# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 28 20:29:01 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4,5-dihydroxytetrahydrofuran-3-yl acetate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)O[C@H]1[C@@H](O)[C@@H](O)O[C@H]1CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 3OD  3OD  '(2S,3S,4R,5S)-2-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4,5-dihydroxytetrahydrofuran-3-yl acetate (non-preferred name)'  ligand  62  39  .  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_3OD
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
 3OD  O15   O  O      0  -0.452   5.6821   3.7153  -0.4991
 3OD  C16   C  C      0   0.573   4.7850   3.3634   0.2231
 3OD  C17   C  CH3    0  -0.773   3.9177   4.2811   1.0313
 3OD  O13   O  O2     0  -0.451   4.4240   2.0942   0.4015
 3OD  C13   C  CH1    0  -0.097   5.1930   1.0597  -0.2014
 3OD  C14   C  CH1    0   0.003   6.2054   0.5134   0.7983
 3OD  O10   O  OH1    0  -0.650   6.8388   1.5328   1.4992
 3OD  C15   C  CH1    0   0.234   5.3507  -0.4538   1.6297
 3OD  O14   O  OH1    0  -0.651   4.7099   0.2364   2.6468
 3OD  O12   O  O2     0  -0.509   4.4578  -1.0044   0.6956
 3OD  C12   C  CH1    0   0.010   4.3240  -0.1683  -0.4531
 3OD  C11   C  CH2    0  -0.134   2.8713   0.1273  -0.7558
 3OD  O11   O  O2     0  -0.627   2.2388  -1.0949  -1.0697
 3OD  P2    P  P      0   1.352   0.7913  -1.0712  -1.8675
 3OD  O8    O  OP    -1  -0.765   0.0812   0.2012  -1.5341
 3OD  O9    O  O      0  -0.799   1.0270  -1.4789  -3.2887
 3OD  O7    O  O2     0  -0.732   0.1403  -2.3208  -1.0333
 3OD  P1    P  P      0   1.375  -0.6554  -3.6070  -1.6636
 3OD  O2    O  OP    -1  -0.791   0.3368  -4.6488  -2.0674
 3OD  O1    O  O      0  -0.789  -1.7339  -3.1582  -2.6042
 3OD  O3    O  O2     0  -0.614  -1.3287  -4.1644  -0.2700
 3OD  C1    C  CH2    0  -0.163  -2.6400  -3.8427   0.1305
 3OD  C2    C  CH1    0  -0.030  -2.6728  -2.7542   1.1897
 3OD  C3    C  CH1    0  -0.035  -4.0903  -2.4848   1.6850
 3OD  O5    O  OH1    0  -0.671  -4.0363  -2.0352   3.0155
 3OD  C4    C  CH1    0  -0.053  -4.5171  -1.3562   0.7456
 3OD  O6    O  OH1    0  -0.653  -5.5384  -0.5359   1.2305
 3OD  C5    C  CH1    0   0.227  -3.2167  -0.5631   0.6285
 3OD  O4    O  O2     0  -0.478  -2.1927  -1.5091   0.6748
 3OD  N1    N  NR5    0  -0.537  -3.1257   0.2081  -0.5853
 3OD  C10   C  CR5    0   0.480  -3.3272   1.5526  -0.6887
 3OD  C7    C  CR5    0  -0.009  -3.2502   1.8257  -2.0457
 3OD  N2    N  N      0  -0.471  -3.0039   0.6819  -2.7584
 3OD  C6    C  CR15   0   0.114  -2.9248  -0.2538  -1.8581
 3OD  N5    N  N      0  -0.458  -3.5544   2.4353   0.2829
 3OD  C9    C  C1     0   0.036  -3.7034   3.6595  -0.1910
 3OD  N4    N  N      0  -0.477  -3.6580   4.0676  -1.4568
 3OD  C8    C  C      0   0.442  -3.4320   3.1672  -2.4210
 3OD  N3    N  NH2    0  -0.821  -3.3953   3.5715  -3.6945
