# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 17:59:23 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  37  24  .  2021-08-24  2022-09-22
;
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  -0.466   5.7190  -3.3465  -0.4086
 UC5  C4    C  CR6    0   0.566   5.1276  -2.3418  -0.0586
 UC5  C5    C  CR16   0  -0.514   5.0960  -1.7953   1.2745
 UC5  C6    C  CR16   0   0.100   4.3965  -0.6738   1.5111
 UC5  N3    N  NR16   0  -0.733   4.3909  -1.6024  -0.9711
 UC5  C2    C  CR6    0   0.745   3.6683  -0.4579  -0.7503
 UC5  O2    O  O      0  -0.465   3.0551   0.0942  -1.6372
 UC5  N1    N  NR6    0  -0.566   3.7071   0.0075   0.5492
 UC5  C1'   C  CR15   0   0.220   2.9370   1.1932   0.9264
 UC5  C2'   C  CH2    0  -0.560   3.2248   2.4715   0.1333
 UC5  C3'   C  CR15   0   0.026   1.9286   2.7594  -0.6264
 UC5  O3'   O  OH1    0  -0.670   1.5673   4.1175  -0.6737
 UC5  O4'   O  O      0  -0.489   1.5751   0.9118   0.7945
 UC5  C4'   C  CR15   0   0.013   0.8871   1.9971   0.1922
 UC5  C5'   C  CH2    0  -0.141  -0.2657   1.4742  -0.6304
 UC5  O5'   O  O2     0  -0.641  -1.1789   0.8214   0.2107
 UC5  PA    P  P      0   1.258  -2.7120   0.4854  -0.4036
 UC5  O1A   O  O      0  -0.830  -3.4314   1.8068  -0.5328
 UC5  O2A   O  OP    -1  -0.827  -2.5116  -0.3425  -1.6484
 UC5  C3A   C  CH2    0  -0.995  -3.3208  -0.4788   1.0006
 UC5  PB    P  P      0   1.167  -4.8466  -1.5150   0.6650
 UC5  O1B   O  OP    -1  -0.912  -4.3551  -2.7347  -0.1206
 UC5  O2B   O  OP    -1  -0.921  -5.3683  -1.8706   2.0659
 UC5  O3B   O  O      0  -0.909  -5.7890  -0.6004  -0.1252
 UC5  H5    H  HCR6   0   0.292   5.6276  -2.2903   2.0719
 UC5  H6    H  HCR6   0   0.327   4.3500  -0.2454   2.5024
 UC5  HN3   H  HNR6   0   0.425   4.3722  -1.9425  -1.9249
 UC5  H1'   H  HCR5   0   0.252   3.1914   1.3498   1.9779
 UC5  H2'1  H  HCH2   0   0.274   4.1012   2.3934  -0.5078
 UC5  H2'2  H  HCH2   0   0.265   3.4063   3.2817   0.8416
 UC5  H3'   H  HCR5   0   0.229   1.9874   2.3412  -1.6354
 UC5  HO3'  H  HOH1   0   0.456   2.0786   4.5421  -1.3683
 UC5  H4'   H  HCR5   0   0.219   0.5011   2.6671   0.9750
 UC5  H5'1  H  HCH2   0   0.193  -0.7198   2.3322  -1.1444
 UC5  H5'2  H  HCH2   0   0.195   0.1263   0.8037  -1.4058
 UC5  H3A1  H  HCH2   0   0.209  -2.5236  -1.1353   1.3630
 UC5  H3A2  H  HCH2   0   0.207  -3.5294   0.2232   1.8143

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  1.217  0.020  1.217
 UC5  C4   C5    single  1.441  0.020  1.441
 UC5  C4   N3    single  1.386  0.020  1.386
 UC5  C5   C6    double  1.343  0.020  1.343
 UC5  C5   H5    single  0.930  0.020  1.080
 UC5  C6   N1    single  1.366  0.020  1.366
 UC5  C6   H6    single  0.930  0.020  1.080
 UC5  N3   C2    single  1.371  0.020  1.371
 UC5  N3   HN3   single  0.860  0.020  1.020
 UC5  C2   O2    double  1.211  0.020  1.211
 UC5  C2   N1    single  1.381  0.020  1.381
 UC5  N1   C1'   single  1.463  0.020  1.463
 UC5  C1'  C2'   single  1.532  0.020  1.532
 UC5  C1'  O4'   single  1.397  0.020  1.397
 UC5  C1'  H1'   single  0.970  0.020  1.090
 UC5  C2'  C3'   single  1.530  0.020  1.530
 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  1.406  0.020  1.406
 UC5  C3'  C4'   single  1.528  0.020  1.528
 UC5  C3'  H3'   single  0.970  0.020  1.090
 UC5  O3'  HO3'  single  0.850  0.020  0.980
 UC5  O4'  C4'   single  1.419  0.020  1.419
 UC5  C4'  C5'   single  1.510  0.020  1.510
 UC5  C4'  H4'   single  0.970  0.020  1.090
 UC5  C5'  O5'   single  1.403  0.020  1.403
