# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 20:49:09 2021
#   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  62  34  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.450  -3.4488  12.1400   3.1690
 3R2  C4   C  CR6   0   0.562  -3.1095  10.9848   2.9940
 3R2  N3   N  NR16  0  -0.736  -3.4939  10.3015   1.8548
 3R2  C2   C  CR6   0   0.735  -3.2000   9.0110   1.5009
 3R2  O2   O  O     0  -0.481  -3.6045   8.5218   0.4661
 3R2  C5   C  CR6   0  -0.185  -2.2999  10.2077   3.9129
 3R2  C5M  C  CH3   0  -0.708  -1.8370  10.8412   5.1827
 3R2  C6   C  CR16  0   0.075  -2.0047   8.9431   3.5725
 3R2  N1   N  NR6   0  -0.567  -2.4115   8.3400   2.4099
 3R2  C1C  C  CH1   0   0.201  -2.0449   6.9567   2.1516
 3R2  O4C  O  O2    0  -0.498  -2.5150   6.1564   3.2148
 3R2  C2C  C  CH2   0  -0.531  -0.5496   6.6931   2.0702
 3R2  C3C  C  CH1   0  -0.028  -0.4755   5.2215   2.4506
 3R2  O3C  O  OH1   0  -0.705  -0.7967   4.4387   1.3308
 3R2  C4C  C  CH1   0  -0.019  -1.5705   5.1416   3.5316
 3R2  C5C  C  CH2   0  -0.208  -1.0597   5.3945   4.9425
 3R2  O5C  O  O2    0  -0.599  -0.2066   4.2900   5.2612
 3R2  PA   P  P     0   1.514   0.1741   3.6830   6.6735
 3R2  O1A  O  O     0  -0.670   1.5464   3.1497   6.6773
 3R2  O2A  O  OH1   0  -0.718  -0.2391   4.7301   7.7894
 3R2  O3A  O  O2    0  -0.701  -0.9041   2.5195   6.9663
 3R2  PB   P  P     0   1.497  -2.3504   2.1652   6.3043
 3R2  O1B  O  OH1   0  -0.722  -2.8039   0.9433   7.2028
 3R2  O2B  O  O     0  -0.675  -3.2296   3.3399   6.2027
 3R2  O3B  O  O2    0  -0.589  -2.0520   1.5063   4.9081
 3R2  C1'  C  CH1   0  -0.005  -1.4030   0.2405   4.6051
 3R2  C2'  C  CH2   0  -0.526   0.1063   0.3668   4.7002
 3R2  C3'  C  CH1   0   0.015   0.6353   1.3918   3.7049
 3R2  O3'  O  OH1   0  -0.681   2.0430   1.4943   3.7543
 3R2  C4'  C  CH1   0   0.084   0.2425   1.0196   2.2819
 3R2  O4'  O  OH1   0  -0.683   0.6665   2.0252   1.3747
 3R2  C5'  C  CH1   0  -0.291  -1.2703   0.8613   2.1402
 3R2  C6'  C  CH3   0  -0.652  -1.6636   0.4086   0.7388
 3R2  C7'  C  CH2   0  -0.442  -1.8115  -0.1136   3.1871
 3R2  H1   H  HNR6  0   0.427  -4.0683  10.8083   1.1922
 3R2  H2   H  HCH3  0   0.249  -1.2020  11.7059   4.9860
 3R2  H3   H  HCH3  0   0.249  -2.6780  11.1891   5.7838
 3R2  H4   H  HCH3  0   0.247  -1.2644  10.1353   5.7818
 3R2  H5   H  HCR6  0   0.302  -1.4100   8.3303   4.2348
 3R2  H6   H  HCH1  0   0.276  -2.5369   6.6785   1.2200
 3R2  H7   H  HCH2  0   0.267   0.0073   7.3015   2.7862
