# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 14:04:26 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)C[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
 UC5  UC5  2'-deoxy-5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]uridine  ligand  40  24  .  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_UC5
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
 UC5  O4    O  O     0  -0.459   4.3966  -3.6672  -1.0374
 UC5  C4    C  CR6   0   0.570   3.9773  -2.6406  -0.5389
 UC5  C5    C  CR16  0  -0.509   3.9738  -2.3191   0.8674
 UC5  C6    C  CR16  0   0.100   3.4798  -1.1407   1.2749
 UC5  N3    N  NR16  0  -0.732   3.4325  -1.6413  -1.3328
 UC5  C2    C  CR6   0   0.746   2.9302  -0.4298  -0.9408
 UC5  O2    O  O     0  -0.464   2.4824   0.3716  -1.7317
 UC5  N1    N  NR6   0  -0.573   2.9748  -0.1979   0.4208
 UC5  C1'   C  CR15  0   0.231   2.4618   1.0538   0.9640
 UC5  C2'   C  CH2   0  -0.560   3.0817   2.3407   0.4198
 UC5  C3'   C  CR15  0   0.025   1.9710   3.0334  -0.3733
 UC5  O3'   O  OH1   0  -0.664   1.8923   4.4216  -0.1847
 UC5  O4'   O  O     0  -0.536   1.0762   1.1323   0.7230
 UC5  C4'   C  CR15  0   0.037   0.6977   2.3967   0.1880
 UC5  C5'   C  CH2   0  -0.222  -0.3721   2.2117  -0.8621
 UC5  O5'   O  O2    0  -0.593  -1.5470   1.6310  -0.2812
 UC5  PA    P  P     0   1.367  -1.9359   0.0957  -0.5631
 UC5  O1A   O  O     0  -0.691  -2.3446  -0.2363  -1.9458
 UC5  O2A   O  OH1   0  -0.771  -0.6785  -0.7700  -0.0865
 UC5  C3A   C  CH2   0  -1.034  -3.2354  -0.1407   0.6701
 UC5  PB    P  P     0   1.373  -4.1467  -1.6842   0.4297
 UC5  O1B   O  OH1   0  -0.744  -3.0456  -2.8297   0.1995
 UC5  O2B   O  OH1   0  -0.739  -4.7449  -1.8932   1.9032
 UC5  O3B   O  O     0  -0.699  -5.1229  -1.6981  -0.6798
 UC5  H5    H  HCR6  0   0.297   4.3630  -3.0279   1.5815
 UC5  H6    H  HCR6  0   0.332   3.4605  -0.8735   2.3220
 UC5  HN3   H  HNR6  0   0.429   3.4017  -1.8168  -2.3302
 UC5  H1'   H  HCR5  0   0.275   2.6352   0.9775   2.0379
 UC5  H2'1  H  HCH2  0   0.286   3.9822   2.1614  -0.1645
 UC5  H2'2  H  HCH2  0   0.278   3.3615   2.9706   1.2658
 UC5  H3'   H  HCR5  0   0.242   2.0723   2.7940  -1.4351
 UC5  HO3'  H  HOH1  0   0.460   2.5768   4.8384  -0.7165
 UC5  H4'   H  HCR5  0   0.259   0.3130   3.0241   1.0017
 UC5  H5'1  H  HCH2  0   0.274  -0.6522   3.1880  -1.2582
 UC5  H5'2  H  HCH2  0   0.252   0.0034   1.6099  -1.6944
 UC5  HO2A  H  HOH1  0   0.494  -0.0036  -0.2580   0.4058
 UC5  H3A1  H  HCH2  0   0.336  -2.8016  -0.1047   1.6717
 UC5  H3A2  H  HCH2  0   0.340  -3.9499   0.6822   0.5924
 UC5  HO1B  H  HOH1  0   0.491  -2.4021  -2.9522   0.9099
 UC5  HO2B  H  HOH1  0   0.498  -5.4194  -2.5850   1.9589

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
 UC5  O4   C4    double  1.216  0.020  1.216
 UC5  C4   C5    single  1.443  0.020  1.443
