# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 09:44:17 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 5'-O-[(R)-{[(S)-[(6-aminohexyl)oxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)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
 UDH  UDH  5'-O-[(R)-{[(S)-[(6-aminohexyl)oxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]uridine  ligand  57  32  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UDH
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
 UDH  N1    N  NR6    0  -0.566    4.8984  -0.5385  -0.0525
 UDH  C2    C  CR6    0   0.734    6.1237  -1.1353  -0.2748
 UDH  N3    N  NR16   0  -0.733    6.4036  -1.3847  -1.5925
 UDH  C4    C  CR6    0   0.568    5.6169  -1.1153  -2.7029
 UDH  C5    C  CR16   0  -0.525    4.3558  -0.5024  -2.3727
 UDH  C6    C  CR16   0   0.082    4.0570  -0.2462  -1.0889
 UDH  O2    O  O      0  -0.479    6.8999  -1.4224   0.6127
 UDH  O4    O  O      0  -0.467    6.0095  -1.3974  -3.8203
 UDH  C1B   C  CR15   0   0.208    4.5106  -0.2118   1.3157
 UDH  C2B   C  CR15   0  -0.044    4.5831   1.2805   1.6369
 UDH  O2'   O  OH1    0  -0.653    5.8858   1.6280   1.9984
 UDH  C3B   C  CR15   0  -0.033    3.5471   1.3865   2.7604
 UDH  C4B   C  CR15   0  -0.039    2.4793   0.4239   2.2598
 UDH  O4'   O  O      0  -0.489    3.1788  -0.5811   1.5171
 UDH  O3'   O  OH1    0  -0.668    4.0673   0.9019   3.9707
 UDH  C5B   C  CH2    0  -0.159    1.4514   1.1306   1.3936
 UDH  O5'   O  O2     0  -0.617    0.6094   0.1730   0.8010
 UDH  PA    P  P      0   1.347   -0.0484   0.5583  -0.6628
 UDH  O1A   O  O      0  -0.792   -1.0406   1.6615  -0.4867
 UDH  O2A   O  OP    -1  -0.777    1.0525   0.6921  -1.6740
 UDH  O3A   O  O2     0  -0.732   -0.7756  -0.9006  -0.8226
 UDH  PB    P  P      0   1.354   -2.0672  -1.2289  -1.7810
 UDH  O1B   O  O      0  -0.804   -2.1335  -0.2790  -2.9346
 UDH  O2B   O  O2     0  -0.622   -3.2244  -0.8723  -0.6763
 UDH  O3B   O  OP    -1  -0.793   -2.0486  -2.7074  -2.0181
 UDH  C1'   C  CH2    0  -0.135   -4.5758  -0.8841  -1.1049
 UDH  C2'   C  CH2    0  -0.456   -5.4727  -1.1503   0.0881
 UDH  C3'   C  CH2    0  -0.423   -6.9513  -1.1006  -0.2746
 UDH  C4'   C  CH2    0  -0.415   -7.8559  -1.4025   0.9139
 UDH  C5'   C  CH2    0  -0.426   -9.3387  -1.3234   0.5769
 UDH  C6'   C  CH2    0  -0.270  -10.2289  -1.6464   1.7669
 UDH  N6'   N  NH2    0  -0.801  -11.6382  -1.5415   1.4127
 UDH  HN3   H  HNR6   0   0.425    7.2999  -1.8237  -1.7650
 UDH  H5    H  HCR6   0   0.286    3.6499  -0.2629  -3.1528
 UDH  H6    H  HCR6   0   0.345    3.0989   0.1887  -0.8392
 UDH  H1'   H  HCR5   0   0.271    5.1820  -0.7700   1.9714
 UDH  H2'   H  HCR5   0   0.249    4.2369   1.8634   0.7729
 UDH  HO2'  H  HOH1   0   0.469    5.9813   2.5837   1.9355
 UDH  H3'   H  HCR5   0   0.253    3.1595   2.4090   2.8655
 UDH  H4'   H  HCR5   0   0.263    1.9713  -0.0680   3.0942
 UDH  HO3'  H  HOH1   0   0.449    4.9394   1.2937   4.0986
 UDH  H5'1  H  HCH2   0   0.235    0.8824   1.8161   2.0324
 UDH  H5'2  H  HCH2   0   0.203    1.9559   1.7490   0.6395
