# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 18 18:35:46 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-({(5R)-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methyl-2,4-dioxohexahydropyrimidin-5-yl}methyl)pyrimidine-2,4(1H,3H)-dione (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O)CC3=CN([C@H]4C[C@H](O)[C@@H](CO)O4)C(=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
 0TT  0TT  '1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-({(5R)-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methyl-2,4-dioxohexahydropyrimidin-5-yl}methyl)pyrimidine-2,4(1H,3H)-dione (non-preferred name)'  ligand  62  34  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0TT
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
 0TT  O8   O  OH1   0  -0.673   4.9817   3.3860  -0.6933
 0TT  C6   C  CH2   0  -0.162   5.6310   2.1728  -0.9932
 0TT  C5   C  CH1   0   0.026   5.7589   1.3432   0.2605
 0TT  O7   O  O2    0  -0.493   4.4807   0.9316   0.7045
 0TT  C4   C  CH1   0   0.018   6.5762   0.0694   0.0407
 0TT  O9   O  OH1   0  -0.671   7.9325   0.3475   0.2931
 0TT  C3   C  CH2   0  -0.550   5.9302  -0.9111   1.0171
 0TT  C2   C  CH1   0   0.226   4.5193  -0.3585   1.2640
 0TT  N3   N  NR6   0  -0.522   3.4108  -1.1408   0.7554
 0TT  CJ   C  C     0  -0.266   2.4157  -1.6739   1.6678
 0TT  CK   C  CR6   0   0.729   3.3292  -1.4428  -0.5580
 0TT  O5   O  O     0  -0.482   4.1794  -1.1912  -1.3895
 0TT  N4   N  NR16  0  -0.716   2.1675  -2.1112  -0.9362
 0TT  CL   C  CR6   0   0.618   0.9748  -2.1403  -0.2656
 0TT  O6   O  O     0  -0.437  -0.0130  -2.6347  -0.7631
 0TT  CI   C  CR6   0  -0.280   1.0017  -1.5179   1.1157
 0TT  C1   C  CH3   0  -0.650   0.0249  -2.2480   2.0288
 0TT  CH   C  CH2   0  -0.481   0.6472  -0.0095   1.0323
 0TT  CF   C  CR6   0  -0.160  -0.6153   0.3002   0.2945
 0TT  CE   C  CR16  0   0.053  -1.8029   0.4364   0.9106
 0TT  CG   C  CR6   0   0.568  -0.5743   0.4658  -1.1440
 0TT  O4   O  O     0  -0.450   0.4305   0.4024  -1.8281
 0TT  N2   N  NR16  0  -0.735  -1.8049   0.7182  -1.7203
 0TT  CB   C  CR6   0   0.740  -3.0206   0.8478  -1.1002
 0TT  O3   O  O     0  -0.469  -4.0363   1.0748  -1.7220
 0TT  N1   N  NR6   0  -0.571  -2.9805   0.7090   0.2697
 0TT  CD   C  CH1   0   0.219  -4.2153   0.8039   1.0500
 0TT  OB   O  O2    0  -0.490  -5.0660  -0.2453   0.6908
 0TT  CM   C  CH2   0  -0.560  -5.0012   2.1104   0.9047
 0TT  CA   C  CH1   0   0.023  -6.3098   1.7073   0.2235
 0TT  O1   O  OH1   0  -0.669  -7.4568   2.3423   0.7298
 0TT  C9   C  CH1   0   0.022  -6.3988   0.2115   0.5287
 0TT  C8   C  CH2   0  -0.165  -7.0852  -0.5709  -0.5632
