# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 13:36:13 2021
#   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  59  32  .  2021-08-24  2022-11-18
;
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  -0.567  37.7274  50.7935  40.8394
 UDH  C2    C  CR6   0   0.741  38.9823  51.1920  40.4266
 UDH  N3    N  NR16  0  -0.731  39.7173  50.2263  39.7962
 UDH  C4    C  CR6   0   0.567  39.3419  48.9206  39.5135
 UDH  C5    C  CR16  0  -0.512  38.0169  48.5958  39.9764
 UDH  C6    C  CR16  0   0.080  37.2822  49.5253  40.6114
 UDH  O2    O  O     0  -0.478  39.3973  52.3185  40.6079
 UDH  O4    O  O     0  -0.465  40.1033  48.1719  38.9293
 UDH  C1B   C  CH1   0   0.168  36.9160  51.8201  41.5218
 UDH  C2B   C  CH1   0  -0.067  36.2817  52.8035  40.5246
 UDH  O2'   O  OH1   0  -0.655  36.2004  54.1141  41.0223
 UDH  C3B   C  CH1   0  -0.003  34.8936  52.1827  40.3275
 UDH  C4B   C  CH1   0  -0.019  34.6029  51.6587  41.7357
 UDH  O4'   O  O2    0  -0.493  35.8686  51.2075  42.2135
 UDH  O3'   O  OH1   0  -0.651  33.9242  53.0383  39.8151
 UDH  C5B   C  CH2   0  -0.203  33.5752  50.5620  41.8434
 UDH  O5'   O  O2    0  -0.580  34.0014  49.4263  41.0871
 UDH  PA    P  P     0   1.479  33.0599  48.6469  40.0723
 UDH  O1A   O  O     0  -0.677  32.2008  49.4661  39.2056
 UDH  O2A   O  OH1   0  -0.716  34.0932  47.6589  39.3883
 UDH  O3A   O  O2    0  -0.698  32.2804  47.6676  41.0920
 UDH  PB    P  P     0   1.497  31.1381  46.5310  40.8450
 UDH  O1B   O  O     0  -0.679  30.7346  45.9925  42.1523
 UDH  O2B   O  O2    0  -0.585  31.7656  45.5487  39.7798
 UDH  O3B   O  OH1   0  -0.720  30.0405  47.2008  39.9222
 UDH  C1'   C  CH2   0  -0.190  32.8084  44.6223  40.1633
 UDH  C2'   C  CH2   0  -0.460  33.4623  44.0893  38.9115
 UDH  C3'   C  CH2   0  -0.415  32.5516  43.2514  38.0234
 UDH  C4'   C  CH2   0  -0.419  33.2673  42.7599  36.7713
 UDH  C5'   C  CH2   0  -0.426  32.3892  41.8983  35.8748
 UDH  C6'   C  CH2   0  -0.271  33.1041  41.4499  34.6095
 UDH  N6'   N  NH2   0  -0.801  32.2349  40.6284  33.7786
 UDH  HN3   H  HNR6  0   0.428  40.6381  50.5154  39.4883
 UDH  H5    H  HCR6  0   0.290  37.6241  47.6033  39.8187
 UDH  H6    H  HCR6  0   0.335  36.2958  49.2950  40.9785
 UDH  H1'   H  HCH1  0   0.292  37.5799  52.3329  42.2216
 UDH  H2'   H  HCH1  0   0.291  36.8441  52.8606  39.5929
 UDH  HO2'  H  HOH1  0   0.462  35.9365  54.1191  41.9491
 UDH  H3'   H  HCH1  0   0.259  34.9807  51.3435  39.6302
 UDH  H4'   H  HCH1  0   0.259  34.2355  52.4787  42.3705
 UDH  HO3'  H  HOH1  0   0.448  34.0368  53.9075  40.2194
