# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:50:21 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C/[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
 QVR  QVR  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol  ligand  35  20  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QVR
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
 QVR  C24  C  CH3   0  -0.707   4.5251  -2.9575  -0.1764
 QVR  C28  C  C1    0  -0.227   3.6271  -1.8109  -0.5057
 QVR  C31  C  C1    0  -0.259   3.7777  -0.5786  -0.0310
 QVR  C36  C  CH1   0   0.008   2.9117   0.5999  -0.3181
 QVR  C38  C  CH1   0   0.168   0.6639   0.9319  -0.8158
 QVR  C39  C  CH1   0  -0.048   1.0377   1.9114   0.2971
 QVR  C40  C  CH1   0  -0.011   2.2281   1.1925   0.9267
 QVR  C49  C  CR15  0   0.105  -0.1076  -1.2888   0.1640
 QVR  C50  C  CR56  0  -0.005  -2.2012  -1.0172   0.1646
 QVR  C51  C  CR56  0   0.488  -1.6683   0.1438  -0.3722
 QVR  C53  C  CR16  0   0.042  -3.6504   1.0421  -0.6528
 QVR  C55  C  CR6   0   0.458  -3.6041  -1.0683   0.2656
 QVR  N47  N  NR5   0  -0.533  -0.3175  -0.0459  -0.3685
 QVR  N48  N  N     0  -0.451  -1.2076  -1.9013   0.4925
 QVR  N52  N  N     0  -0.459  -2.3468   1.2087  -0.7954
 QVR  N54  N  N     0  -0.474  -4.3011  -0.0081  -0.1588
 QVR  N57  N  NH2   0  -0.817  -4.2535  -2.1208   0.7634
 QVR  O37  O  O2    0  -0.494   1.8360   0.2705  -1.1902
 QVR  O41  O  OH1   0  -0.662   1.4166   3.1108  -0.3210
 QVR  O42  O  OH1   0  -0.662   3.0255   2.0770   1.6543
 QVR  H1   H  HCH3  0   0.239   3.9695  -3.7608   0.3121
 QVR  H30  H  HCH3  0   0.239   4.9582  -3.3869  -1.0820
 QVR  H29  H  HCH3  0   0.236   5.3413  -2.6616   0.4827
 QVR  H28  H  H     0   0.243   2.8089  -2.0272  -1.1858
 QVR  H31  H  H     0   0.252   4.6119  -0.3585   0.6317
 QVR  H61  H  HCH1  0   0.249   3.5253   1.3871  -0.7780
 QVR  H62  H  HCH1  0   0.284   0.2217   1.4536  -1.6688
 QVR  H44  H  HCH1  0   0.267   0.2137   2.0566   1.0060
 QVR  H43  H  HCH1  0   0.242   1.8540   0.3751   1.5570
 QVR  H58  H  HCR5  0   0.294   0.8830  -1.7007   0.2814
 QVR  H56  H  HCR6  0   0.252  -4.2763   1.8662  -0.9785
 QVR  H59  H  HNH2  0   0.412  -3.7577  -2.9297   1.0937
 QVR  H60  H  HNH2  0   0.404  -5.2574  -2.1216   0.8145
 QVR  H46  H  HOH1  0   0.460   1.8239   3.6808   0.3401
 QVR  H45  H  HOH1  0   0.467   3.5374   1.5846   2.3020

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
 QVR  N57  C55  single    1.333  0.020  1.333
 QVR  C55  C50  aromatic  1.407  0.020  1.407
 QVR  C55  N54  aromatic  1.338  0.020  1.338
 QVR  N48  C50  aromatic  1.370  0.020  1.370
 QVR  N48  C49  aromatic  1.301  0.020  1.301
 QVR  C50  C51  aromatic  1.386  0.020  1.386
 QVR  N54  C53  aromatic  1.331  0.020  1.331
 QVR  C49  N47  aromatic  1.368  0.020  1.368
 QVR  C51  N47  aromatic  1.364  0.020  1.364
 QVR  C51  N52  aromatic  1.332  0.020  1.332
 QVR  C53  N52  aromatic  1.322  0.020  1.322
 QVR  N47  C38  single    1.456  0.020  1.456
 QVR  C38  C39  single    1.529  0.020  1.529
 QVR  C38  O37  single    1.397  0.020  1.397
 QVR  C24  C28  single    1.493  0.020  1.493
 QVR  C39  O41  single    1.402  0.020  1.402
 QVR  C39  C40  single    1.526  0.020  1.526
 QVR  C31  C28  double    1.329  0.020  1.329
 QVR  C31  C36  single    1.490  0.020  1.490
 QVR  O37  C36  single    1.423  0.020  1.423
 QVR  C36  C40  single    1.539  0.020  1.539
 QVR  C40  O42  single    1.396  0.020  1.396
 QVR  C24  H1   single    0.970  0.020  1.090
 QVR  C24  H30  single    0.970  0.020  1.090
 QVR  C24  H29  single    0.970  0.020  1.090
 QVR  C28  H28  single    0.930  0.020  1.080
 QVR  C31  H31  single    0.930  0.020  1.080
 QVR  C36  H61  single    0.970  0.020  1.090
 QVR  C38  H62  single    0.970  0.020  1.090
 QVR  C39  H44  single    0.970  0.020  1.090
 QVR  C40  H43  single    0.970  0.020  1.090
 QVR  C49  H58  single    0.930  0.020  1.080
 QVR  C53  H56  single    0.930  0.020  1.080
