# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul 11 19:16:31 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3R)-2,3-dihydroxy-4-oxo-pentoxy]-oxido-phosphoryl] phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H](O)[C@H](O)CO[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 ZZC  ZZC  '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3R)-2,3-dihydroxy-4-oxo-pentoxy]-oxido-phosphoryl] phosphate'  ligand  56  35  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZZC
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
 ZZC  N1    N  N      0  -0.475  -4.0945   3.9711  -0.2232
 ZZC  C2    C  CR16   0   0.037  -4.1606   3.3250   0.9386
 ZZC  N3    N  N      0  -0.456  -3.8302   2.0730   1.2012
 ZZC  C4    C  CR56   0   0.482  -3.3774   1.4427   0.1190
 ZZC  C5    C  CR56   0  -0.005  -3.2507   1.9815  -1.1524
 ZZC  C6    C  CR6    0   0.436  -3.6401   3.3223  -1.3011
 ZZC  N6    N  NH2    0  -0.819  -3.5931   3.9617  -2.4776
 ZZC  N7    N  N      0  -0.467  -2.7462   1.0542  -2.0255
 ZZC  C8    C  CR15   0   0.113  -2.5652  -0.0111  -1.3021
 ZZC  N9    N  NR5    0  -0.539  -2.9417   0.1557   0.0040
 ZZC  PA    P  P      0   1.375   0.3123  -2.8060  -1.5119
 ZZC  PB    P  P      0   1.353   1.2478  -0.0550  -1.1673
 ZZC  C2'A  C  C      0   0.387   6.2697   2.2793   1.9726
 ZZC  C3'A  C  CH1    0  -0.099   5.2929   2.3445   0.7976
 ZZC  C4'A  C  CH1    0  -0.029   4.4002   1.0873   0.8263
 ZZC  C5'A  C  CH2    0  -0.161   3.5019   1.0337  -0.3976
 ZZC  O2'A  O  O      0  -0.401   5.8983   2.6483   3.0641
 ZZC  O4'A  O  OH1    0  -0.658   5.1725  -0.0793   0.9842
 ZZC  O5'A  O  O2     0  -0.619   2.6497  -0.0819  -0.2891
 ZZC  C1'   C  CH1    0   0.225  -2.9542  -0.8362   1.0498
 ZZC  O1A   O  O      0  -0.789  -0.7807  -2.4541  -2.4767
 ZZC  O1B   O  OP    -1  -0.768   0.3685   1.0298  -0.6338
 ZZC  C2'   C  CH1    0  -0.049  -4.0584  -1.8817   0.8924
 ZZC  O2'   O  OH1    0  -0.653  -5.2603  -1.3918   1.4078
 ZZC  O2A   O  OP    -1  -0.791   1.5484  -3.5121  -1.9655
 ZZC  O2B   O  O      0  -0.807   1.5777  -0.1252  -2.6262
 ZZC  C3'   C  CH1    0  -0.036  -3.4560  -3.0606   1.6577
 ZZC  O3'   O  OH1    0  -0.670  -3.5730  -2.8716   3.0451
 ZZC  O3A   O  O2     0  -0.728   0.7282  -1.5003  -0.6131
 ZZC  C4'   C  CH1    0  -0.031  -1.9879  -2.9420   1.2643
 ZZC  O4'   O  O2     0  -0.478  -1.7549  -1.5491   1.0426
 ZZC  C5'   C  CH2    0  -0.164  -1.6656  -3.7658   0.0294
 ZZC  O5'   O  O2     0  -0.613  -0.2958  -3.7309  -0.2956
 ZZC  H2    H  HCR6   0   0.247  -4.5333   3.9071   1.7750
 ZZC  HN6   H  HNH2   0   0.398  -3.7397   4.9563  -2.5039
 ZZC  HN6A  H  HNH2   0   0.405  -3.1064   3.5476  -3.2536
