# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 30 12:20:58 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 5'-deoxy-5'-{[(2R)-3-hydroxy-2-(4-phenyl-1H-1,2,3-triazol-1-yl)propanoyl]amino}uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](n1cc(nn1)c2ccccc2)C(=O)NC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=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
 48E  48E  5'-deoxy-5'-{[(2R)-3-hydroxy-2-(4-phenyl-1H-1,2,3-triazol-1-yl)propanoyl]amino}uridine  ligand  55  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_48E
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
 48E  OAG  O  O     0  -0.479   6.7050  -0.7222   0.3544
 48E  CAB  C  CR6   0   0.741   5.8267  -1.1790  -0.3485
 48E  NAA  N  NR16  0  -0.731   6.0426  -2.2083  -1.2233
 48E  CAC  C  CR6   0   0.567   5.1303  -2.7955  -2.0879
 48E  OAH  O  O     0  -0.464   5.4716  -3.7010  -2.8259
 48E  CAE  C  CR16  0  -0.509   3.8104  -2.2248  -1.9960
 48E  CAF  C  CR16  0   0.091   3.5738  -1.2223  -1.1327
 48E  NAD  N  NR6   0  -0.568   4.5356  -0.6933  -0.3253
 48E  CAI  C  CR15  0   0.188   4.2763   0.4196   0.6114
 48E  OAL  O  O     0  -0.502   2.9051   0.5248   0.8422
 48E  CAK  C  CR15  0  -0.043   4.7369   1.7629   0.0414
 48E  OAN  O  OH1   0  -0.663   5.1170   2.5708   1.1204
 48E  CAJ  C  CR15  0  -0.029   3.4444   2.2793  -0.6029
 48E  OAO  O  OH1   0  -0.655   3.3772   3.6717  -0.7036
 48E  CAM  C  CR15  0   0.005   2.3892   1.7706   0.3720
 48E  CAP  C  CH2   0  -0.281   1.0297   1.5635  -0.2568
 48E  NAQ  N  NH1   0  -0.642   0.0875   1.0241   0.6973
 48E  C    C  C     0   0.584  -1.2199   1.3019   0.6711
 48E  O    O  O     0  -0.471  -1.7542   2.0522  -0.1269
 48E  CA   C  CH1   0  -0.288  -2.0376   0.6302   1.7743
 48E  CB   C  CH2   0  -0.132  -2.4864   1.6780   2.7842
 48E  OG   O  OH1   0  -0.658  -3.2171   1.0229   3.7835
 48E  N    N  NR5   0  -0.253  -3.1651  -0.0614   1.1859
 48E  CAY  C  CR15  0  -0.071  -4.2783   0.4454   0.6349
 48E  NAX  N  N     0  -0.083  -3.1602  -1.3839   1.1152
 48E  NAZ  N  N     0  -0.320  -4.2438  -1.7517   0.5345
 48E  CBA  C  CR5   0   0.158  -4.9787  -0.6606   0.2132
 48E  CBB  C  CR6   0   0.064  -6.2721  -0.7481  -0.4599
 48E  CBF  C  CR16  0  -0.290  -6.8337  -1.9905  -0.7583
 48E  CBD  C  CR16  0  -0.239  -8.0614  -2.0733  -1.3975
 48E  CBC  C  CR16  0  -0.266  -8.7490  -0.9194  -1.7508
 48E  CBE  C  CR16  0  -0.235  -8.1969   0.3210  -1.4575
 48E  CBG  C  CR16  0  -0.337  -6.9694   0.4063  -0.8190
 48E  H1   H  HNR6  0   0.428   6.9902  -2.5652  -1.2442
 48E  H2   H  HCR6  0   0.293   3.0156  -2.6110  -2.6147
 48E  H3   H  HCR6  0   0.327   2.5843  -0.8037  -1.0400
