# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 12:36:21 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@@H](O[C@H]1CN2CCCCC2)N3C=CC(=O)NC3=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
 U3S  U3S  1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione  ligand  43  22  .  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_U3S
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
 U3S  C4    C  CR6   0   0.567  -4.2083   1.9464   0.1856
 U3S  C5    C  CR16  0  -0.513  -4.0639   1.1779   1.3967
 U3S  C6    C  CR16  0   0.101  -3.0685   0.2828   1.4958
 U3S  N1    N  NR6   0  -0.568  -2.1680   0.0389   0.4978
 U3S  N3    N  NR16  0  -0.734  -3.2506   1.6466  -0.7718
 U3S  CAV   C  CH2   0  -0.441   5.0643   2.1947  -0.0926
 U3S  CAK   C  CH2   0  -0.435   3.9277   2.0280  -1.0928
 U3S  CAM   C  CH2   0  -0.287   3.4233   0.5931  -1.0953
 U3S  CAJ   C  CH2   0  -0.437   4.6314   1.6835   1.2757
 U3S  CAL   C  CH2   0  -0.278   4.1006   0.2612   1.1793
 U3S  NBA   N  NT    0  -0.421   3.0024   0.1764   0.2316
 U3S  C5'   C  CH2   0  -0.279   2.3933  -1.1380   0.2239
 U3S  C4'   C  CH1   0   0.014   0.9683  -1.1243  -0.2882
 U3S  O4'   O  O2    0  -0.484   0.1473  -0.3760   0.6070
 U3S  C3'   C  CH1   0  -0.004   0.3241  -2.5051  -0.3370
 U3S  O3'   O  OH1   0  -0.663   0.6993  -3.1743  -1.5085
 U3S  C2'   C  CH1   0  -0.048  -1.1598  -2.1553  -0.2352
 U3S  O2'   O  OH1   0  -0.661  -1.9890  -3.1378   0.3213
 U3S  C1'   C  CH1   0   0.210  -1.1162  -0.9534   0.7103
 U3S  O4    O  O     0  -0.464  -5.0589   2.7885  -0.0330
 U3S  C2    C  CR6   0   0.747  -2.2292   0.7363  -0.6942
 U3S  O2    O  O     0  -0.469  -1.4510   0.5632  -1.6071
 U3S  H5    H  HCR6  0   0.294  -4.7491   1.3312   2.2155
 U3S  H6    H  HCR6  0   0.328  -2.9313  -0.3012   2.3952
 U3S  HN3   H  HNR6  0   0.427  -3.2989   2.1618  -1.6428
 U3S  HAVA  H  HCH2  0   0.230   5.3802   3.2385  -0.0343
 U3S  HAK   H  HCH2  0   0.215   3.1032   2.6994  -0.8350
 U3S  HAKA  H  HCH2  0   0.229   4.2533   2.2953  -2.1006
 U3S  HAM   H  HCH2  0   0.235   2.5821   0.5036  -1.7852
 U3S  HAMA  H  HCH2  0   0.185   4.2186  -0.0697  -1.4835
 U3S  HAJ   H  HCH2  0   0.229   5.4641   1.7114   1.9820
 U3S  HAJA  H  HCH2  0   0.214   3.8456   2.3287   1.6799
 U3S  HAL   H  HCH2  0   0.182   4.9283  -0.4184   0.9055
 U3S  HALA  H  HCH2  0   0.233   3.7409  -0.0639   2.1585
 U3S  H5'   H  HCH2  0   0.209   2.9703  -1.8624  -0.3764
 U3S  H5'A  H  HCH2  0   0.235   2.3802  -1.5261   1.2465
 U3S  H4'   H  HCH1  0   0.233   0.9170  -0.6764  -1.2883
 U3S  H3'   H  HCH1  0   0.224   0.6147  -3.0724   0.5604
 U3S  HO3'  H  HOH1  0   0.460   0.4982  -4.1095  -1.4099
 U3S  H2'   H  HCH1  0   0.252  -1.5071  -1.8570  -1.2300
 U3S  HO2'  H  HOH1  0   0.462  -2.2252  -3.7658  -0.3674
 U3S  H1'   H  HCH1  0   0.261  -1.2775  -1.3109   1.7329
 U3S  HAV   H  HCH2  0   0.210   5.9332   1.6217  -0.4341

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
 U3S  C4   C5    single  1.442  0.020  1.442
 U3S  C4   N3    single  1.387  0.020  1.387
 U3S  C4   O4    double  1.217  0.020  1.217
 U3S  C5   C6    double  1.342  0.020  1.342
 U3S  C6   N1    single  1.366  0.020  1.366
