# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:39:15 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1,2-dihydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(Cc2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@H](O)CO)c(N)n1
#
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
 1U0  1U0  '2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1,2-dihydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate'  ligand  53  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1U0
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
 1U0  O3B  O  OH1   0  -0.730  35.1762   0.8047  20.6028
 1U0  PB   P  P     0   1.472  34.3547   1.5537  19.4731
 1U0  O1B  O  O     0  -0.677  34.4349   1.0667  18.0883
 1U0  O2B  O  OH1   0  -0.724  34.8598   3.0283  19.7741
 1U0  O3A  O  O2    0  -0.697  32.8043   1.5198  19.9559
 1U0  PA   P  P     0   1.488  32.0834   1.5167  21.4098
 1U0  O1A  O  O     0  -0.679  30.6351   1.6933  21.2258
 1U0  O2A  O  OH1   0  -0.721  32.5994   0.2122  22.1459
 1U0  O7   O  O2    0  -0.589  32.8645   2.5978  22.2652
 1U0  C7   C  CH2   0  -0.156  32.6122   3.9984  22.0474
 1U0  C6   C  CH2   0  -0.553  33.7593   4.7872  22.6529
 1U0  C5   C  CR5   0  -0.247  33.5661   6.2463  22.3900
 1U0  C4   C  CR5   0   0.147  32.7865   7.1372  23.0690
 1U0  CM4  C  CH3   0  -0.762  32.0079   6.7794  24.2949
 1U0  S1   S  S2    0   0.199  34.3260   6.9815  21.0356
 1U0  C2   C  CR5   0  -0.241  33.6121   8.5125  21.3728
 1U0  C8   C  CH1   0  -0.082  33.8804   9.6518  20.4360
 1U0  O9   O  OH1   0  -0.670  33.2242   9.4671  19.2032
 1U0  C3   C  CR5   0   0.220  32.8065   8.4485  22.4755
 1U0  C7'  C  CH2   0  -0.677  31.9955   9.5941  23.0333
 1U0  C5'  C  CR6   0   0.013  30.5309   9.4612  22.7038
 1U0  C6'  C  CR16  0  -0.092  29.6173   8.9811  23.6185
 1U0  N1'  N  N     0  -0.433  28.3361   8.7383  23.3477
 1U0  C2'  C  CR6   0   0.356  27.9462   8.9810  22.1045
 1U0  CM2  C  CH3   0  -0.731  26.5450   8.6169  21.7299
 1U0  N3'  N  N     0  -0.453  28.7100   9.5170  21.1607
 1U0  C4'  C  CR6   0   0.441  29.9775   9.7859  21.4514
 1U0  N4'  N  NH2   0  -0.859  30.7211  10.3792  20.4651
 1U0  C9   C  CH2   0  -0.169  35.3599   9.8252  20.1210
 1U0  O10  O  OH1   0  -0.664  36.0476  10.0076  21.3316
 1U0  H1   H  HOH1  0   0.509  35.1088  -0.1603  20.5834
 1U0  H2   H  HOH1  0   0.508  34.7307   3.6454  19.0409
 1U0  H3   H  HOH1  0   0.511  32.0625  -0.5756  21.9813
 1U0  H4   H  HCH2  0   0.240  32.5333   4.2175  20.9801
 1U0  H5   H  HCH2  0   0.259  31.6656   4.2692  22.5185
 1U0  H6   H  HCH2  0   0.272  33.8113   4.6040  23.7285
 1U0  H7   H  HCH2  0   0.273  34.7031   4.4429  22.2273
 1U0  H8   H  HCH3  0   0.248  32.0629   7.5638  25.0506
 1U0  H9   H  HCH3  0   0.253  30.9516   6.6172  24.0725
 1U0  H10  H  HCH3  0   0.256  32.3806   5.8649  24.7553
 1U0  H11  H  HCH1  0   0.212  33.5500  10.5772  20.9277
 1U0  H12  H  HOH1  0   0.460  32.2730   9.4937  19.3903
 1U0  H13  H  HCH2  0   0.287  32.1058   9.6175  24.1204