 3R2  H8   H  HCH2  0   0.284  -0.1453   6.8962   1.0799
 3R2  H9   H  HCH1  0   0.257   0.5070   4.9591   2.8555
 3R2  H10  H  HOH1  0   0.460  -0.3112   3.5967   1.3726
 3R2  H11  H  HCH1  0   0.260  -2.0736   4.1691   3.5069
 3R2  H12  H  HCH2  0   0.250  -0.4705   6.3133   5.0011
 3R2  H13  H  HCH2  0   0.271  -1.8940   5.4679   5.6393
 3R2  H14  H  HOH1  0   0.513   0.4236   5.4129   7.9693
 3R2  H15  H  HOH1  0   0.513  -3.1671   1.1741   8.0696
 3R2  H16  H  HCH1  0   0.280  -1.7697  -0.5180   5.2994
 3R2  H17  H  HCH2  0   0.258   0.5276  -0.6174   4.4744
 3R2  H18  H  HCH2  0   0.261   0.4306   0.6103   5.7140
 3R2  H19  H  HCH1  0   0.213   0.1824   2.3665   3.9140
 3R2  H20  H  HOH1  0   0.449   2.2769   1.9868   4.5491
 3R2  H21  H  HCH1  0   0.214   0.7239   0.0626   2.0231
 3R2  H22  H  HOH1  0   0.461   1.6065   2.1868   1.5194
 3R2  H23  H  HCH1  0   0.234  -1.7254   1.8419   2.3225
 3R2  H24  H  HCH3  0   0.232  -2.7451   0.2870   0.6650
 3R2  H25  H  HCH3  0   0.237  -1.3622   1.1271  -0.0224
 3R2  H26  H  HCH3  0   0.220  -1.2040  -0.5518   0.4960
 3R2  H27  H  HCH2  0   0.261  -2.9001  -0.1666   3.1120
 3R2  H28  H  HCH2  0   0.243  -1.4399  -1.1230   2.9851

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  1.403  0.020  1.403
 3R2  O2   C2   double  1.214  0.020  1.214
 3R2  C6'  C5'  single  1.524  0.020  1.524
 3R2  C3C  C2C  single  1.522  0.020  1.522
 3R2  C3C  C4C  single  1.541  0.020  1.541
 3R2  C2C  C1C  single  1.520  0.020  1.520
 3R2  C1C  O4C  single  1.411  0.020  1.411
 3R2  C1C  N1   single  1.454  0.020  1.454
 3R2  C2   N1   single  1.378  0.020  1.378
 3R2  C2   N3   single  1.370  0.020  1.370
 3R2  C4C  O4C  single  1.422  0.020  1.422
 3R2  C4C  C5C  single  1.522  0.020  1.522
 3R2  O4'  C4'  single  1.419  0.020  1.419
 3R2  N1   C6   single  1.371  0.020  1.371
 3R2  C5'  C4'  single  1.528  0.020  1.528
 3R2  C5'  C7'  single  1.529  0.020  1.529
 3R2  N3   C4   single  1.383  0.020  1.383
 3R2  C4'  C3'  single  1.522  0.020  1.522
 3R2  O5C  C5C  single  1.432  0.020  1.432
 3R2  O5C  PA   single  1.584  0.020  1.584
 3R2  C7'  C1'  single  1.518  0.020  1.518
 3R2  O1A  PA   double  1.472  0.020  1.472
 3R2  C6   C5   double  1.342  0.020  1.342
 3R2  C4   C5   single  1.450  0.020  1.450
 3R2  C4   O4   double  1.217  0.020  1.217
 3R2  PA   O3A  single  1.613  0.020  1.613
 3R2  PA   O2A  single  1.585  0.020  1.585
 3R2  O3B  C1'  single  1.454  0.020  1.454
 3R2  O3B  PB   single  1.572  0.020  1.572