 0TT  OA   O  OH1   0  -0.672  -7.2391  -1.9092  -0.1533
 0TT  H1   H  HOH1  0   0.455   4.8744   3.8771  -1.5127
 0TT  H2   H  HCH2  0   0.202   5.0834   1.5879  -1.7429
 0TT  H3   H  HCH2  0   0.198   6.6430   2.3413  -1.3854
 0TT  H4   H  HCH1  0   0.217   6.2543   1.9382   1.0433
 0TT  H5   H  HCH1  0   0.228   6.4409  -0.2835  -0.9852
 0TT  H6   H  HOH1  0   0.455   8.4554  -0.3872  -0.0403
 0TT  H7   H  HCH2  0   0.266   5.9245  -1.9407   0.6636
 0TT  H8   H  HCH2  0   0.256   6.4866  -0.8909   1.9564
 0TT  H9   H  HCH1  0   0.242   4.3384  -0.2969   2.3406
 0TT  H10  H  H     0   0.270   2.6146  -2.7309   1.8774
 0TT  H11  H  H     0   0.274   2.4950  -1.1400   2.6142
 0TT  H12  H  HNR6  0   0.412   2.1516  -2.4162  -1.9010
 0TT  H13  H  HCH3  0   0.248   0.2497  -3.3139   2.0812
 0TT  H14  H  HCH3  0   0.242   0.0895  -1.8442   3.0401
 0TT  H15  H  HCH3  0   0.251  -1.0040  -2.1411   1.6889
 0TT  H16  H  HCH2  0   0.272   0.5652   0.3476   2.0615
 0TT  H17  H  HCH2  0   0.275   1.4739   0.5418   0.5796
 0TT  H18  H  HCR6  0   0.321  -1.8823   0.3389   1.9852
 0TT  H19  H  HNR6  0   0.426  -1.8217   0.8290  -2.7267
 0TT  H20  H  HCH1  0   0.255  -3.8860   0.6833   2.0852
 0TT  H21  H  HCH2  0   0.268  -5.2217   2.4962   1.9015
 0TT  H22  H  HCH2  0   0.275  -4.4505   2.8817   0.3689
 0TT  H23  H  HCH1  0   0.232  -6.2272   1.8613  -0.8559
 0TT  H24  H  HOH1  0   0.457  -7.4982   3.2288   0.3600
 0TT  H25  H  HCH1  0   0.227  -6.9500   0.0829   1.4725
 0TT  H26  H  HCH2  0   0.203  -8.0528  -0.0895  -0.7577
 0TT  H27  H  HCH2  0   0.203  -6.4917  -0.4900  -1.4828
 0TT  H28  H  HOH1  0   0.456  -7.6580  -2.3944  -0.8697

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
 0TT  C1  CI   single  1.523  0.020  1.523
 0TT  O6  CL   double  1.211  0.020  1.211
 0TT  CI  CL   single  1.515  0.020  1.515
 0TT  CI  CH   single  1.552  0.020  1.552
 0TT  CI  CJ   single  1.526  0.020  1.526
 0TT  CL  N4   single  1.369  0.020  1.369
 0TT  CH  CF   single  1.495  0.020  1.495
 0TT  CJ  N3   single  1.452  0.020  1.452
 0TT  N4  CK   single  1.393  0.020  1.393
 0TT  CF  CE   double  1.345  0.020  1.345
 0TT  CF  CG   single  1.449  0.020  1.449
 0TT  O4  CG   double  1.217  0.020  1.217
 0TT  CE  N1   single  1.368  0.020  1.368
 0TT  CG  N2   single  1.382  0.020  1.382
 0TT  N3  CK   single  1.350  0.020  1.350
 0TT  N3  C2   single  1.449  0.020  1.449
 0TT  CK  O5   double  1.216  0.020  1.216
 0TT  CM  CD   single  1.532  0.020  1.532
 0TT  CM  CA   single  1.529  0.020  1.529
 0TT  N1  CD   single  1.464  0.020  1.464
 0TT  N1  CB   single  1.377  0.020  1.377
