# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 11:28:50 2020
#   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  41  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.910  -5.1449  -2.5010  -1.1978
 UNP  PG    P  P      0   1.192  -5.5038  -1.9707   0.1865
 UNP  O3G   O  OP    -1  -0.915  -6.7711  -1.1150   0.2175
 UNP  O1G   O  OP    -1  -0.920  -5.4509  -3.0255   1.2958
 UNP  N2B   N  NH1    0  -0.970  -4.1536  -0.9144   0.6540
 UNP  PB    P  P      0   1.299  -3.9088   0.6230   0.0388
 UNP  O1B   O  OP    -1  -0.825  -4.4098   0.7345  -1.3711
 UNP  O3B   O  O      0  -0.829  -4.2529   1.6907   1.0446
 UNP  O3A   O  O2     0  -0.755  -2.2192   0.5882  -0.0346
 UNP  PA    P  P      0   1.336  -1.3350   1.4821  -1.0516
 UNP  O1A   O  OP    -1  -0.813  -1.0436   0.7409  -2.3226
 UNP  O2A   O  O      0  -0.813  -1.8120   2.9016  -1.1149
 UNP  O5'   O  O2     0  -0.625   0.0261   1.4222  -0.0981
 UNP  C5'   C  CH2    0  -0.143   1.2318   1.8594  -0.6689
 UNP  C4'   C  CR15   0  -0.006   2.2861   1.9349   0.4064
 UNP  C3'   C  CR15   0  -0.038   3.6519   2.3822  -0.0994
 UNP  O3'   O  OH1    0  -0.656   3.7151   3.7785  -0.1646
 UNP  C2'   C  CR15   0  -0.041   4.5869   1.7692   0.9499
 UNP  O2'   O  OH1    0  -0.665   4.5941   2.5356   2.1226
 UNP  O4'   O  O      0  -0.495   2.5212   0.6416   0.9665
 UNP  C1'   C  CR15   0   0.187   3.8694   0.4528   1.2565
 UNP  N1    N  NT     0  -0.567   4.4019  -0.6608   0.4410
 UNP  C2    C  C      0   0.740   5.5802  -1.2259   0.8816
 UNP  O2    O  O      0  -0.480   6.1604  -0.8320   1.8730
 UNP  C6    C  C1     0   0.091   3.7842  -1.1170  -0.6843
 UNP  C5    C  C1     0  -0.510   4.2671  -2.1269  -1.4290
 UNP  C4    C  C      0   0.566   5.4892  -2.7831  -1.0396
 UNP  N3    N  NH1    0  -0.731   6.0480  -2.2595   0.1171
 UNP  O4    O  O      0  -0.466   6.0267  -3.7073  -1.6219
 UNP  HN2B  H  HNH1   0   0.340  -3.9977  -0.9552   1.6534
 UNP  H5'   H  HCH2   0   0.204   1.5640   1.1899  -1.4730
 UNP  H5'A  H  HCH2   0   0.217   1.1413   2.8617  -1.1081
 UNP  H4'   H  HCR5   0   0.247   1.9455   2.6132   1.1988
 UNP  H3'   H  HCR5   0   0.244   3.8554   1.9251  -1.0774
 UNP  HO3'  H  HOH1   0   0.470   4.4356   4.0305  -0.7510
 UNP  H2'   H  HCR5   0   0.260   5.5999   1.6085   0.5632
 UNP  HO2'  H  HOH1   0   0.451   4.5652   3.4657   1.8654
 UNP  H1'   H  HCR5   0   0.285   3.9952   0.1638   2.3015
 UNP  H6    H  H      0   0.325   2.8606  -0.6288  -0.9539
 UNP  H5    H  H      0   0.292   3.7397  -2.4569  -2.3106
 UNP  HN3   H  HNH1   0   0.427   6.9131  -2.6777   0.4378

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    deloc   1.525  0.020  1.525
 UNP  PG   O3G   deloc   1.529  0.020  1.529
 UNP  PG   O1G   deloc   1.532  0.020  1.532
 UNP  PG   N2B   single  1.777  0.020  1.777
 UNP  N2B  PB    single  1.674  0.020  1.674
 UNP  PB   O1B   deloc   1.500  0.020  1.500
 UNP  PB   O3B   deloc   1.507  0.020  1.507
 UNP  PB   O3A   single  1.692  0.020  1.692
 UNP  O3A  PA    single  1.617  0.020  1.617
 UNP  PA   O1A   deloc   1.500  0.020  1.500
 UNP  PA   O2A   deloc   1.499  0.020  1.499
 UNP  PA   O5'   single  1.663  0.020  1.663
 UNP  O5'  C5'   single  1.404  0.020  1.404
 UNP  C5'  C4'   single  1.508  0.020  1.508
 UNP  C4'  C3'   single  1.524  0.020  1.524
 UNP  C4'  O4'   single  1.429  0.020  1.429
 UNP  C3'  O3'   single  1.399  0.020  1.399
 UNP  C3'  C2'   single  1.533  0.020  1.533
 UNP  C2'  O2'   single  1.401  0.020  1.401
 UNP  C2'  C1'   single  1.530  0.020  1.530
