# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:15:46 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-{3-[(3S)-oxolan-3-yl]propyl}-3H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncn(CCC[C@H]2CCOC2)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
 W8J  W8J  3-{3-[(3S)-oxolan-3-yl]propyl}-3H-purin-6-amine  ligand  35  18  .  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_W8J
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
 W8J  C10   C  CH2   0  -0.457  -45.7558  -30.8987   1.7164
 W8J  C13   C  CH2   0  -0.180  -42.8159  -31.7915   2.1417
 W8J  C15   C  CH2   0  -0.156  -41.6914  -31.1559   0.2219
 W8J  C17   C  CR16  0   0.154  -47.3882  -28.4861   3.3649
 W8J  C02   C  CR6   0   0.448  -47.9471  -28.6896   5.5874
 W8J  C03   C  CR56  0   0.033  -46.7965  -29.4625   5.7829
 W8J  C05   C  CR15  0   0.006  -45.1680  -30.6347   6.3724
 W8J  C07   C  CR56  0   0.435  -45.9653  -29.7157   4.6879
 W8J  C09   C  CH2   0  -0.331  -45.4459  -29.5209   2.2892
 W8J  C11   C  CH2   0  -0.439  -44.7950  -31.2690   0.5805
 W8J  C12   C  CR15  0  -0.297  -43.6814  -32.2430   0.9738
 W8J  C16   C  CH2   0  -0.508  -42.6120  -32.3327  -0.1166
 W8J  N01   N  NH2   0  -0.805  -48.8064  -28.3944   6.5552
 W8J  N04   N  N     0  -0.472  -46.2565  -30.0723   6.8729
 W8J  N06   N  N     0  -0.484  -44.9284  -30.4588   5.0500
 W8J  N08   N  NR6   0  -0.483  -46.2687  -29.2131   3.4552
 W8J  N18   N  N     0  -0.475  -48.2026  -28.2152   4.3462
 W8J  O14   O  O     0  -0.503  -41.9043  -30.8528   1.5962
 W8J  H101  H  HCH2  0   0.250  -46.7866  -30.8940   1.3557
 W8J  H102  H  HCH2  0   0.248  -45.7112  -31.6478   2.5117
 W8J  H131  H  HCH2  0   0.209  -42.2846  -32.6566   2.5623
 W8J  H151  H  HCH2  0   0.216  -40.6396  -31.3987   0.0434
 W8J  H152  H  HCH2  0   0.209  -41.9323  -30.2725  -0.3775
 W8J  H171  H  HCR6  0   0.300  -47.6173  -28.0952   2.3813
 W8J  H051  H  HCR5  0   0.237  -44.4895  -31.2136   6.9857
 W8J  H092  H  HCH2  0   0.275  -44.4024  -29.4335   2.5890
 W8J  H091  H  HCH2  0   0.280  -45.6292  -28.7489   1.5419
 W8J  H112  H  HCH2  0   0.233  -44.3663  -30.3567   0.1505
 W8J  H111  H  HCH2  0   0.248  -45.3591  -31.7298  -0.2330
 W8J  H121  H  HCR5  0   0.248  -44.1246  -33.2190   1.1872
 W8J  H161  H  HCH2  0   0.247  -42.0737  -33.2801  -0.0475
 W8J  H162  H  HCH2  0   0.248  -43.0213  -32.2606  -1.1253
 W8J  H012  H  HNH2  0   0.410  -49.6191  -27.8336   6.3636
 W8J  H011  H  HNH2  0   0.417  -48.6627  -28.7236   7.4941
 W8J  H132  H  HCH2  0   0.241  -43.3647  -31.3201   2.9602

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
 W8J  C16  C12   single    1.530  0.020  1.530
 W8J  C16  C15   single    1.532  0.020  1.532
 W8J  C11  C12   single    1.531  0.020  1.531
 W8J  C11  C10   single    1.533  0.020  1.533
 W8J  C12  C13   single    1.522  0.020  1.522
 W8J  C15  O14   single    1.423  0.020  1.423
 W8J  C10  C09   single    1.524  0.020  1.524
 W8J  C13  O14   single    1.418  0.020  1.418
 W8J  C09  N08   single    1.460  0.020  1.460
 W8J  C17  N08   aromatic  1.338  0.020  1.338