 1U0  H14  H  HCH2  0   0.278  32.3941  10.5510  22.6904
 1U0  H15  H  HCR6  0   0.265  29.9380   8.7778  24.6354
 1U0  H16  H  HCH3  0   0.249  26.1718   9.2517  20.9293
 1U0  H17  H  HCH3  0   0.259  26.5135   7.5849  21.3729
 1U0  H18  H  HCH3  0   0.249  25.8801   8.6863  22.5881
 1U0  H19  H  HNH2  0   0.398  30.1630  10.7462  19.7068
 1U0  H20  H  HNH2  0   0.401  31.3963  11.0585  20.7834
 1U0  H21  H  HCH2  0   0.200  35.7224   8.9464  19.5691
 1U0  H22  H  HCH2  0   0.223  35.4691  10.6880  19.4519
 1U0  H23  H  HOH1  0   0.460  36.9844  10.0899  21.1333

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
 1U0  O1B  PB   double    1.470  0.020  1.470
 1U0  O9   C8   single    1.409  0.020  1.409
 1U0  O2B  PB   single    1.588  0.020  1.588
 1U0  PB   O3A  single    1.624  0.020  1.624
 1U0  PB   O3B  single    1.585  0.020  1.585
 1U0  O3A  PA   single    1.623  0.020  1.623
 1U0  C9   C8   single    1.523  0.020  1.523
 1U0  C9   O10  single    1.404  0.020  1.404
 1U0  N4'  C4'  single    1.370  0.020  1.370
 1U0  C8   C2   single    1.499  0.020  1.499
 1U0  O1A  PA   double    1.470  0.020  1.470
 1U0  S1   C2   aromatic  1.723  0.020  1.723
 1U0  S1   C5   aromatic  1.718  0.020  1.718
 1U0  PA   O2A  single    1.584  0.020  1.584
 1U0  PA   O7   single    1.585  0.020  1.585
 1U0  N3'  C4'  aromatic  1.328  0.020  1.328
 1U0  N3'  C2'  aromatic  1.327  0.020  1.327
 1U0  C2   C3   aromatic  1.367  0.020  1.367
 1U0  C4'  C5'  aromatic  1.407  0.020  1.407
 1U0  C7   O7   single    1.440  0.020  1.440
 1U0  C7   C6   single    1.518  0.020  1.518
 1U0  CM2  C2'  single    1.495  0.020  1.495
 1U0  C2'  N1'  aromatic  1.325  0.020  1.325
 1U0  C5   C6   single    1.495  0.020  1.495
 1U0  C5   C4   aromatic  1.365  0.020  1.365
 1U0  C3   C7'  single    1.510  0.020  1.510
 1U0  C3   C4   aromatic  1.440  0.020  1.440
 1U0  C5'  C7'  single    1.507  0.020  1.507
 1U0  C5'  C6'  aromatic  1.379  0.020  1.379
 1U0  C4   CM4  single    1.496  0.020  1.496
 1U0  N1'  C6'  aromatic  1.332  0.020  1.332
 1U0  O3B  H1   single    0.850  0.020  0.980
 1U0  O2B  H2   single    0.850  0.020  0.980
 1U0  O2A  H3   single    0.850  0.020  0.980
 1U0  C7   H4   single    0.970  0.020  1.090
 1U0  C7   H5   single    0.970  0.020  1.090
 1U0  C6   H6   single    0.970  0.020  1.090
 1U0  C6   H7   single    0.970  0.020  1.090
 1U0  CM4  H8   single    0.970  0.020  1.090
 1U0  CM4  H9   single    0.970  0.020  1.090
 1U0  CM4  H10  single    0.970  0.020  1.090
 1U0  C8   H11  single    0.970  0.020  1.090
 1U0  O9   H12  single    0.850  0.020  0.980
 1U0  C7'  H13  single    0.970  0.020  1.090
 1U0  C7'  H14  single    0.970  0.020  1.090
 1U0  C6'  H15  single    0.930  0.020  1.080
 1U0  CM2  H16  single    0.970  0.020  1.090
 1U0  CM2  H17  single    0.970  0.020  1.090
 1U0  CM2  H18  single    0.970  0.020  1.090
 1U0  N4'  H19  single    0.890  0.020  1.040
 1U0  N4'  H20  single    0.890  0.020  1.040
