# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 13:24:15 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-(5-deoxy-5-pyrrolidin-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]1CN2CCCC2)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
 U4S  U4S  1-(5-deoxy-5-pyrrolidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione  ligand  40  21  .  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_U4S
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
 U4S  C4    C  CR6   0   0.567  -4.1363   1.6917   0.0479
 U4S  C5    C  CR16  0  -0.513  -3.9645   0.9564   1.2757
 U4S  C6    C  CR16  0   0.101  -2.8956   0.1580   1.4232
 U4S  N1    N  NR6   0  -0.568  -1.9418  -0.0146   0.4606
 U4S  N3    N  NR16  0  -0.734  -3.1198   1.4723  -0.8699
 U4S  CAJ   C  CH2   0  -0.272   4.4682   0.6442   1.0562
 U4S  C5'   C  CH2   0  -0.276   2.7066  -0.8324   0.3165
 U4S  C4'   C  CH1   0   0.008   1.2972  -0.9379  -0.2215
 U4S  O4'   O  O2    0  -0.486   0.3981  -0.2398   0.6383
 U4S  C3'   C  CH1   0  -0.001   0.7662  -2.3668  -0.2548
 U4S  O3'   O  OH1   0  -0.663   1.2256  -3.0272  -1.4006
 U4S  C2'   C  CH1   0  -0.048  -0.7423  -2.1331  -0.1979
 U4S  O2'   O  OH1   0  -0.662  -1.5047  -3.1682   0.3590
 U4S  C1'   C  CH1   0   0.209  -0.8191  -0.9126   0.7217
 U4S  O4    O  O     0  -0.464  -5.0547   2.4458  -0.2143
 U4S  C2    C  CR6   0   0.746  -2.0250   0.6577  -0.7445
 U4S  O2    O  O     0  -0.468  -1.2041   0.5426  -1.6288
 U4S  CAI   C  CH2   0  -0.283   3.4193   1.1404  -0.9336
 U4S  CAG   C  CH2   0  -0.469   4.3006   2.3606  -0.6306
 U4S  CAH   C  CH2   0  -0.462   4.8890   2.0803   0.7670
 U4S  NAT   N  NT    0  -0.432   3.1973   0.5231   0.3648
 U4S  H5    H  HCR6  0   0.294  -4.6889   1.0574   2.0685
 U4S  H6    H  HCR6  0   0.328  -2.7372  -0.3994   2.3358
 U4S  HN3   H  HNR6  0   0.427  -3.1860   1.9675  -1.7515
 U4S  HAJA  H  HCH2  0   0.233   4.3555   0.4306   2.1214
 U4S  H5'   H  HCH2  0   0.235   2.7236  -1.2453   1.3299
 U4S  H5'A  H  HCH2  0   0.203   3.3528  -1.4808  -0.3023
 U4S  H4'   H  HCH1  0   0.236   1.2395  -0.5166  -1.2326
 U4S  H3'   H  HCH1  0   0.223   1.0770  -2.8891   0.6630
 U4S  HO3'  H  HOH1  0   0.460   1.0731  -3.9711  -1.2976
 U4S  H2'   H  HCH1  0   0.253  -1.0858  -1.8846  -1.2077
 U4S  HO2'  H  HOH1  0   0.463  -1.7206  -3.7990  -0.3336
 U4S  H1'   H  HCH1  0   0.261  -0.9788  -1.2617   1.7476
 U4S  HAI   H  HCH2  0   0.232   2.4780   1.4158  -1.4131
 U4S  HAIA  H  HCH2  0   0.194   3.9440   0.4519  -1.6176
 U4S  HAG   H  HCH2  0   0.234   5.0764   2.4721  -1.3877
 U4S  HAGA  H  HCH2  0   0.236   3.7176   3.2816  -0.6326
 U4S  HAH   H  HCH2  0   0.232   4.4594   2.7562   1.5074
 U4S  HAHA  H  HCH2  0   0.233   5.9711   2.2028   0.8046
 U4S  HAJ   H  HCH2  0   0.189   5.2185  -0.0602   0.6567

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
 U4S  C4   C5    single  1.441  0.020  1.441
 U4S  C4   N3    single  1.387  0.020  1.387
 U4S  C4   O4    double  1.217  0.020  1.217
