# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 18:18:12 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (2~{R},3~{S},5~{R})-5-(2-azanyl-6-methoxy-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc(N)nc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)O3
#
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
 J03  J03  "(2~{R},3~{S},5~{R})-5-(2-azanyl-6-methoxy-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol"
  ligand  35  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J03
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
 J03  O5'  O  OH1   0  -0.663  -18.2889  21.6076   4.2264
 J03  N9   N  NR5   0  -0.544  -15.1461  20.9073   1.1230
 J03  C4   C  CR56  0   0.507  -14.1042  20.0980   0.7755
 J03  N3   N  N     0  -0.499  -12.8147  20.2809   1.0190
 J03  C2   C  CR6   0   0.540  -12.0585  19.2996   0.5360
 J03  N2   N  NH2   0  -0.820  -10.7292  19.3606   0.7665
 J03  N1   N  N     0  -0.524  -12.4903  18.2162  -0.1418
 J03  C6   C  CR6   0   0.513  -13.7760  18.0706  -0.3642
 J03  O6   O  O2    0  -0.449  -14.2363  17.0232  -1.0207
 J03  C5   C  CR56  0  -0.043  -14.6830  19.0327   0.0966
 J03  N7   N  N     0  -0.442  -16.0488  19.1755   0.0374
 J03  C8   C  CR15  0   0.099  -16.2821  20.2897   0.6571
 J03  C2'  C  CH2   0  -0.544  -15.7318  23.3256   1.2689
 J03  C5'  C  CH2   0  -0.158  -18.0167  22.6818   3.3612
 J03  C4'  C  CH1   0  -0.030  -16.5442  23.0294   3.4643
 J03  O4'  O  O2    0  -0.491  -15.7221  21.9118   3.1393
 J03  C1'  C  CH1   0   0.218  -15.0666  22.1131   1.9111
 J03  C3'  C  CH1   0  -0.006  -16.1408  24.1368   2.4840
 J03  O3'  O  OH1   0  -0.668  -15.0085  24.8497   2.9228
 J03  C    C  CH3   0  -0.418  -13.3045  16.0538  -1.4920
 J03  H1   H  HOH1  0   0.454  -19.2230  21.3928   4.1530
 J03  H2   H  HNH2  0   0.394  -10.1238  18.7631   0.2307
 J03  H3   H  HNH2  0   0.393  -10.3398  20.2336   1.0783
 J03  H4   H  HCR5  0   0.295  -17.2621  20.7171   0.8113
 J03  H5   H  HCH2  0   0.281  -15.0601  23.8633   0.6012
 J03  H6   H  HCH2  0   0.272  -16.6140  23.0379   0.6947
 J03  H7   H  HCH2  0   0.205  -18.5889  23.5801   3.6294
 J03  H8   H  HCH2  0   0.202  -18.2756  22.4409   2.3208
 J03  H9   H  HCH1  0   0.249  -16.3266  23.3224   4.4982
 J03  H10  H  HCH1  0   0.257  -13.9994  22.2893   2.0716
 J03  H11  H  HCH1  0   0.246  -16.9804  24.8097   2.2701
 J03  H12  H  HOH1  0   0.452  -15.2274  25.3002   3.7449
 J03  H13  H  HCH3  0   0.251  -13.8967  15.3009  -2.0043
 J03  H14  H  HCH3  0   0.236  -12.5909  16.4914  -2.1897
 J03  H15  H  HCH3  0   0.236  -12.7589  15.5903  -0.6703

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
 J03  C    O6   single    1.425  0.020  1.425
 J03  O6   C6   single    1.319  0.020  1.319
 J03  N7   C5   aromatic  1.375  0.020  1.375
 J03  N7   C8   aromatic  1.296  0.020  1.296
 J03  C6   C5   aromatic  1.400  0.020  1.400
 J03  C6   N1   aromatic  1.313  0.020  1.313
 J03  C5   C4   aromatic  1.390  0.020  1.390
 J03  C8   N9   aromatic  1.374  0.020  1.374
