# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 08:56:25 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)N[P](O)(O)=O)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
 UNP  UNP  5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine  ligand  45  29  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UNP
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
 UNP  O2G   O  O     0  -0.674  16.6528  37.1613  34.7036
 UNP  PG    P  P     0   1.465  15.4877  36.4965  35.3097
 UNP  O3G   O  OH1   0  -0.739  14.3929  37.3468  36.0859
 UNP  O1G   O  OH1   0  -0.766  15.8445  35.4073  36.4457
 UNP  N2B   N  NH1   0  -0.951  14.5230  35.7481  34.1666
 UNP  PB    P  P     0   1.464  13.0107  35.0578  34.3152
 UNP  O1B   O  OH1   0  -0.747  11.9446  36.1712  34.6624
 UNP  O3B   O  O     0  -0.656  12.6640  34.2307  33.1519
 UNP  O3A   O  O2    0  -0.716  13.1632  34.1895  35.6901
 UNP  PA    P  P     0   1.494  12.6191  34.4344  37.1962
 UNP  O1A   O  OH1   0  -0.728  13.8869  34.1603  38.0882
 UNP  O2A   O  O     0  -0.684  11.9160  35.7302  37.3181
 UNP  O5'   O  O2    0  -0.571  11.6546  33.2264  37.4910
 UNP  C5'   C  CH2   0  -0.217  12.0175  31.8355  37.5003
 UNP  C4'   C  CH1   0   0.009  11.0153  31.0409  36.6958
 UNP  C3'   C  CH1   0  -0.077  10.9074  31.4169  35.2119
 UNP  O3'   O  OH1   0  -0.670  10.7064  30.2376  34.4683
 UNP  C2'   C  CH1   0  -0.003   9.6426  32.2821  35.1878
 UNP  O2'   O  OH1   0  -0.645   8.9998  32.4030  33.9623
 UNP  O4'   O  O2    0  -0.491   9.7141  31.2040  37.2596
 UNP  C1'   C  CH1   0   0.170   8.8029  31.5932  36.2696
 UNP  N1    N  NR6   0  -0.565   7.7897  32.4439  36.8653
 UNP  C2    C  CR6   0   0.739   6.4545  32.1437  36.6652
 UNP  O2    O  O     0  -0.473   6.0741  31.1933  36.0157
 UNP  C6    C  CR16  0   0.101   8.1642  33.5315  37.6057
 UNP  C5    C  CR16  0  -0.512   7.2877  34.3706  38.1768
 UNP  C4    C  CR6   0   0.572   5.8723  34.1355  38.0222
 UNP  N3    N  NR16  0  -0.734   5.5811  33.0141  37.2607
 UNP  O4    O  O     0  -0.460   4.9791  34.8162  38.4887
 UNP  HO3G  H  HOH1  0   0.510  14.6854  37.7761  36.9026
 UNP  HO1G  H  HOH1  0   0.512  16.6140  34.8547  36.2441
 UNP  HN2B  H  HNH1  0   0.455  14.9234  35.6917  33.2368
 UNP  HO1B  H  HOH1  0   0.500  11.8068  36.3577  35.6190
 UNP  HO1A  H  HOH1  0   0.512  14.7092  34.5857  37.7742
 UNP  H5'   H  HCH2  0   0.267  13.0170  31.6706  37.0942
 UNP  H5'A  H  HCH2  0   0.285  12.0175  31.5062  38.5393
 UNP  H4'   H  HCH1  0   0.278  11.3225  29.9927  36.7781
 UNP  H3'   H  HCH1  0   0.266  11.7899  31.9561  34.8560
 UNP  HO3'  H  HOH1  0   0.466  10.9854  30.3894  33.5603
 UNP  H2'   H  HCH1  0   0.245   9.8893  33.2993  35.5074
 UNP  HO2'  H  HOH1  0   0.449   8.8208  31.5222  33.6128
 UNP  H1'   H  HCH1  0   0.279   8.2785  30.7296  35.8518
 UNP  H6    H  HCR6  0   0.321   9.2275  33.6811  37.7206
 UNP  H5    H  HCR6  0   0.295   7.6307  35.2164  38.7519
 UNP  HN3   H  HNR6  0   0.428   4.6012  32.8016  37.1180

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
 UNP  O2G  PG    double  1.472  0.020  1.472
 UNP  PG   O3G   single  1.589  0.020  1.589