 3OD  H171  H  HCH3   0   0.260   4.1490   5.3187   0.8086
 3OD  H172  H  HCH3   0   0.270   2.8624   4.0967   0.8306
 3OD  H173  H  HCH3   0   0.273   4.0800   4.1036   2.0953
 3OD  H13   H  HCH1   0   0.283   5.6527   1.4160  -1.1235
 3OD  H14   H  HCH1   0   0.242   6.9172  -0.1000   0.2281
 3OD  HO10  H  HOH1   0   0.460   7.4995   1.1410   2.0789
 3OD  H15   H  HCH1   0   0.221   5.9423  -1.2829   2.0359
 3OD  HO14  H  HOH1   0   0.458   4.3547  -0.4019   3.2737
 3OD  H12   H  HCH1   0   0.242   4.7505  -0.7006  -1.3123
 3OD  H111  H  HCH2   0   0.212   2.3897   0.6053   0.1011
 3OD  H112  H  HCH2   0   0.208   2.8343   0.8363  -1.5914
 3OD  H11   H  HCH2   0   0.213  -3.2621  -3.5680  -0.7266
 3OD  H12A  H  HCH2   0   0.229  -3.0776  -4.7437   0.5710
 3OD  H2    H  HCH1   0   0.251  -2.0282  -3.0539   2.0230
 3OD  H3    H  HCH1   0   0.247  -4.7362  -3.3671   1.5849
 3OD  HO5   H  HOH1   0   0.447  -4.8283  -1.5094   3.1793
 3OD  H4    H  HCH1   0   0.249  -4.7709  -1.7817  -0.2340
 3OD  HO6   H  HOH1   0   0.468  -6.3861  -0.9475   1.0349
 3OD  H5    H  HCH1   0   0.248  -3.1428   0.1590   1.4507
 3OD  H6    H  HCR5   0   0.312  -2.6924  -1.2914  -2.0614
 3OD  H9    H  H      0   0.246  -3.8884   4.4369   0.5429
 3OD  HN31  H  HNH2   0   0.408  -3.1712   2.9297  -4.4339
 3OD  HN32  H  HNH2   0   0.400  -3.4830   4.5473  -3.9189

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
 3OD  O15  C16   double    1.204  0.020  1.204
 3OD  C16  C17   single    1.499  0.020  1.499
 3OD  C16  O13   single    1.332  0.020  1.332
 3OD  C17  H171  single    0.970  0.020  1.090
 3OD  C17  H172  single    0.970  0.020  1.090
 3OD  C17  H173  single    0.970  0.020  1.090
 3OD  O13  C13   single    1.423  0.020  1.423
 3OD  C13  C14   single    1.524  0.020  1.524
 3OD  C13  C12   single    1.525  0.020  1.525
 3OD  C13  H13   single    0.970  0.020  1.090
 3OD  C14  O10   single    1.390  0.020  1.390
 3OD  C14  C15   single    1.535  0.020  1.535
 3OD  C14  H14   single    0.970  0.020  1.090
 3OD  O10  HO10  single    0.850  0.020  0.980
 3OD  C15  O14   single    1.386  0.020  1.386
 3OD  C15  O12   single    1.405  0.020  1.405
 3OD  C15  H15   single    0.970  0.020  1.090
 3OD  O14  HO14  single    0.850  0.020  0.980
 3OD  O12  C12   single    1.427  0.020  1.427
 3OD  C12  C11   single    1.513  0.020  1.513
 3OD  C12  H12   single    0.970  0.020  1.090
 3OD  C11  O11   single    1.411  0.020  1.411
 3OD  C11  H111  single    0.970  0.020  1.090
 3OD  C11  H112  single    0.970  0.020  1.090
 3OD  O11  P2    single    1.653  0.020  1.653
 3OD  P2   O8    deloc     1.495  0.020  1.495
 3OD  P2   O9    deloc     1.497  0.020  1.497
 3OD  P2   O7    single    1.637  0.020  1.637
 3OD  O7   P1    single    1.638  0.020  1.638
 3OD  P1   O2    deloc     1.494  0.020  1.494
 3OD  P1   O1    deloc     1.500  0.020  1.500