 J03  N1   C2   aromatic  1.349  0.020  1.349
 J03  C4   N9   aromatic  1.364  0.020  1.364
 J03  C4   N3   aromatic  1.325  0.020  1.325
 J03  N9   C1'  single    1.443  0.020  1.443
 J03  C2'  C1'  single    1.525  0.020  1.525
 J03  C2'  C3'  single    1.517  0.020  1.517
 J03  C2   N3   aromatic  1.330  0.020  1.330
 J03  C2   N2   single    1.350  0.020  1.350
 J03  C1'  O4'  single    1.407  0.020  1.407
 J03  C3'  O3'  single    1.408  0.020  1.408
 J03  C3'  C4'  single    1.533  0.020  1.533
 J03  O4'  C4'  single    1.425  0.020  1.425
 J03  C4'  C5'  single    1.516  0.020  1.516
 J03  C5'  O5'  single    1.406  0.020  1.406
 J03  O5'  H1   single    0.850  0.020  0.980
 J03  N2   H2   single    0.890  0.020  1.040
 J03  N2   H3   single    0.890  0.020  1.040
 J03  C8   H4   single    0.930  0.020  1.080
 J03  C2'  H5   single    0.970  0.020  1.090
 J03  C2'  H6   single    0.970  0.020  1.090
 J03  C5'  H7   single    0.970  0.020  1.090
 J03  C5'  H8   single    0.970  0.020  1.090
 J03  C4'  H9   single    0.970  0.020  1.090
 J03  C1'  H10  single    0.970  0.020  1.090
 J03  C3'  H11  single    0.970  0.020  1.090
 J03  O3'  H12  single    0.850  0.020  0.980
 J03  C    H13  single    0.970  0.020  1.090
 J03  C    H14  single    0.970  0.020  1.090
 J03  C    H15  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
 J03  H1   O5'  C5'  108.17  3.000
 J03  C1'  N9   C8   127.32  3.000
 J03  C1'  N9   C4   126.36  3.000
 J03  C8   N9   C4   106.16  3.000
 J03  C5   C4   N3   126.95  3.000
 J03  N3   C4   N9   127.92  3.000
 J03  C5   C4   N9   105.13  3.000
 J03  C2   N3   C4   112.63  3.000
 J03  N1   C2   N2   115.92  3.000
 J03  N2   C2   N3   117.67  3.000
 J03  N1   C2   N3   126.38  3.000
 J03  H3   N2   H2   116.62  3.000
 J03  H3   N2   C2   118.25  3.000
 J03  H2   N2   C2   118.36  3.000
 J03  C6   N1   C2   119.19  3.000
 J03  C5   C6   O6   118.90  3.000
 J03  C5   C6   N1   120.16  3.000
 J03  O6   C6   N1   120.94  3.000
 J03  C    O6   C6   118.47  3.000
 J03  N7   C5   C6   134.50  3.000
 J03  C6   C5   C4   114.69  3.000
 J03  N7   C5   C4   110.81  3.000
 J03  C8   N7   C5   104.33  3.000
 J03  H4   C8   N7   124.87  3.000
 J03  H4   C8   N9   121.58  3.000
 J03  N7   C8   N9   113.55  3.000
 J03  H6   C2'  H5   107.83  3.000
 J03  H6   C2'  C3'  110.15  3.000
 J03  H5   C2'  C3'  113.16  3.000
 J03  H6   C2'  C1'  111.38  3.000
 J03  H5   C2'  C1'  112.44  3.000
 J03  C3'  C2'  C1'  101.86  3.000
 J03  H8   C5'  H7   106.73  3.000
 J03  H8   C5'  C4'  110.08  3.000
 J03  H7   C5'  C4'  107.57  3.000
 J03  H8   C5'  O5'  111.69  3.000
 J03  H7   C5'  O5'  111.95  3.000
 J03  C4'  C5'  O5'  108.74  3.000
 J03  H9   C4'  C3'  110.96  3.000
 J03  H9   C4'  O4'  108.07  3.000
 J03  C3'  C4'  O4'  105.60  3.000
 J03  H9   C4'  C5'  108.55  3.000
 J03  O4'  C4'  C5'  111.40  3.000
 J03  C3'  C4'  C5'  112.19  3.000
 J03  C1'  O4'  C4'  110.84  3.000
 J03  H10  C1'  O4'  110.47  3.000
 J03  H10  C1'  C2'  111.06  3.000
 J03  O4'  C1'  C2'  106.15  3.000