 UNP  PG   O1G   single  1.614  0.020  1.614
 UNP  PG   N2B   single  1.673  0.020  1.673
 UNP  N2B  PB    single  1.669  0.020  1.669
 UNP  PB   O1B   single  1.580  0.020  1.580
 UNP  PB   O3B   double  1.469  0.020  1.469
 UNP  PB   O3A   single  1.633  0.020  1.633
 UNP  O3A  PA    single  1.620  0.020  1.620
 UNP  PA   O1A   single  1.574  0.020  1.574
 UNP  PA   O2A   double  1.479  0.020  1.479
 UNP  PA   O5'   single  1.574  0.020  1.574
 UNP  O5'  C5'   single  1.437  0.020  1.437
 UNP  C5'  C4'   single  1.511  0.020  1.511
 UNP  C4'  C3'   single  1.535  0.020  1.535
 UNP  C4'  O4'   single  1.427  0.020  1.427
 UNP  C3'  O3'   single  1.409  0.020  1.409
 UNP  C3'  C2'   single  1.533  0.020  1.533
 UNP  C2'  O2'   single  1.389  0.020  1.389
 UNP  C2'  C1'   single  1.533  0.020  1.533
 UNP  O4'  C1'   single  1.401  0.020  1.401
 UNP  C1'  N1    single  1.451  0.020  1.451
 UNP  N1   C2    single  1.383  0.020  1.383
 UNP  N1   C6    single  1.368  0.020  1.368
 UNP  C2   O2    double  1.212  0.020  1.212
 UNP  C2   N3    single  1.369  0.020  1.369
 UNP  C6   C5    double  1.341  0.020  1.341
 UNP  C5   C4    single  1.443  0.020  1.443
 UNP  C4   N3    single  1.386  0.020  1.386
 UNP  C4   O4    double  1.216  0.020  1.216
 UNP  O3G  HO3G  single  0.850  0.020  0.980
 UNP  O1G  HO1G  single  0.850  0.020  0.980
 UNP  N2B  HN2B  single  0.860  0.020  1.020
 UNP  O1B  HO1B  single  0.850  0.020  0.980
 UNP  O1A  HO1A  single  0.850  0.020  0.980
 UNP  C5'  H5'   single  0.970  0.020  1.090
 UNP  C5'  H5'A  single  0.970  0.020  1.090
 UNP  C4'  H4'   single  0.970  0.020  1.090
 UNP  C3'  H3'   single  0.970  0.020  1.090
 UNP  O3'  HO3'  single  0.850  0.020  0.980
 UNP  C2'  H2'   single  0.970  0.020  1.090
 UNP  O2'  HO2'  single  0.850  0.020  0.980
 UNP  C1'  H1'   single  0.970  0.020  1.090
 UNP  C6   H6    single  0.930  0.020  1.080
 UNP  C5   H5    single  0.930  0.020  1.080
 UNP  N3   HN3   single  0.860  0.020  1.020

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
 UNP  N2B   PG   O1G  107.86  3.000
 UNP  N2B   PG   O3G  100.13  3.000
 UNP  O1G   PG   O3G   99.77  3.000
 UNP  N2B   PG   O2G  112.16  3.000
 UNP  O1G   PG   O2G  114.82  3.000
 UNP  O3G   PG   O2G  120.32  3.000
 UNP  HO3G  O3G  PG   116.19  3.000
 UNP  HO1G  O1G  PG   114.47  3.000
 UNP  HN2B  N2B  PB   114.61  3.000
 UNP  HN2B  N2B  PG   115.08  3.000
 UNP  PB    N2B  PG   130.30  3.000
 UNP  O3A   PB   O3B  112.92  3.000
 UNP  O3A   PB   O1B  104.63  3.000
 UNP  O3B   PB   O1B  114.30  3.000
 UNP  O3A   PB   N2B  102.14  3.000
 UNP  O3B   PB   N2B  112.10  3.000
 UNP  O1B   PB   N2B  109.84  3.000
 UNP  HO1B  O1B  PB   116.20  3.000
 UNP  PA    O3A  PB   132.14  3.000
 UNP  O5'   PA   O2A  111.45  3.000
 UNP  O5'   PA   O1A  104.70  3.000
 UNP  O2A   PA   O1A  119.25  3.000
 UNP  O5'   PA   O3A  105.30  3.000
 UNP  O2A   PA   O3A  111.63  3.000
 UNP  O1A   PA   O3A  103.30  3.000
 UNP  HO1A  O1A  PA   114.81  3.000
 UNP  C5'   O5'  PA   126.10  3.000
 UNP  H5'A  C5'  H5'  108.01  3.000
 UNP  H5'A  C5'  C4'  110.41  3.000
 UNP  H5'   C5'  C4'  109.26  3.000
 UNP  H5'A  C5'  O5'  107.36  3.000