 UDH  H5'1  H  HCH2  0   0.279  33.4462  50.2511  42.8810
 UDH  H5'2  H  HCH2  0   0.260  32.6201  50.9551  41.4868
 UDH  HOA2  H  HOH1  0   0.512  34.2938  47.8616  38.4641
 UDH  HOB3  H  HOH1  0   0.510  29.4106  47.7654  40.3918
 UDH  H1'1  H  HCH2  0   0.250  33.5498  45.1289  40.7849
 UDH  H1'2  H  HCH2  0   0.247  32.3629  43.8168  40.7507
 UDH  H2'1  H  HCH2  0   0.232  33.8835  44.9243  38.3451
 UDH  H2'2  H  HCH2  0   0.237  34.3127  43.4829  39.2368
 UDH  H3'1  H  HCH2  0   0.215  32.1778  42.3936  38.5926
 UDH  H3'2  H  HCH2  0   0.220  31.6716  43.8307  37.7294
 UDH  H4'1  H  HCH2  0   0.211  33.6288  43.6247  36.2038
 UDH  H4'2  H  HCH2  0   0.212  34.1605  42.1953  37.0603
 UDH  H5B   H  HCH2  0   0.211  32.0532  41.0163  36.4325
 UDH  H5D   H  HCH2  0   0.212  31.4852  42.4499  35.5982
 UDH  H6'1  H  HCH2  0   0.210  33.3934  42.3337  34.0334
 UDH  H6'2  H  HCH2  0   0.186  34.0425  40.9490  34.8904
 UDH  HN'1  H  HNH2  0   0.345  32.7228  40.3728  32.9297
 UDH  HN'2  H  HNH2  0   0.336  32.0495  39.7549  34.2564

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  1.380  0.020  1.380
 UDH  N1   C6    single  1.363  0.020  1.363
 UDH  N1   C1B   single  1.476  0.020  1.476
 UDH  C2   N3    single  1.367  0.020  1.367
 UDH  C2   O2    double  1.214  0.020  1.214
 UDH  N3   C4    single  1.388  0.020  1.388
 UDH  N3   HN3   single  0.860  0.020  1.020
 UDH  C4   C5    single  1.441  0.020  1.441
 UDH  C4   O4    double  1.217  0.020  1.217
 UDH  C5   C6    double  1.344  0.020  1.344
 UDH  C5   H5    single  0.930  0.020  1.080
 UDH  C6   H6    single  0.930  0.020  1.080
 UDH  C1B  C2B   single  1.537  0.020  1.537
 UDH  C1B  O4'   single  1.397  0.020  1.397
 UDH  C1B  H1'   single  0.970  0.020  1.090
 UDH  C2B  O2'   single  1.404  0.020  1.404
 UDH  C2B  C3B   single  1.533  0.020  1.533
 UDH  C2B  H2'   single  0.970  0.020  1.090
 UDH  O2'  HO2'  single  0.850  0.020  0.980
 UDH  C3B  C4B   single  1.530  0.020  1.530
 UDH  C3B  O3'   single  1.391  0.020  1.391
 UDH  C3B  H3'   single  0.970  0.020  1.090
 UDH  C4B  O4'   single  1.426  0.020  1.426
 UDH  C4B  C5B   single  1.507  0.020  1.507
 UDH  C4B  H4'   single  0.970  0.020  1.090
 UDH  O3'  HO3'  single  0.850  0.020  0.980
 UDH  C5B  O5'   single  1.430  0.020  1.430
 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  1.589  0.020  1.589
 UDH  PA   O1A   double  1.470  0.020  1.470
 UDH  PA   O2A   single  1.585  0.020  1.585
 UDH  PA   O3A   single  1.615  0.020  1.615
 UDH  O2A  HOA2  single  0.850  0.020  0.980
 UDH  O3A  PB    single  1.630  0.020  1.630
