# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:40:20 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (1S,2S,5R)-5-(6-amino-9H-purin-9-yl)cyclopent-3-ene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3C=C[C@H](O)[C@H]3O
#
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
 ADC  ADC  (1S,2S,5R)-5-(6-amino-9H-purin-9-yl)cyclopent-3-ene-1,2-diol  ligand  28  17  .  2021-08-06  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ADC
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
 ADC  C5'   C  CR15  0  -0.215   0.5156  -1.6262  -2.1484
 ADC  C4'   C  CR15  0  -0.269   0.5041  -1.2973  -3.4346
 ADC  C3'   C  CR15  0  -0.017  -0.2627  -0.0238  -3.6694
 ADC  O3'   O  OH1   0  -0.668   0.3281   0.8735  -4.5770
 ADC  C2'   C  CR15  0   0.048  -0.2957   0.5974  -2.2647
 ADC  O2'   O  OH1   0  -0.659  -1.4012   1.3978  -1.9693
 ADC  C1'   C  CR15  0  -0.169  -0.2374  -0.6167  -1.3294
 ADC  N9    N  NR5   0  -0.512   0.3658  -0.3386  -0.0430
 ADC  C8    C  CR15  0   0.110   1.6926  -0.1415   0.2175
 ADC  N7    N  N     0  -0.454   1.9461   0.1033   1.4704
 ADC  C5    C  CR56  0  -0.014   0.7167   0.0698   2.0746
 ADC  C6    C  CR6   0   0.457   0.3006   0.2417   3.4077
 ADC  N6    N  NH2   0  -0.818   1.1519   0.5033   4.4009
 ADC  N1    N  N     0  -0.476  -1.0061   0.1382   3.6748
 ADC  C2    C  CR16  0   0.041  -1.8514  -0.1262   2.6810
 ADC  N3    N  N     0  -0.455  -1.5834  -0.3107   1.4009
 ADC  C4    C  CR56  0   0.490  -0.2803  -0.2009   1.1494
 ADC  H5'   H  HCR5  0   0.278   0.9422  -2.5219  -1.7163
 ADC  H4'   H  HCR5  0   0.268   0.9304  -1.8867  -4.2366
 ADC  H3'   H  HCR5  0   0.235  -1.2894  -0.2704  -3.9766
 ADC  HO3   H  HOH1  0   0.459   0.1033   0.5993  -5.4711
 ADC  H2'   H  HCR5  0   0.228   0.6461   1.1556  -2.1487
 ADC  HO2   H  HOH1  0   0.458  -1.3326   2.2132  -2.4759
 ADC  H1'   H  HCR5  0   0.294  -1.2526  -0.9691  -1.1207
 ADC  H8    H  HCR5  0   0.298   2.4332  -0.1964  -0.5670
 ADC  HN61  H  HNH2  0   0.403   0.8203   0.5832   5.3466
 ADC  HN62  H  HNH2  0   0.410   2.1420   0.5478   4.2374
 ADC  H2    H  HCR6  0   0.250  -2.8957  -0.1987   2.9658

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
 ADC  C5'  C4'   double    1.328  0.020  1.328
 ADC  C5'  C1'   single    1.502  0.020  1.502
 ADC  C5'  H5'   single    0.930  0.020  1.080
 ADC  C4'  C3'   single    1.505  0.020  1.505
 ADC  C4'  H4'   single    0.930  0.020  1.080
 ADC  C3'  O3'   single    1.406  0.020  1.406
 ADC  C3'  C2'   single    1.536  0.020  1.536
 ADC  C3'  H3'   single    0.970  0.020  1.090
 ADC  O3'  HO3   single    0.850  0.020  0.980
 ADC  C2'  O2'   single    1.397  0.020  1.397
 ADC  C2'  C1'   single    1.534  0.020  1.534
 ADC  C2'  H2'   single    0.970  0.020  1.090
 ADC  O2'  HO2   single    0.850  0.020  0.980
 ADC  C1'  N9    single    1.448  0.020  1.448
 ADC  C1'  H1'   single    0.970  0.020  1.090
 ADC  N9   C8    aromatic  1.366  0.020  1.366
 ADC  N9   C4    aromatic  1.363  0.020  1.363
 ADC  C8   N7    aromatic  1.301  0.020  1.301
 ADC  C8   H8    single    0.930  0.020  1.080
 ADC  N7   C5    aromatic  1.370  0.020  1.370
 ADC  C5   C6    aromatic  1.407  0.020  1.407
 ADC  C5   C4    aromatic  1.387  0.020  1.387
 ADC  C6   N6    single    1.334  0.020  1.334
 ADC  C6   N1    aromatic  1.338  0.020  1.338
 ADC  N6   HN61  single    0.860  0.020  1.020
 ADC  N6   HN62  single    0.860  0.020  1.020
 ADC  N1   C2    aromatic  1.331  0.020  1.331
 ADC  C2   N3    aromatic  1.321  0.020  1.321
 ADC  C2   H2    single    0.930  0.020  1.080
 ADC  N3   C4    aromatic  1.332  0.020  1.332

