# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:32:54 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[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
 FWK  FWK  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol  ligand  34  19  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FWK
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
 FWK  C5'  C  CH2   0  -0.458   3.6278   1.3388  -0.2966
 FWK  C4'  C  CH1   0  -0.004   3.2601   0.0699   0.4572
 FWK  O4'  O  O2    0  -0.495   1.9477   0.1703   1.0351
 FWK  C3'  C  CH1   0  -0.012   3.2033  -1.1652  -0.4309
 FWK  O3'  O  OH1   0  -0.671   3.4086  -2.3070   0.3611
 FWK  C2'  C  CH1   0  -0.058   1.7576  -1.1002  -0.9245
 FWK  O2'  O  OH1   0  -0.654   1.2182  -2.3183  -1.3447
 FWK  C1'  C  CH1   0   0.216   1.0348  -0.6233   0.3376
 FWK  N9   N  NR5   0  -0.538  -0.1601   0.1405   0.0615
 FWK  C8   C  CR15  0   0.108  -0.2325   1.3855  -0.5018
 FWK  N7   N  N     0  -0.450  -1.4490   1.8209  -0.6404
 FWK  C5   C  CR56  0  -0.012  -2.2300   0.8096  -0.1435
 FWK  C4   C  CR56  0   0.491  -1.4477  -0.2442   0.3026
 FWK  N3   N  N     0  -0.456  -1.8841  -1.3769   0.8489
 FWK  C2   C  CR16  0   0.044  -3.2030  -1.4037   0.9293
 FWK  N1   N  N     0  -0.475  -4.0757  -0.4780   0.5394
 FWK  C6   C  CR6   0   0.459  -3.6221   0.6552  -0.0080
 FWK  N6   N  NH2   0  -0.817  -4.4931   1.5881  -0.3949
 FWK  C6'  C  CH3   0  -0.663   3.5861   2.5857   0.5745
 FWK  H1   H  HCH2  0   0.244   4.6376   1.2043  -0.6934
 FWK  H2   H  HCH2  0   0.225   2.9768   1.4674  -1.1676
 FWK  H3   H  HCH1  0   0.253   3.9713  -0.0749   1.2764
 FWK  H4   H  HCH1  0   0.247   3.9244  -1.1066  -1.2563
 FWK  H5   H  HOH1  0   0.448   3.0197  -3.0611  -0.0972
 FWK  H6   H  HCH1  0   0.251   1.6799  -0.3358  -1.7082
 FWK  H7   H  HOH1  0   0.469   1.4553  -2.4628  -2.2663
 FWK  H8   H  HCH1  0   0.261   0.7103  -1.4828   0.9345
 FWK  H9   H  HCR5  0   0.296   0.6540   1.9319  -0.7875
 FWK  H10  H  HCR6  0   0.252  -3.6370  -2.2961   1.3675
 FWK  H11  H  HNH2  0   0.411  -4.1868   2.4285  -0.8527
 FWK  H12  H  HNH2  0   0.404  -5.4816   1.4230  -0.3136
 FWK  H13  H  HCH3  0   0.226   2.5847   2.7811   0.9580
 FWK  H14  H  HCH3  0   0.224   4.2576   2.4902   1.4296
 FWK  H15  H  HCH3  0   0.235   3.8977   3.4629   0.0080

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
 FWK  C6'  C5'  single    1.522  0.020  1.522
 FWK  C5'  C4'  single    1.521  0.020  1.521
 FWK  C3'  O3'  single    1.405  0.020  1.405
 FWK  C3'  C4'  single    1.522  0.020  1.522
 FWK  C3'  C2'  single    1.529  0.020  1.529
 FWK  C4'  O4'  single    1.437  0.020  1.437
 FWK  C2'  O2'  single    1.397  0.020  1.397
 FWK  C2'  C1'  single    1.531  0.020  1.531
 FWK  O4'  C1'  single    1.396  0.020  1.396
 FWK  C1'  N9   single    1.445  0.020  1.445
