO5   O2   C2    109.54  3.000
 U3H  H3    N3   C4    116.60  3.000
 U3H  H3    N3   C2    115.49  3.000
 U3H  C4    N3   C2    125.36  3.000
 U3H  C5    C4   O4    124.97  3.000
 U3H  C5    C4   N3    113.98  3.000
 U3H  O4    C4   N3    120.95  3.000
 U3H  H5    C5   C4    119.86  3.000
 U3H  H5    C5   C6    119.84  3.000
 U3H  C4    C5   C6    120.02  3.000
 U3H  H1'   C1'  O4'   110.27  3.000
 U3H  H1'   C1'  C2'   108.89  3.000
 U3H  O4'   C1'  C2'   105.91  3.000
 U3H  H1'   C1'  N1    106.22  3.000
 U3H  O4'   C1'  N1    109.67  3.000
 U3H  C2'   C1'  N1    115.88  3.000
 U3H  H2''  C2'  C3'   109.75  3.000
 U3H  H2''  C2'  O2'   105.34  3.000
 U3H  C3'   C2'  O2'   116.06  3.000
 U3H  H2''  C2'  C1'   111.33  3.000
 U3H  C3'   C2'  C1'   101.37  3.000
 U3H  O2'   C2'  C1'   113.11  3.000
 U3H  HA    O2'  C2'   108.72  3.000
 U3H  H3'2  C3'  H3'   109.07  3.000
 U3H  H3'2  C3'  C4'   112.05  3.000
 U3H  H3'   C3'  C4'   110.56  3.000
 U3H  H3'2  C3'  C2'   111.80  3.000
 U3H  H3'   C3'  C2'   110.34  3.000
 U3H  C4'   C3'  C2'   102.92  3.000
 U3H  H4'   C4'  C5'   109.01  3.000
 U3H  H4'   C4'  O4'   108.40  3.000
 U3H  C5'   C4'  O4'   107.70  3.000
 U3H  H4'   C4'  C3'   111.04  3.000
 U3H  C5'   C4'  C3'   114.05  3.000
 U3H  O4'   C4'  C3'   106.42  3.000
 U3H  C4'   O4'  C1'   110.56  3.000
 U3H  H5'2  C5'  H5'1  107.98  3.000
 U3H  H5'2  C5'  O5'   111.81  3.000
 U3H  H5'1  C5'  O5'   110.59  3.000
 U3H  H5'2  C5'  C4'   109.97  3.000
 U3H  H5'1  C5'  C4'   108.97  3.000
 U3H  O5'   C5'  C4'   107.49  3.000
 U3H  PA    O5'  C5'   119.53  3.000
 U3H  O3A   PA   O2A   105.31  3.000
 U3H  O3A   PA   O1A   111.54  3.000
 U3H  O2A   PA   O1A   120.70  3.000
 U3H  O3A   PA   O5'   103.62  3.000
 U3H  O2A   PA   O5'   109.24  3.000
 U3H  O1A   PA   O5'   105.20  3.000
 U3H  PB    O3A  PA    128.16  3.000
 U3H  O3B   PB   O2B   106.40  3.000
 U3H  O3B   PB   O1B   113.72  3.000
 U3H  O2B   PB   O1B   118.76  3.000
 U3H  O3B   PB   O3A    99.34  3.000
 U3H  O2B   PB   O3A   107.27  3.000
 U3H  O1B   PB   O3A   109.45  3.000
 U3H  PG    O3B  PB    133.15  3.000
 U3H  O3G   PG   O2G   114.67  3.000
 U3H  O3G   PG   O1G   115.61  3.000
 U3H  O2G   PG   O1G   113.85  3.000
 U3H  O3G   PG   O3B   105.52  3.000
 U3H  O2G   PG   O3B    99.99  3.000
 U3H  O1G   PG   O3B   104.96  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
 U3H  CONST_03  H3    N3   C4   C5    180.00   0.0  0
 U3H  Var_01    C4    C5   C6   N1      6.32  30.0  1
 U3H  Var_02    N3    C4   C5   C6     -3.14  30.0  1
 U3H  Var_03    C5    C6   N1   C2     11.45  30.0  1
 U3H  Var_04    O1A   PA   O5'  C5'  -171.38  30.0  3
 U3H  Var_05    O1B   PB   O3A  PA     40.63  30.0  3
 U3H  Var_06    O1G   PG   O3B  PB     59.43  30.0  3
 U3H  Var_07    H5'1  C5'  O5'  PA    -71.03  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
 U3H  chir_01  C2   N1   O2   N3   positiv
 U3H  chir_02  C1'  O4'  N1   C2'  negativ
 U3H  chir_03  C2'  O2'  C1'  C3'  negativ
 U3H  chir_04  C4'  O4'  C5'  C3'  positiv

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
 U3H  plan-1  N1   0.020
 U3H  plan-1  C6   0.020
 U3H  plan-1  C2   0.020
 U3H  plan-1  C1'  0.020
 U3H  plan-2  C2   0.020
 U3H  plan-2  N3   0.020
 U3H  plan-2  C4   0.020
 U3H  plan-2  O4   0.020
 U3H  plan-2  C5   0.020
 U3H  plan-2  H3   0.020