 48E  H4   H  HCR5  0   0.290   4.7951   0.1786   1.5406
 48E  H5   H  HCR5  0   0.264   5.5448   1.6481  -0.6897
 48E  H6   H  HOH1  0   0.453   4.9758   3.4909   0.8652
 48E  H7   H  HCR5  0   0.248   3.3092   1.7992  -1.5812
 48E  H8   H  HOH1  0   0.471   3.7935   3.9483  -1.5262
 48E  H9   H  HCR5  0   0.261   2.2968   2.4640   1.2164
 48E  H10  H  HCH2  0   0.280   0.6659   2.5289  -0.6081
 48E  H11  H  HCH2  0   0.252   1.1069   0.9110  -1.1335
 48E  H12  H  HNH1  0   0.414   0.4128   0.2978   1.3160
 48E  H13  H  HCH1  0   0.314  -1.4533  -0.1347   2.2889
 48E  H14  H  HCH2  0   0.238  -1.5842   2.1655   3.1735
 48E  H15  H  HCH2  0   0.221  -3.0756   2.4512   2.2784
 48E  H16  H  HOH1  0   0.465  -3.5822   1.6877   4.3747
 48E  H17  H  HCR5  0   0.313  -4.4866   1.4996   0.5877
 48E  H18  H  HCR6  0   0.255  -6.3084  -2.8976  -0.4899
 48E  H19  H  HCR6  0   0.259  -8.4829  -3.0452  -1.6192
 48E  H20  H  HCR6  0   0.258  -9.7064  -0.9861  -2.2508
 48E  H21  H  HCR6  0   0.260  -8.7225   1.2279  -1.7266
 48E  H22  H  HCR6  0   0.248  -6.5553   1.3834  -0.6033

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
 48E  OAN  CAK  single    1.400  0.020  1.400
 48E  OAO  CAJ  single    1.398  0.020  1.398
 48E  CAK  CAJ  single    1.534  0.020  1.534
 48E  CAK  CAI  single    1.530  0.020  1.530
 48E  CAJ  CAM  single    1.524  0.020  1.524
 48E  CAM  CAP  single    1.512  0.020  1.512
 48E  CAM  OAL  single    1.428  0.020  1.428
 48E  CAP  NAQ  single    1.445  0.020  1.445
 48E  OAL  CAI  single    1.394  0.020  1.394
 48E  CAI  NAD  single    1.478  0.020  1.478
 48E  NAQ  C    single    1.337  0.020  1.337
 48E  OAG  CAB  double    1.214  0.020  1.214
 48E  C    CA   single    1.529  0.020  1.529
 48E  C    O    double    1.219  0.020  1.219
 48E  NAD  CAB  single    1.380  0.020  1.380
 48E  NAD  CAF  single    1.363  0.020  1.363
 48E  CA   CB   single    1.523  0.020  1.523
 48E  CA   N    single    1.448  0.020  1.448
 48E  CAB  NAA  single    1.368  0.020  1.368
 48E  CB   OG   single    1.401  0.020  1.401
 48E  NAX  N    aromatic  1.324  0.020  1.324
 48E  NAX  NAZ  aromatic  1.283  0.020  1.283
 48E  CAF  CAE  double    1.344  0.020  1.344
 48E  N    CAY  aromatic  1.342  0.020  1.342
 48E  NAA  CAC  single    1.387  0.020  1.387
 48E  NAZ  CBA  aromatic  1.354  0.020  1.354
 48E  CAE  CAC  single    1.441  0.020  1.441
 48E  CAY  CBA  aromatic  1.375  0.020  1.375
 48E  CAC  OAH  double    1.217  0.020  1.217
 48E  CBA  CBB  single    1.461  0.020  1.461
 48E  CBB  CBF  aromatic  1.396  0.020  1.396
 48E  CBB  CBG  aromatic  1.396  0.020  1.396
 48E  CBF  CBD  aromatic  1.387  0.020  1.387