 UNP  O4'  C1'   single  1.392  0.020  1.392
 UNP  C1'  N1    single  1.479  0.020  1.479
 UNP  N1   C2    single  1.379  0.020  1.379
 UNP  N1   C6    single  1.362  0.020  1.362
 UNP  C2   O2    double  1.214  0.020  1.214
 UNP  C2   N3    single  1.368  0.020  1.368
 UNP  C6   C5    double  1.344  0.020  1.344
 UNP  C5   C4    single  1.441  0.020  1.441
 UNP  C4   N3    single  1.387  0.020  1.387
 UNP  C4   O4    double  1.217  0.020  1.217
 UNP  N2B  HN2B  single  0.890  0.020  1.040
 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  101.11  3.000
 UNP  N2B   PG   O3G  106.96  3.000
 UNP  O1G   PG   O3G  113.53  3.000
 UNP  N2B   PG   O2G  105.47  3.000
 UNP  O1G   PG   O2G  114.19  3.000
 UNP  O3G   PG   O2G  114.07  3.000
 UNP  HN2B  N2B  PB   112.17  3.000
 UNP  HN2B  N2B  PG   110.66  3.000
 UNP  PB    N2B  PG   124.08  3.000
 UNP  O3A   PB   O3B  105.77  3.000
 UNP  O3A   PB   O1B  107.11  3.000
 UNP  O3B   PB   O1B  119.89  3.000
 UNP  O3A   PB   N2B   98.23  3.000
 UNP  O3B   PB   N2B  111.84  3.000
 UNP  O1B   PB   N2B  111.39  3.000
 UNP  PA    O3A  PB   124.20  3.000
 UNP  O5'   PA   O2A  108.59  3.000
 UNP  O5'   PA   O1A  108.01  3.000
 UNP  O2A   PA   O1A  119.60  3.000
 UNP  O5'   PA   O3A   93.85  3.000
 UNP  O2A   PA   O3A  112.09  3.000
 UNP  O1A   PA   O3A  111.47  3.000
 UNP  C5'   O5'  PA   117.30  3.000
 UNP  H5'A  C5'  H5'  106.78  3.000
 UNP  H5'A  C5'  C4'  107.29  3.000
 UNP  H5'   C5'  C4'  109.95  3.000
 UNP  H5'A  C5'  O5'  112.10  3.000
 UNP  H5'   C5'  O5'  111.58  3.000
 UNP  C4'   C5'  O5'  109.04  3.000
 UNP  H4'   C4'  O4'  109.12  3.000
 UNP  H4'   C4'  C3'  109.66  3.000
 UNP  O4'   C4'  C3'  104.39  3.000
 UNP  H4'   C4'  C5'  109.20  3.000
 UNP  O4'   C4'  C5'  110.44  3.000
 UNP  C3'   C4'  C5'  113.88  3.000
 UNP  H3'   C3'  C2'  109.26  3.000
 UNP  H3'   C3'  O3'  111.44  3.000
 UNP  C2'   C3'  O3'  113.78  3.000
 UNP  H3'   C3'  C4'  109.84  3.000
 UNP  C2'   C3'  C4'  101.66  3.000
 UNP  O3'   C3'  C4'  110.43  3.000
 UNP  HO3'  O3'  C3'  108.87  3.000
 UNP  H2'   C2'  C1'  112.20  3.000
 UNP  H2'   C2'  O2'  111.76  3.000
 UNP  C1'   C2'  O2'  107.77  3.000
 UNP  H2'   C2'  C3'  112.38  3.000
 UNP  C1'   C2'  C3'  101.25  3.000
 UNP  O2'   C2'  C3'  110.93  3.000
 UNP  HO2'  O2'  C2'  107.69  3.000
 UNP  C1'   O4'  C4'  111.33  3.000
 UNP  H1'   C1'  N1   106.68  3.000
 UNP  H1'   C1'  O4'  110.30  3.000
 UNP  N1    C1'  O4'  109.63  3.000
 UNP  H1'   C1'  C2'  111.44  3.000
 UNP  N1    C1'  C2'  111.61  3.000
 UNP  O4'   C1'  C2'  107.20  3.000
 UNP  C6    N1   C2   120.94  3.000
 UNP  C6    N1   C1'  122.97  3.000
 UNP  C2    N1   C1'  116.10  3.000
 UNP  N3    C2   O2   122.54  3.000
 UNP  N3    C2   N1   115.04  3.000
 UNP  O2    C2   N1   122.42  3.000
 UNP  H6    C6   C5   120.59  3.000
 UNP  H6    C6   N1   116.30  3.000
 UNP  C5    C6   N1   123.11  3.000
 UNP  H5    C5   C4   119.74  3.000
 UNP  H5    C5   C6   120.45  3.000
 UNP  C4    C5   C6   119.81  3.000
 UNP  O4    C4   N3   120.50  3.000
 UNP  O4    C4   C5   126.23  3.000
 UNP  N3    C4   C5   113.27  3.000
 UNP  HN3   N3   C4   116.89  3.000
 UNP  HN3   N3   C2   115.27  3.000
 UNP  C4    N3   C2   127.83  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   171.06  30.0  3
 UNP  Var_02    PB   N2B  PG   O2G   75.63  30.0  3
 UNP  Var_03    O1B  PB   N2B  PG   -30.97  30.0  3
 UNP  Var_04    O1A  PA   O3A  PB   -92.62  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

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