 UDH  PB   O1B   double  1.470  0.020  1.470
 UDH  PB   O2B   single  1.579  0.020  1.579
 UDH  PB   O3B   single  1.583  0.020  1.583
 UDH  O2B  C1'   single  1.447  0.020  1.447
 UDH  O3B  HOB3  single  0.850  0.020  0.980
 UDH  C1'  C2'   single  1.510  0.020  1.510
 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  1.522  0.020  1.522
 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  1.456  0.020  1.456
 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    123.02  3.000
 UDH  C1B   N1   C2    115.94  3.000
 UDH  C6    N1   C2    121.04  3.000
 UDH  O2    C2   N3    122.71  3.000
 UDH  O2    C2   N1    122.28  3.000
 UDH  N3    C2   N1    115.01  3.000
 UDH  HN3   N3   C4    116.90  3.000
 UDH  HN3   N3   C2    115.28  3.000
 UDH  C4    N3   C2    127.81  3.000
 UDH  O4    C4   C5    126.22  3.000
 UDH  O4    C4   N3    120.49  3.000
 UDH  C5    C4   N3    113.29  3.000
 UDH  H5    C5   C6    120.40  3.000
 UDH  H5    C5   C4    119.69  3.000
 UDH  C6    C5   C4    119.91  3.000
 UDH  H6    C6   C5    120.90  3.000
 UDH  H6    C6   N1    116.16  3.000
 UDH  C5    C6   N1    122.94  3.000
 UDH  H1'   C1B  O4'   110.15  3.000
 UDH  H1'   C1B  C2B   111.47  3.000
 UDH  O4'   C1B  C2B   107.00  3.000
 UDH  H1'   C1B  N1    106.78  3.000
 UDH  O4'   C1B  N1    109.64  3.000
 UDH  C2B   C1B  N1    111.83  3.000
 UDH  H2'   C2B  C3B   112.24  3.000
 UDH  H2'   C2B  O2'   106.50  3.000
 UDH  C3B   C2B  O2'   111.78  3.000
 UDH  H2'   C2B  C1B   112.03  3.000
 UDH  C3B   C2B  C1B   101.41  3.000
 UDH  O2'   C2B  C1B   113.01  3.000
 UDH  HO2'  O2'  C2B   111.20  3.000
 UDH  H3'   C3B  O3'   107.00  3.000
 UDH  H3'   C3B  C4B   109.80  3.000
 UDH  O3'   C3B  C4B   114.66  3.000
 UDH  H3'   C3B  C2B   108.68  3.000
 UDH  O3'   C3B  C2B   115.42  3.000
 UDH  C4B   C3B  C2B   101.09  3.000
 UDH  H4'   C4B  C5B   105.87  3.000
 UDH  H4'   C4B  O4'   109.81  3.000
 UDH  C5B   C4B  O4'   110.56  3.000
 UDH  H4'   C4B  C3B   109.83  3.000
 UDH  C5B   C4B  C3B   116.39  3.000
 UDH  O4'   C4B  C3B   104.36  3.000
 UDH  C4B   O4'  C1B   111.15  3.000
 UDH  HO3'  O3'  C3B   108.57  3.000
 UDH  H5'2  C5B  H5'1  108.04  3.000
 UDH  H5'2  C5B  O5'   111.95  3.000
 UDH  H5'1  C5B  O5'   108.18  3.000
 UDH  H5'2  C5B  C4B   108.12  3.000
 UDH  H5'1  C5B  C4B   110.86  3.000
 UDH  O5'   C5B  C4B   109.70  3.000
 UDH  PA    O5'  C5B   123.44  3.000
 UDH  O3A   PA   O2A   102.08  3.000
 UDH  O3A   PA   O1A   115.36  3.000
 UDH  O2A   PA   O1A   118.30  3.000
 UDH  O3A   PA   O5'   100.39  3.000
 UDH  O2A   PA   O5'   101.25  3.000
 UDH  O1A   PA   O5'   116.72  3.000
