# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:41:56 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-{[(2R)-oxolan-2-yl]methyl}-3H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncn(C[C@H]2CCCO2)c3ncnc13
#
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
 W8D  W8D  3-{[(2R)-oxolan-2-yl]methyl}-3H-purin-6-amine  ligand  29  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W8D
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
 W8D  C10   C  CH1   0   0.041  -44.3430  -27.9734   1.8770
 W8D  C13   C  CH2   0  -0.477  -43.8536  -26.7515  -0.1348
 W8D  C15   C  CR16  0   0.161  -47.2230  -29.0009   3.0951
 W8D  C02   C  CR6   0   0.448  -47.6865  -28.9805   5.3490
 W8D  C03   C  CR56  0   0.039  -46.3404  -29.2638   5.6066
 W8D  C05   C  CR15  0   0.001  -44.4073  -29.6718   6.2921
 W8D  C07   C  CR56  0   0.426  -45.4658  -29.4019   4.5253
 W8D  C09   C  CH2   0  -0.359  -45.0112  -29.3213   2.1092
 W8D  C12   C  CH2   0  -0.174  -45.3082  -26.6145   0.2784
 W8D  C14   C  CH2   0  -0.504  -43.4336  -28.0011   0.6374
 W8D  N01   N  NH2   0  -0.804  -48.5976  -28.8233   6.3015
 W8D  N04   N  N     0  -0.472  -45.6273  -29.4450   6.7517
 W8D  N06   N  N     0  -0.490  -44.2353  -29.6587   4.9475
 W8D  N08   N  NR6   0  -0.479  -45.9213  -29.2747   3.2443
 W8D  N16   N  N     0  -0.477  -48.0866  -28.8621   4.0618
 W8D  O11   O  O2    0  -0.495  -45.3251  -26.9762   1.6503
 W8D  H101  H  HCH1  0   0.251  -43.7829  -27.6941   2.7752
 W8D  H132  H  HCH2  0   0.248  -43.7284  -26.8549  -1.2121
 W8D  H131  H  HCH2  0   0.240  -43.2815  -25.8805   0.1908
 W8D  H051  H  HCR5  0   0.237  -43.5729  -29.8620   6.9551
 W8D  H092  H  HCH2  0   0.282  -45.5807  -29.6263   1.2301
 W8D  H091  H  HCH2  0   0.286  -44.2622  -30.0891   2.3006
 W8D  H121  H  HCH2  0   0.236  -45.7011  -25.6014   0.1832
 W8D  H122  H  HCH2  0   0.206  -45.9454  -27.2827  -0.3152
 W8D  H141  H  HCH2  0   0.246  -43.6151  -28.8970   0.0377
 W8D  H142  H  HCH2  0   0.260  -42.3797  -28.0015   0.9107
 W8D  H011  H  HNH2  0   0.409  -49.5549  -28.6225   6.0671
 W8D  H012  H  HNH2  0   0.417  -48.3471  -28.8926   7.2725
 W8D  H151  H  HCR6  0   0.296  -47.5721  -28.9031   2.0754

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
 W8D  C13  C12   single    1.518  0.020  1.518
 W8D  C13  C14   single    1.528  0.020  1.528
 W8D  C12  O11   single    1.419  0.020  1.419
 W8D  C14  C10   single    1.538  0.020  1.538
 W8D  O11  C10   single    1.418  0.020  1.418
 W8D  C10  C09   single    1.522  0.020  1.522
 W8D  C09  N08   single    1.456  0.020  1.456
 W8D  C15  N08   aromatic  1.338  0.020  1.338
 W8D  C15  N16   aromatic  1.304  0.020  1.304
 W8D  N08  C07   aromatic  1.366  0.020  1.366
 W8D  N16  C02   aromatic  1.353  0.020  1.353
 W8D  C07  N06   aromatic  1.326  0.020  1.326
 W8D  C07  C03   aromatic  1.398  0.020  1.398
 W8D  N06  C05   aromatic  1.356  0.020  1.356
 W8D  C02  C03   aromatic  1.400  0.020  1.400
 W8D  C02  N01   single    1.327  0.020  1.327
 W8D  C03  N04   aromatic  1.361  0.020  1.361
 W8D  C05  N04   aromatic  1.323  0.020  1.323
 W8D  C10  H101  single    0.970  0.020  1.090
 W8D  C13  H132  single    0.970  0.020  1.090
 W8D  C13  H131  single    0.970  0.020  1.090
 W8D  C15  H151  single    0.930  0.020  1.080
 W8D  C05  H051  single    0.930  0.020  1.080
 W8D  C09  H092  single    0.970  0.020  1.090
 W8D  C09  H091  single    0.970  0.020  1.090
 W8D  C12  H121  single    0.970  0.020  1.090
 W8D  C12  H122  single    0.970  0.020  1.090
 W8D  C14  H141  single    0.970  0.020  1.090
 W8D  C14  H142  single    0.970  0.020  1.090
 W8D  N01  H011  single    0.860  0.020  1.020
 W8D  N01  H012  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
 W8D  H101  C10  O11   107.82  3.000
 W8D  H101  C10  C14   111.31  3.000
 W8D  O11   C10  C14   107.06  3.000
 W8D  H101  C10  C09   108.99  3.000
 W8D  O11   C10  C09   110.06  3.000
 W8D  C14   C10  C09   111.51  3.000
 W8D  H131  C13  H132  108.09  3.000
 W8D  H131  C13  C14   110.95  3.000