 3R2  C3'  O3'  single  1.412  0.020  1.412
 3R2  C3'  C2'  single  1.524  0.020  1.524
 3R2  C5   C5M  single  1.493  0.020  1.493
 3R2  C1'  C2'  single  1.518  0.020  1.518
 3R2  O2B  PB   double  1.471  0.020  1.471
 3R2  O3A  PB   single  1.630  0.020  1.630
 3R2  PB   O1B  single  1.583  0.020  1.583
 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  O2A  H14  single  0.850  0.020  0.980
 3R2  O1B  H15  single  0.850  0.020  0.980
 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   114.35  3.000
 3R2  C5   C4   O4   124.98  3.000
 3R2  N3   C4   O4   120.67  3.000
 3R2  H1   N3   C2   115.09  3.000
 3R2  H1   N3   C4   116.70  3.000
 3R2  C2   N3   C4   128.21  3.000
 3R2  N1   C2   O2   123.84  3.000
 3R2  N1   C2   N3   114.27  3.000
 3R2  O2   C2   N3   121.89  3.000
 3R2  C6   C5   C5M  123.18  3.000
 3R2  C5M  C5   C4   118.99  3.000
 3R2  C6   C5   C4   117.83  3.000
 3R2  H4   C5M  H3   108.01  3.000
 3R2  H4   C5M  H2   107.89  3.000
 3R2  H3   C5M  H2   107.18  3.000
 3R2  H4   C5M  C5   110.86  3.000
 3R2  H3   C5M  C5   111.41  3.000
 3R2  H2   C5M  C5   111.32  3.000
 3R2  H5   C6   N1   115.68  3.000
 3R2  H5   C6   C5   119.98  3.000
 3R2  N1   C6   C5   124.33  3.000
 3R2  C1C  N1   C6   119.61  3.000
 3R2  C6   N1   C2   120.99  3.000
 3R2  C1C  N1   C2   119.36  3.000
 3R2  H6   C1C  C2C  110.73  3.000
 3R2  H6   C1C  O4C  110.42  3.000
 3R2  C2C  C1C  O4C  105.64  3.000
 3R2  H6   C1C  N1   106.32  3.000
 3R2  O4C  C1C  N1   108.76  3.000
 3R2  C2C  C1C  N1   114.98  3.000
 3R2  C4C  O4C  C1C  110.56  3.000
 3R2  H8   C2C  H7   107.64  3.000
 3R2  H8   C2C  C3C  112.93  3.000
 3R2  H7   C2C  C3C  110.48  3.000
 3R2  H8   C2C  C1C  112.43  3.000
 3R2  H7   C2C  C1C  111.70  3.000
 3R2  C3C  C2C  C1C  101.66  3.000
 3R2  H9   C3C  C4C  111.47  3.000
 3R2  H9   C3C  O3C  111.52  3.000
 3R2  C4C  C3C  O3C  111.60  3.000
 3R2  H9   C3C  C2C  111.59  3.000
 3R2  C4C  C3C  C2C  101.01  3.000
 3R2  O3C  C3C  C2C  109.19  3.000
 3R2  H10  O3C  C3C  109.53  3.000
 3R2  H11  C4C  C5C  108.83  3.000
 3R2  H11  C4C  C3C  110.89  3.000
 3R2  C5C  C4C  C3C  113.79  3.000
 3R2  H11  C4C  O4C  108.88  3.000
 3R2  C5C  C4C  O4C  108.12  3.000
 3R2  C3C  C4C  O4C  106.18  3.000
 3R2  H13  C5C  H12  108.78  3.000
 3R2  H13  C5C  O5C  111.47  3.000
 3R2  H12  C5C  O5C  108.38  3.000
 3R2  H13  C5C  C4C  110.31  3.000
 3R2  H12  C5C  C4C  111.74  3.000
 3R2  O5C  C5C  C4C  106.16  3.000
 3R2  PA   O5C  C5C  129.61  3.000
