# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 10:54:59 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy(phenoxy)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)Oc2ccccc2)N3C=CC(=O)NC3=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
 UPP  UPP  5'-O-[(R)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]uridine  ligand  49  31  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UPP
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
 UPP  N1    N  NR6   0  -0.568   -7.8274  27.2874  -20.6272
 UPP  C2    C  CR6   0   0.740   -9.1431  27.2440  -21.0536
 UPP  N3    N  NR16  0  -0.735   -9.9495  26.4118  -20.3235
 UPP  C4    C  CR6   0   0.571   -9.6077  25.6156  -19.2412
 UPP  C5    C  CR16  0  -0.513   -8.2145  25.7113  -18.8786
 UPP  C6    C  CR16  0   0.102   -7.4047  26.5220  -19.5751
 UPP  O2    O  O     0  -0.474   -9.5641  27.8862  -21.9916
 UPP  O4    O  O     0  -0.460  -10.4444  24.9245  -18.6924
 UPP  C1B   C  CH1   0   0.185   -6.8793  28.1262  -21.3367
 UPP  C2B   C  CH1   0   0.000   -6.2293  29.2089  -20.4785
 UPP  O2'   O  OH1   0  -0.650   -7.1096  30.2785  -20.3494
 UPP  C3B   C  CH1   0  -0.063   -4.9438  29.4700  -21.2661
 UPP  C4B   C  CH1   0  -0.022   -4.6030  28.0633  -21.7908
 UPP  O4'   O  O2    0  -0.492   -5.8269  27.3301  -21.8093
 UPP  O3'   O  OH1   0  -0.666   -5.2609  30.3507  -22.3119
 UPP  C5B   C  CH2   0  -0.210   -3.5577  27.3069  -21.0058
 UPP  O5'   O  O2    0  -0.602   -4.0152  27.1563  -19.6565
 UPP  PA    P  P     0   1.522   -3.1959  26.4675  -18.4817
 UPP  O1A   O  O     0  -0.660   -4.0716  26.0893  -17.3675
 UPP  O2A   O  OH1   0  -0.719   -2.2472  25.3694  -19.1159
 UPP  O3A   O  O2    0  -0.700   -2.0339  27.5420  -18.1269
 UPP  PB    P  P     0   1.489   -2.1182  29.1375  -17.9237
 UPP  O1B   O  O     0  -0.650   -1.9401  29.9453  -19.1367
 UPP  O2B   O  OH1   0  -0.728   -3.4944  29.2534  -17.1451
 UPP  O3B   O  O2    0  -0.596   -0.9324  29.3908  -16.8859
 UPP  C1'   C  CR6   0   0.346   -0.7988  28.6827  -15.7011
 UPP  C2'   C  CR16  0  -0.303    0.0380  27.5792  -15.6751
 UPP  C3'   C  CR16  0  -0.252    0.2118  26.8971  -14.4789
 UPP  C4'   C  CR16  0  -0.254   -0.4470  27.3149  -13.3299
 UPP  C5'   C  CR16  0  -0.251   -1.2793  28.4253  -13.3763
 UPP  C6'   C  CR16  0  -0.305   -1.4617  29.1182  -14.5659
 UPP  HN3   H  HNR6  0   0.428  -10.9159  26.3798  -20.6247
 UPP  H5    H  HCR6  0   0.293   -7.8334  25.1288  -18.0544
 UPP  H6    H  HCR6  0   0.322   -6.3569  26.5989  -19.3285
 UPP  H1'   H  HCH1  0   0.277   -7.4287  28.5913  -22.1578
 UPP  H2B   H  HCH1  0   0.241   -5.9522  28.7956  -19.5010
 UPP  HO2'  H  HOH1  0   0.463   -6.7397  30.9139  -19.7288
 UPP  H3B   H  HCH1  0   0.258   -4.1387  29.8686  -20.6377
 UPP  H4B   H  HCH1  0   0.273   -4.2108  28.1398  -22.8116
 UPP  HO3'  H  HOH1  0   0.458   -4.4615  30.5181  -22.8210