 UNP  H5'   C5'  O5'  112.02  3.000
 UNP  C4'   C5'  O5'  109.75  3.000
 UNP  H4'   C4'  O4'  109.59  3.000
 UNP  H4'   C4'  C3'  109.08  3.000
 UNP  O4'   C4'  C3'  106.85  3.000
 UNP  H4'   C4'  C5'  106.09  3.000
 UNP  O4'   C4'  C5'  109.53  3.000
 UNP  C3'   C4'  C5'  115.64  3.000
 UNP  H3'   C3'  C2'  112.48  3.000
 UNP  H3'   C3'  O3'  110.86  3.000
 UNP  C2'   C3'  O3'  110.28  3.000
 UNP  H3'   C3'  C4'  112.26  3.000
 UNP  C2'   C3'  C4'  102.21  3.000
 UNP  O3'   C3'  C4'  108.38  3.000
 UNP  HO3'  O3'  C3'  108.95  3.000
 UNP  H2'   C2'  C1'  109.58  3.000
 UNP  H2'   C2'  O2'  106.32  3.000
 UNP  C1'   C2'  O2'  114.09  3.000
 UNP  H2'   C2'  C3'  109.52  3.000
 UNP  C1'   C2'  C3'  100.79  3.000
 UNP  O2'   C2'  C3'  116.42  3.000
 UNP  HO2'  O2'  C2'  109.03  3.000
 UNP  C1'   O4'  C4'  110.22  3.000
 UNP  H1'   C1'  N1   106.56  3.000
 UNP  H1'   C1'  O4'  111.26  3.000
 UNP  N1    C1'  O4'  109.09  3.000
 UNP  H1'   C1'  C2'  110.37  3.000
 UNP  N1    C1'  C2'  114.13  3.000
 UNP  O4'   C1'  C2'  105.50  3.000
 UNP  C6    N1   C2   121.01  3.000
 UNP  C6    N1   C1'  119.81  3.000
 UNP  C2    N1   C1'  119.18  3.000
 UNP  N3    C2   O2   122.09  3.000
 UNP  N3    C2   N1   114.51  3.000
 UNP  O2    C2   N1   123.40  3.000
 UNP  H6    C6   C5   120.77  3.000
 UNP  H6    C6   N1   115.94  3.000
 UNP  C5    C6   N1   123.30  3.000
 UNP  H5    C5   C4   119.78  3.000
 UNP  H5    C5   C6   120.65  3.000
 UNP  C4    C5   C6   119.57  3.000
 UNP  O4    C4   N3   120.61  3.000
 UNP  O4    C4   C5   126.02  3.000
 UNP  N3    C4   C5   113.37  3.000
 UNP  HN3   N3   C4   116.76  3.000
 UNP  HN3   N3   C2   114.99  3.000
 UNP  C4    N3   C2   128.25  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
 UNP  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 UNP  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 UNP  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 UNP  CONST_04  N3   C2   N1   C6      0.00   0.0  0
 UNP  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 UNP  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 UNP  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 UNP  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 UNP  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 UNP  Var_01    C4'  C5'  O5'  PA   -132.26  30.0  3
 UNP  Var_02    PB   N2B  PG   O2G  -170.52  30.0  3
 UNP  Var_03    O1B  PB   N2B  PG     65.64  30.0  3
 UNP  Var_04    O1A  PA   O3A  PB   -132.81  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
 UNP  chir_03  C4'  C5'  C3'  O4'  positiv
 UNP  chir_04  C3'  O3'  C4'  C2'  positiv
 UNP  chir_05  C2'  O2'  C3'  C1'  positiv
 UNP  chir_06  C1'  O4'  N1   C2'  negativ
 UNP  chir_07  PB   O1B  O3B  O3A  both
 UNP  chir_08  PA   O1A  O2A  O5'  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
 UNP  plan-1  C1'  0.020
 UNP  plan-1  N1   0.020
 UNP  plan-1  C2   0.020
 UNP  plan-1  O2   0.020
 UNP  plan-1  C6   0.020
 UNP  plan-1  C5   0.020
 UNP  plan-1  C4   0.020
 UNP  plan-1  N3   0.020
 UNP  plan-1  O4   0.020
 UNP  plan-1  H6   0.020
 UNP  plan-1  H5   0.020
 UNP  plan-1  HN3  0.020