 J03  H10  C1'  N9   105.58  3.000
 J03  O4'  C1'  N9   109.37  3.000
 J03  C2'  C1'  N9   114.24  3.000
 J03  H11  C3'  O3'  111.45  3.000
 J03  H11  C3'  C4'  111.49  3.000
 J03  O3'  C3'  C4'  112.21  3.000
 J03  H11  C3'  C2'  112.22  3.000
 J03  C4'  C3'  C2'  101.35  3.000
 J03  O3'  C3'  C2'  107.66  3.000
 J03  H12  O3'  C3'  108.67  3.000
 J03  H15  C    H14  109.00  3.000
 J03  H15  C    H13  109.49  3.000
 J03  H14  C    H13  109.47  3.000
 J03  H15  C    O6   111.55  3.000
 J03  H14  C    O6   111.53  3.000
 J03  H13  C    O6   105.73  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
 J03  CONST_01  C5   N7  C8  N9      0.00   0.0  0
 J03  CONST_02  N7   C5  C4  N9      0.00   0.0  0
 J03  CONST_03  C6   C5  C4  N9    180.00   0.0  0
 J03  CONST_04  C2   N3  C4  N9    180.00   0.0  0
 J03  CONST_05  C8   N7  C5  C4      0.00   0.0  0
 J03  CONST_06  N1   C6  C5  C4      0.00   0.0  0
 J03  CONST_07  N7   C8  N9  C4      0.00   0.0  0
 J03  CONST_08  N1   C2  N3  C4      0.00   0.0  0
 J03  CONST_09  N7   C5  C4  N3    180.00   0.0  0
 J03  CONST_10  C6   C5  C4  N3      0.00   0.0  0
 J03  CONST_11  C8   N9  C4  N3    180.00   0.0  0
 J03  CONST_12  C6   N1  C2  N3      0.00   0.0  0
 J03  CONST_13  C5   C6  N1  C2      0.00   0.0  0
 J03  CONST_14  C5   C4  N3  C2      0.00   0.0  0
 J03  CONST_15  N7   C5  C6  N1    180.00   0.0  0
 J03  CONST_16  C8   N7  C5  C6    180.00   0.0  0
 J03  CONST_17  C8   N9  C4  C5      0.00   0.0  0
 J03  CONST_18  C1'  N9  C4  N3      0.00   0.0  0
 J03  CONST_19  C1'  N9  C4  C5    180.00   0.0  0
 J03  CONST_20  C1'  N9  C8  N7    180.00   0.0  0
 J03  CONST_21  O6   C6  C5  C4    180.00   0.0  0
 J03  CONST_22  N2   C2  N3  C4    180.00   0.0  0
 J03  CONST_23  O6   C6  N1  C2    180.00   0.0  0
 J03  CONST_24  C6   N1  C2  N2    180.00   0.0  0
 J03  CONST_25  N7   C5  C6  O6      0.00   0.0  0
 J03  CONST_26  H4   C8  N9  C4    180.00   0.0  0
 J03  CONST_27  H4   C8  N7  C5    180.00   0.0  0
 J03  CONST_28  H4   C8  N9  C1'     0.00   0.0  0
 J03  CONST_29  H2   N2  C2  N3    180.00   0.0  0
 J03  CONST_32  H3   N2  C2  N1    180.00   0.0  0
 J03  Var_01    C    O6  C6  N1     -0.37  30.0  1
 J03  Var_02    C    O6  C6  C5    179.65  30.0  1
 J03  Var_03    H13  C   O6  C6   -179.33  30.0  3
 J03  Var_04    H14  C   O6  C6    -60.43  30.0  3
 J03  Var_05    H15  C   O6  C6     61.72  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
 J03  chir_01  C4'  C3'  O4'  C5'  positiv
 J03  chir_02  C1'  O4'  N9   C2'  negativ
 J03  chir_03  C3'  O3'  C4'  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
 J03  plan-1  N9   0.020
 J03  plan-1  C4   0.020
 J03  plan-1  N3   0.020
 J03  plan-1  C2   0.020
 J03  plan-1  N2   0.020
 J03  plan-1  N1   0.020
 J03  plan-1  C6   0.020
 J03  plan-1  O6   0.020
 J03  plan-1  C5   0.020
 J03  plan-1  N7   0.020
 J03  plan-1  C8   0.020
 J03  plan-1  C1'  0.020
 J03  plan-1  H4   0.020
 J03  plan-2  C2   0.020
 J03  plan-2  N2   0.020
 J03  plan-2  H2   0.020
 J03  plan-2  H3   0.020