 UPP  H5'1  H  HCH2  0   0.274   -3.3933  26.3241  -21.4506
 UPP  H5'2  H  HCH2  0   0.256   -2.6175  27.8622  -21.0383
 UPP  HOA2  H  HOH1  0   0.514   -2.6245  24.4781  -19.1341
 UPP  HOB2  H  HOH1  0   0.513   -3.8565  30.1494  -17.0816
 UPP  H2'   H  HCR6  0   0.277    0.5531  27.2613  -16.5723
 UPP  H3'   H  HCR6  0   0.268    0.8646  26.0350  -14.4493
 UPP  H4'   H  HCR6  0   0.264   -0.3088  26.7791  -12.4003
 UPP  H5'   H  HCR6  0   0.267   -1.7936  28.7572  -12.4843
 UPP  H6'   H  HCR6  0   0.276   -2.1016  29.9900  -14.6029

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
 UPP  N1   C2    single    1.384  0.020  1.384
 UPP  N1   C6    single    1.368  0.020  1.368
 UPP  N1   C1B   single    1.451  0.020  1.451
 UPP  C2   N3    single    1.370  0.020  1.370
 UPP  C2   O2    double    1.212  0.020  1.212
 UPP  N3   C4    single    1.387  0.020  1.387
 UPP  N3   HN3   single    0.860  0.020  1.020
 UPP  C4   C5    single    1.443  0.020  1.443
 UPP  C4   O4    double    1.216  0.020  1.216
 UPP  C5   C6    double    1.341  0.020  1.341
 UPP  C5   H5    single    0.930  0.020  1.080
 UPP  C6   H6    single    0.930  0.020  1.080
 UPP  C1B  C2B   single    1.527  0.020  1.527
 UPP  C1B  O4'   single    1.402  0.020  1.402
 UPP  C1B  H1'   single    0.970  0.020  1.090
 UPP  C2B  O2'   single    1.391  0.020  1.391
 UPP  C2B  C3B   single    1.530  0.020  1.530
 UPP  C2B  H2B   single    0.970  0.020  1.090
 UPP  O2'  HO2'  single    0.850  0.020  0.980
 UPP  C3B  C4B   single    1.539  0.020  1.539
 UPP  C3B  O3'   single    1.404  0.020  1.404
 UPP  C3B  H3B   single    0.970  0.020  1.090
 UPP  C4B  O4'   single    1.427  0.020  1.427
 UPP  C4B  C5B   single    1.510  0.020  1.510
 UPP  C4B  H4B   single    0.970  0.020  1.090
 UPP  O3'  HO3'  single    0.850  0.020  0.980
 UPP  C5B  O5'   single    1.433  0.020  1.433
 UPP  C5B  H5'1  single    0.970  0.020  1.090
 UPP  C5B  H5'2  single    0.970  0.020  1.090
 UPP  O5'  PA    single    1.589  0.020  1.589
 UPP  PA   O1A   double    1.467  0.020  1.467
 UPP  PA   O2A   single    1.584  0.020  1.584
 UPP  PA   O3A   single    1.622  0.020  1.622
 UPP  O2A  HOA2  single    0.850  0.020  0.980
 UPP  O3A  PB    single    1.611  0.020  1.611
 UPP  PB   O1B   double    1.468  0.020  1.468
 UPP  PB   O2B   single    1.585  0.020  1.585
 UPP  PB   O3B   single    1.596  0.020  1.596
 UPP  O2B  HOB2  single    0.850  0.020  0.980
 UPP  O3B  C1'   single    1.387  0.020  1.387
 UPP  C1'  C2'   aromatic  1.385  0.020  1.385
 UPP  C1'  C6'   aromatic  1.385  0.020  1.385
 UPP  C2'  C3'   aromatic  1.388  0.020  1.388
 UPP  C2'  H2'   single    0.930  0.020  1.080
 UPP  C3'  C4'   aromatic  1.389  0.020  1.389
 UPP  C3'  H3'   single    0.930  0.020  1.080
 UPP  C4'  C5'   aromatic  1.388  0.020  1.388
 UPP  C4'  H4'   single    0.930  0.020  1.080
 UPP  C5'  C6'   aromatic  1.389  0.020  1.389