 3R2  O3A  PA   O2A  100.05  3.000
 3R2  O2A  PA   O1A  118.71  3.000
 3R2  O3A  PA   O1A  111.18  3.000
 3R2  O2A  PA   O5C  108.18  3.000
 3R2  O3A  PA   O5C  106.13  3.000
 3R2  O1A  PA   O5C  111.42  3.000
 3R2  H14  O2A  PA   114.72  3.000
 3R2  PB   O3A  PA   132.56  3.000
 3R2  O3B  PB   O2B  112.75  3.000
 3R2  O2B  PB   O1B  118.97  3.000
 3R2  O3B  PB   O1B  103.59  3.000
 3R2  O1B  PB   O3A  101.04  3.000
 3R2  O2B  PB   O3A  112.64  3.000
 3R2  O3B  PB   O3A  106.47  3.000
 3R2  H15  O1B  PB   115.59  3.000
 3R2  C1'  O3B  PB   129.37  3.000
 3R2  H16  C1'  C7'  109.98  3.000
 3R2  H16  C1'  C2'  110.61  3.000
 3R2  C7'  C1'  C2'  110.22  3.000
 3R2  H16  C1'  O3B  108.80  3.000
 3R2  C2'  C1'  O3B  111.00  3.000
 3R2  C7'  C1'  O3B  106.12  3.000
 3R2  H18  C2'  H17  106.13  3.000
 3R2  H18  C2'  C3'  110.69  3.000
 3R2  H17  C2'  C3'  109.67  3.000
 3R2  H18  C2'  C1'  111.85  3.000
 3R2  H17  C2'  C1'  107.17  3.000
 3R2  C3'  C2'  C1'  111.12  3.000
 3R2  H19  C3'  C4'  106.82  3.000
 3R2  H19  C3'  O3'  109.94  3.000
 3R2  C4'  C3'  O3'  107.91  3.000
 3R2  H19  C3'  C2'  109.30  3.000
 3R2  O3'  C3'  C2'  111.85  3.000
 3R2  C4'  C3'  C2'  110.89  3.000
 3R2  H20  O3'  C3'  107.93  3.000
 3R2  H21  C4'  C5'  108.71  3.000
 3R2  H21  C4'  O4'  109.56  3.000
 3R2  C5'  C4'  O4'  108.06  3.000
 3R2  H21  C4'  C3'  108.61  3.000
 3R2  C5'  C4'  C3'  111.56  3.000
 3R2  O4'  C4'  C3'  110.32  3.000
 3R2  H22  O4'  C4'  108.29  3.000
 3R2  H23  C5'  C7'  108.02  3.000
 3R2  H23  C5'  C6'  108.14  3.000
 3R2  C7'  C5'  C6'  110.40  3.000
 3R2  H23  C5'  C4'  107.64  3.000
 3R2  C7'  C5'  C4'  110.68  3.000
 3R2  C6'  C5'  C4'  111.81  3.000
 3R2  H26  C6'  H25  107.96  3.000
 3R2  H26  C6'  H24  107.71  3.000
 3R2  H25  C6'  H24  107.49  3.000
 3R2  H26  C6'  C5'  110.92  3.000
 3R2  H25  C6'  C5'  112.03  3.000
 3R2  H24  C6'  C5'  110.56  3.000
 3R2  H28  C7'  H27  106.32  3.000
 3R2  H28  C7'  C5'  109.96  3.000
 3R2  H27  C7'  C5'  109.67  3.000
 3R2  H28  C7'  C1'  107.23  3.000
 3R2  H27  C7'  C1'  110.10  3.000
 3R2  C5'  C7'  C1'  113.30  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    -61.38  30.0  3
 3R2  Var_02    O1A  PA   O5C  C5C  -147.18  30.0  3
 3R2  Var_03    O3B  PB   O3A  PA     75.45  30.0  3
 3R2  Var_04    H12  C5C  O5C  PA     85.60  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
 3R2  chir_10  PA   O1A  O3A  O2A  both
 3R2  chir_11  PB   O2B  O3A  O1B  both

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