 UC5  C4   N3    single  1.388  0.020  1.388
 UC5  C5   C6    double  1.341  0.020  1.341
 UC5  C5   H5    single  0.930  0.020  1.080
 UC5  C6   N1    single  1.369  0.020  1.369
 UC5  C6   H6    single  0.930  0.020  1.080
 UC5  N3   C2    single  1.369  0.020  1.369
 UC5  N3   HN3   single  0.860  0.020  1.020
 UC5  C2   O2    double  1.212  0.020  1.212
 UC5  C2   N1    single  1.382  0.020  1.382
 UC5  N1   C1'   single  1.458  0.020  1.458
 UC5  C1'  C2'   single  1.529  0.020  1.529
 UC5  C1'  O4'   single  1.409  0.020  1.409
 UC5  C1'  H1'   single  0.970  0.020  1.090
 UC5  C2'  C3'   single  1.531  0.020  1.531
 UC5  C2'  H2'1  single  0.970  0.020  1.090
 UC5  C2'  H2'2  single  0.970  0.020  1.090
 UC5  C3'  O3'   single  1.403  0.020  1.403
 UC5  C3'  C4'   single  1.530  0.020  1.530
 UC5  C3'  H3'   single  0.970  0.020  1.090
 UC5  O3'  HO3'  single  0.850  0.020  0.980
 UC5  O4'  C4'   single  1.424  0.020  1.424
 UC5  C4'  C5'   single  1.510  0.020  1.510
 UC5  C4'  H4'   single  0.970  0.020  1.090
 UC5  C5'  O5'   single  1.434  0.020  1.434
 UC5  C5'  H5'1  single  0.970  0.020  1.090
 UC5  C5'  H5'2  single  0.970  0.020  1.090
 UC5  O5'  PA    single  1.609  0.020  1.609
 UC5  PA   O1A   double  1.480  0.020  1.480
 UC5  PA   O2A   single  1.599  0.020  1.599
 UC5  PA   C3A   single  1.807  0.020  1.807
 UC5  O2A  HO2A  single  0.850  0.020  0.980
 UC5  C3A  PB    single  1.808  0.020  1.808
 UC5  C3A  H3A1  single  0.970  0.020  1.090
 UC5  C3A  H3A2  single  0.970  0.020  1.090
 UC5  PB   O1B   single  1.605  0.020  1.605
 UC5  PB   O2B   single  1.604  0.020  1.604
 UC5  PB   O3B   double  1.478  0.020  1.478
 UC5  O1B  HO1B  single  0.850  0.020  0.980
 UC5  O2B  HO2B  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
 UC5  N3    C4   C5    113.35  3.000
 UC5  N3    C4   O4    120.59  3.000
 UC5  C5    C4   O4    126.07  3.000
 UC5  H5    C5   C6    120.60  3.000
 UC5  H5    C5   C4    119.87  3.000
 UC5  C6    C5   C4    119.53  3.000
 UC5  H6    C6   N1    115.32  3.000
 UC5  H6    C6   C5    121.20  3.000
 UC5  N1    C6   C5    123.47  3.000
 UC5  HN3   N3   C2    115.09  3.000
 UC5  HN3   N3   C4    116.77  3.000
 UC5  C2    N3   C4    128.14  3.000
 UC5  N1    C2   O2    122.96  3.000
 UC5  N1    C2   N3    114.76  3.000
 UC5  O2    C2   N3    122.28  3.000
 UC5  C1'   N1   C2    119.99  3.000
 UC5  C1'   N1   C6    119.26  3.000
 UC5  C2    N1   C6    120.74  3.000
 UC5  H1'   C1'  O4'   109.20  3.000
 UC5  H1'   C1'  C2'   110.18  3.000
 UC5  O4'   C1'  C2'   106.92  3.000
 UC5  H1'   C1'  N1    104.53  3.000
 UC5  O4'   C1'  N1    109.29  3.000
 UC5  C2'   C1'  N1    116.58  3.000
 UC5  H2'2  C2'  H2'1  107.41  3.000
 UC5  H2'2  C2'  C3'   109.06  3.000
 UC5  H2'1  C2'  C3'   113.38  3.000
 UC5  H2'2  C2'  C1'   108.30  3.000
 UC5  H2'1  C2'  C1'   112.83  3.000
 UC5  C3'   C2'  C1'   105.73  3.000
