# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 02:40:31 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 1-(5-deoxy-5-morpholin-4-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]1CN2CCOCC2)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
 U2S  U2S  1-(5-deoxy-5-morpholin-4-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione  ligand  41  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 PERFECT
;

data_comp_U2S
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
 U2S  C4    C  CR6   0   0.567  -4.1987   1.9195   0.1401
 U2S  C5    C  CR16  0  -0.512  -4.0716   1.1597   1.3585
 U2S  C6    C  CR16  0   0.101  -3.0895   0.2518   1.4712
 U2S  N1    N  NR6   0  -0.570  -2.1895  -0.0172   0.4785
 U2S  N3    N  NR16  0  -0.734  -3.2392   1.5987  -0.8089
 U2S  OAM   O  O2    0  -0.485   5.0447   2.0406  -0.0637
 U2S  CAK   C  CH2   0  -0.185   3.9724   1.9441  -0.9746
 U2S  CAM   C  CH2   0  -0.313   3.4093   0.5372  -1.0276
 U2S  CAJ   C  CH2   0  -0.187   4.6477   1.6287   1.2257
 U2S  CAL   C  CH2   0  -0.304   4.1008   0.2138   1.2190
 U2S  NBA   N  NT    0  -0.430   2.9843   0.1205   0.2963
 U2S  C5'   C  CH2   0  -0.279   2.3753  -1.1933   0.3018
 U2S  C4'   C  CH1   0   0.015   0.9621  -1.1836  -0.2416
 U2S  O4'   O  O2    0  -0.482   0.1212  -0.4284   0.6278
 U2S  C3'   C  CH1   0   0.005   0.3211  -2.5650  -0.2967
 U2S  O3'   O  OH1   0  -0.661   0.7304  -3.2475  -1.4464
 U2S  C2'   C  CH1   0  -0.049  -1.1612  -2.2202  -0.2410
 U2S  O2'   O  OH1   0  -0.659  -1.9229  -3.2896   0.2433
 U2S  C1'   C  CH1   0   0.192  -1.1436  -1.0117   0.7092
 U2S  O4    O  O     0  -0.463  -5.0369   2.7712  -0.0903
 U2S  C2    C  CR6   0   0.748  -2.2318   0.6745  -0.7180
 U2S  O2    O  O     0  -0.469  -1.4491   0.4844  -1.6237
 U2S  H5    H  HCR6  0   0.294  -4.7579   1.3307   2.1731
 U2S  H6    H  HCR6  0   0.329  -2.9653  -0.3255   2.3767
 U2S  HN3   H  HNR6  0   0.427  -3.2760   2.1067  -1.6847
 U2S  HAKA  H  HCH2  0   0.236   4.3508   2.2321  -1.9564
 U2S  HAM   H  HCH2  0   0.244   2.5615   0.5311  -1.7154
 U2S  HAMA  H  HCH2  0   0.199   4.1666  -0.1493  -1.4449
 U2S  HAJ   H  HCH2  0   0.236   5.5240   1.6897   1.8731
 U2S  HAJA  H  HCH2  0   0.200   3.8822   2.3076   1.6275
 U2S  HAL   H  HCH2  0   0.197   4.9085  -0.4949   0.9660
 U2S  HALA  H  HCH2  0   0.242   3.7606  -0.0336   2.2277
 U2S  H5'   H  HCH2  0   0.213   2.9651  -1.9276  -0.2728
 U2S  H5'A  H  HCH2  0   0.240   2.3417  -1.5586   1.3323
 U2S  H4'   H  HCH1  0   0.235   0.9353  -0.7449  -1.2468
 U2S  H3'   H  HCH1  0   0.225   0.5859  -3.1216   0.6161
 U2S  HO3'  H  HOH1  0   0.460   0.4608  -4.1676  -1.3695
 U2S  H2'   H  HCH1  0   0.254  -1.4819  -1.9223  -1.2438
 U2S  HO2'  H  HOH1  0   0.462  -2.8379  -3.1707  -0.0274
 U2S  H1'   H  HCH1  0   0.261  -1.3240  -1.3722   1.7273
 U2S  HAK   H  HCH2  0   0.200   3.1705   2.6455  -0.7034

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
 U2S  C4   C5    single  1.442  0.020  1.442
 U2S  C4   N3    single  1.387  0.020  1.387
 U2S  C4   O4    double  1.217  0.020  1.217