 UDH  H1'1  H  HCH2   0   0.201   -4.8348   0.0783  -1.5608
 UDH  H1'2  H  HCH2   0   0.197   -4.7502  -1.6560  -1.8648
 UDH  H2'1  H  HCH2   0   0.218   -5.2299  -2.1320   0.5064
 UDH  H2'2  H  HCH2   0   0.219   -5.2648  -0.4125   0.8696
 UDH  H3'1  H  HCH2   0   0.213   -7.1962  -0.1112  -0.6755
 UDH  H3'2  H  HCH2   0   0.213   -7.1590  -1.8157  -1.0779
 UDH  H4'1  H  HCH2   0   0.210   -7.6219  -2.4007   1.2995
 UDH  H4'2  H  HCH2   0   0.210   -7.6305  -0.7025   1.7257
 UDH  H5B   H  HCH2   0   0.212   -9.5822  -0.3221   0.2084
 UDH  H5D   H  HCH2   0   0.210   -9.5640  -2.0181  -0.2407
 UDH  H6'1  H  HCH2   0   0.186   -9.9501  -2.6357   2.1595
 UDH  H6'2  H  HCH2   0   0.209  -10.0238  -0.9314   2.5691
 UDH  HN'1  H  HNH2   0   0.336  -11.8555  -2.2441   0.7159
 UDH  HN'2  H  HNH2   0   0.344  -12.2038  -1.7793   2.2176

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
 UDH  N1   C2    single  1.381  0.020  1.381
 UDH  N1   C6    single  1.367  0.020  1.367
 UDH  N1   C1B   single  1.459  0.020  1.459
 UDH  C2   N3    single  1.370  0.020  1.370
 UDH  C2   O2    double  1.213  0.020  1.213
 UDH  N3   C4    single  1.387  0.020  1.387
 UDH  N3   HN3   single  0.860  0.020  1.020
 UDH  C4   C5    single  1.441  0.020  1.441
 UDH  C4   O4    double  1.218  0.020  1.218
 UDH  C5   C6    double  1.343  0.020  1.343
 UDH  C5   H5    single  0.930  0.020  1.080
 UDH  C6   H6    single  0.930  0.020  1.080
 UDH  C1B  C2B   single  1.528  0.020  1.528
 UDH  C1B  O4'   single  1.397  0.020  1.397
 UDH  C1B  H1'   single  0.970  0.020  1.090
 UDH  C2B  O2'   single  1.396  0.020  1.396
 UDH  C2B  C3B   single  1.532  0.020  1.532
 UDH  C2B  H2'   single  0.970  0.020  1.090
 UDH  O2'  HO2'  single  0.850  0.020  0.980
 UDH  C3B  C4B   single  1.522  0.020  1.522
 UDH  C3B  O3'   single  1.404  0.020  1.404
 UDH  C3B  H3'   single  0.970  0.020  1.090
 UDH  C4B  O4'   single  1.432  0.020  1.432
 UDH  C4B  C5B   single  1.519  0.020  1.519
 UDH  C4B  H4'   single  0.970  0.020  1.090
 UDH  O3'  HO3'  single  0.850  0.020  0.980
 UDH  C5B  O5'   single  1.406  0.020  1.406
 UDH  C5B  H5'1  single  0.970  0.020  1.090
 UDH  C5B  H5'2  single  0.970  0.020  1.090
 UDH  O5'  PA    single  1.650  0.020  1.650
 UDH  PA   O1A   deloc   1.494  0.020  1.494
 UDH  PA   O2A   deloc   1.501  0.020  1.501
 UDH  PA   O3A   single  1.638  0.020  1.638
 UDH  O3A  PB    single  1.641  0.020  1.641
 UDH  PB   O1B   deloc   1.496  0.020  1.496
 UDH  PB   O2B   single  1.639  0.020  1.639
 UDH  PB   O3B   deloc   1.498  0.020  1.498
 UDH  O2B  C1'   single  1.418  0.020  1.418
 UDH  C1'  C2'   single  1.516  0.020  1.516
 UDH  C1'  H1'1  single  0.970  0.020  1.090
 UDH  C1'  H1'2  single  0.970  0.020  1.090
 UDH  C2'  C3'   single  1.523  0.020  1.523
 UDH  C2'  H2'1  single  0.970  0.020  1.090
 UDH  C2'  H2'2  single  0.970  0.020  1.090
 UDH  C3'  C4'   single  1.524  0.020  1.524
 UDH  C3'  H3'1  single  0.970  0.020  1.090
 UDH  C3'  H3'2  single  0.970  0.020  1.090