 UPP  C5'  H5'   single    0.930  0.020  1.080
 UPP  C6'  H6'   single    0.930  0.020  1.080

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
 UPP  C1B   N1   C6    119.84  3.000
 UPP  C1B   N1   C2    119.25  3.000
 UPP  C6    N1   C2    120.88  3.000
 UPP  O2    C2   N3    122.00  3.000
 UPP  O2    C2   N1    123.51  3.000
 UPP  N3    C2   N1    114.50  3.000
 UPP  HN3   N3   C4    116.69  3.000
 UPP  HN3   N3   C2    114.99  3.000
 UPP  C4    N3   C2    128.31  3.000
 UPP  O4    C4   C5    126.07  3.000
 UPP  O4    C4   N3    120.60  3.000
 UPP  C5    C4   N3    113.33  3.000
 UPP  H5    C5   C6    120.66  3.000
 UPP  H5    C5   C4    119.82  3.000
 UPP  C6    C5   C4    119.53  3.000
 UPP  H6    C6   C5    120.72  3.000
 UPP  H6    C6   N1    115.84  3.000
 UPP  C5    C6   N1    123.44  3.000
 UPP  H1'   C1B  O4'   111.48  3.000
 UPP  H1'   C1B  C2B   109.56  3.000
 UPP  O4'   C1B  C2B   105.82  3.000
 UPP  H1'   C1B  N1    106.57  3.000
 UPP  O4'   C1B  N1    109.10  3.000
 UPP  C2B   C1B  N1    114.41  3.000
 UPP  H2B   C2B  C3B   108.11  3.000
 UPP  H2B   C2B  O2'   111.52  3.000
 UPP  C3B   C2B  O2'   116.63  3.000
 UPP  H2B   C2B  C1B   109.96  3.000
 UPP  C3B   C2B  C1B   100.92  3.000
 UPP  O2'   C2B  C1B   109.14  3.000
 UPP  HO2'  O2'  C2B   108.92  3.000
 UPP  H3B   C3B  O3'   111.40  3.000
 UPP  H3B   C3B  C4B   111.41  3.000
 UPP  O3'   C3B  C4B   111.68  3.000
 UPP  H3B   C3B  C2B   112.58  3.000
 UPP  O3'   C3B  C2B   107.51  3.000
 UPP  C4B   C3B  C2B   101.86  3.000
 UPP  H4B   C4B  C5B   105.75  3.000
 UPP  H4B   C4B  O4'   109.31  3.000
 UPP  C5B   C4B  O4'   110.06  3.000
 UPP  H4B   C4B  C3B   109.44  3.000
 UPP  C5B   C4B  C3B   115.71  3.000
 UPP  O4'   C4B  C3B   106.50  3.000
 UPP  C4B   O4'  C1B   110.36  3.000
 UPP  HO3'  O3'  C3B   108.40  3.000
 UPP  H5'2  C5B  H5'1  108.42  3.000
 UPP  H5'2  C5B  O5'   110.87  3.000
 UPP  H5'1  C5B  O5'   109.71  3.000
 UPP  H5'2  C5B  C4B   109.00  3.000
 UPP  H5'1  C5B  C4B   110.09  3.000
 UPP  O5'   C5B  C4B   108.73  3.000
 UPP  PA    O5'  C5B   125.25  3.000
 UPP  O3A   PA   O2A    96.76  3.000
 UPP  O3A   PA   O1A   115.62  3.000
 UPP  O2A   PA   O1A   118.88  3.000
 UPP  O3A   PA   O5'   104.12  3.000
 UPP  O2A   PA   O5'   108.26  3.000
 UPP  O1A   PA   O5'   111.44  3.000
 UPP  HOA2  O2A  PA    114.36  3.000
 UPP  PB    O3A  PA    130.26  3.000
 UPP  O3B   PB   O2B   108.30  3.000
 UPP  O3B   PB   O1B   111.08  3.000
 UPP  O2B   PB   O1B   118.09  3.000
 UPP  O3B   PB   O3A   101.56  3.000
 UPP  O2B   PB   O3A   100.36  3.000
 UPP  O1B   PB   O3A   115.75  3.000
 UPP  HOB2  O2B  PB    115.11  3.000
 UPP  C1'   O3B  PB    123.10  3.000
 UPP  C6'   C1'  C2'   121.63  3.000
 UPP  C6'   C1'  O3B   119.59  3.000
 UPP  C2'   C1'  O3B   118.75  3.000
 UPP  H2'   C2'  C3'   120.70  3.000
 UPP  H2'   C2'  C1'   120.40  3.000
 UPP  C3'   C2'  C1'   118.90  3.000