 U2S  C5   C6    double  1.342  0.020  1.342
 U2S  C6   N1    single  1.367  0.020  1.367
 U2S  N1   C1'   single  1.462  0.020  1.462
 U2S  N1   C2    single  1.383  0.020  1.383
 U2S  N3   C2    single  1.370  0.020  1.370
 U2S  OAM  CAK   single  1.410  0.020  1.410
 U2S  OAM  CAJ   single  1.411  0.020  1.411
 U2S  CAK  CAM   single  1.516  0.020  1.516
 U2S  CAM  NBA   single  1.452  0.020  1.452
 U2S  CAJ  CAL   single  1.517  0.020  1.517
 U2S  CAL  NBA   single  1.451  0.020  1.451
 U2S  NBA  C5'   single  1.448  0.020  1.448
 U2S  C5'  C4'   single  1.514  0.020  1.514
 U2S  C4'  O4'   single  1.426  0.020  1.426
 U2S  C4'  C3'   single  1.524  0.020  1.524
 U2S  O4'  C1'   single  1.395  0.020  1.395
 U2S  C3'  O3'   single  1.398  0.020  1.398
 U2S  C3'  C2'   single  1.523  0.020  1.523
 U2S  C2'  O2'   single  1.399  0.020  1.399
 U2S  C2'  C1'   single  1.537  0.020  1.537
 U2S  C2   O2    double  1.212  0.020  1.212
 U2S  C5   H5    single  0.930  0.020  1.080
 U2S  C6   H6    single  0.930  0.020  1.080
 U2S  N3   HN3   single  0.860  0.020  1.020
 U2S  CAK  HAK   single  0.970  0.020  1.090
 U2S  CAK  HAKA  single  0.970  0.020  1.090
 U2S  CAM  HAM   single  0.970  0.020  1.090
 U2S  CAM  HAMA  single  0.970  0.020  1.090
 U2S  CAJ  HAJ   single  0.970  0.020  1.090
 U2S  CAJ  HAJA  single  0.970  0.020  1.090
 U2S  CAL  HAL   single  0.970  0.020  1.090
 U2S  CAL  HALA  single  0.970  0.020  1.090
 U2S  C5'  H5'   single  0.970  0.020  1.090
 U2S  C5'  H5'A  single  0.970  0.020  1.090
 U2S  C4'  H4'   single  0.970  0.020  1.090
 U2S  C3'  H3'   single  0.970  0.020  1.090
 U2S  O3'  HO3'  single  0.850  0.020  0.980
 U2S  C2'  H2'   single  0.970  0.020  1.090
 U2S  O2'  HO2'  single  0.850  0.020  0.980
 U2S  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
 U2S  O4    C4   N3   120.58  3.000
 U2S  O4    C4   C5   126.12  3.000
 U2S  N3    C4   C5   113.29  3.000
 U2S  H5    C5   C6   120.62  3.000
 U2S  H5    C5   C4   119.91  3.000
 U2S  C6    C5   C4   119.47  3.000
 U2S  H6    C6   N1   115.32  3.000
 U2S  H6    C6   C5   121.04  3.000
 U2S  N1    C6   C5   123.64  3.000
 U2S  C2    N1   C1'  119.92  3.000
 U2S  C2    N1   C6   120.66  3.000
 U2S  C1'   N1   C6   119.37  3.000
 U2S  HN3   N3   C2   114.97  3.000
 U2S  HN3   N3   C4   116.77  3.000
 U2S  C2    N3   C4   128.26  3.000
 U2S  CAJ   OAM  CAK  110.88  3.000
 U2S  HAKA  CAK  HAK  107.86  3.000
 U2S  HAKA  CAK  CAM  110.01  3.000
 U2S  HAK   CAK  CAM  109.25  3.000
 U2S  HAKA  CAK  OAM  107.43  3.000
 U2S  HAK   CAK  OAM  110.59  3.000
 U2S  CAM   CAK  OAM  111.62  3.000
 U2S  HAMA  CAM  HAM  106.92  3.000
 U2S  HAMA  CAM  NBA  111.54  3.000
 U2S  HAM   CAM  NBA  110.23  3.000
 U2S  HAMA  CAM  CAK  109.59  3.000
 U2S  HAM   CAM  CAK  108.39  3.000
 U2S  NBA   CAM  CAK  110.07  3.000
 U2S  HAJA  CAJ  HAJ  107.93  3.000
 U2S  HAJA  CAJ  CAL  109.06  3.000
 U2S  HAJ   CAJ  CAL  110.14  3.000
 U2S  HAJA  CAJ  OAM  110.47  3.000
 U2S  HAJ   CAJ  OAM  107.46  3.000
 U2S  CAL   CAJ  OAM  111.70  3.000
 U2S  HALA  CAL  HAL  107.10  3.000