 UDH  C4'  C5'   single  1.523  0.020  1.523
 UDH  C4'  H4'1  single  0.970  0.020  1.090
 UDH  C4'  H4'2  single  0.970  0.020  1.090
 UDH  C5'  C6'   single  1.521  0.020  1.521
 UDH  C5'  H5B   single  0.970  0.020  1.090
 UDH  C5'  H5D   single  0.970  0.020  1.090
 UDH  C6'  N6'   single  1.457  0.020  1.457
 UDH  C6'  H6'1  single  0.970  0.020  1.090
 UDH  C6'  H6'2  single  0.970  0.020  1.090
 UDH  N6'  HN'1  single  0.890  0.020  1.040
 UDH  N6'  HN'2  single  0.890  0.020  1.040

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
 UDH  C1B   N1   C6    119.97  3.000
 UDH  C1B   N1   C2    118.92  3.000
 UDH  C6    N1   C2    121.11  3.000
 UDH  O2    C2   N3    121.99  3.000
 UDH  O2    C2   N1    123.51  3.000
 UDH  N3    C2   N1    114.51  3.000
 UDH  HN3   N3   C4    116.72  3.000
 UDH  HN3   N3   C2    115.06  3.000
 UDH  C4    N3   C2    128.22  3.000
 UDH  O4    C4   C5    126.25  3.000
 UDH  O4    C4   N3    120.45  3.000
 UDH  C5    C4   N3    113.30  3.000
 UDH  H5    C5   C6    120.22  3.000
 UDH  H5    C5   C4    120.10  3.000
 UDH  C6    C5   C4    119.68  3.000
 UDH  H6    C6   C5    119.65  3.000
 UDH  H6    C6   N1    117.15  3.000
 UDH  C5    C6   N1    123.18  3.000
 UDH  H1'   C1B  O4'   111.38  3.000
 UDH  H1'   C1B  C2B   110.10  3.000
 UDH  O4'   C1B  C2B   105.85  3.000
 UDH  H1'   C1B  N1    106.57  3.000
 UDH  O4'   C1B  N1    109.24  3.000
 UDH  C2B   C1B  N1    113.78  3.000
 UDH  H2'   C2B  C3B   109.09  3.000
 UDH  H2'   C2B  O2'   111.45  3.000
 UDH  C3B   C2B  O2'   115.09  3.000
 UDH  H2'   C2B  C1B   109.75  3.000
 UDH  C3B   C2B  C1B   100.94  3.000
 UDH  O2'   C2B  C1B   109.99  3.000
 UDH  HO2'  O2'  C2B   108.83  3.000
 UDH  H3'   C3B  O3'   111.69  3.000
 UDH  H3'   C3B  C4B   111.87  3.000
 UDH  O3'   C3B  C4B   108.97  3.000
 UDH  H3'   C3B  C2B   111.92  3.000
 UDH  O3'   C3B  C2B   110.97  3.000
 UDH  C4B   C3B  C2B   100.92  3.000
 UDH  H4'   C4B  C5B   109.27  3.000
 UDH  H4'   C4B  O4'   107.88  3.000
 UDH  C5B   C4B  O4'   111.18  3.000
 UDH  H4'   C4B  C3B   111.06  3.000
 UDH  C5B   C4B  C3B   111.60  3.000
 UDH  O4'   C4B  C3B   105.76  3.000
 UDH  C4B   O4'  C1B   110.79  3.000
 UDH  HO3'  O3'  C3B   108.01  3.000
 UDH  H5'2  C5B  H5'1  106.65  3.000
 UDH  H5'2  C5B  O5'   111.67  3.000
 UDH  H5'1  C5B  O5'   111.14  3.000
 UDH  H5'2  C5B  C4B   110.05  3.000
 UDH  H5'1  C5B  C4B   108.05  3.000
 UDH  O5'   C5B  C4B   109.19  3.000
 UDH  PA    O5'  C5B   116.96  3.000
 UDH  O3A   PA   O2A   109.84  3.000
 UDH  O3A   PA   O1A   111.98  3.000
 UDH  O2A   PA   O1A   120.04  3.000
 UDH  O3A   PA   O5'    93.18  3.000
 UDH  O2A   PA   O5'   109.03  3.000
 UDH  O1A   PA   O5'   109.42  3.000
 UDH  PB    O3A  PA    125.76  3.000
 UDH  O3B   PB   O2B   109.28  3.000
 UDH  O3B   PB   O1B   120.36  3.000
 UDH  O2B   PB   O1B   110.51  3.000
 UDH  O3B   PB   O3A   106.27  3.000
 UDH  O2B   PB   O3A    96.80  3.000
 UDH  O1B   PB   O3A   110.99  3.000
 UDH  C1'   O2B  PB    117.87  3.000
 UDH  H1'2  C1'  H1'1  106.99  3.000
 UDH  H1'2  C1'  C2'   109.11  3.000