 U3S  N1   C1'   single  1.462  0.020  1.462
 U3S  N1   C2    single  1.382  0.020  1.382
 U3S  N3   C2    single  1.370  0.020  1.370
 U3S  CAV  CAK   single  1.523  0.020  1.523
 U3S  CAV  CAJ   single  1.523  0.020  1.523
 U3S  CAK  CAM   single  1.521  0.020  1.521
 U3S  CAM  NBA   single  1.453  0.020  1.453
 U3S  CAJ  CAL   single  1.521  0.020  1.521
 U3S  CAL  NBA   single  1.453  0.020  1.453
 U3S  NBA  C5'   single  1.449  0.020  1.449
 U3S  C5'  C4'   single  1.514  0.020  1.514
 U3S  C4'  O4'   single  1.427  0.020  1.427
 U3S  C4'  C3'   single  1.524  0.020  1.524
 U3S  O4'  C1'   single  1.393  0.020  1.393
 U3S  C3'  O3'   single  1.400  0.020  1.400
 U3S  C3'  C2'   single  1.528  0.020  1.528
 U3S  C2'  O2'   single  1.401  0.020  1.401
 U3S  C2'  C1'   single  1.530  0.020  1.530
 U3S  C2   O2    double  1.212  0.020  1.212
 U3S  C5   H5    single  0.930  0.020  1.080
 U3S  C6   H6    single  0.930  0.020  1.080
 U3S  N3   HN3   single  0.860  0.020  1.020
 U3S  CAV  HAV   single  0.970  0.020  1.090
 U3S  CAV  HAVA  single  0.970  0.020  1.090
 U3S  CAK  HAK   single  0.970  0.020  1.090
 U3S  CAK  HAKA  single  0.970  0.020  1.090
 U3S  CAM  HAM   single  0.970  0.020  1.090
 U3S  CAM  HAMA  single  0.970  0.020  1.090
 U3S  CAJ  HAJ   single  0.970  0.020  1.090
 U3S  CAJ  HAJA  single  0.970  0.020  1.090
 U3S  CAL  HAL   single  0.970  0.020  1.090
 U3S  CAL  HALA  single  0.970  0.020  1.090
 U3S  C5'  H5'   single  0.970  0.020  1.090
 U3S  C5'  H5'A  single  0.970  0.020  1.090
 U3S  C4'  H4'   single  0.970  0.020  1.090
 U3S  C3'  H3'   single  0.970  0.020  1.090
 U3S  O3'  HO3'  single  0.850  0.020  0.980
 U3S  C2'  H2'   single  0.970  0.020  1.090
 U3S  O2'  HO2'  single  0.850  0.020  0.980
 U3S  C1'  H1'   single  0.970  0.020  1.090

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
 U3S  O4    C4   N3   120.55  3.000
 U3S  O4    C4   C5   126.15  3.000
 U3S  N3    C4   C5   113.30  3.000
 U3S  H5    C5   C6   120.65  3.000
 U3S  H5    C5   C4   119.89  3.000
 U3S  C6    C5   C4   119.46  3.000
 U3S  H6    C6   N1   115.32  3.000
 U3S  H6    C6   C5   121.05  3.000
 U3S  N1    C6   C5   123.63  3.000
 U3S  C2    N1   C1'  119.98  3.000
 U3S  C2    N1   C6   120.71  3.000
 U3S  C1'   N1   C6   119.30  3.000
 U3S  HN3   N3   C2   114.96  3.000
 U3S  HN3   N3   C4   116.78  3.000
 U3S  C2    N3   C4   128.26  3.000
 U3S  HAVA  CAV  HAV  106.69  3.000
 U3S  HAVA  CAV  CAJ  110.79  3.000
 U3S  HAV   CAV  CAJ  109.26  3.000
 U3S  HAVA  CAV  CAK  110.82  3.000
 U3S  HAV   CAV  CAK  109.26  3.000
 U3S  CAJ   CAV  CAK  109.94  3.000
 U3S  HAKA  CAK  HAK  106.97  3.000
 U3S  HAKA  CAK  CAM  109.17  3.000
 U3S  HAK   CAK  CAM  109.23  3.000
 U3S  HAKA  CAK  CAV  110.89  3.000
 U3S  HAK   CAK  CAV  109.90  3.000
 U3S  CAM   CAK  CAV  110.60  3.000
 U3S  HAMA  CAM  HAM  106.45  3.000
 U3S  HAMA  CAM  NBA  110.92  3.000
 U3S  HAM   CAM  NBA  109.29  3.000
 U3S  HAMA  CAM  CAK  109.12  3.000
 U3S  HAM   CAM  CAK  109.51  3.000
 U3S  NBA   CAM  CAK  111.42  3.000
 U3S  HAJA  CAJ  HAJ  107.07  3.000
 U3S  HAJA  CAJ  CAL  108.91  3.000
 U3S  HAJ   CAJ  CAL  109.33  3.000
 U3S  HAJA  CAJ  CAV  109.76  3.000