 W8D  H132  C13  C14   112.99  3.000
 W8D  H131  C13  C12   110.42  3.000
 W8D  H132  C13  C12   112.82  3.000
 W8D  C14   C13  C12   101.51  3.000
 W8D  H151  C15  N16   118.38  3.000
 W8D  H151  C15  N08   115.93  3.000
 W8D  N16   C15  N08   125.69  3.000
 W8D  N16   C02  N01   117.99  3.000
 W8D  N01   C02  C03   123.51  3.000
 W8D  N16   C02  C03   118.50  3.000
 W8D  N04   C03  C07   108.05  3.000
 W8D  N04   C03  C02   133.29  3.000
 W8D  C07   C03  C02   118.66  3.000
 W8D  H051  C05  N06   120.75  3.000
 W8D  H051  C05  N04   121.88  3.000
 W8D  N06   C05  N04   117.37  3.000
 W8D  N08   C07  N06   128.78  3.000
 W8D  N06   C07  C03   110.71  3.000
 W8D  N08   C07  C03   120.52  3.000
 W8D  H091  C09  H092  107.67  3.000
 W8D  H091  C09  N08   108.38  3.000
 W8D  H092  C09  N08   108.12  3.000
 W8D  H091  C09  C10   110.42  3.000
 W8D  H092  C09  C10   110.72  3.000
 W8D  N08   C09  C10   111.41  3.000
 W8D  H122  C12  H121  108.00  3.000
 W8D  H122  C12  O11   111.15  3.000
 W8D  H121  C12  O11   108.48  3.000
 W8D  H122  C12  C13   110.73  3.000
 W8D  H121  C12  C13   113.90  3.000
 W8D  O11   C12  C13   104.57  3.000
 W8D  H142  C14  H141  107.34  3.000
 W8D  H142  C14  C13   113.16  3.000
 W8D  H141  C14  C13   110.32  3.000
 W8D  H142  C14  C10   111.73  3.000
 W8D  H141  C14  C10   111.03  3.000
 W8D  C13   C14  C10   103.31  3.000
 W8D  H012  N01  H011  118.43  3.000
 W8D  H012  N01  C02   120.92  3.000
 W8D  H011  N01  C02   120.64  3.000
 W8D  C05   N04  C03   102.34  3.000
 W8D  C07   N06  C05   101.53  3.000
 W8D  C09   N08  C07   121.33  3.000
 W8D  C07   N08  C15   116.62  3.000
 W8D  C09   N08  C15   121.85  3.000
 W8D  C02   N16  C15   120.01  3.000
 W8D  C12   O11  C10   109.00  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
 W8D  CONST_01  N06   C07  N08  C15  180.00   0.0  0
 W8D  CONST_02  C03   C07  N08  C15    0.00   0.0  0
 W8D  CONST_03  C03   C02  N16  C15    0.00   0.0  0
 W8D  CONST_04  N08   C15  N16  C02    0.00   0.0  0
 W8D  CONST_05  N08   C07  C03  C02    0.00   0.0  0
 W8D  CONST_06  N06   C07  C03  C02  180.00   0.0  0
 W8D  CONST_07  C05   N04  C03  C02  180.00   0.0  0
 W8D  CONST_08  C05   N06  C07  C03    0.00   0.0  0
 W8D  CONST_09  N06   C05  N04  C03    0.00   0.0  0
 W8D  CONST_10  N08   C07  N06  C05  180.00   0.0  0
 W8D  CONST_11  C07   C03  N04  C05    0.00   0.0  0
 W8D  CONST_12  N16   C15  N08  C07    0.00   0.0  0
 W8D  CONST_13  N04   C05  N06  C07    0.00   0.0  0
 W8D  CONST_14  N16   C02  C03  C07    0.00   0.0  0
 W8D  CONST_15  N08   C07  C03  N04  180.00   0.0  0
 W8D  CONST_16  N06   C07  C03  N04    0.00   0.0  0
 W8D  CONST_17  N16   C02  C03  N04  180.00   0.0  0
 W8D  CONST_18  N01   C02  N16  C15  180.00   0.0  0
 W8D  CONST_19  C09   N08  C07  C03  180.00   0.0  0
 W8D  CONST_20  N01   C02  C03  C07  180.00   0.0  0
 W8D  CONST_21  N16   C15  N08  C09  180.00   0.0  0
 W8D  CONST_22  N06   C07  N08  C09    0.00   0.0  0
 W8D  CONST_23  N04   C03  C02  N01    0.00   0.0  0
 W8D  CONST_24  H151  C15  N16  C02  180.00   0.0  0
 W8D  CONST_25  H051  C05  N04  C03  180.00   0.0  0
 W8D  CONST_26  H011  N01  C02  C03  180.00   0.0  0
 W8D  CONST_27  H012  N01  C02  C03    0.00   0.0  0
 W8D  Var_01    C12   C13  C14  C10  -29.05  30.0  1
 W8D  Var_02    C13   C12  O11  C10  -33.23  30.0  1
 W8D  Var_03    O11   C12  C13  C14   38.31  30.0  1
 W8D  Var_04    C15   N08  C09  C10   92.62  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
 W8D  chir_01  C10  C14  O11  C09  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
 W8D  plan-1  C15   0.020
 W8D  plan-1  C02   0.020
 W8D  plan-1  C03   0.020
 W8D  plan-1  C05   0.020
 W8D  plan-1  C07   0.020
 W8D  plan-1  C09   0.020
 W8D  plan-1  N01   0.020
 W8D  plan-1  N04   0.020
 W8D  plan-1  N06   0.020
 W8D  plan-1  N08   0.020
 W8D  plan-1  N16   0.020
 W8D  plan-1  H051  0.020
 W8D  plan-1  H151  0.020
 W8D  plan-2  C02   0.020
 W8D  plan-2  N01   0.020
 W8D  plan-2  H011  0.020
 W8D  plan-2  H012  0.020