 U2S  HALA  CAL  NBA  109.43  3.000
 U2S  HAL   CAL  NBA  112.08  3.000
 U2S  HALA  CAL  CAJ  108.62  3.000
 U2S  HAL   CAL  CAJ  109.63  3.000
 U2S  NBA   CAL  CAJ  109.88  3.000
 U2S  C5'   NBA  CAL  112.30  3.000
 U2S  C5'   NBA  CAM  112.77  3.000
 U2S  CAL   NBA  CAM  109.65  3.000
 U2S  H5'A  C5'  H5'  106.55  3.000
 U2S  H5'A  C5'  C4'  108.16  3.000
 U2S  H5'   C5'  C4'  108.44  3.000
 U2S  H5'A  C5'  NBA  108.63  3.000
 U2S  H5'   C5'  NBA  112.15  3.000
 U2S  C4'   C5'  NBA  112.67  3.000
 U2S  H4'   C4'  C3'  108.61  3.000
 U2S  H4'   C4'  O4'  109.42  3.000
 U2S  C3'   C4'  O4'  104.72  3.000
 U2S  H4'   C4'  C5'  110.75  3.000
 U2S  C3'   C4'  C5'  113.56  3.000
 U2S  O4'   C4'  C5'  109.57  3.000
 U2S  C1'   O4'  C4'  110.41  3.000
 U2S  H3'   C3'  C2'  108.55  3.000
 U2S  H3'   C3'  O3'  111.37  3.000
 U2S  C2'   C3'  O3'  115.18  3.000
 U2S  H3'   C3'  C4'  109.09  3.000
 U2S  C2'   C3'  C4'  101.71  3.000
 U2S  O3'   C3'  C4'  110.43  3.000
 U2S  HO3'  O3'  C3'  108.61  3.000
 U2S  H2'   C2'  C1'  110.84  3.000
 U2S  H2'   C2'  O2'  111.45  3.000
 U2S  C1'   C2'  O2'  113.14  3.000
 U2S  H2'   C2'  C3'  108.27  3.000
 U2S  C1'   C2'  C3'  100.92  3.000
 U2S  O2'   C2'  C3'  111.68  3.000
 U2S  HO2'  O2'  C2'  109.03  3.000
 U2S  H1'   C1'  C2'  108.30  3.000
 U2S  H1'   C1'  O4'  109.96  3.000
 U2S  C2'   C1'  O4'  107.63  3.000
 U2S  H1'   C1'  N1   104.64  3.000
 U2S  C2'   C1'  N1   115.41  3.000
 U2S  O4'   C1'  N1   110.80  3.000
 U2S  O2    C2   N3   122.07  3.000
 U2S  O2    C2   N1   123.26  3.000
 U2S  N3    C2   N1   114.67  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
 U2S  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 U2S  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 U2S  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 U2S  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 U2S  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 U2S  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 U2S  CONST_07  O2   C2   N1   C1'    0.00   0.0  0
 U2S  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 U2S  CONST_09  HN3  N3   C4   C5   180.00   0.0  0
 U2S  Var_01    NBA  CAM  CAK  OAM   57.18  30.0  1
 U2S  Var_02    NBA  CAL  CAJ  OAM  -57.33  30.0  1
 U2S  Var_03    CAL  CAJ  OAM  CAK   57.01  30.0  1
 U2S  Var_04    CAL  NBA  CAM  CAK  -56.91  30.0  1
 U2S  Var_05    CAJ  CAL  NBA  CAM   56.90  30.0  1
 U2S  Var_06    C4'  C5'  NBA  CAM  -76.05  30.0  3
 U2S  Var_07    HAK  CAK  OAM  CAJ   64.99  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
 U2S  chir_01  C4'  C5'  O4'  C3'  positiv
 U2S  chir_02  C3'  O3'  C4'  C2'  negativ
 U2S  chir_03  C2'  O2'  C3'  C1'  positiv
 U2S  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
 U2S  plan-1  C4   0.020
 U2S  plan-1  C5   0.020
 U2S  plan-1  C6   0.020
 U2S  plan-1  N1   0.020
 U2S  plan-1  N3   0.020
 U2S  plan-1  C1'  0.020
 U2S  plan-1  O4   0.020
 U2S  plan-1  C2   0.020
 U2S  plan-1  O2   0.020
 U2S  plan-1  H5   0.020
 U2S  plan-1  H6   0.020
 U2S  plan-1  HN3  0.020