 ZZC  H8    H  HCR5   0   0.310  -2.1358  -0.9376  -1.6614
 ZZC  H1'A  H  HCH3   0   0.275   8.2031   2.5961   1.1881
 ZZC  H1'B  H  HCH3   0   0.263   8.1873   1.5506   2.6189
 ZZC  H1'C  H  HCH3   0   0.256   7.6598   0.9403   1.0301
 ZZC  H3'A  H  HCH1   0   0.258   5.8548   2.3706  -0.1432
 ZZC  H4'A  H  HCH1   0   0.241   3.7698   1.1503   1.7210
 ZZC  H5'A  H  HCH2   0   0.217   2.9412   1.9718  -0.4616
 ZZC  H5'B  H  HCH2   0   0.206   4.1222   0.9665  -1.3030
 ZZC  H4'B  H  HOH1   0   0.450   5.6117  -0.2819   0.1508
 ZZC  H1'   H  HCH1   0   0.249  -3.0936  -0.2846   1.9871
 ZZC  H2'   H  HCH1   0   0.247  -4.1536  -2.1551  -0.1669
 ZZC  HO2'  H  HOH1   0   0.468  -5.9843  -1.9256   1.0658
 ZZC  H3'   H  HCH1   0   0.248  -3.8896  -4.0192   1.3431
 ZZC  HO3'  H  HOH1   0   0.448  -4.4799  -2.6012   3.2309
 ZZC  H4'   H  HCH1   0   0.252  -1.3440  -3.2720   2.0863
 ZZC  H5'   H  HCH2   0   0.229  -1.9247  -4.8058   0.2508
 ZZC  H5'C  H  HCH2   0   0.212  -2.2831  -3.4542  -0.8187
 ZZC  O3'A  O  OH1    0  -0.653   4.5325   3.5213   0.8464
 ZZC  H3'B  H  HOH1   0   0.447   4.1143   3.5759   1.7144
 ZZC  C1'A  C  CH3    0  -0.775   7.6586   1.7981   1.7007

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
 ZZC  N1    C2    aromatic  1.331  0.020  1.331
 ZZC  N1    C6    aromatic  1.338  0.020  1.338
 ZZC  C2    N3    aromatic  1.321  0.020  1.321
 ZZC  N3    C4    aromatic  1.332  0.020  1.332
 ZZC  C4    C5    aromatic  1.387  0.020  1.387
 ZZC  C4    N9    aromatic  1.364  0.020  1.364
 ZZC  C5    C6    aromatic  1.404  0.020  1.404
 ZZC  C5    N7    aromatic  1.370  0.020  1.370
 ZZC  C6    N6    single    1.340  0.020  1.340
 ZZC  N7    C8    aromatic  1.300  0.020  1.300
 ZZC  C8    N9    aromatic  1.369  0.020  1.369
 ZZC  N9    C1'   single    1.441  0.020  1.441
 ZZC  PA    O1A   deloc     1.500  0.020  1.500
 ZZC  PA    O2A   deloc     1.494  0.020  1.494
 ZZC  PA    O3A   single    1.639  0.020  1.639
 ZZC  PA    O5'   single    1.645  0.020  1.645
 ZZC  PB    O5'A  single    1.654  0.020  1.654
 ZZC  PB    O1B   deloc     1.495  0.020  1.495
 ZZC  PB    O2B   deloc     1.497  0.020  1.497
 ZZC  PB    O3A   single    1.633  0.020  1.633
 ZZC  C1'A  C2'A  single    1.495  0.020  1.495
 ZZC  C2'A  C3'A  single    1.529  0.020  1.529
 ZZC  C2'A  O2'A  double    1.211  0.020  1.211
 ZZC  C3'A  C4'A  single    1.542  0.020  1.542
 ZZC  C3'A  O3'A  single    1.402  0.020  1.402
 ZZC  C4'A  C5'A  single    1.519  0.020  1.519
 ZZC  C4'A  O4'A  single    1.408  0.020  1.408
 ZZC  C5'A  O5'A  single    1.408  0.020  1.408
 ZZC  C1'   C2'   single    1.529  0.020  1.529
 ZZC  C1'   O4'   single    1.395  0.020  1.395