 UC5  H3'   C3'  C4'   110.01  3.000
 UC5  H3'   C3'  O3'   110.64  3.000
 UC5  C4'   C3'  O3'   108.40  3.000
 UC5  H3'   C3'  C2'   109.69  3.000
 UC5  C4'   C3'  C2'   103.03  3.000
 UC5  O3'   C3'  C2'   114.76  3.000
 UC5  HO3'  O3'  C3'   108.33  3.000
 UC5  C4'   O4'  C1'   112.03  3.000
 UC5  H4'   C4'  C5'   109.71  3.000
 UC5  H4'   C4'  O4'   108.81  3.000
 UC5  C5'   C4'  O4'   109.91  3.000
 UC5  H4'   C4'  C3'   109.02  3.000
 UC5  C5'   C4'  C3'   112.66  3.000
 UC5  O4'   C4'  C3'   106.63  3.000
 UC5  H5'2  C5'  H5'1  107.73  3.000
 UC5  H5'2  C5'  O5'   111.52  3.000
 UC5  H5'1  C5'  O5'   107.42  3.000
 UC5  H5'2  C5'  C4'   110.69  3.000
 UC5  H5'1  C5'  C4'   108.96  3.000
 UC5  O5'   C5'  C4'   110.39  3.000
 UC5  PA    O5'  C5'   120.91  3.000
 UC5  C3A   PA   O2A   106.93  3.000
 UC5  C3A   PA   O1A   114.19  3.000
 UC5  O2A   PA   O1A   111.98  3.000
 UC5  C3A   PA   O5'   100.32  3.000
 UC5  O2A   PA   O5'   105.92  3.000
 UC5  O1A   PA   O5'   116.40  3.000
 UC5  HO2A  O2A  PA    114.11  3.000
 UC5  H3A2  C3A  H3A1  107.47  3.000
 UC5  H3A2  C3A  PB    107.69  3.000
 UC5  H3A1  C3A  PB    110.50  3.000
 UC5  H3A2  C3A  PA    108.86  3.000
 UC5  H3A1  C3A  PA    109.63  3.000
 UC5  PB    C3A  PA    112.54  3.000
 UC5  O3B   PB   O2B   116.24  3.000
 UC5  O3B   PB   O1B   109.80  3.000
 UC5  O2B   PB   O1B   107.13  3.000
 UC5  O3B   PB   C3A   116.15  3.000
 UC5  O2B   PB   C3A   100.20  3.000
 UC5  O1B   PB   C3A   106.41  3.000
 UC5  HO1B  O1B  PB    116.22  3.000
 UC5  HO2B  O2B  PB    113.95  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
 UC5  CONST_01  N1    C2   N3   C4     0.00   0.0  0
 UC5  CONST_02  C2    N3   C4   C5     0.00   0.0  0
 UC5  CONST_03  N3    C2   N1   C6     0.00   0.0  0
 UC5  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 UC5  CONST_05  C2    N3   C4   O4   180.00   0.0  0
 UC5  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 UC5  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 UC5  CONST_08  C1'   N1   C2   O2     0.00   0.0  0
 UC5  CONST_09  HN3   N3   C4   C5   180.00   0.0  0
 UC5  Var_01    O1A   PA   O5'  C5'  -67.84  30.0  3
 UC5  Var_02    PB    C3A  PA   O5'  168.68  30.0  3
 UC5  Var_03    O1B   PB   C3A  PA    46.85  30.0  3
 UC5  Var_04    H5'1  C5'  O5'  PA   134.63  30.0  2

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
 UC5  chir_01  C1'  N1   C2'  O4'  negativ
 UC5  chir_02  C3'  O3'  C4'  C2'  positiv
 UC5  chir_03  C4'  O4'  C3'  C5'  negativ
 UC5  chir_04  PA   O1A  O2A  C3A  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
 UC5  plan-1  O4   0.020
 UC5  plan-1  C4   0.020
 UC5  plan-1  C5   0.020
 UC5  plan-1  C6   0.020
 UC5  plan-1  N3   0.020
 UC5  plan-1  C2   0.020
 UC5  plan-1  O2   0.020
 UC5  plan-1  N1   0.020
 UC5  plan-1  C1'  0.020
 UC5  plan-1  H5   0.020
 UC5  plan-1  H6   0.020
 UC5  plan-1  HN3  0.020

