# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 14:26:47 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C[C@@H](C[C@@H](O)[C@@H]1O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)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
 3R2  3R2  2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine  ligand  60  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3R2
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
 3R2  O4   O  O      0  -0.456   5.7054   3.5462   2.0265
 3R2  C4   C  CR6    0   0.558   5.3472   2.7308   1.1958
 3R2  N3   N  NR16   0  -0.733   5.1605   1.4059   1.5443
 3R2  C2   C  CR6    0   0.745   4.7685   0.3660   0.7412
 3R2  O2   O  O      0  -0.472   4.6387  -0.7605   1.1714
 3R2  C5   C  CR6    0  -0.185   5.0782   3.0243  -0.1971
 3R2  C5M  C  CH3    0  -0.707   5.2378   4.4269  -0.6835
 3R2  C6   C  CR16   0   0.060   4.6936   2.0089  -0.9895
 3R2  N1   N  NR6    0  -0.567   4.5490   0.7109  -0.5721
 3R2  C1C  C  CH1    0   0.216   4.0822  -0.2958  -1.5269
 3R2  O4C  O  O2     0  -0.488   2.7973  -0.7137  -1.1689
 3R2  C2C  C  CH2    0  -0.560   4.9522  -1.5469  -1.6697
 3R2  C3C  C  CH1    0   0.020   4.1046  -2.6853  -1.1015
 3R2  O3C  O  OH1    0  -0.669   4.1703  -3.8858  -1.8311
 3R2  C4C  C  CH1    0   0.015   2.6835  -2.1266  -1.1958
 3R2  C5C  C  CH2    0  -0.155   1.7987  -2.5949  -0.0672
 3R2  O5C  O  O2     0  -0.622   0.4717  -2.1687  -0.2938
 3R2  PA   P  P      0   1.341  -0.5346  -2.1537   1.0115
 3R2  O1A  O  O      0  -0.804  -0.8197  -3.5592   1.4408
 3R2  O2A  O  OP    -1  -0.792  -0.0456  -1.1450   2.0013
 3R2  O3A  O  O2     0  -0.736  -1.7962  -1.5512   0.1515
 3R2  PB   P  P      0   1.339  -3.3588  -1.6864   0.6406
 3R2  O1B  O  OP    -1  -0.793  -4.0088  -2.8366  -0.0638
 3R2  O2B  O  O      0  -0.801  -3.4567  -1.5698   2.1307
 3R2  O3B  O  O2     0  -0.626  -3.8233  -0.2822  -0.0723
 3R2  C1'  C  CH1    0   0.020  -5.1610   0.1535   0.1531
 3R2  C2'  C  CH2    0  -0.488  -5.7434   0.6410  -1.1653
 3R2  C3'  C  CH1    0   0.032  -5.0513   1.9044  -1.6603
 3R2  O3'  O  OH1    0  -0.685  -5.6664   2.4156  -2.8305
 3R2  C4'  C  CH1    0   0.089  -5.1137   3.0065  -0.6083
 3R2  O4'  O  OH1    0  -0.683  -4.4470   4.1678  -1.0522
 3R2  C5'  C  CH1    0  -0.274  -4.4864   2.5441   0.7036
 3R2  C6'  C  CH3    0  -0.653  -4.5395   3.6257   1.7764
 3R2  C7'  C  CH2    0  -0.427  -5.1795   1.2705   1.1873
 3R2  H1   H  HNR6   0   0.425   5.3310   1.1611   2.5123
 3R2  H2   H  HCH3   0   0.247   6.2552   4.7874  -0.5261
 3R2  H3   H  HCH3   0   0.247   5.0190   4.4983  -1.7477
 3R2  H4   H  HCH3   0   0.247   4.5685   5.1099  -0.1585
 3R2  H5   H  HCR6   0   0.315   4.4763   2.1749  -2.0360
 3R2  H6   H  HCH1   0   0.253   4.0499   0.2392  -2.4791
 3R2  H7   H  HCH2   0   0.267   5.1192  -1.7297  -2.7328
 3R2  H8   H  HCH2   0   0.275   5.9282  -1.4470  -1.1978
 3R2  H9   H  HCH1   0   0.234   4.3671  -2.8591  -0.0549
 3R2  H10  H  HOH1   0   0.456   4.9692  -4.3514  -1.5688
 3R2  H11  H  HCH1   0   0.226   2.2530  -2.4413  -2.1578