 48E  CBG  CBE  aromatic  1.386  0.020  1.386
 48E  CBD  CBC  aromatic  1.389  0.020  1.389
 48E  CBE  CBC  aromatic  1.389  0.020  1.389
 48E  NAA  H1   single    0.860  0.020  1.020
 48E  CAE  H2   single    0.930  0.020  1.080
 48E  CAF  H3   single    0.930  0.020  1.080
 48E  CAI  H4   single    0.970  0.020  1.090
 48E  CAK  H5   single    0.970  0.020  1.090
 48E  OAN  H6   single    0.850  0.020  0.980
 48E  CAJ  H7   single    0.970  0.020  1.090
 48E  OAO  H8   single    0.850  0.020  0.980
 48E  CAM  H9   single    0.970  0.020  1.090
 48E  CAP  H10  single    0.970  0.020  1.090
 48E  CAP  H11  single    0.970  0.020  1.090
 48E  NAQ  H12  single    0.860  0.020  1.020
 48E  CA   H13  single    0.970  0.020  1.090
 48E  CB   H14  single    0.970  0.020  1.090
 48E  CB   H15  single    0.970  0.020  1.090
 48E  OG   H16  single    0.850  0.020  0.980
 48E  CAY  H17  single    0.930  0.020  1.080
 48E  CBF  H18  single    0.930  0.020  1.080
 48E  CBD  H19  single    0.930  0.020  1.080
 48E  CBC  H20  single    0.930  0.020  1.080
 48E  CBE  H21  single    0.930  0.020  1.080
 48E  CBG  H22  single    0.930  0.020  1.080

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
 48E  NAD  CAB  NAA  115.04  3.000
 48E  NAA  CAB  OAG  122.63  3.000
 48E  NAD  CAB  OAG  122.33  3.000
 48E  H1   NAA  CAC  116.95  3.000
 48E  H1   NAA  CAB  115.21  3.000
 48E  CAC  NAA  CAB  127.83  3.000
 48E  CAE  CAC  OAH  126.18  3.000
 48E  OAH  CAC  NAA  120.56  3.000
 48E  CAE  CAC  NAA  113.26  3.000
 48E  H2   CAE  CAF  120.38  3.000
 48E  H2   CAE  CAC  119.77  3.000
 48E  CAF  CAE  CAC  119.84  3.000
 48E  H3   CAF  NAD  116.49  3.000
 48E  H3   CAF  CAE  120.41  3.000
 48E  NAD  CAF  CAE  123.09  3.000
 48E  CAI  NAD  CAF  122.97  3.000
 48E  CAF  NAD  CAB  120.93  3.000
 48E  CAI  NAD  CAB  116.11  3.000
 48E  H4   CAI  CAK  111.59  3.000
 48E  H4   CAI  OAL  110.08  3.000
 48E  CAK  CAI  OAL  106.94  3.000
 48E  H4   CAI  NAD  106.86  3.000
 48E  OAL  CAI  NAD  109.53  3.000
 48E  CAK  CAI  NAD  111.85  3.000
 48E  CAM  OAL  CAI  111.51  3.000
 48E  H5   CAK  CAJ  112.11  3.000
 48E  H5   CAK  OAN  111.99  3.000
 48E  CAJ  CAK  OAN  110.99  3.000
 48E  H5   CAK  CAI  112.24  3.000
 48E  CAJ  CAK  CAI  101.44  3.000
 48E  OAN  CAK  CAI  107.53  3.000
 48E  H6   OAN  CAK  107.85  3.000
 48E  H7   CAJ  CAM  109.80  3.000
 48E  H7   CAJ  OAO  111.43  3.000
 48E  CAM  CAJ  OAO  110.20  3.000
 48E  H7   CAJ  CAK  109.33  3.000
 48E  CAM  CAJ  CAK  101.68  3.000
 48E  OAO  CAJ  CAK  113.97  3.000
 48E  H8   OAO  CAJ  109.09  3.000
 48E  H9   CAM  CAP  109.33  3.000
 48E  H9   CAM  CAJ  109.87  3.000