 3OD  P1   O3    single    1.645  0.020  1.645
 3OD  O3   C1    single    1.408  0.020  1.408
 3OD  C1   C2    single    1.519  0.020  1.519
 3OD  C1   H11   single    0.970  0.020  1.090
 3OD  C1   H12A  single    0.970  0.020  1.090
 3OD  C2   C3    single    1.525  0.020  1.525
 3OD  C2   O4    single    1.430  0.020  1.430
 3OD  C2   H2    single    0.970  0.020  1.090
 3OD  C3   O5    single    1.405  0.020  1.405
 3OD  C3   C4    single    1.529  0.020  1.529
 3OD  C3   H3    single    0.970  0.020  1.090
 3OD  O5   HO5   single    0.850  0.020  0.980
 3OD  C4   O6    single    1.397  0.020  1.397
 3OD  C4   C5    single    1.528  0.020  1.528
 3OD  C4   H4    single    0.970  0.020  1.090
 3OD  O6   HO6   single    0.850  0.020  0.980
 3OD  C5   O4    single    1.395  0.020  1.395
 3OD  C5   N1    single    1.441  0.020  1.441
 3OD  C5   H5    single    0.970  0.020  1.090
 3OD  N1   C10   aromatic  1.363  0.020  1.363
 3OD  N1   C6    aromatic  1.369  0.020  1.369
 3OD  C10  C7    aromatic  1.386  0.020  1.386
 3OD  C10  N5    aromatic  1.332  0.020  1.332
 3OD  C7   N2    aromatic  1.370  0.020  1.370
 3OD  C7   C8    aromatic  1.405  0.020  1.405
 3OD  N2   C6    aromatic  1.301  0.020  1.301
 3OD  C6   H6    single    0.930  0.020  1.080
 3OD  N5   C9    aromatic  1.321  0.020  1.321
 3OD  C9   N4    aromatic  1.331  0.020  1.331
 3OD  C9   H9    single    0.930  0.020  1.080
 3OD  N4   C8    aromatic  1.338  0.020  1.338
 3OD  C8   N3    single    1.337  0.020  1.337
 3OD  N3   HN31  single    0.860  0.020  1.020
 3OD  N3   HN32  single    0.860  0.020  1.020

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
 3OD  O13   C16  C17   110.76  3.000
 3OD  O13   C16  O15   124.12  3.000
 3OD  C17   C16  O15   125.13  3.000
 3OD  H173  C17  H172  107.23  3.000
 3OD  H173  C17  H171  108.89  3.000
 3OD  H172  C17  H171  109.27  3.000
 3OD  H173  C17  C16   109.88  3.000
 3OD  H172  C17  C16   110.94  3.000
 3OD  H171  C17  C16   110.55  3.000
 3OD  C13   O13  C16   119.31  3.000
 3OD  H13   C13  C12   111.33  3.000
 3OD  H13   C13  C14   113.07  3.000
 3OD  C12   C13  C14   101.42  3.000
 3OD  H13   C13  O13   110.41  3.000
 3OD  C12   C13  O13   110.32  3.000
 3OD  C14   C13  O13   109.98  3.000
 3OD  H14   C14  C15   106.85  3.000
 3OD  H14   C14  O10   112.08  3.000
 3OD  C15   C14  O10   116.28  3.000
 3OD  H14   C14  C13   106.86  3.000
 3OD  C15   C14  C13   102.20  3.000
 3OD  O10   C14  C13   111.75  3.000
 3OD  HO10  O10  C14   108.54  3.000
 3OD  H15   C15  O12   107.04  3.000
 3OD  H15   C15  O14   110.74  3.000
 3OD  O12   C15  O14   112.90  3.000
 3OD  H15   C15  C14   112.13  3.000
 3OD  O12   C15  C14   103.93  3.000
 3OD  O14   C15  C14   109.94  3.000
 3OD  HO14  O14  C15   108.56  3.000
 3OD  C12   O12  C15   111.43  3.000
 3OD  H12   C12  C11   108.15  3.000
 3OD  H12   C12  O12   108.04  3.000
 3OD  C11   C12  O12   111.44  3.000