 3R2  H12  H  HCH2   0   0.211   1.8552  -3.6891  -0.0208
 3R2  H13  H  HCH2   0   0.215   2.1942  -2.2005   0.8754
 3R2  H16  H  HCH1   0   0.228  -5.7819  -0.6753   0.5155
 3R2  H17  H  HCH2   0   0.243  -5.6763  -0.1486  -1.9191
 3R2  H18  H  HCH2   0   0.226  -6.8077   0.8503  -1.0174
 3R2  H19  H  HCH1   0   0.203  -3.9930   1.6841  -1.8572
 3R2  H20  H  HOH1   0   0.454  -5.4466   1.8378  -3.5675
 3R2  H21  H  HCH1   0   0.179  -6.1795   3.2267  -0.4158
 3R2  H22  H  HOH1   0   0.443  -4.7721   4.3681  -1.9365
 3R2  H23  H  HCH1   0   0.222  -3.4338   2.3076   0.5078
 3R2  H24  H  HCH3   0   0.211  -5.5703   3.9123   1.9984
 3R2  H25  H  HCH3   0   0.226  -4.0919   3.2652   2.7041
 3R2  H26  H  HCH3   0   0.232  -3.9990   4.5234   1.4786
 3R2  H27  H  HCH2   0   0.214  -6.2235   1.4965   1.4310
 3R2  H28  H  HCH2   0   0.242  -4.7133   0.9188   2.1100

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
 3R2  O3C  C3C  single  1.406  0.020  1.406
 3R2  O2   C2   double  1.213  0.020  1.213
 3R2  C6'  C5'  single  1.524  0.020  1.524
 3R2  C3C  C2C  single  1.529  0.020  1.529
 3R2  C3C  C4C  single  1.530  0.020  1.530
 3R2  C2C  C1C  single  1.530  0.020  1.530
 3R2  C1C  O4C  single  1.398  0.020  1.398
 3R2  C1C  N1   single  1.464  0.020  1.464
 3R2  C2   N1   single  1.375  0.020  1.375
 3R2  C2   N3   single  1.371  0.020  1.371
 3R2  C4C  O4C  single  1.418  0.020  1.418
 3R2  C4C  C5C  single  1.509  0.020  1.509
 3R2  O4'  C4'  single  1.411  0.020  1.411
 3R2  N1   C6   single  1.371  0.020  1.371
 3R2  C5'  C4'  single  1.526  0.020  1.526
 3R2  C5'  C7'  single  1.528  0.020  1.528
 3R2  N3   C4   single  1.383  0.020  1.383
 3R2  C4'  C3'  single  1.525  0.020  1.525
 3R2  O5C  C5C  single  1.412  0.020  1.412
 3R2  O5C  PA   single  1.648  0.020  1.648
 3R2  C7'  C1'  single  1.522  0.020  1.522
 3R2  O1A  PA   deloc   1.497  0.020  1.497
 3R2  C6   C5   double  1.344  0.020  1.344
 3R2  C4   C5   single  1.449  0.020  1.449
 3R2  C4   O4   double  1.218  0.020  1.218
 3R2  PA   O3A  single  1.641  0.020  1.641
 3R2  PA   O2A  deloc   1.495  0.020  1.495
 3R2  O3B  C1'  single  1.425  0.020  1.425
 3R2  O3B  PB   single  1.642  0.020  1.642
 3R2  C3'  O3'  single  1.417  0.020  1.417
 3R2  C3'  C2'  single  1.523  0.020  1.523
 3R2  C5   C5M  single  1.493  0.020  1.493
 3R2  C1'  C2'  single  1.521  0.020  1.521
 3R2  O2B  PB   deloc   1.498  0.020  1.498
 3R2  O3A  PB   single  1.643  0.020  1.643
 3R2  PB   O1B  deloc   1.497  0.020  1.497
 3R2  N3   H1   single  0.860  0.020  1.020
 3R2  C5M  H2   single  0.970  0.020  1.090
 3R2  C5M  H3   single  0.970  0.020  1.090
 3R2  C5M  H4   single  0.970  0.020  1.090
 3R2  C6   H5   single  0.930  0.020  1.080
 3R2  C1C  H6   single  0.970  0.020  1.090
 3R2  C2C  H7   single  0.970  0.020  1.090
 3R2  C2C  H8   single  0.970  0.020  1.090
 3R2  C3C  H9   single  0.970  0.020  1.090
 3R2  O3C  H10  single  0.850  0.020  0.980
 3R2  C4C  H11  single  0.970  0.020  1.090
 3R2  C5C  H12  single  0.970  0.020  1.090