 U4S  C5   C6    double  1.342  0.020  1.342
 U4S  C6   N1    single  1.366  0.020  1.366
 U4S  N1   C1'   single  1.461  0.020  1.461
 U4S  N1   C2    single  1.382  0.020  1.382
 U4S  N3   C2    single  1.370  0.020  1.370
 U4S  CAJ  CAH   single  1.524  0.020  1.524
 U4S  CAJ  NAT   single  1.452  0.020  1.452
 U4S  C5'  C4'   single  1.512  0.020  1.512
 U4S  C5'  NAT   single  1.442  0.020  1.442
 U4S  C4'  O4'   single  1.427  0.020  1.427
 U4S  C4'  C3'   single  1.525  0.020  1.525
 U4S  O4'  C1'   single  1.393  0.020  1.393
 U4S  C3'  O3'   single  1.400  0.020  1.400
 U4S  C3'  C2'   single  1.528  0.020  1.528
 U4S  C2'  O2'   single  1.401  0.020  1.401
 U4S  C2'  C1'   single  1.530  0.020  1.530
 U4S  C2   O2    double  1.212  0.020  1.212
 U4S  CAI  CAG   single  1.535  0.020  1.535
 U4S  CAI  NAT   single  1.455  0.020  1.455
 U4S  CAG  CAH   single  1.542  0.020  1.542
 U4S  C5   H5    single  0.930  0.020  1.080
 U4S  C6   H6    single  0.930  0.020  1.080
 U4S  N3   HN3   single  0.860  0.020  1.020
 U4S  CAJ  HAJ   single  0.970  0.020  1.090
 U4S  CAJ  HAJA  single  0.970  0.020  1.090
 U4S  C5'  H5'   single  0.970  0.020  1.090
 U4S  C5'  H5'A  single  0.970  0.020  1.090
 U4S  C4'  H4'   single  0.970  0.020  1.090
 U4S  C3'  H3'   single  0.970  0.020  1.090
 U4S  O3'  HO3'  single  0.850  0.020  0.980
 U4S  C2'  H2'   single  0.970  0.020  1.090
 U4S  O2'  HO2'  single  0.850  0.020  0.980
 U4S  C1'  H1'   single  0.970  0.020  1.090
 U4S  CAI  HAI   single  0.970  0.020  1.090
 U4S  CAI  HAIA  single  0.970  0.020  1.090
 U4S  CAG  HAG   single  0.970  0.020  1.090
 U4S  CAG  HAGA  single  0.970  0.020  1.090
 U4S  CAH  HAH   single  0.970  0.020  1.090
 U4S  CAH  HAHA  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
 U4S  O4    C4   N3   120.57  3.000
 U4S  O4    C4   C5   126.13  3.000
 U4S  N3    C4   C5   113.30  3.000
 U4S  H5    C5   C6   120.64  3.000
 U4S  H5    C5   C4   119.89  3.000
 U4S  C6    C5   C4   119.47  3.000
 U4S  H6    C6   N1   115.30  3.000
 U4S  H6    C6   C5   121.08  3.000
 U4S  N1    C6   C5   123.62  3.000
 U4S  C2    N1   C1'  120.06  3.000
 U4S  C2    N1   C6   120.72  3.000
 U4S  C1'   N1   C6   119.22  3.000
 U4S  HN3   N3   C2   114.98  3.000
 U4S  HN3   N3   C4   116.78  3.000
 U4S  C2    N3   C4   128.24  3.000
 U4S  HAJA  CAJ  HAJ  107.35  3.000
 U4S  HAJA  CAJ  NAT  110.97  3.000
 U4S  HAJ   CAJ  NAT  111.68  3.000
 U4S  HAJA  CAJ  CAH  113.44  3.000
 U4S  HAJ   CAJ  CAH  110.18  3.000
 U4S  NAT   CAJ  CAH  103.30  3.000
 U4S  H5'A  C5'  H5'  106.74  3.000
 U4S  H5'A  C5'  NAT  111.79  3.000
 U4S  H5'   C5'  NAT  108.56  3.000
 U4S  H5'A  C5'  C4'  107.75  3.000
 U4S  H5'   C5'  C4'  108.51  3.000
 U4S  NAT   C5'  C4'  113.24  3.000
 U4S  H4'   C4'  C3'  108.75  3.000
 U4S  H4'   C4'  O4'  109.54  3.000
 U4S  C3'   C4'  O4'  104.61  3.000
 U4S  H4'   C4'  C5'  110.50  3.000
 U4S  C3'   C4'  C5'  113.44  3.000
 U4S  O4'   C4'  C5'  109.80  3.000
 U4S  C1'   O4'  C4'  110.51  3.000