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
 ADC  H5'   C5'  C1'   122.42  3.000
 ADC  H5'   C5'  C4'   126.53  3.000
 ADC  C1'   C5'  C4'   110.94  3.000
 ADC  H4'   C4'  C3'   123.07  3.000
 ADC  H4'   C4'  C5'   125.40  3.000
 ADC  C3'   C4'  C5'   111.42  3.000
 ADC  H3'   C3'  C2'   109.02  3.000
 ADC  H3'   C3'  O3'   110.79  3.000
 ADC  C2'   C3'  O3'   109.94  3.000
 ADC  H3'   C3'  C4'   109.24  3.000
 ADC  C2'   C3'  C4'   102.15  3.000
 ADC  O3'   C3'  C4'   115.25  3.000
 ADC  HO3   O3'  C3'   108.65  3.000
 ADC  H2'   C2'  C1'   107.74  3.000
 ADC  H2'   C2'  O2'   111.36  3.000
 ADC  C1'   C2'  O2'   110.78  3.000
 ADC  H2'   C2'  C3'   106.44  3.000
 ADC  C1'   C2'  C3'   103.69  3.000
 ADC  O2'   C2'  C3'   116.24  3.000
 ADC  HO2   O2'  C2'   108.53  3.000
 ADC  H1'   C1'  N9    106.19  3.000
 ADC  H1'   C1'  C2'   109.63  3.000
 ADC  N9    C1'  C2'   113.93  3.000
 ADC  H1'   C1'  C5'   110.64  3.000
 ADC  N9    C1'  C5'   113.87  3.000
 ADC  C2'   C1'  C5'   102.62  3.000
 ADC  C4    N9   C8    106.20  3.000
 ADC  C4    N9   C1'   126.81  3.000
 ADC  C8    N9   C1'   126.99  3.000
 ADC  H8    C8   N7    125.10  3.000
 ADC  H8    C8   N9    121.33  3.000
 ADC  N7    C8   N9    113.57  3.000
 ADC  C5    N7   C8    104.19  3.000
 ADC  C4    C5   C6    116.31  3.000
 ADC  C4    C5   N7    110.83  3.000
 ADC  C6    C5   N7    132.85  3.000
 ADC  N1    C6   N6    119.33  3.000
 ADC  N1    C6   C5    117.95  3.000
 ADC  N6    C6   C5    122.73  3.000
 ADC  HN62  N6   HN61  118.34  3.000
 ADC  HN62  N6   C6    121.10  3.000
 ADC  HN61  N6   C6    120.37  3.000
 ADC  C2    N1   C6    119.11  3.000
 ADC  H2    C2   N3    116.13  3.000
 ADC  H2    C2   N1    115.38  3.000
 ADC  N3    C2   N1    128.50  3.000
 ADC  C4    N3   C2    111.72  3.000
 ADC  N3    C4   C5    126.41  3.000
 ADC  N3    C4   N9    128.37  3.000
 ADC  C5    C4   N9    105.22  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
 ADC  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 ADC  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 ADC  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 ADC  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 ADC  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 ADC  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 ADC  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 ADC  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 ADC  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 ADC  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 ADC  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 ADC  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 ADC  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 ADC  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 ADC  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 ADC  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 ADC  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 ADC  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 ADC  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 ADC  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 ADC  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 ADC  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 ADC  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 ADC  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 ADC  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 ADC  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 ADC  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 ADC  Var_01    C1'   C5'  C4'  C3'   -0.26  30.0  1

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
 ADC  chir_01  C3'  C4'  O3'  C2'  positiv
 ADC  chir_02  C2'  O2'  C1'  C3'  negativ
 ADC  chir_03  C1'  N9   C5'  C2'  positiv

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
 ADC  plan-1  C1'   0.020
 ADC  plan-1  N9    0.020
 ADC  plan-1  C8    0.020
 ADC  plan-1  N7    0.020
 ADC  plan-1  C5    0.020
 ADC  plan-1  C6    0.020
 ADC  plan-1  N6    0.020
 ADC  plan-1  N1    0.020
 ADC  plan-1  C2    0.020
 ADC  plan-1  N3    0.020
 ADC  plan-1  C4    0.020
 ADC  plan-1  H8    0.020
 ADC  plan-1  H2    0.020
 ADC  plan-2  C6    0.020
 ADC  plan-2  N6    0.020
 ADC  plan-2  HN61  0.020
 ADC  plan-2  HN62  0.020