 3R2  C5C  H13  single  0.970  0.020  1.090
 3R2  C1'  H16  single  0.970  0.020  1.090
 3R2  C2'  H17  single  0.970  0.020  1.090
 3R2  C2'  H18  single  0.970  0.020  1.090
 3R2  C3'  H19  single  0.970  0.020  1.090
 3R2  O3'  H20  single  0.850  0.020  0.980
 3R2  C4'  H21  single  0.970  0.020  1.090
 3R2  O4'  H22  single  0.850  0.020  0.980
 3R2  C5'  H23  single  0.970  0.020  1.090
 3R2  C6'  H24  single  0.970  0.020  1.090
 3R2  C6'  H25  single  0.970  0.020  1.090
 3R2  C6'  H26  single  0.970  0.020  1.090
 3R2  C7'  H27  single  0.970  0.020  1.090
 3R2  C7'  H28  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
 3R2  C5   C4   N3   114.30  3.000
 3R2  C5   C4   O4   125.09  3.000
 3R2  N3   C4   O4   120.62  3.000
 3R2  H1   N3   C2   115.13  3.000
 3R2  H1   N3   C4   116.73  3.000
 3R2  C2   N3   C4   128.14  3.000
 3R2  N1   C2   O2   123.68  3.000
 3R2  N1   C2   N3   114.51  3.000
 3R2  O2   C2   N3   121.82  3.000
 3R2  C6   C5   C5M  123.24  3.000
 3R2  C5M  C5   C4   118.93  3.000
 3R2  C6   C5   C4   117.83  3.000
 3R2  H4   C5M  H3   107.83  3.000
 3R2  H4   C5M  H2   107.21  3.000
 3R2  H3   C5M  H2   107.87  3.000
 3R2  H4   C5M  C5   111.45  3.000
 3R2  H3   C5M  C5   111.01  3.000
 3R2  H2   C5M  C5   111.29  3.000
 3R2  H5   C6   N1   114.75  3.000
 3R2  H5   C6   C5   120.79  3.000
 3R2  N1   C6   C5   124.47  3.000
 3R2  C1C  N1   C6   119.09  3.000
 3R2  C6   N1   C2   120.74  3.000
 3R2  C1C  N1   C2   120.08  3.000
 3R2  H6   C1C  C2C  109.62  3.000
 3R2  H6   C1C  O4C  110.02  3.000
 3R2  C2C  C1C  O4C  107.58  3.000
 3R2  H6   C1C  N1   103.95  3.000
 3R2  O4C  C1C  N1   109.37  3.000
 3R2  C2C  C1C  N1   116.21  3.000
 3R2  C4C  O4C  C1C  111.53  3.000
 3R2  H8   C2C  H7   107.48  3.000
 3R2  H8   C2C  C3C  113.85  3.000
 3R2  H7   C2C  C3C  108.79  3.000
 3R2  H8   C2C  C1C  113.21  3.000
 3R2  H7   C2C  C1C  108.35  3.000
 3R2  C3C  C2C  C1C  105.00  3.000
 3R2  H9   C3C  C4C  109.89  3.000
 3R2  H9   C3C  O3C  110.48  3.000
 3R2  C4C  C3C  O3C  108.85  3.000
 3R2  H9   C3C  C2C  109.95  3.000
 3R2  C4C  C3C  C2C  102.72  3.000
 3R2  O3C  C3C  C2C  114.64  3.000
 3R2  H10  O3C  C3C  108.11  3.000
 3R2  H11  C4C  C5C  109.63  3.000
 3R2  H11  C4C  C3C  108.24  3.000
 3R2  C5C  C4C  C3C  112.66  3.000
 3R2  H11  C4C  O4C  109.46  3.000
 3R2  C5C  C4C  O4C  110.01  3.000
 3R2  C3C  C4C  O4C  106.75  3.000
 3R2  H13  C5C  H12  107.70  3.000
 3R2  H13  C5C  O5C  111.63  3.000
 3R2  H12  C5C  O5C  110.87  3.000
 3R2  H13  C5C  C4C  108.68  3.000
 3R2  H12  C5C  C4C  108.13  3.000
 3R2  O5C  C5C  C4C  109.72  3.000
 3R2  PA   O5C  C5C  116.71  3.000
 3R2  O3A  PA   O2A  110.52  3.000
 3R2  O2A  PA   O1A  120.38  3.000
 3R2  O3A  PA   O1A  110.40  3.000
 3R2  O2A  PA   O5C  109.31  3.000
 3R2  O3A  PA   O5C   93.31  3.000
 3R2  O1A  PA   O5C  109.56  3.000
 3R2  PB   O3A  PA   123.01  3.000
 3R2  O3B  PB   O2B  110.29  3.000
 3R2  O2B  PB   O1B  119.97  3.000
 3R2  O3B  PB   O1B  109.27  3.000
 3R2  O1B  PB   O3A  109.64  3.000
 3R2  O2B  PB   O3A  110.60  3.000