 3OD  H12   C12  C13   107.36  3.000
 3OD  C11   C12  C13   115.00  3.000
 3OD  O12   C12  C13   106.58  3.000
 3OD  H112  C11  H111  107.45  3.000
 3OD  H112  C11  O11   112.04  3.000
 3OD  H111  C11  O11   110.83  3.000
 3OD  H112  C11  C12   108.13  3.000
 3OD  H111  C11  C12   110.59  3.000
 3OD  O11   C11  C12   107.79  3.000
 3OD  P2    O11  C11   119.16  3.000
 3OD  O7    P2   O9    109.77  3.000
 3OD  O7    P2   O8    110.31  3.000
 3OD  O9    P2   O8    121.22  3.000
 3OD  O7    P2   O11    95.24  3.000
 3OD  O9    P2   O11   108.45  3.000
 3OD  O8    P2   O11   108.69  3.000
 3OD  P1    O7   P2    126.60  3.000
 3OD  O3    P1   O1    109.78  3.000
 3OD  O3    P1   O2    105.34  3.000
 3OD  O1    P1   O2    121.11  3.000
 3OD  O3    P1   O7     97.98  3.000
 3OD  O1    P1   O7    110.83  3.000
 3OD  O2    P1   O7    109.19  3.000
 3OD  C1    O3   P1    123.00  3.000
 3OD  H12A  C1   H11   107.14  3.000
 3OD  H12A  C1   C2    107.50  3.000
 3OD  H11   C1   C2    110.74  3.000
 3OD  H12A  C1   O3    107.38  3.000
 3OD  H11   C1   O3    111.34  3.000
 3OD  C2    C1   O3    112.46  3.000
 3OD  H2    C2   O4    108.33  3.000
 3OD  H2    C2   C3    110.38  3.000
 3OD  O4    C2   C3    105.96  3.000
 3OD  H2    C2   C1    108.76  3.000
 3OD  O4    C2   C1    111.44  3.000
 3OD  C3    C2   C1    111.90  3.000
 3OD  H3    C3   C4    111.89  3.000
 3OD  H3    C3   O5    111.46  3.000
 3OD  C4    C3   O5    110.87  3.000
 3OD  H3    C3   C2    112.03  3.000
 3OD  C4    C3   C2    100.97  3.000
 3OD  O5    C3   C2    109.15  3.000
 3OD  HO5   O5   C3    107.67  3.000
 3OD  H4    C4   C5    109.25  3.000
 3OD  H4    C4   O6    111.61  3.000
 3OD  C5    C4   O6    110.13  3.000
 3OD  H4    C4   C3    109.06  3.000
 3OD  C5    C4   C3    101.11  3.000
 3OD  O6    C4   C3    115.10  3.000
 3OD  HO6   O6   C4    108.81  3.000
 3OD  H5    C5   N1    105.95  3.000
 3OD  H5    C5   O4    111.85  3.000
 3OD  N1    C5   O4    110.16  3.000
 3OD  H5    C5   C4    109.98  3.000
 3OD  N1    C5   C4    113.34  3.000
 3OD  O4    C5   C4    105.68  3.000
 3OD  C5    O4   C2    110.85  3.000
 3OD  C6    N1   C10   106.49  3.000
 3OD  C6    N1   C5    127.73  3.000
 3OD  C10   N1   C5    125.61  3.000
 3OD  N5    C10  C7    126.36  3.000
 3OD  N5    C10  N1    128.56  3.000
 3OD  C7    C10  N1    105.09  3.000
 3OD  C8    C7   N2    132.96  3.000
 3OD  C8    C7   C10   116.26  3.000
 3OD  N2    C7   C10   110.78  3.000
 3OD  C6    N2   C7    104.56  3.000
 3OD  H6    C6   N2    124.92  3.000
 3OD  H6    C6   N1    121.98  3.000
 3OD  N2    C6   N1    113.08  3.000
 3OD  C9    N5   C10   111.81  3.000
 3OD  H9    C9   N4    115.44  3.000
 3OD  H9    C9   N5    116.14  3.000
 3OD  N4    C9   N5    128.43  3.000
 3OD  C8    N4   C9    118.99  3.000
 3OD  N3    C8   N4    119.18  3.000
 3OD  N3    C8   C7    122.67  3.000
 3OD  N4    C8   C7    118.15  3.000