 ZZC  C2'   O2'   single    1.396  0.020  1.396
 ZZC  C2'   C3'   single    1.529  0.020  1.529
 ZZC  C3'   O3'   single    1.405  0.020  1.405
 ZZC  C3'   C4'   single    1.524  0.020  1.524
 ZZC  C4'   O4'   single    1.430  0.020  1.430
 ZZC  C4'   C5'   single    1.519  0.020  1.519
 ZZC  C5'   O5'   single    1.408  0.020  1.408
 ZZC  C2    H2    single    0.930  0.020  1.080
 ZZC  N6    HN6   single    0.890  0.020  1.040
 ZZC  N6    HN6A  single    0.890  0.020  1.040
 ZZC  C8    H8    single    0.930  0.020  1.080
 ZZC  C1'A  H1'A  single    0.970  0.020  1.090
 ZZC  C1'A  H1'B  single    0.970  0.020  1.090
 ZZC  C1'A  H1'C  single    0.970  0.020  1.090
 ZZC  C3'A  H3'A  single    0.970  0.020  1.090
 ZZC  C4'A  H4'A  single    0.970  0.020  1.090
 ZZC  C5'A  H5'A  single    0.970  0.020  1.090
 ZZC  C5'A  H5'B  single    0.970  0.020  1.090
 ZZC  O3'A  H3'B  single    0.850  0.020  0.980
 ZZC  O4'A  H4'B  single    0.850  0.020  0.980
 ZZC  C1'   H1'   single    0.970  0.020  1.090
 ZZC  C2'   H2'   single    0.970  0.020  1.090
 ZZC  O2'   HO2'  single    0.850  0.020  0.980
 ZZC  C3'   H3'   single    0.970  0.020  1.090
 ZZC  O3'   HO3'  single    0.850  0.020  0.980
 ZZC  C4'   H4'   single    0.970  0.020  1.090
 ZZC  C5'   H5'   single    0.970  0.020  1.090
 ZZC  C5'   H5'C  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
 ZZC  C6    N1    C2    119.00  3.000
 ZZC  H2    C2    N3    116.17  3.000
 ZZC  H2    C2    N1    115.43  3.000
 ZZC  N3    C2    N1    128.40  3.000
 ZZC  C4    N3    C2    111.84  3.000
 ZZC  N9    C4    C5    105.08  3.000
 ZZC  N9    C4    N3    128.60  3.000
 ZZC  C5    C4    N3    126.32  3.000
 ZZC  N7    C5    C6    132.92  3.000
 ZZC  N7    C5    C4    110.79  3.000
 ZZC  C6    C5    C4    116.28  3.000
 ZZC  N6    C6    C5    122.61  3.000
 ZZC  N6    C6    N1    119.21  3.000
 ZZC  C5    C6    N1    118.17  3.000
 ZZC  HN6A  N6    HN6   117.24  3.000
 ZZC  HN6A  N6    C6    119.89  3.000
 ZZC  HN6   N6    C6    119.32  3.000
 ZZC  C8    N7    C5    104.55  3.000
 ZZC  H8    C8    N9    122.00  3.000
 ZZC  H8    C8    N7    124.87  3.000
 ZZC  N9    C8    N7    113.11  3.000
 ZZC  C1'   N9    C8    127.63  3.000
 ZZC  C1'   N9    C4    125.84  3.000
 ZZC  C8    N9    C4    106.45  3.000
 ZZC  O5'   PA    O3A    97.83  3.000
 ZZC  O5'   PA    O2A   105.35  3.000
 ZZC  O3A   PA    O2A   109.46  3.000
 ZZC  O5'   PA    O1A   109.77  3.000
 ZZC  O3A   PA    O1A   110.54  3.000
 ZZC  O2A   PA    O1A   121.23  3.000
 ZZC  O3A   PB    O2B   111.06  3.000
 ZZC  O3A   PB    O1B   109.51  3.000
 ZZC  O2B   PB    O1B   120.76  3.000
 ZZC  O3A   PB    O5'A   94.31  3.000