 3R2  O3B  PB   O3A   93.98  3.000
 3R2  C1'  O3B  PB   117.29  3.000
 3R2  H16  C1'  C7'  108.84  3.000
 3R2  H16  C1'  C2'  108.16  3.000
 3R2  C7'  C1'  C2'  110.42  3.000
 3R2  H16  C1'  O3B  110.65  3.000
 3R2  C2'  C1'  O3B  108.68  3.000
 3R2  C7'  C1'  O3B  110.07  3.000
 3R2  H18  C2'  H17  106.90  3.000
 3R2  H18  C2'  C3'  109.09  3.000
 3R2  H17  C2'  C3'  110.30  3.000
 3R2  H18  C2'  C1'  108.44  3.000
 3R2  H17  C2'  C1'  110.02  3.000
 3R2  C3'  C2'  C1'  111.93  3.000
 3R2  H19  C3'  C4'  107.94  3.000
 3R2  H19  C3'  O3'  110.02  3.000
 3R2  C4'  C3'  O3'  106.93  3.000
 3R2  H19  C3'  C2'  109.24  3.000
 3R2  O3'  C3'  C2'  111.73  3.000
 3R2  C4'  C3'  C2'  110.90  3.000
 3R2  H20  O3'  C3'  108.47  3.000
 3R2  H21  C4'  C5'  107.88  3.000
 3R2  H21  C4'  O4'  110.28  3.000
 3R2  C5'  C4'  O4'  109.01  3.000
 3R2  H21  C4'  C3'  107.67  3.000
 3R2  C5'  C4'  C3'  110.94  3.000
 3R2  O4'  C4'  C3'  111.01  3.000
 3R2  H22  O4'  C4'  107.49  3.000
 3R2  H23  C5'  C7'  108.19  3.000
 3R2  H23  C5'  C6'  108.19  3.000
 3R2  C7'  C5'  C6'  110.66  3.000
 3R2  H23  C5'  C4'  107.84  3.000
 3R2  C7'  C5'  C4'  109.76  3.000
 3R2  C6'  C5'  C4'  112.07  3.000
 3R2  H26  C6'  H25  107.52  3.000
 3R2  H26  C6'  H24  107.91  3.000
 3R2  H25  C6'  H24  107.51  3.000
 3R2  H26  C6'  C5'  112.03  3.000
 3R2  H25  C6'  C5'  110.46  3.000
 3R2  H24  C6'  C5'  111.22  3.000
 3R2  H28  C7'  H27  106.57  3.000
 3R2  H28  C7'  C5'  110.01  3.000
 3R2  H27  C7'  C5'  109.31  3.000
 3R2  H28  C7'  C1'  109.42  3.000
 3R2  H27  C7'  C1'  108.30  3.000
 3R2  C5'  C7'  C1'  113.01  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
 3R2  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 3R2  CONST_02  C1C  N1   C2   N3   180.00   0.0  0
 3R2  CONST_03  C6   N1   C2   N3     0.00   0.0  0
 3R2  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 3R2  CONST_05  C2   N3   C4   O4   180.00   0.0  0
 3R2  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 3R2  CONST_07  C1C  N1   C2   O2     0.00   0.0  0
 3R2  CONST_08  C6   N1   C2   O2   180.00   0.0  0
 3R2  CONST_09  H1   N3   C4   C5   180.00   0.0  0
 3R2  Var_01    H2   C5M  C5   C4    58.95  30.0  3
 3R2  Var_02    O1A  PA   O5C  C5C  -69.06  30.0  3
 3R2  Var_03    O3B  PB   O3A  PA   149.54  30.0  3
 3R2  Var_04    H12  C5C  O5C  PA    79.43  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
 3R2  chir_01  C1C  C2C  O4C  N1   negativ
 3R2  chir_02  C3C  O3C  C2C  C4C  negativ
 3R2  chir_03  C4C  O4C  C3C  C5C  negativ
 3R2  chir_06  C1'  C7'  O3B  C2'  positiv
 3R2  chir_07  C3'  O3'  C4'  C2'  negativ
 3R2  chir_08  C4'  O4'  C3'  C5'  negativ
 3R2  chir_09  C5'  C7'  C4'  C6'  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
 3R2  plan-1  O4   0.020
 3R2  plan-1  C4   0.020
 3R2  plan-1  N3   0.020
 3R2  plan-1  C2   0.020
 3R2  plan-1  O2   0.020
 3R2  plan-1  C5   0.020
 3R2  plan-1  C5M  0.020
 3R2  plan-1  C6   0.020
 3R2  plan-1  N1   0.020
 3R2  plan-1  C1C  0.020
 3R2  plan-1  H1   0.020
 3R2  plan-1  H5   0.020