 48E  CAP  CAM  CAJ  113.72  3.000
 48E  H9   CAM  OAL  109.18  3.000
 48E  CAP  CAM  OAL  110.02  3.000
 48E  CAJ  CAM  OAL  104.57  3.000
 48E  H11  CAP  H10  107.05  3.000
 48E  H11  CAP  NAQ  110.60  3.000
 48E  H10  CAP  NAQ  109.01  3.000
 48E  H11  CAP  CAM  110.55  3.000
 48E  H10  CAP  CAM  108.23  3.000
 48E  NAQ  CAP  CAM  111.27  3.000
 48E  H12  NAQ  C    118.51  3.000
 48E  H12  NAQ  CAP  117.62  3.000
 48E  C    NAQ  CAP  123.17  3.000
 48E  CA   C    O    120.57  3.000
 48E  O    C    NAQ  124.72  3.000
 48E  CA   C    NAQ  114.69  3.000
 48E  H13  CA   N    105.89  3.000
 48E  H13  CA   CB   109.10  3.000
 48E  N    CA   CB   111.64  3.000
 48E  H13  CA   C    111.21  3.000
 48E  N    CA   C    109.46  3.000
 48E  CB   CA   C    109.51  3.000
 48E  H15  CB   H14  107.01  3.000
 48E  H15  CB   OG   112.27  3.000
 48E  H14  CB   OG   112.57  3.000
 48E  H15  CB   CA   109.74  3.000
 48E  H14  CB   CA   107.38  3.000
 48E  OG   CB   CA   107.76  3.000
 48E  H16  OG   CB   108.26  3.000
 48E  NAX  N    CAY  111.00  3.000
 48E  CAY  N    CA   129.25  3.000
 48E  NAX  N    CA   119.73  3.000
 48E  H17  CAY  CBA  132.53  3.000
 48E  H17  CAY  N    123.30  3.000
 48E  CBA  CAY  N    104.17  3.000
 48E  NAZ  NAX  N    107.90  3.000
 48E  CBA  NAZ  NAX  109.55  3.000
 48E  CBB  CBA  NAZ  122.79  3.000
 48E  CBB  CBA  CAY  129.82  3.000
 48E  NAZ  CBA  CAY  107.39  3.000
 48E  CBG  CBB  CBF  118.70  3.000
 48E  CBG  CBB  CBA  120.76  3.000
 48E  CBF  CBB  CBA  120.54  3.000
 48E  H18  CBF  CBD  119.61  3.000
 48E  H18  CBF  CBB  119.86  3.000
 48E  CBD  CBF  CBB  120.53  3.000
 48E  H19  CBD  CBC  120.08  3.000
 48E  H19  CBD  CBF  119.53  3.000
 48E  CBC  CBD  CBF  120.39  3.000
 48E  H20  CBC  CBE  120.28  3.000
 48E  H20  CBC  CBD  120.28  3.000
 48E  CBE  CBC  CBD  119.44  3.000
 48E  H21  CBE  CBG  119.54  3.000
 48E  H21  CBE  CBC  120.19  3.000
 48E  CBG  CBE  CBC  120.27  3.000
 48E  H22  CBG  CBE  119.06  3.000
 48E  H22  CBG  CBB  120.27  3.000
 48E  CBE  CBG  CBB  120.67  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
 48E  CONST_01  CBA  NAZ  NAX  N      0.00   0.0  0
 48E  CONST_02  NAZ  CBA  CAY  N      0.00   0.0  0
 48E  CONST_03  CBB  CBA  CAY  N    180.00   0.0  0
 48E  CONST_04  NAZ  NAX  N    CAY    0.00   0.0  0
 48E  CONST_05  NAX  NAZ  CBA  CAY    0.00   0.0  0
 48E  CONST_06  CBF  CBB  CBA  CAY  180.00   0.0  0
 48E  CONST_07  CBG  CBB  CBA  CAY    0.00   0.0  0
 48E  CONST_08  CBA  CAY  N    NAX    0.00   0.0  0
 48E  CONST_09  CBB  CBA  NAZ  NAX  180.00   0.0  0
 48E  CONST_10  CBF  CBB  CBA  NAZ    0.00   0.0  0
 48E  CONST_11  CBG  CBB  CBA  NAZ  180.00   0.0  0