 FWK  C8   N9   aromatic  1.368  0.020  1.368
 FWK  C8   N7   aromatic  1.300  0.020  1.300
 FWK  N9   C4   aromatic  1.365  0.020  1.365
 FWK  N7   C5   aromatic  1.371  0.020  1.371
 FWK  C4   C5   aromatic  1.386  0.020  1.386
 FWK  C4   N3   aromatic  1.331  0.020  1.331
 FWK  C5   C6   aromatic  1.407  0.020  1.407
 FWK  N3   C2   aromatic  1.322  0.020  1.322
 FWK  C6   N1   aromatic  1.338  0.020  1.338
 FWK  C6   N6   single    1.334  0.020  1.334
 FWK  C2   N1   aromatic  1.331  0.020  1.331
 FWK  C5'  H1   single    0.970  0.020  1.090
 FWK  C5'  H2   single    0.970  0.020  1.090
 FWK  C4'  H3   single    0.970  0.020  1.090
 FWK  C3'  H4   single    0.970  0.020  1.090
 FWK  O3'  H5   single    0.850  0.020  0.980
 FWK  C2'  H6   single    0.970  0.020  1.090
 FWK  O2'  H7   single    0.850  0.020  0.980
 FWK  C1'  H8   single    0.970  0.020  1.090
 FWK  C8   H9   single    0.930  0.020  1.080
 FWK  C2   H10  single    0.930  0.020  1.080
 FWK  N6   H11  single    0.860  0.020  1.020
 FWK  N6   H12  single    0.860  0.020  1.020
 FWK  C6'  H13  single    0.970  0.020  1.090
 FWK  C6'  H14  single    0.970  0.020  1.090
 FWK  C6'  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
 FWK  H2   C5'  H1   105.96  3.000
 FWK  H2   C5'  C6'  110.05  3.000
 FWK  H1   C5'  C6'  109.51  3.000
 FWK  H2   C5'  C4'  110.40  3.000
 FWK  H1   C5'  C4'  107.49  3.000
 FWK  C6'  C5'  C4'  113.16  3.000
 FWK  H3   C4'  C3'  110.71  3.000
 FWK  H3   C4'  O4'  107.55  3.000
 FWK  C3'  C4'  O4'  104.90  3.000
 FWK  H3   C4'  C5'  108.92  3.000
 FWK  O4'  C4'  C5'  111.20  3.000
 FWK  C3'  C4'  C5'  113.37  3.000
 FWK  C1'  O4'  C4'  110.88  3.000
 FWK  H4   C3'  C2'  112.10  3.000
 FWK  H4   C3'  O3'  111.80  3.000
 FWK  C2'  C3'  O3'  110.78  3.000
 FWK  H4   C3'  C4'  111.77  3.000
 FWK  C2'  C3'  C4'  100.90  3.000
 FWK  O3'  C3'  C4'  108.97  3.000
 FWK  H5   O3'  C3'  107.98  3.000
 FWK  H6   C2'  C1'  109.78  3.000
 FWK  H6   C2'  O2'  111.42  3.000
 FWK  C1'  C2'  O2'  109.72  3.000
 FWK  H6   C2'  C3'  109.09  3.000
 FWK  C1'  C2'  C3'  101.16  3.000
 FWK  O2'  C2'  C3'  115.16  3.000
 FWK  H7   O2'  C2'  108.89  3.000
 FWK  H8   C1'  N9   105.90  3.000
 FWK  H8   C1'  C2'  110.16  3.000
 FWK  N9   C1'  C2'  113.43  3.000
 FWK  H8   C1'  O4'  111.55  3.000
 FWK  N9   C1'  O4'  109.62  3.000
 FWK  C2'  C1'  O4'  106.27  3.000
 FWK  C4   N9   C8   106.21  3.000
 FWK  C4   N9   C1'  126.67  3.000
 FWK  C8   N9   C1'  127.11  3.000
 FWK  H9   C8   N7   124.81  3.000
 FWK  H9   C8   N9   121.73  3.000
 FWK  N7   C8   N9   113.46  3.000
 FWK  C5   N7   C8   104.33  3.000
 FWK  C6   C5   C4   116.36  3.000
 FWK  C6   C5   N7   132.79  3.000
 FWK  C4   C5   N7   110.85  3.000
 FWK  N3   C4   C5   126.43  3.000
 FWK  N3   C4   N9   128.42  3.000
 FWK  C5   C4   N9   105.14  3.000
 FWK  C2   N3   C4   111.68  3.000