 3OD  HN32  N3   HN31  118.39  3.000
 3OD  HN32  N3   C8    120.26  3.000
 3OD  HN31  N3   C8    120.95  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
 3OD  CONST_01  N2    C7   C10  N1      0.00   0.0  0
 3OD  CONST_02  C8    C7   C10  N1    180.00   0.0  0
 3OD  CONST_03  C9    N5   C10  N1    180.00   0.0  0
 3OD  CONST_04  C7    N2   C6   N1      0.00   0.0  0
 3OD  CONST_05  N2    C6   N1   C10     0.00   0.0  0
 3OD  CONST_06  C6    N2   C7   C10     0.00   0.0  0
 3OD  CONST_07  N4    C8   C7   C10     0.00   0.0  0
 3OD  CONST_08  N4    C9   N5   C10     0.00   0.0  0
 3OD  CONST_09  C6    N1   C10  C7      0.00   0.0  0
 3OD  CONST_10  C9    N5   C10  C7      0.00   0.0  0
 3OD  CONST_11  C9    N4   C8   C7      0.00   0.0  0
 3OD  CONST_12  N5    C10  C7   N2    180.00   0.0  0
 3OD  CONST_13  N4    C8   C7   N2    180.00   0.0  0
 3OD  CONST_14  N5    C10  N1   C6    180.00   0.0  0
 3OD  CONST_15  C8    C7   N2   C6    180.00   0.0  0
 3OD  CONST_16  C8    C7   C10  N5      0.00   0.0  0
 3OD  CONST_17  C8    N4   C9   N5      0.00   0.0  0
 3OD  CONST_18  C7    C10  N1   C5    180.00   0.0  0
 3OD  CONST_19  N5    C10  N1   C5      0.00   0.0  0
 3OD  CONST_20  N2    C6   N1   C5    180.00   0.0  0
 3OD  CONST_21  N3    C8   C7   C10   180.00   0.0  0
 3OD  CONST_22  N3    C8   C7   N2      0.00   0.0  0
 3OD  CONST_23  N3    C8   N4   C9    180.00   0.0  0
 3OD  CONST_24  H6    C6   N1   C5      0.00   0.0  0
 3OD  CONST_25  H9    C9   N5   C10   180.00   0.0  0
 3OD  CONST_26  HN31  N3   C8   C7      0.00   0.0  0
 3OD  CONST_27  HN32  N3   C8   C7    180.00   0.0  0
 3OD  Var_01    C2    C1   O3   P1   -101.06  30.0  3
 3OD  Var_02    O8    P2   O11  C11   -28.05  30.0  3
 3OD  Var_03    O2    P1   O7   P2     85.04  30.0  3
 3OD  Var_04    H171  C17  C16  O15     5.14  30.0  3
 3OD  Var_05    H111  C11  O11  P2     76.76  30.0  2

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
 3OD  chir_01  C13  O13  C14  C12  negativ
 3OD  chir_02  C14  O10  C15  C13  negativ
 3OD  chir_03  C15  O12  O14  C14  positiv
 3OD  chir_04  C12  O12  C11  C13  negativ
 3OD  chir_07  C2   C1   C3   O4   positiv
 3OD  chir_08  C3   O5   C4   C2   negativ
 3OD  chir_09  C4   O6   C5   C3   negativ
 3OD  chir_10  C5   O4   N1   C4   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
 3OD  plan-1  C8    0.020
 3OD  plan-1  N3    0.020
 3OD  plan-1  HN31  0.020
 3OD  plan-1  HN32  0.020
 3OD  plan-2  C5    0.020
 3OD  plan-2  N1    0.020
 3OD  plan-2  C10   0.020
 3OD  plan-2  C7    0.020
 3OD  plan-2  N2    0.020
 3OD  plan-2  C6    0.020
 3OD  plan-2  N5    0.020
 3OD  plan-2  C9    0.020
 3OD  plan-2  N4    0.020
 3OD  plan-2  C8    0.020
 3OD  plan-2  N3    0.020
 3OD  plan-2  H6    0.020
 3OD  plan-2  H9    0.020
 3OD  plan-3  O15   0.020
 3OD  plan-3  C16   0.020
 3OD  plan-3  C17   0.020
 3OD  plan-3  O13   0.020