 UPP  H3'   C3'  C4'   120.22  3.000
 UPP  H3'   C3'  C2'   119.40  3.000
 UPP  C4'   C3'  C2'   120.39  3.000
 UPP  H4'   C4'  C5'   120.09  3.000
 UPP  H4'   C4'  C3'   120.09  3.000
 UPP  C5'   C4'  C3'   119.82  3.000
 UPP  H5'   C5'  C6'   119.39  3.000
 UPP  H5'   C5'  C4'   120.18  3.000
 UPP  C6'   C5'  C4'   120.43  3.000
 UPP  H6'   C6'  C5'   120.60  3.000
 UPP  H6'   C6'  C1'   120.56  3.000
 UPP  C5'   C6'  C1'   118.84  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
 UPP  CONST_01  C4'   C3'  C2'  C1'     0.00   0.0  0
 UPP  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 UPP  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 UPP  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 UPP  CONST_05  C6'   C1'  C2'  C3'     0.00   0.0  0
 UPP  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 UPP  CONST_07  C4    N3   C2   N1      0.00   0.0  0
 UPP  CONST_08  C5    C4   N3   C2      0.00   0.0  0
 UPP  CONST_09  C6    N1   C2   N3      0.00   0.0  0
 UPP  CONST_10  C1B   N1   C2   N3    180.00   0.0  0
 UPP  CONST_11  C3'   C2'  C1'  O3B   180.00   0.0  0
 UPP  CONST_12  C5'   C6'  C1'  O3B   180.00   0.0  0
 UPP  CONST_13  O4    C4   N3   C2    180.00   0.0  0
 UPP  CONST_14  O2    C2   N3   C4    180.00   0.0  0
 UPP  CONST_15  O2    C2   N1   C6    180.00   0.0  0
 UPP  CONST_16  C1B   N1   C2   O2      0.00   0.0  0
 UPP  CONST_17  H3'   C3'  C2'  C1'   180.00   0.0  0
 UPP  CONST_18  H5'   C5'  C6'  C1'   180.00   0.0  0
 UPP  CONST_19  H6'   C6'  C1'  C2'   180.00   0.0  0
 UPP  CONST_20  H4'   C4'  C3'  C2'   180.00   0.0  0
 UPP  CONST_21  H2'   C2'  C3'  C4'   180.00   0.0  0
 UPP  CONST_22  HN3   N3   C2   N1    180.00   0.0  0
 UPP  Var_01    C2'   C1'  O3B  PB     95.62  30.0  2
 UPP  Var_02    O1A   PA   O5'  C5B  -161.83  30.0  3
 UPP  Var_03    O1B   PB   O3A  PA    -89.15  30.0  3
 UPP  Var_04    H5'1  C5B  O5'  PA     61.96  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
 UPP  chir_01  C1B  N1   C2B  O4'  negativ
 UPP  chir_02  C2B  O2'  C3B  C1B  positiv
 UPP  chir_03  C3B  O3'  C2B  C4B  negativ
 UPP  chir_04  C4B  O4'  C3B  C5B  negativ
 UPP  chir_05  PA   O1A  O2A  O3A  both
 UPP  chir_06  PB   O1B  O2B  O3B  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
 UPP  plan-1  N1   0.020
 UPP  plan-1  C2   0.020
 UPP  plan-1  N3   0.020
 UPP  plan-1  C4   0.020
 UPP  plan-1  C5   0.020
 UPP  plan-1  C6   0.020
 UPP  plan-1  O2   0.020
 UPP  plan-1  O4   0.020
 UPP  plan-1  C1B  0.020
 UPP  plan-1  HN3  0.020
 UPP  plan-1  H5   0.020
 UPP  plan-1  H6   0.020
 UPP  plan-2  O3B  0.020
 UPP  plan-2  C1'  0.020
 UPP  plan-2  C2'  0.020
 UPP  plan-2  C3'  0.020
 UPP  plan-2  C4'  0.020
 UPP  plan-2  C5'  0.020
 UPP  plan-2  C6'  0.020
 UPP  plan-2  H2'  0.020
 UPP  plan-2  H3'  0.020
 UPP  plan-2  H4'  0.020
 UPP  plan-2  H5'  0.020
 UPP  plan-2  H6'  0.020