 U4S  H3'   C3'  C2'  108.68  3.000
 U4S  H3'   C3'  O3'  111.47  3.000
 U4S  C2'   C3'  O3'  115.26  3.000
 U4S  H3'   C3'  C4'  109.15  3.000
 U4S  C2'   C3'  C4'  101.52  3.000
 U4S  O3'   C3'  C4'  110.22  3.000
 U4S  HO3'  O3'  C3'  108.86  3.000
 U4S  H2'   C2'  C1'  110.94  3.000
 U4S  H2'   C2'  O2'  111.32  3.000
 U4S  C1'   C2'  O2'  108.85  3.000
 U4S  H2'   C2'  C3'  108.06  3.000
 U4S  C1'   C2'  C3'  101.19  3.000
 U4S  O2'   C2'  C3'  116.05  3.000
 U4S  HO2'  O2'  C2'  108.70  3.000
 U4S  H1'   C1'  C2'  108.42  3.000
 U4S  H1'   C1'  O4'  109.72  3.000
 U4S  C2'   C1'  O4'  107.78  3.000
 U4S  H1'   C1'  N1   104.55  3.000
 U4S  C2'   C1'  N1   114.92  3.000
 U4S  O4'   C1'  N1   111.33  3.000
 U4S  O2    C2   N3   122.06  3.000
 U4S  O2    C2   N1   123.30  3.000
 U4S  N3    C2   N1   114.64  3.000
 U4S  HAIA  CAI  HAI  107.17  3.000
 U4S  HAIA  CAI  NAT  111.16  3.000
 U4S  HAI   CAI  NAT  111.56  3.000
 U4S  HAIA  CAI  CAG  110.20  3.000
 U4S  HAI   CAI  CAG  112.40  3.000
 U4S  NAT   CAI  CAG  104.40  3.000
 U4S  HAGA  CAG  HAG  107.04  3.000
 U4S  HAGA  CAG  CAH  111.06  3.000
 U4S  HAG   CAG  CAH  112.12  3.000
 U4S  HAGA  CAG  CAI  111.35  3.000
 U4S  HAG   CAG  CAI  110.66  3.000
 U4S  CAH   CAG  CAI  104.68  3.000
 U4S  HAHA  CAH  HAH  107.33  3.000
 U4S  HAHA  CAH  CAG  112.94  3.000
 U4S  HAH   CAH  CAG  110.63  3.000
 U4S  HAHA  CAH  CAJ  111.94  3.000
 U4S  HAH   CAH  CAJ  110.26  3.000
 U4S  CAG   CAH  CAJ  103.76  3.000
 U4S  CAI   NAT  C5'  114.89  3.000
 U4S  CAI   NAT  CAJ  104.84  3.000
 U4S  C5'   NAT  CAJ  113.09  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
 U4S  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 U4S  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 U4S  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 U4S  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 U4S  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 U4S  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 U4S  CONST_07  O2   C2   N1   C1'    0.00   0.0  0
 U4S  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 U4S  CONST_09  HN3  N3   C4   C5   180.00   0.0  0
 U4S  Var_01    CAI  CAG  CAH  CAJ    8.14  30.0  1
 U4S  Var_02    CAG  CAI  NAT  CAJ  -39.11  30.0  1
 U4S  Var_03    CAH  CAJ  NAT  CAI   44.57  30.0  1
 U4S  Var_04    NAT  CAJ  CAH  CAG  -31.60  30.0  1
 U4S  Var_05    NAT  CAI  CAG  CAH   18.05  30.0  1
 U4S  Var_06    C4'  C5'  NAT  CAJ  171.65  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
 U4S  chir_01  C4'  C5'  O4'  C3'  positiv
 U4S  chir_02  C3'  O3'  C4'  C2'  negativ
 U4S  chir_03  C2'  O2'  C3'  C1'  positiv
 U4S  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
 U4S  plan-1  C4   0.020
 U4S  plan-1  C5   0.020
 U4S  plan-1  C6   0.020
 U4S  plan-1  N1   0.020
 U4S  plan-1  N3   0.020
 U4S  plan-1  C1'  0.020
 U4S  plan-1  O4   0.020
 U4S  plan-1  C2   0.020
 U4S  plan-1  O2   0.020
 U4S  plan-1  H5   0.020
 U4S  plan-1  H6   0.020
 U4S  plan-1  HN3  0.020