 FWK  H10  C2   N1   115.36  3.000
 FWK  H10  C2   N3   116.14  3.000
 FWK  N1   C2   N3   128.51  3.000
 FWK  C6   N1   C2   119.13  3.000
 FWK  N6   C6   N1   119.33  3.000
 FWK  N6   C6   C5   122.78  3.000
 FWK  N1   C6   C5   117.89  3.000
 FWK  H12  N6   H11  118.28  3.000
 FWK  H12  N6   C6   120.25  3.000
 FWK  H11  N6   C6   121.20  3.000
 FWK  H15  C6'  H14  107.57  3.000
 FWK  H15  C6'  H13  107.54  3.000
 FWK  H14  C6'  H13  107.78  3.000
 FWK  H15  C6'  C5'  110.74  3.000
 FWK  H14  C6'  C5'  111.10  3.000
 FWK  H13  C6'  C5'  111.93  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
 FWK  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 FWK  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 FWK  CONST_03  C6   C5   C4   N9   180.00   0.0  0
 FWK  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 FWK  CONST_05  C5   C4   N9   C8     0.00   0.0  0
 FWK  CONST_06  N3   C4   N9   C8   180.00   0.0  0
 FWK  CONST_07  C4   C5   N7   C8     0.00   0.0  0
 FWK  CONST_08  C6   C5   N7   C8   180.00   0.0  0
 FWK  CONST_09  C4   N9   C8   N7     0.00   0.0  0
 FWK  CONST_10  N3   C4   C5   N7   180.00   0.0  0
 FWK  CONST_11  N1   C6   C5   N7   180.00   0.0  0
 FWK  CONST_12  C2   N3   C4   C5     0.00   0.0  0
 FWK  CONST_13  C2   N1   C6   C5     0.00   0.0  0
 FWK  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 FWK  CONST_15  N1   C2   N3   C4     0.00   0.0  0
 FWK  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 FWK  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 FWK  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 FWK  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 FWK  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 FWK  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 FWK  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 FWK  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 FWK  CONST_24  H9   C8   N9   C1'    0.00   0.0  0
 FWK  CONST_25  H10  C2   N3   C4   180.00   0.0  0
 FWK  CONST_26  H11  N6   C6   C5     0.00   0.0  0
 FWK  CONST_27  H12  N6   C6   C5   180.00   0.0  0
 FWK  Var_01    H13  C6'  C5'  C4'  -62.50  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
 FWK  chir_01  C4'  C5'  C3'  O4'  positiv
 FWK  chir_02  C3'  O3'  C2'  C4'  negativ
 FWK  chir_03  C2'  O2'  C1'  C3'  negativ
 FWK  chir_04  C1'  O4'  N9   C2'  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
 FWK  plan-1  C1'  0.020
 FWK  plan-1  N9   0.020
 FWK  plan-1  C8   0.020
 FWK  plan-1  N7   0.020
 FWK  plan-1  C5   0.020
 FWK  plan-1  C4   0.020
 FWK  plan-1  N3   0.020
 FWK  plan-1  C2   0.020
 FWK  plan-1  N1   0.020
 FWK  plan-1  C6   0.020
 FWK  plan-1  N6   0.020
 FWK  plan-1  H9   0.020
 FWK  plan-1  H10  0.020
 FWK  plan-2  C6   0.020
 FWK  plan-2  N6   0.020
 FWK  plan-2  H11  0.020
 FWK  plan-2  H12  0.020