 0TT  N2  CB   single  1.371  0.020  1.371
 0TT  C2  O7   single  1.407  0.020  1.407
 0TT  C2  C3   single  1.535  0.020  1.535
 0TT  CD  OB   single  1.398  0.020  1.398
 0TT  CA  O1   single  1.405  0.020  1.405
 0TT  CA  C9   single  1.529  0.020  1.529
 0TT  CB  O3   double  1.212  0.020  1.212
 0TT  O7  C5   single  1.414  0.020  1.414
 0TT  C3  C4   single  1.527  0.020  1.527
 0TT  OB  C9   single  1.418  0.020  1.418
 0TT  C9  C8   single  1.508  0.020  1.508
 0TT  C8  OA   single  1.408  0.020  1.408
 0TT  C5  C4   single  1.529  0.020  1.529
 0TT  C5  C6   single  1.509  0.020  1.509
 0TT  C4  O9   single  1.407  0.020  1.407
 0TT  O8  C6   single  1.408  0.020  1.408
 0TT  O8  H1   single  0.850  0.020  0.980
 0TT  C6  H2   single  0.970  0.020  1.090
 0TT  C6  H3   single  0.970  0.020  1.090
 0TT  C5  H4   single  0.970  0.020  1.090
 0TT  C4  H5   single  0.970  0.020  1.090
 0TT  O9  H6   single  0.850  0.020  0.980
 0TT  C3  H7   single  0.970  0.020  1.090
 0TT  C3  H8   single  0.970  0.020  1.090
 0TT  C2  H9   single  0.970  0.020  1.090
 0TT  CJ  H10  single  0.970  0.020  1.090
 0TT  CJ  H11  single  0.970  0.020  1.090
 0TT  N4  H12  single  0.860  0.020  1.020
 0TT  C1  H13  single  0.970  0.020  1.090
 0TT  C1  H14  single  0.970  0.020  1.090
 0TT  C1  H15  single  0.970  0.020  1.090
 0TT  CH  H16  single  0.970  0.020  1.090
 0TT  CH  H17  single  0.970  0.020  1.090
 0TT  CE  H18  single  0.930  0.020  1.080
 0TT  N2  H19  single  0.860  0.020  1.020
 0TT  CD  H20  single  0.970  0.020  1.090
 0TT  CM  H21  single  0.970  0.020  1.090
 0TT  CM  H22  single  0.970  0.020  1.090
 0TT  CA  H23  single  0.970  0.020  1.090
 0TT  O1  H24  single  0.850  0.020  0.980
 0TT  C9  H25  single  0.970  0.020  1.090
 0TT  C8  H26  single  0.970  0.020  1.090
 0TT  C8  H27  single  0.970  0.020  1.090
 0TT  OA  H28  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
 0TT  H1   O8  C6   108.06  3.000
 0TT  H3   C6  H2   107.32  3.000
 0TT  H3   C6  C5   107.63  3.000
 0TT  H2   C6  C5   108.48  3.000
 0TT  H3   C6  O8   111.64  3.000
 0TT  H2   C6  O8   112.00  3.000
 0TT  C5   C6  O8   109.62  3.000
 0TT  H4   C5  C4   108.17  3.000
 0TT  H4   C5  O7   109.92  3.000
 0TT  C4   C5  O7   106.60  3.000
 0TT  H4   C5  C6   109.38  3.000
 0TT  C4   C5  C6   112.57  3.000
 0TT  O7   C5  C6   110.14  3.000
 0TT  C2   O7  C5   111.53  3.000
 0TT  H5   C4  C3   109.90  3.000
 0TT  H5   C4  O9   110.57  3.000
 0TT  C3   C4  O9   114.83  3.000
 0TT  H5   C4  C5   109.73  3.000
 0TT  O9   C4  C5   108.94  3.000
 0TT  C3   C4  C5   102.52  3.000