 1U0  C9   H21  single    0.970  0.020  1.090
 1U0  C9   H22  single    0.970  0.020  1.090
 1U0  O10  H23  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
 1U0  H1   O3B  PB   114.89  3.000
 1U0  O3A  PB   O2B  105.47  3.000
 1U0  O3A  PB   O1B  108.97  3.000
 1U0  O2B  PB   O1B  117.97  3.000
 1U0  O3A  PB   O3B  105.84  3.000
 1U0  O2B  PB   O3B   97.99  3.000
 1U0  O1B  PB   O3B  119.12  3.000
 1U0  H2   O2B  PB   113.99  3.000
 1U0  PA   O3A  PB   133.66  3.000
 1U0  O7   PA   O2A   98.65  3.000
 1U0  O7   PA   O1A  118.11  3.000
 1U0  O2A  PA   O1A  118.54  3.000
 1U0  O7   PA   O3A  105.27  3.000
 1U0  O2A  PA   O3A  105.85  3.000
 1U0  O1A  PA   O3A  108.98  3.000
 1U0  H3   O2A  PA   114.25  3.000
 1U0  C7   O7   PA   119.71  3.000
 1U0  H5   C7   H4   108.01  3.000
 1U0  H5   C7   C6   110.75  3.000
 1U0  H4   C7   C6   109.88  3.000
 1U0  H5   C7   O7   109.15  3.000
 1U0  H4   C7   O7   110.83  3.000
 1U0  C6   C7   O7   108.22  3.000
 1U0  H7   C6   H6   106.86  3.000
 1U0  H7   C6   C5   110.55  3.000
 1U0  H6   C6   C5   110.06  3.000
 1U0  H7   C6   C7   109.51  3.000
 1U0  H6   C6   C7   109.97  3.000
 1U0  C5   C6   C7   109.84  3.000
 1U0  S1   C5   C4   111.44  3.000
 1U0  C4   C5   C6   128.56  3.000
 1U0  S1   C5   C6   119.94  3.000
 1U0  C3   C4   CM4  124.27  3.000
 1U0  CM4  C4   C5   123.30  3.000
 1U0  C3   C4   C5   112.43  3.000
 1U0  H10  CM4  H9   107.00  3.000
 1U0  H10  CM4  H8   107.07  3.000
 1U0  H9   CM4  H8   107.26  3.000
 1U0  H10  CM4  C4   111.66  3.000
 1U0  H9   CM4  C4   111.86  3.000
 1U0  H8   CM4  C4   111.69  3.000
 1U0  C2   S1   C5    92.44  3.000
 1U0  C3   C2   C8   130.17  3.000
 1U0  C3   C2   S1   111.13  3.000
 1U0  C8   C2   S1   118.61  3.000
 1U0  H11  C8   C9   106.79  3.000
 1U0  H11  C8   O9   111.22  3.000
 1U0  C9   C8   O9   106.65  3.000
 1U0  H11  C8   C2   107.85  3.000
 1U0  C9   C8   C2   112.94  3.000
 1U0  O9   C8   C2   111.33  3.000
 1U0  H12  O9   C8   106.52  3.000
 1U0  C7'  C3   C2   125.37  3.000
 1U0  C7'  C3   C4   122.09  3.000
 1U0  C2   C3   C4   112.54  3.000
 1U0  H14  C7'  H13  104.87  3.000
 1U0  H14  C7'  C5'  111.31  3.000
 1U0  H13  C7'  C5'  108.51  3.000
 1U0  H14  C7'  C3   110.65  3.000
 1U0  H13  C7'  C3   109.23  3.000
 1U0  C5'  C7'  C3   111.98  3.000
 1U0  C4'  C5'  C6'  114.21  3.000
 1U0  C6'  C5'  C7'  121.98  3.000
 1U0  C4'  C5'  C7'  123.81  3.000
 1U0  H15  C6'  N1'  116.14  3.000
 1U0  H15  C6'  C5'  119.39  3.000
 1U0  N1'  C6'  C5'  124.47  3.000
 1U0  C2'  N1'  C6'  116.13  3.000
 1U0  N3'  C2'  CM2  117.35  3.000
 1U0  CM2  C2'  N1'  117.78  3.000
 1U0  N3'  C2'  N1'  124.87  3.000
 1U0  H18  CM2  H17  107.48  3.000
 1U0  H18  CM2  H16  109.50  3.000
 1U0  H17  CM2  H16  107.51  3.000
 1U0  H18  CM2  C2'  111.07  3.000
 1U0  H17  CM2  C2'  109.81  3.000
 1U0  H16  CM2  C2'  111.33  3.000
 1U0  C4'  N3'  C2'  118.38  3.000
 1U0  N4'  C4'  N3'  116.62  3.000
 1U0  N3'  C4'  C5'  121.57  3.000
 1U0  N4'  C4'  C5'  121.81  3.000