 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  1.685  0.020  1.685
 UC5  PA   O1A   deloc   1.510  0.020  1.510
 UC5  PA   O2A   deloc   1.508  0.020  1.508
 UC5  PA   C3A   single  1.809  0.020  1.809
 UC5  C3A  PB    single  1.875  0.020  1.875
 UC5  C3A  H3A1  single  0.970  0.020  1.090
 UC5  C3A  H3A2  single  0.970  0.020  1.090
 UC5  PB   O1B   deloc   1.532  0.020  1.532
 UC5  PB   O2B   deloc   1.537  0.020  1.537
 UC5  PB   O3B   deloc   1.533  0.020  1.533

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    113.26  3.000
 UC5  N3    C4   O4    120.60  3.000
 UC5  C5    C4   O4    126.14  3.000
 UC5  H5    C5   C6    120.65  3.000
 UC5  H5    C5   C4    119.93  3.000
 UC5  C6    C5   C4    119.42  3.000
 UC5  H6    C6   N1    115.25  3.000
 UC5  H6    C6   C5    121.00  3.000
 UC5  N1    C6   C5    123.75  3.000
 UC5  HN3   N3   C2    114.97  3.000
 UC5  HN3   N3   C4    116.78  3.000
 UC5  C2    N3   C4    128.25  3.000
 UC5  N1    C2   O2    123.34  3.000
 UC5  N1    C2   N3    114.71  3.000
 UC5  O2    C2   N3    121.95  3.000
 UC5  C1'   N1   C2    120.06  3.000
 UC5  C1'   N1   C6    119.23  3.000
 UC5  C2    N1   C6    120.59  3.000
 UC5  H1'   C1'  O4'   110.28  3.000
 UC5  H1'   C1'  C2'   109.56  3.000
 UC5  O4'   C1'  C2'   107.61  3.000
 UC5  H1'   C1'  N1    103.98  3.000
 UC5  O4'   C1'  N1    109.00  3.000
 UC5  C2'   C1'  N1    116.35  3.000
 UC5  H2'2  C2'  H2'1  107.56  3.000
 UC5  H2'2  C2'  C3'   108.87  3.000
 UC5  H2'1  C2'  C3'   113.78  3.000
 UC5  H2'2  C2'  C1'   108.35  3.000
 UC5  H2'1  C2'  C1'   113.35  3.000
 UC5  C3'   C2'  C1'   104.77  3.000
 UC5  H3'   C3'  C4'   109.88  3.000
 UC5  H3'   C3'  O3'   110.61  3.000
 UC5  C4'   C3'  O3'   108.94  3.000
 UC5  H3'   C3'  C2'   109.91  3.000
 UC5  C4'   C3'  C2'   102.57  3.000
 UC5  O3'   C3'  C2'   114.59  3.000
 UC5  HO3'  O3'  C3'   108.31  3.000
 UC5  C4'   O4'  C1'   111.02  3.000
 UC5  H4'   C4'  C5'   109.31  3.000
 UC5  H4'   C4'  O4'   109.50  3.000
 UC5  C5'   C4'  O4'   109.67  3.000
 UC5  H4'   C4'  C3'   108.44  3.000
 UC5  C5'   C4'  C3'   113.66  3.000
 UC5  O4'   C4'  C3'   106.16  3.000
 UC5  H5'2  C5'  H5'1  107.11  3.000
 UC5  H5'2  C5'  O5'   111.83  3.000
 UC5  H5'1  C5'  O5'   112.03  3.000
 UC5  H5'2  C5'  C4'   108.89  3.000
 UC5  H5'1  C5'  C4'   107.46  3.000
 UC5  O5'   C5'  C4'   109.37  3.000
 UC5  PA    O5'  C5'   117.80  3.000
 UC5  C3A   PA   O2A   113.13  3.000
 UC5  C3A   PA   O1A   111.87  3.000
 UC5  O2A   PA   O1A   118.22  3.000
 UC5  C3A   PA   O5'    97.44  3.000
 UC5  O2A   PA   O5'   106.82  3.000
 UC5  O1A   PA   O5'   106.87  3.000
 UC5  H3A2  C3A  H3A1  106.10  3.000
 UC5  H3A2  C3A  PB    109.41  3.000
 UC5  H3A1  C3A  PB    108.70  3.000
 UC5  H3A2  C3A  PA    107.42  3.000
 UC5  H3A1  C3A  PA    109.37  3.000
 UC5  PB    C3A  PA    115.44  3.000
 UC5  O3B   PB   O2B   113.54  3.000
 UC5  O3B   PB   O1B   114.08  3.000
 UC5  O2B   PB   O1B   113.09  3.000
 UC5  O3B   PB   C3A   105.24  3.000
 UC5  O2B   PB   C3A   103.95  3.000
 UC5  O1B   PB   C3A   105.71  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'   -70.42  30.0  3
 UC5  Var_02    PB    C3A  PA   O5'  -163.87  30.0  3
 UC5  Var_03    O1B   PB   C3A  PA     76.83  30.0  3
 UC5  Var_04    H5'1  C5'  O5'  PA     46.37  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
 UC5  chir_01  C1'  N1   C2'  O4'  negativ
 UC5  chir_02  C3'  O3'  C4'  C2'  positiv
 UC5  chir_03  C4'  O4'  C3'  C5'  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
 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