 ZZC  O2B   PB    O5'A  109.25  3.000
 ZZC  O1B   PB    O5'A  108.71  3.000
 ZZC  O2'A  C2'A  C3'A  118.93  3.000
 ZZC  O2'A  C2'A  C1'A  123.18  3.000
 ZZC  C3'A  C2'A  C1'A  117.87  3.000
 ZZC  H3'A  C3'A  O3'A  106.74  3.000
 ZZC  H3'A  C3'A  C4'A  109.40  3.000
 ZZC  O3'A  C3'A  C4'A  111.69  3.000
 ZZC  H3'A  C3'A  C2'A  109.45  3.000
 ZZC  O3'A  C3'A  C2'A  110.82  3.000
 ZZC  C4'A  C3'A  C2'A  108.70  3.000
 ZZC  H4'A  C4'A  O4'A  105.75  3.000
 ZZC  H4'A  C4'A  C5'A  108.63  3.000
 ZZC  O4'A  C4'A  C5'A  112.68  3.000
 ZZC  H4'A  C4'A  C3'A  107.53  3.000
 ZZC  O4'A  C4'A  C3'A  111.10  3.000
 ZZC  C5'A  C4'A  C3'A  110.86  3.000
 ZZC  H5'B  C5'A  H5'A  107.05  3.000
 ZZC  H5'B  C5'A  O5'A  110.88  3.000
 ZZC  H5'A  C5'A  O5'A  111.93  3.000
 ZZC  H5'B  C5'A  C4'A  109.39  3.000
 ZZC  H5'A  C5'A  C4'A  108.65  3.000
 ZZC  O5'A  C5'A  C4'A  108.89  3.000
 ZZC  H4'B  O4'A  C4'A  109.10  3.000
 ZZC  C5'A  O5'A  PB    117.32  3.000
 ZZC  H1'   C1'   O4'   111.76  3.000
 ZZC  H1'   C1'   C2'   109.89  3.000
 ZZC  O4'   C1'   C2'   105.72  3.000
 ZZC  H1'   C1'   N9    105.96  3.000
 ZZC  O4'   C1'   N9    109.90  3.000
 ZZC  C2'   C1'   N9    113.72  3.000
 ZZC  H2'   C2'   C3'   108.96  3.000
 ZZC  H2'   C2'   O2'   111.64  3.000
 ZZC  C3'   C2'   O2'   115.13  3.000
 ZZC  H2'   C2'   C1'   109.40  3.000
 ZZC  C3'   C2'   C1'   101.02  3.000
 ZZC  O2'   C2'   C1'   110.11  3.000
 ZZC  HO2'  O2'   C2'   108.77  3.000
 ZZC  H3'   C3'   C4'   111.98  3.000
 ZZC  H3'   C3'   O3'   111.56  3.000
 ZZC  C4'   C3'   O3'   108.94  3.000
 ZZC  H3'   C3'   C2'   111.97  3.000
 ZZC  C4'   C3'   C2'   100.96  3.000
 ZZC  O3'   C3'   C2'   110.96  3.000
 ZZC  HO3'  O3'   C3'   107.83  3.000
 ZZC  PB    O3A   PA    126.86  3.000
 ZZC  H4'   C4'   C5'   108.78  3.000
 ZZC  H4'   C4'   O4'   108.32  3.000
 ZZC  C5'   C4'   O4'   111.57  3.000
 ZZC  H4'   C4'   C3'   110.43  3.000
 ZZC  C5'   C4'   C3'   111.83  3.000
 ZZC  O4'   C4'   C3'   105.83  3.000
 ZZC  C4'   O4'   C1'   110.91  3.000
 ZZC  H5'C  C5'   H5'   107.08  3.000
 ZZC  H5'C  C5'   O5'   111.28  3.000
 ZZC  H5'   C5'   O5'   107.49  3.000
 ZZC  H5'C  C5'   C4'   110.85  3.000
 ZZC  H5'   C5'   C4'   107.50  3.000
 ZZC  O5'   C5'   C4'   112.37  3.000
 ZZC  C5'   O5'   PA    122.97  3.000
 ZZC  H3'B  O3'A  C3'A  108.30  3.000
 ZZC  H1'C  C1'A  H1'B  109.88  3.000
 ZZC  H1'C  C1'A  H1'A  106.59  3.000
 ZZC  H1'B  C1'A  H1'A  108.64  3.000
 ZZC  H1'C  C1'A  C2'A  111.51  3.000
 ZZC  H1'B  C1'A  C2'A  111.79  3.000
 ZZC  H1'A  C1'A  C2'A  108.24  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
 ZZC  CONST_01  C4    N3    C2    N1       0.00   0.0  0