 UDH  HOA2  O2A  PA    114.64  3.000
 UDH  PB    O3A  PA    131.72  3.000
 UDH  O3B   PB   O2B    98.37  3.000
 UDH  O3B   PB   O1B   118.89  3.000
 UDH  O2B   PB   O1B   118.75  3.000
 UDH  O3B   PB   O3A   106.21  3.000
 UDH  O2B   PB   O3A   104.92  3.000
 UDH  O1B   PB   O3A   108.24  3.000
 UDH  C1'   O2B  PB    120.39  3.000
 UDH  HOB3  O3B  PB    114.55  3.000
 UDH  H1'2  C1'  H1'1  108.24  3.000
 UDH  H1'2  C1'  C2'   111.25  3.000
 UDH  H1'1  C1'  C2'   109.98  3.000
 UDH  H1'2  C1'  O2B   108.72  3.000
 UDH  H1'1  C1'  O2B   110.07  3.000
 UDH  C2'   C1'  O2B   108.57  3.000
 UDH  H2'2  C2'  H2'1  106.14  3.000
 UDH  H2'2  C2'  C3'   109.46  3.000
 UDH  H2'1  C2'  C3'   110.38  3.000
 UDH  H2'2  C2'  C1'   106.61  3.000
 UDH  H2'1  C2'  C1'   109.08  3.000
 UDH  C3'   C2'  C1'   114.76  3.000
 UDH  H3'2  C3'  H3'1  106.25  3.000
 UDH  H3'2  C3'  C4'   109.14  3.000
 UDH  H3'1  C3'  C4'   109.56  3.000
 UDH  H3'2  C3'  C2'   110.27  3.000
 UDH  H3'1  C3'  C2'   109.38  3.000
 UDH  C4'   C3'  C2'   112.07  3.000
 UDH  H4'2  C4'  H4'1  105.93  3.000
 UDH  H4'2  C4'  C5'   109.51  3.000
 UDH  H4'1  C4'  C5'   109.39  3.000
 UDH  H4'2  C4'  C3'   109.42  3.000
 UDH  H4'1  C4'  C3'   109.02  3.000
 UDH  C5'   C4'  C3'   113.30  3.000
 UDH  H5D   C5'  H5B   106.32  3.000
 UDH  H5D   C5'  C6'   109.06  3.000
 UDH  H5B   C5'  C6'   109.27  3.000
 UDH  H5D   C5'  C4'   109.88  3.000
 UDH  H5B   C5'  C4'   109.43  3.000
 UDH  C6'   C5'  C4'   112.68  3.000
 UDH  H6'2  C6'  H6'1  106.06  3.000
 UDH  H6'2  C6'  N6'   113.45  3.000
 UDH  H6'1  C6'  N6'   108.25  3.000
 UDH  H6'2  C6'  C5'   108.83  3.000
 UDH  H6'1  C6'  C5'   108.92  3.000
 UDH  N6'   C6'  C5'   111.13  3.000
 UDH  HN'2  N6'  HN'1  105.44  3.000
 UDH  HN'2  N6'  C6'   109.06  3.000
 UDH  HN'1  N6'  C6'   109.47  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    42.12  30.0  3
 UDH  Var_02    O1B   PB   O3A  PA   -177.11  30.0  3
 UDH  Var_03    C2'   C1'  O2B  PB   -165.08  30.0  3
 UDH  Var_04    C3'   C2'  C1'  O2B   -64.79  30.0  3
 UDH  Var_05    C4'   C3'  C2'  C1'   179.30  30.0  3
 UDH  Var_06    C5'   C4'  C3'  C2'   178.98  30.0  3
 UDH  Var_07    C6'   C5'  C4'  C3'   178.28  30.0  3
 UDH  Var_08    N6'   C6'  C5'  C4'   179.96  30.0  3
 UDH  Var_09    H5'1  C5B  O5'  PA    106.55  30.0  1
 UDH  Var_10    HN'1  N6'  C6'  C5'   177.93  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
 UDH  chir_05  PA   O1A  O2A  O3A  both
 UDH  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
 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