 U3S  HAJ   CAJ  CAV  110.83  3.000
 U3S  CAL   CAJ  CAV  110.85  3.000
 U3S  HALA  CAL  HAL  106.59  3.000
 U3S  HALA  CAL  NBA  108.56  3.000
 U3S  HAL   CAL  NBA  111.62  3.000
 U3S  HALA  CAL  CAJ  109.65  3.000
 U3S  HAL   CAL  CAJ  109.22  3.000
 U3S  NBA   CAL  CAJ  111.08  3.000
 U3S  C5'   NBA  CAL  111.97  3.000
 U3S  C5'   NBA  CAM  112.16  3.000
 U3S  CAL   NBA  CAM  111.09  3.000
 U3S  H5'A  C5'  H5'  106.37  3.000
 U3S  H5'A  C5'  C4'  107.94  3.000
 U3S  H5'   C5'  C4'  108.30  3.000
 U3S  H5'A  C5'  NBA  108.79  3.000
 U3S  H5'   C5'  NBA  112.25  3.000
 U3S  C4'   C5'  NBA  112.91  3.000
 U3S  H4'   C4'  C3'  108.72  3.000
 U3S  H4'   C4'  O4'  109.33  3.000
 U3S  C3'   C4'  O4'  104.60  3.000
 U3S  H4'   C4'  C5'  110.85  3.000
 U3S  C3'   C4'  C5'  113.59  3.000
 U3S  O4'   C4'  C5'  109.51  3.000
 U3S  C1'   O4'  C4'  110.56  3.000
 U3S  H3'   C3'  C2'  108.67  3.000
 U3S  H3'   C3'  O3'  111.41  3.000
 U3S  C2'   C3'  O3'  115.17  3.000
 U3S  H3'   C3'  C4'  109.22  3.000
 U3S  C2'   C3'  C4'  101.59  3.000
 U3S  O3'   C3'  C4'  110.27  3.000
 U3S  HO3'  O3'  C3'  108.84  3.000
 U3S  H2'   C2'  C1'  110.89  3.000
 U3S  H2'   C2'  O2'  111.36  3.000
 U3S  C1'   C2'  O2'  108.80  3.000
 U3S  H2'   C2'  C3'  108.05  3.000
 U3S  C1'   C2'  C3'  101.15  3.000
 U3S  O2'   C2'  C3'  116.15  3.000
 U3S  HO2'  O2'  C2'  108.60  3.000
 U3S  H1'   C1'  C2'  108.45  3.000
 U3S  H1'   C1'  O4'  109.76  3.000
 U3S  C2'   C1'  O4'  107.80  3.000
 U3S  H1'   C1'  N1   104.56  3.000
 U3S  C2'   C1'  N1   115.02  3.000
 U3S  O4'   C1'  N1   111.13  3.000
 U3S  O2    C2   N3   122.06  3.000
 U3S  O2    C2   N1   123.30  3.000
 U3S  N3    C2   N1   114.64  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
 U3S  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 U3S  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 U3S  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 U3S  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 U3S  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 U3S  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 U3S  CONST_07  O2   C2   N1   C1'    0.00   0.0  0
 U3S  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 U3S  CONST_09  HN3  N3   C4   C5   180.00   0.0  0
 U3S  Var_01    NBA  CAM  CAK  CAV   56.53  30.0  1
 U3S  Var_02    NBA  CAL  CAJ  CAV  -56.64  30.0  1
 U3S  Var_03    CAL  CAJ  CAV  CAK   53.24  30.0  1
 U3S  Var_04    CAL  NBA  CAM  CAK  -59.70  30.0  1
 U3S  Var_05    CAJ  CAV  CAK  CAM  -53.02  30.0  1
 U3S  Var_06    CAJ  CAL  NBA  CAM   59.58  30.0  1
 U3S  Var_07    C4'  C5'  NBA  CAM  -77.43  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
 U3S  chir_01  C4'  C5'  O4'  C3'  positiv
 U3S  chir_02  C3'  O3'  C4'  C2'  negativ
 U3S  chir_03  C2'  O2'  C3'  C1'  positiv
 U3S  chir_04  C1'  O4'  N1   C2'  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
 U3S  plan-1  C4   0.020
 U3S  plan-1  C5   0.020
 U3S  plan-1  C6   0.020
 U3S  plan-1  N1   0.020
 U3S  plan-1  N3   0.020
 U3S  plan-1  C1'  0.020
 U3S  plan-1  O4   0.020
 U3S  plan-1  C2   0.020
 U3S  plan-1  O2   0.020
 U3S  plan-1  H5   0.020
 U3S  plan-1  H6   0.020
 U3S  plan-1  HN3  0.020