 W8J  C17  N18   aromatic  1.304  0.020  1.304
 W8J  N08  C07   aromatic  1.365  0.020  1.365
 W8J  N18  C02   aromatic  1.353  0.020  1.353
 W8J  C07  N06   aromatic  1.326  0.020  1.326
 W8J  C07  C03   aromatic  1.398  0.020  1.398
 W8J  N06  C05   aromatic  1.355  0.020  1.355
 W8J  C02  C03   aromatic  1.400  0.020  1.400
 W8J  C02  N01   single    1.327  0.020  1.327
 W8J  C03  N04   aromatic  1.361  0.020  1.361
 W8J  C05  N04   aromatic  1.323  0.020  1.323
 W8J  C10  H101  single    0.970  0.020  1.090
 W8J  C10  H102  single    0.970  0.020  1.090
 W8J  C13  H132  single    0.970  0.020  1.090
 W8J  C13  H131  single    0.970  0.020  1.090
 W8J  C15  H151  single    0.970  0.020  1.090
 W8J  C15  H152  single    0.970  0.020  1.090
 W8J  C17  H171  single    0.930  0.020  1.080
 W8J  C05  H051  single    0.930  0.020  1.080
 W8J  C09  H092  single    0.970  0.020  1.090
 W8J  C09  H091  single    0.970  0.020  1.090
 W8J  C11  H112  single    0.970  0.020  1.090
 W8J  C11  H111  single    0.970  0.020  1.090
 W8J  C12  H121  single    0.970  0.020  1.090
 W8J  C16  H161  single    0.970  0.020  1.090
 W8J  C16  H162  single    0.970  0.020  1.090
 W8J  N01  H012  single    0.860  0.020  1.020
 W8J  N01  H011  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
 W8J  H102  C10  H101  106.36  3.000
 W8J  H102  C10  C11   110.36  3.000
 W8J  H101  C10  C11   110.35  3.000
 W8J  H102  C10  C09   109.74  3.000
 W8J  H101  C10  C09   108.19  3.000
 W8J  C11   C10  C09   111.68  3.000
 W8J  H131  C13  H132  107.21  3.000
 W8J  H131  C13  O14   110.96  3.000
 W8J  H132  C13  O14   109.01  3.000
 W8J  H131  C13  C12   109.58  3.000
 W8J  H132  C13  C12   114.66  3.000
 W8J  O14   C13  C12   105.47  3.000
 W8J  H152  C15  H151  107.54  3.000
 W8J  H152  C15  O14   108.90  3.000
 W8J  H151  C15  O14   110.40  3.000
 W8J  H152  C15  C16   111.52  3.000
 W8J  H151  C15  C16   111.79  3.000
 W8J  O14   C15  C16   106.68  3.000
 W8J  H171  C17  N18   118.46  3.000
 W8J  H171  C17  N08   115.75  3.000
 W8J  N18   C17  N08   125.79  3.000
 W8J  N18   C02  N01   117.94  3.000
 W8J  N01   C02  C03   123.58  3.000
 W8J  N18   C02  C03   118.48  3.000
 W8J  N04   C03  C07   108.07  3.000
 W8J  N04   C03  C02   133.28  3.000
 W8J  C07   C03  C02   118.65  3.000
 W8J  H051  C05  N06   120.76  3.000
 W8J  H051  C05  N04   121.91  3.000
 W8J  N06   C05  N04   117.33  3.000
 W8J  N08   C07  N06   128.80  3.000
 W8J  N06   C07  C03   110.64  3.000
 W8J  N08   C07  C03   120.56  3.000
 W8J  H091  C09  H092  107.04  3.000
 W8J  H091  C09  N08   107.67  3.000
 W8J  H092  C09  N08   107.65  3.000
 W8J  H091  C09  C10   110.39  3.000
 W8J  H092  C09  C10   111.77  3.000
 W8J  N08   C09  C10   112.10  3.000
 W8J  H111  C11  H112  105.14  3.000
 W8J  H111  C11  C12   107.38  3.000
 W8J  H112  C11  C12   110.24  3.000
 W8J  H111  C11  C10   109.28  3.000
 W8J  H112  C11  C10   109.56  3.000
 W8J  C12   C11  C10   114.78  3.000
 W8J  H121  C12  C16   111.73  3.000
 W8J  H121  C12  C11   108.87  3.000
 W8J  C16   C12  C11   111.26  3.000
 W8J  H121  C12  C13   110.22  3.000