 48E  CONST_12  CBD  CBF  CBB  CBA  180.00   0.0  0
 48E  CONST_13  CBE  CBG  CBB  CBA  180.00   0.0  0
 48E  CONST_14  CBC  CBD  CBF  CBB    0.00   0.0  0
 48E  CONST_15  CBC  CBE  CBG  CBB    0.00   0.0  0
 48E  CONST_16  CBE  CBG  CBB  CBF    0.00   0.0  0
 48E  CONST_17  CBE  CBC  CBD  CBF    0.00   0.0  0
 48E  CONST_18  CBG  CBB  CBF  CBD    0.00   0.0  0
 48E  CONST_19  CBG  CBE  CBC  CBD    0.00   0.0  0
 48E  CONST_20  CAI  NAD  CAB  NAA  180.00   0.0  0
 48E  CONST_21  CAF  NAD  CAB  NAA    0.00   0.0  0
 48E  CONST_22  NAD  CAB  NAA  CAC    0.00   0.0  0
 48E  CONST_23  NAZ  NAX  N    CA   180.00   0.0  0
 48E  CONST_24  CBA  CAY  N    CA   180.00   0.0  0
 48E  CONST_25  CAI  NAD  CAB  OAG    0.00   0.0  0
 48E  CONST_26  CAF  NAD  CAB  OAG  180.00   0.0  0
 48E  CONST_27  CAC  NAA  CAB  OAG  180.00   0.0  0
 48E  CONST_28  H17  CAY  N    NAX  180.00   0.0  0
 48E  CONST_29  H18  CBF  CBB  CBA    0.00   0.0  0
 48E  CONST_30  H22  CBG  CBB  CBA    0.00   0.0  0
 48E  CONST_31  H19  CBD  CBF  CBB  180.00   0.0  0
 48E  CONST_32  H21  CBE  CBG  CBB  180.00   0.0  0
 48E  CONST_33  H20  CBC  CBD  CBF  180.00   0.0  0
 48E  CONST_34  H1   NAA  CAB  NAD  180.00   0.0  0
 48E  CONST_35  CA   C    NAQ  CAP  180.00   0.0  0
 48E  CONST_36  O    C    NAQ  CAP    0.00   0.0  0
 48E  CONST_37  H12  NAQ  C    O    180.00   0.0  0
 48E  Var_01    C    NAQ  CAP  CAM  147.86  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
 48E  chir_01  CAI  CAK  OAL  NAD  negativ
 48E  chir_02  CAK  OAN  CAI  CAJ  negativ
 48E  chir_03  CAJ  OAO  CAK  CAM  negativ
 48E  chir_04  CAM  OAL  CAJ  CAP  negativ
 48E  chir_05  CA   N    C    CB   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
 48E  plan-1  CA   0.020
 48E  plan-1  N    0.020
 48E  plan-1  CAY  0.020
 48E  plan-1  NAX  0.020
 48E  plan-1  NAZ  0.020
 48E  plan-1  CBA  0.020
 48E  plan-1  CBB  0.020
 48E  plan-1  H17  0.020
 48E  plan-2  OAG  0.020
 48E  plan-2  CAB  0.020
 48E  plan-2  NAA  0.020
 48E  plan-2  CAC  0.020
 48E  plan-2  OAH  0.020
 48E  plan-2  CAE  0.020
 48E  plan-2  CAF  0.020
 48E  plan-2  NAD  0.020
 48E  plan-2  CAI  0.020
 48E  plan-2  H1   0.020
 48E  plan-2  H2   0.020
 48E  plan-2  H3   0.020
 48E  plan-3  CBA  0.020
 48E  plan-3  CBB  0.020
 48E  plan-3  CBF  0.020
 48E  plan-3  CBD  0.020
 48E  plan-3  CBC  0.020
 48E  plan-3  CBE  0.020
 48E  plan-3  CBG  0.020
 48E  plan-3  H18  0.020
 48E  plan-3  H19  0.020
 48E  plan-3  H20  0.020
 48E  plan-3  H21  0.020
 48E  plan-3  H22  0.020
 48E  plan-4  CAP  0.020
 48E  plan-4  NAQ  0.020
 48E  plan-4  C    0.020
 48E  plan-4  O    0.020
 48E  plan-4  CA   0.020
 48E  plan-4  H12  0.020