 ZZC  CONST_02  C4    C5    C6    N1       0.00   0.0  0
 ZZC  CONST_03  N7    C5    C6    N1     180.00   0.0  0
 ZZC  CONST_04  C5    C6    N1    C2       0.00   0.0  0
 ZZC  CONST_05  C5    C4    N3    C2       0.00   0.0  0
 ZZC  CONST_06  N9    C4    N3    C2     180.00   0.0  0
 ZZC  CONST_07  C6    N1    C2    N3       0.00   0.0  0
 ZZC  CONST_08  C6    C5    C4    N3       0.00   0.0  0
 ZZC  CONST_09  N7    C5    C4    N3     180.00   0.0  0
 ZZC  CONST_10  C8    N9    C4    N3     180.00   0.0  0
 ZZC  CONST_11  C8    N7    C5    C4       0.00   0.0  0
 ZZC  CONST_12  N7    C8    N9    C4       0.00   0.0  0
 ZZC  CONST_13  C8    N9    C4    C5       0.00   0.0  0
 ZZC  CONST_14  N9    C8    N7    C5       0.00   0.0  0
 ZZC  CONST_15  N9    C4    C5    C6     180.00   0.0  0
 ZZC  CONST_16  C8    N7    C5    C6     180.00   0.0  0
 ZZC  CONST_17  N9    C4    C5    N7       0.00   0.0  0
 ZZC  CONST_18  C1'   N9    C4    N3       0.00   0.0  0
 ZZC  CONST_19  C1'   N9    C4    C5     180.00   0.0  0
 ZZC  CONST_20  C1'   N9    C8    N7     180.00   0.0  0
 ZZC  CONST_21  N6    C6    N1    C2     180.00   0.0  0
 ZZC  CONST_22  N6    C6    C5    C4     180.00   0.0  0
 ZZC  CONST_23  N7    C5    C6    N6       0.00   0.0  0
 ZZC  CONST_24  H2    C2    N3    C4     180.00   0.0  0
 ZZC  CONST_25  H8    C8    N9    C4     180.00   0.0  0
 ZZC  CONST_26  HN6   N6    C6    N1       0.00   0.0  0
 ZZC  CONST_27  HN6A  N6    C6    N1     180.00   0.0  0
 ZZC  Var_01    C4'   C5'   O5'   PA    -102.47  30.0  1
 ZZC  Var_02    O5'A  PB    O3A   PA    -124.18  30.0  2
 ZZC  Var_03    C4'A  C5'A  O5'A  PB     158.03  30.0  1
 ZZC  Var_04    O1A   PA    O3A   PB     -57.32  30.0  2
 ZZC  Var_05    H1'A  C1'A  C2'A  C3'A    74.84  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
 ZZC  chir_01  C3'A  C2'A  C4'A  O3'A  negativ
 ZZC  chir_02  C4'A  O4'A  C3'A  C5'A  negativ
 ZZC  chir_03  C1'   N9    C2'   O4'   negativ
 ZZC  chir_04  C2'   O2'   C3'   C1'   positiv
 ZZC  chir_05  C3'   O3'   C4'   C2'   positiv
 ZZC  chir_06  C4'   O4'   C3'   C5'   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
 ZZC  plan-1  N1    0.020
 ZZC  plan-1  C2    0.020
 ZZC  plan-1  N3    0.020
 ZZC  plan-1  C4    0.020
 ZZC  plan-1  C5    0.020
 ZZC  plan-1  C6    0.020
 ZZC  plan-1  N6    0.020
 ZZC  plan-1  N7    0.020
 ZZC  plan-1  C8    0.020
 ZZC  plan-1  N9    0.020
 ZZC  plan-1  C1'   0.020
 ZZC  plan-1  H2    0.020
 ZZC  plan-1  H8    0.020
 ZZC  plan-2  C6    0.020
 ZZC  plan-2  N6    0.020
 ZZC  plan-2  HN6   0.020
 ZZC  plan-2  HN6A  0.020
 ZZC  plan-3  C2'A  0.020
 ZZC  plan-3  C3'A  0.020
 ZZC  plan-3  O2'A  0.020
 ZZC  plan-3  C1'A  0.020