 UDH  H1'1  C1'  C2'   109.98  3.000
 UDH  H1'2  C1'  O2B   111.52  3.000
 UDH  H1'1  C1'  O2B   110.10  3.000
 UDH  C2'   C1'  O2B   109.11  3.000
 UDH  H2'2  C2'  H2'1  106.83  3.000
 UDH  H2'2  C2'  C3'   109.42  3.000
 UDH  H2'1  C2'  C3'   109.61  3.000
 UDH  H2'2  C2'  C1'   109.33  3.000
 UDH  H2'1  C2'  C1'   109.08  3.000
 UDH  C3'   C2'  C1'   112.40  3.000
 UDH  H3'2  C3'  H3'1  106.20  3.000
 UDH  H3'2  C3'  C4'   109.27  3.000
 UDH  H3'1  C3'  C4'   109.38  3.000
 UDH  H3'2  C3'  C2'   109.72  3.000
 UDH  H3'1  C3'  C2'   109.49  3.000
 UDH  C4'   C3'  C2'   112.58  3.000
 UDH  H4'2  C4'  H4'1  106.11  3.000
 UDH  H4'2  C4'  C5'   109.34  3.000
 UDH  H4'1  C4'  C5'   109.47  3.000
 UDH  H4'2  C4'  C3'   109.22  3.000
 UDH  H4'1  C4'  C3'   109.17  3.000
 UDH  C5'   C4'  C3'   113.28  3.000
 UDH  H5D   C5'  H5B   106.44  3.000
 UDH  H5D   C5'  C6'   109.19  3.000
 UDH  H5B   C5'  C6'   109.12  3.000
 UDH  H5D   C5'  C4'   109.41  3.000
 UDH  H5B   C5'  C4'   109.80  3.000
 UDH  C6'   C5'  C4'   112.70  3.000
 UDH  H6'2  C6'  H6'1  106.18  3.000
 UDH  H6'2  C6'  N6'   108.22  3.000
 UDH  H6'1  C6'  N6'   113.37  3.000
 UDH  H6'2  C6'  C5'   108.98  3.000
 UDH  H6'1  C6'  C5'   108.77  3.000
 UDH  N6'   C6'  C5'   111.14  3.000
 UDH  HN'2  N6'  HN'1  105.32  3.000
 UDH  HN'2  N6'  C6'   109.28  3.000
 UDH  HN'1  N6'  C6'   108.95  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
 UDH  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 UDH  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 UDH  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 UDH  CONST_04  C1B   N1   C2   N3   180.00   0.0  0
 UDH  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 UDH  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 UDH  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 UDH  CONST_08  C1B   N1   C2   O2     0.00   0.0  0
 UDH  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 UDH  Var_01    O1A   PA   O5'  C5B  -68.68  30.0  3
 UDH  Var_02    O1B   PB   O3A  PA    26.15  30.0  3
 UDH  Var_03    C2'   C1'  O2B  PB   154.96  30.0  3
 UDH  Var_04    C3'   C2'  C1'  O2B  176.75  30.0  3
 UDH  Var_05    C4'   C3'  C2'  C1'  178.54  30.0  3
 UDH  Var_06    C5'   C4'  C3'  C2'  178.58  30.0  3
 UDH  Var_07    C6'   C5'  C4'  C3'  179.18  30.0  3
 UDH  Var_08    N6'   C6'  C5'  C4'  179.16  30.0  3
 UDH  Var_09    H5'1  C5B  O5'  PA    90.03  30.0  1
 UDH  Var_10    HN'1  N6'  C6'  C5'   64.30  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
 UDH  chir_01  C1B  N1   C2B  O4'  negativ
 UDH  chir_02  C2B  O2'  C3B  C1B  positiv
 UDH  chir_03  C3B  O3'  C2B  C4B  negativ
 UDH  chir_04  C4B  O4'  C3B  C5B  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
 UDH  plan-1  N1   0.020
 UDH  plan-1  C2   0.020
 UDH  plan-1  N3   0.020
 UDH  plan-1  C4   0.020
 UDH  plan-1  C5   0.020
 UDH  plan-1  C6   0.020
 UDH  plan-1  O2   0.020
 UDH  plan-1  O4   0.020
 UDH  plan-1  C1B  0.020
 UDH  plan-1  HN3  0.020
 UDH  plan-1  H5   0.020
 UDH  plan-1  H6   0.020