 0TT  H6   O9  C4   108.12  3.000
 0TT  H8   C3  H7   107.43  3.000
 0TT  H8   C3  C2   108.86  3.000
 0TT  H7   C3  C2   112.82  3.000
 0TT  H8   C3  C4   108.82  3.000
 0TT  H7   C3  C4   113.69  3.000
 0TT  C2   C3  C4   105.10  3.000
 0TT  H9   C2  N3   104.44  3.000
 0TT  H9   C2  C3   109.31  3.000
 0TT  N3   C2  C3   116.89  3.000
 0TT  H9   C2  O7   109.60  3.000
 0TT  C3   C2  O7   106.94  3.000
 0TT  N3   C2  O7   109.55  3.000
 0TT  CK   N3  CJ   119.20  3.000
 0TT  CK   N3  C2   120.56  3.000
 0TT  CJ   N3  C2   120.14  3.000
 0TT  H11  CJ  H10  107.06  3.000
 0TT  H11  CJ  CI   109.37  3.000
 0TT  H10  CJ  CI   109.64  3.000
 0TT  H11  CJ  N3   108.43  3.000
 0TT  H10  CJ  N3   110.49  3.000
 0TT  CI   CJ  N3   111.73  3.000
 0TT  N4   CK  O5   119.81  3.000
 0TT  O5   CK  N3   125.23  3.000
 0TT  N4   CK  N3   114.96  3.000
 0TT  H12  N4  CL   116.55  3.000
 0TT  H12  N4  CK   114.62  3.000
 0TT  CL   N4  CK   127.17  3.000
 0TT  CI   CL  O6   123.81  3.000
 0TT  CI   CL  N4   114.99  3.000
 0TT  O6   CL  N4   121.20  3.000
 0TT  CH   CI  C1   110.58  3.000
 0TT  CH   CI  CL   110.26  3.000
 0TT  C1   CI  CL   109.76  3.000
 0TT  CH   CI  CJ   109.30  3.000
 0TT  CL   CI  CJ   107.72  3.000
 0TT  C1   CI  CJ   109.16  3.000
 0TT  H15  C1  H14  108.00  3.000
 0TT  H15  C1  H13  107.80  3.000
 0TT  H14  C1  H13  107.76  3.000
 0TT  H15  C1  CI   111.82  3.000
 0TT  H14  C1  CI   109.89  3.000
 0TT  H13  C1  CI   111.41  3.000
 0TT  H17  CH  H16  106.40  3.000
 0TT  H17  CH  CF   109.29  3.000
 0TT  H16  CH  CF   109.51  3.000
 0TT  H17  CH  CI   109.88  3.000
 0TT  H16  CH  CI   106.51  3.000
 0TT  CF   CH  CI   114.89  3.000
 0TT  CG   CF  CE   117.92  3.000
 0TT  CG   CF  CH   119.34  3.000
 0TT  CE   CF  CH   122.74  3.000
 0TT  H18  CE  N1   114.84  3.000
 0TT  H18  CE  CF   120.71  3.000
 0TT  N1   CE  CF   124.45  3.000
 0TT  N2   CG  O4   120.67  3.000
 0TT  N2   CG  CF   114.19  3.000
 0TT  O4   CG  CF   125.13  3.000
 0TT  H19  N2  CB   115.12  3.000
 0TT  H19  N2  CG   116.69  3.000
 0TT  CB   N2  CG   128.19  3.000
 0TT  N1   CB  O3   123.59  3.000
 0TT  O3   CB  N2   121.91  3.000
 0TT  N1   CB  N2   114.49  3.000
 0TT  CD   N1  CB   119.94  3.000
 0TT  CB   N1  CE   120.73  3.000
 0TT  CD   N1  CE   119.29  3.000
 0TT  H20  CD  CM   109.80  3.000
 0TT  H20  CD  OB   110.12  3.000
 0TT  CM   CD  OB   107.68  3.000
 0TT  H20  CD  N1   104.10  3.000
 0TT  OB   CD  N1   109.13  3.000
 0TT  CM   CD  N1   115.95  3.000
 0TT  C9   OB  CD   111.07  3.000
 0TT  H22  CM  H21  107.53  3.000
 0TT  H22  CM  CA   113.60  3.000
 0TT  H21  CM  CA   109.10  3.000