 W8J  C11   C12  C13   114.97  3.000
 W8J  C16   C12  C13    99.60  3.000
 W8J  H162  C16  H161  107.51  3.000
 W8J  H162  C16  C12   113.13  3.000
 W8J  H161  C16  C12   110.51  3.000
 W8J  H162  C16  C15   112.27  3.000
 W8J  H161  C16  C15   110.88  3.000
 W8J  C12   C16  C15   102.56  3.000
 W8J  H011  N01  H012  118.42  3.000
 W8J  H011  N01  C02   121.03  3.000
 W8J  H012  N01  C02   120.55  3.000
 W8J  C05   N04  C03   102.35  3.000
 W8J  C07   N06  C05   101.59  3.000
 W8J  C09   N08  C07   121.21  3.000
 W8J  C07   N08  C17   116.54  3.000
 W8J  C09   N08  C17   122.16  3.000
 W8J  C02   N18  C17   119.98  3.000
 W8J  C15   O14  C13   109.07  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
 W8J  CONST_01  N06   C07  N08  C17   180.00   0.0  0
 W8J  CONST_02  C03   C07  N08  C17     0.00   0.0  0
 W8J  CONST_03  C03   C02  N18  C17     0.00   0.0  0
 W8J  CONST_04  N08   C17  N18  C02     0.00   0.0  0
 W8J  CONST_05  N08   C07  C03  C02     0.00   0.0  0
 W8J  CONST_06  N06   C07  C03  C02   180.00   0.0  0
 W8J  CONST_07  C05   N04  C03  C02   180.00   0.0  0
 W8J  CONST_08  C05   N06  C07  C03     0.00   0.0  0
 W8J  CONST_09  N06   C05  N04  C03     0.00   0.0  0
 W8J  CONST_10  N08   C07  N06  C05   180.00   0.0  0
 W8J  CONST_11  C07   C03  N04  C05     0.00   0.0  0
 W8J  CONST_12  N18   C17  N08  C07     0.00   0.0  0
 W8J  CONST_13  N04   C05  N06  C07     0.00   0.0  0
 W8J  CONST_14  N18   C02  C03  C07     0.00   0.0  0
 W8J  CONST_15  N08   C07  C03  N04   180.00   0.0  0
 W8J  CONST_16  N06   C07  C03  N04     0.00   0.0  0
 W8J  CONST_17  N18   C02  C03  N04   180.00   0.0  0
 W8J  CONST_18  N01   C02  N18  C17   180.00   0.0  0
 W8J  CONST_19  C09   N08  C07  C03   180.00   0.0  0
 W8J  CONST_20  N01   C02  C03  C07   180.00   0.0  0
 W8J  CONST_21  N18   C17  N08  C09   180.00   0.0  0
 W8J  CONST_22  N06   C07  N08  C09     0.00   0.0  0
 W8J  CONST_23  N04   C03  C02  N01     0.00   0.0  0
 W8J  CONST_24  H171  C17  N18  C02   180.00   0.0  0
 W8J  CONST_25  H051  C05  N04  C03   180.00   0.0  0
 W8J  CONST_26  H012  N01  C02  C03   180.00   0.0  0
 W8J  CONST_27  H011  N01  C02  C03     0.00   0.0  0
 W8J  Var_01    C16   C15  O14  C13     3.35  30.0  1
 W8J  Var_02    C12   C13  O14  C15   -27.75  30.0  1
 W8J  Var_03    O14   C15  C16  C12    21.88  30.0  1
 W8J  Var_04    C17   N08  C09  C10   -96.99  30.0  2
 W8J  Var_05    C12   C11  C10  C09   102.03  30.0  2
 W8J  Var_06    N08   C09  C10  C11  -174.41  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
 W8J  chir_01  C12  C16  C11  C13  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
 W8J  plan-1  C17   0.020
 W8J  plan-1  C02   0.020
 W8J  plan-1  C03   0.020
 W8J  plan-1  C05   0.020
 W8J  plan-1  C07   0.020
 W8J  plan-1  C09   0.020
 W8J  plan-1  N01   0.020
 W8J  plan-1  N04   0.020
 W8J  plan-1  N06   0.020
 W8J  plan-1  N08   0.020
 W8J  plan-1  N18   0.020
 W8J  plan-1  H171  0.020
 W8J  plan-1  H051  0.020
 W8J  plan-2  C02   0.020
 W8J  plan-2  N01   0.020
 W8J  plan-2  H012  0.020
 W8J  plan-2  H011  0.020