 1U0  H20  N4'  H19  111.20  3.000
 1U0  H20  N4'  C4'  115.31  3.000
 1U0  H19  N4'  C4'  113.43  3.000
 1U0  H22  C9   H21  106.84  3.000
 1U0  H22  C9   O10  112.02  3.000
 1U0  H21  C9   O10  112.03  3.000
 1U0  H22  C9   C8   108.20  3.000
 1U0  H21  C9   C8   109.47  3.000
 1U0  O10  C9   C8   108.20  3.000
 1U0  H23  O10  C9   108.09  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
 1U0  CONST_01  C3   C2   S1   C5      0.00   0.0  0
 1U0  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 1U0  CONST_03  C2   S1   C5   C4      0.00   0.0  0
 1U0  CONST_04  S1   C2   C3   C4      0.00   0.0  0
 1U0  CONST_05  C3   C4   C5   S1      0.00   0.0  0
 1U0  CONST_06  C2'  N3'  C4'  C5'     0.00   0.0  0
 1U0  CONST_07  C2'  N1'  C6'  C5'     0.00   0.0  0
 1U0  CONST_08  N3'  C4'  C5'  C6'     0.00   0.0  0
 1U0  CONST_09  N3'  C2'  N1'  C6'     0.00   0.0  0
 1U0  CONST_10  C4'  N3'  C2'  N1'     0.00   0.0  0
 1U0  CONST_11  C4'  C5'  C6'  N1'     0.00   0.0  0
 1U0  CONST_12  C2   S1   C5   C6    180.00   0.0  0
 1U0  CONST_13  C3   C4   C5   C6    180.00   0.0  0
 1U0  CONST_14  C8   C2   S1   C5    180.00   0.0  0
 1U0  CONST_15  C7'  C3   C4   C5    180.00   0.0  0
 1U0  CONST_16  C8   C2   C3   C4    180.00   0.0  0
 1U0  CONST_17  S1   C5   C4   CM4   180.00   0.0  0
 1U0  CONST_18  C2   C3   C4   CM4   180.00   0.0  0
 1U0  CONST_19  C7'  C3   C2   S1    180.00   0.0  0
 1U0  CONST_20  N3'  C4'  C5'  C7'   180.00   0.0  0
 1U0  CONST_21  N1'  C6'  C5'  C7'   180.00   0.0  0
 1U0  CONST_22  N4'  C4'  C5'  C6'   180.00   0.0  0
 1U0  CONST_23  CM2  C2'  N1'  C6'   180.00   0.0  0
 1U0  CONST_24  N4'  C4'  N3'  C2'   180.00   0.0  0
 1U0  CONST_25  C4'  N3'  C2'  CM2   180.00   0.0  0
 1U0  CONST_26  H15  C6'  N1'  C2'   180.00   0.0  0
 1U0  CONST_27  H19  N4'  C4'  C5'   180.00   0.0  0
 1U0  Var_01    C5'  C7'  C3   C4    -75.07  30.0  2
 1U0  Var_02    C4'  C5'  C7'  C3    -78.72  30.0  1
 1U0  Var_03    S1   C5   C6   C7    -95.12  30.0  1
 1U0  Var_04    H8   CM4  C4   C5    138.60  30.0  2
 1U0  Var_05    H16  CM2  C2'  N1'   152.15  30.0  2
 1U0  Var_06    C5   C6   C7   O7    177.32  30.0  3
 1U0  Var_07    O1A  PA   O3A  PB    171.12  30.0  3
 1U0  Var_08    C6   C7   O7   PA   -162.63  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
 1U0  chir_02  C8  O9   C9   C2  positiv
 1U0  chir_03  PA  O1A  O2A  O7  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
 1U0  plan-1  C6   0.020
 1U0  plan-1  C5   0.020
 1U0  plan-1  C4   0.020
 1U0  plan-1  CM4  0.020
 1U0  plan-1  S1   0.020
 1U0  plan-1  C2   0.020
 1U0  plan-1  C8   0.020
 1U0  plan-1  C3   0.020
 1U0  plan-1  C7'  0.020
 1U0  plan-2  C7'  0.020
 1U0  plan-2  C5'  0.020
 1U0  plan-2  C6'  0.020
 1U0  plan-2  N1'  0.020
 1U0  plan-2  C2'  0.020
 1U0  plan-2  CM2  0.020
 1U0  plan-2  N3'  0.020
 1U0  plan-2  C4'  0.020
 1U0  plan-2  N4'  0.020
 1U0  plan-2  H15  0.020
 1U0  plan-3  C4'  0.020
 1U0  plan-3  N4'  0.020
 1U0  plan-3  H19  0.020
 1U0  plan-3  H20  0.020