 0TT  H22  CM  CD   113.04  3.000
 0TT  H21  CM  CD   108.57  3.000
 0TT  CA   CM  CD   104.86  3.000
 0TT  H23  CA  C9   109.83  3.000
 0TT  H23  CA  O1   110.72  3.000
 0TT  C9   CA  O1   108.81  3.000
 0TT  H23  CA  CM   109.75  3.000
 0TT  C9   CA  CM   102.63  3.000
 0TT  O1   CA  CM   114.75  3.000
 0TT  H24  O1  CA   108.25  3.000
 0TT  H25  C9  C8   109.40  3.000
 0TT  H25  C9  CA   108.34  3.000
 0TT  C8   C9  CA   112.91  3.000
 0TT  H25  C9  OB   109.57  3.000
 0TT  C8   C9  OB   110.08  3.000
 0TT  CA   C9  OB   106.45  3.000
 0TT  H27  C8  H26  107.20  3.000
 0TT  H27  C8  OA   111.91  3.000
 0TT  H26  C8  OA   111.83  3.000
 0TT  H27  C8  C9   108.80  3.000
 0TT  H26  C8  C9   107.57  3.000
 0TT  OA   C8  C9   109.39  3.000
 0TT  H28  OA  C8   108.08  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
 0TT  CONST_01  N4   CK  N3  C2  180.00   0.0  0
 0TT  CONST_03  N4   CK  N3  CJ    0.00   0.0  0
 0TT  CONST_04  CI   CL  N4  CK    0.00   0.0  0
 0TT  CONST_05  CB   N2  CG  CF    0.00   0.0  0
 0TT  CONST_06  N2   CB  N1  CE    0.00   0.0  0
 0TT  CONST_07  N1   CB  N2  CG    0.00   0.0  0
 0TT  CONST_08  CD   N1  CB  N2  180.00   0.0  0
 0TT  CONST_09  O5   CK  N3  C2    0.00   0.0  0
 0TT  CONST_10  O5   CK  N3  CJ  180.00   0.0  0
 0TT  CONST_11  O6   CL  N4  CK  180.00   0.0  0
 0TT  CONST_13  O3   CB  N1  CE  180.00   0.0  0
 0TT  CONST_14  O3   CB  N2  CG  180.00   0.0  0
 0TT  CONST_15  CB   N2  CG  O4  180.00   0.0  0
 0TT  CONST_16  CD   N1  CB  O3    0.00   0.0  0
 0TT  CONST_17  H12  N4  CK  N3  180.00   0.0  0
 0TT  CONST_18  H19  N2  CG  CF  180.00   0.0  0
 0TT  Var_01    CE   CF  CH  CI   93.61  30.0  3
 0TT  Var_02    H10  CJ  N3  C2  -99.88  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
 0TT  chir_01  C5  O7  C4  C6  negativ
 0TT  chir_02  C4  O9  C5  C3  positiv
 0TT  chir_03  C2  O7  N3  C3  negativ
 0TT  chir_04  CI  CJ  CL  C1  negativ
 0TT  chir_05  CD  OB  N1  CM  negativ
 0TT  chir_06  CA  O1  C9  CM  positiv
 0TT  chir_07  C9  OB  CA  C8  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
 0TT  plan-1  C2   0.020
 0TT  plan-1  N3   0.020
 0TT  plan-1  CJ   0.020
 0TT  plan-1  CK   0.020
 0TT  plan-1  O5   0.020
 0TT  plan-1  N4   0.020
 0TT  plan-1  CL   0.020
 0TT  plan-1  O6   0.020
 0TT  plan-1  CI   0.020
 0TT  plan-1  H12  0.020
 0TT  plan-2  CH   0.020
 0TT  plan-2  CF   0.020
 0TT  plan-2  CE   0.020
 0TT  plan-2  CG   0.020
 0TT  plan-2  O4   0.020
 0TT  plan-2  N2   0.020
 0TT  plan-2  CB   0.020
 0TT  plan-2  O3   0.020
 0TT  plan-2  N1   0.020
 0TT  plan-2  CD   0.020
 0TT  plan-2  H18  0.020
 0TT  plan-2  H19  0.020