 QVR  N57  H59  single    0.860  0.020  1.020
 QVR  N57  H60  single    0.860  0.020  1.020
 QVR  O41  H46  single    0.850  0.020  0.980
 QVR  O42  H45  single    0.850  0.020  0.980

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
 QVR  H29  C24  H30  108.14  3.000
 QVR  H29  C24  H1   108.07  3.000
 QVR  H30  C24  H1   106.47  3.000
 QVR  H29  C24  C28  112.04  3.000
 QVR  H30  C24  C28  110.95  3.000
 QVR  H1   C24  C28  110.94  3.000
 QVR  H28  C28  C31  119.59  3.000
 QVR  H28  C28  C24  116.00  3.000
 QVR  C31  C28  C24  124.40  3.000
 QVR  H31  C31  C36  113.76  3.000
 QVR  H31  C31  C28  119.47  3.000
 QVR  C36  C31  C28  126.76  3.000
 QVR  H61  C36  O37  109.35  3.000
 QVR  H61  C36  C40  108.10  3.000
 QVR  O37  C36  C40  104.42  3.000
 QVR  H61  C36  C31  108.82  3.000
 QVR  C40  C36  C31  114.01  3.000
 QVR  O37  C36  C31  111.97  3.000
 QVR  H62  C38  O37  110.86  3.000
 QVR  H62  C38  N47  106.71  3.000
 QVR  O37  C38  N47  109.27  3.000
 QVR  H62  C38  C39  111.17  3.000
 QVR  O37  C38  C39  107.06  3.000
 QVR  N47  C38  C39  111.81  3.000
 QVR  H44  C39  O41  112.02  3.000
 QVR  H44  C39  C40  112.44  3.000
 QVR  O41  C39  C40  111.97  3.000
 QVR  H44  C39  C38  111.82  3.000
 QVR  C40  C39  C38  100.90  3.000
 QVR  O41  C39  C38  107.06  3.000
 QVR  H43  C40  O42  111.55  3.000
 QVR  H43  C40  C39  108.76  3.000
 QVR  O42  C40  C39  111.23  3.000
 QVR  H43  C40  C36  109.21  3.000
 QVR  O42  C40  C36  114.33  3.000
 QVR  C39  C40  C36  101.20  3.000
 QVR  H58  C49  N48  124.67  3.000
 QVR  H58  C49  N47  122.00  3.000
 QVR  N48  C49  N47  113.33  3.000
 QVR  N48  C50  C55  133.03  3.000
 QVR  N48  C50  C51  110.76  3.000
 QVR  C55  C50  C51  116.21  3.000
 QVR  N52  C51  N47  128.07  3.000
 QVR  N52  C51  C50  126.67  3.000
 QVR  N47  C51  C50  105.27  3.000
 QVR  H56  C53  N54  115.39  3.000
 QVR  H56  C53  N52  116.16  3.000
 QVR  N54  C53  N52  128.45  3.000
 QVR  N57  C55  N54  119.36  3.000
 QVR  N54  C55  C50  117.89  3.000
 QVR  N57  C55  C50  122.75  3.000
 QVR  C51  N47  C49  106.22  3.000
 QVR  C51  N47  C38  124.98  3.000
 QVR  C49  N47  C38  128.77  3.000
 QVR  C50  N48  C49  104.42  3.000
 QVR  C53  N52  C51  111.55  3.000
 QVR  C55  N54  C53  119.24  3.000
 QVR  H60  N57  H59  118.40  3.000
 QVR  H60  N57  C55  120.40  3.000
 QVR  H59  N57  C55  121.20  3.000
 QVR  C38  O37  C36  111.12  3.000
 QVR  H46  O41  C39  108.54  3.000
 QVR  H45  O42  C40  109.33  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
 QVR  CONST_01  C55  C50  N48  C49   180.00   0.0  0
 QVR  CONST_02  C51  C50  N48  C49     0.00   0.0  0
 QVR  CONST_03  C50  C51  N47  C49     0.00   0.0  0
 QVR  CONST_04  N52  C51  N47  C49   180.00   0.0  0
 QVR  CONST_05  C53  N54  C55  C50     0.00   0.0  0
 QVR  CONST_06  N47  C49  N48  C50     0.00   0.0  0
 QVR  CONST_07  C53  N52  C51  C50     0.00   0.0  0
 QVR  CONST_08  N54  C55  C50  C51     0.00   0.0  0
 QVR  CONST_09  N48  C49  N47  C51     0.00   0.0  0
 QVR  CONST_10  N54  C53  N52  C51     0.00   0.0  0
 QVR  CONST_11  N47  C51  N52  C53   180.00   0.0  0
 QVR  CONST_12  N47  C51  C50  C55   180.00   0.0  0
 QVR  CONST_13  N52  C51  C50  C55     0.00   0.0  0
 QVR  CONST_14  N52  C53  N54  C55     0.00   0.0  0
 QVR  CONST_15  N48  C50  C51  N47     0.00   0.0  0
 QVR  CONST_16  N54  C55  C50  N48   180.00   0.0  0
 QVR  CONST_17  N52  C51  C50  N48   180.00   0.0  0
 QVR  CONST_18  N48  C49  N47  C38   180.00   0.0  0
 QVR  CONST_19  C50  C51  N47  C38   180.00   0.0  0
 QVR  CONST_20  N52  C51  N47  C38     0.00   0.0  0
 QVR  CONST_21  N57  C55  C50  C51   180.00   0.0  0
 QVR  CONST_22  N57  C55  N54  C53   180.00   0.0  0
 QVR  CONST_23  N57  C55  C50  N48     0.00   0.0  0
 QVR  CONST_24  H58  C49  N47  C38     0.00   0.0  0
 QVR  CONST_25  H56  C53  N52  C51   180.00   0.0  0
 QVR  CONST_26  H59  N57  C55  C50     0.00   0.0  0
 QVR  CONST_27  H60  N57  C55  C50   180.00   0.0  0
 QVR  Var_01    C36  C31  C28  C24  -179.67   0.0  2
 QVR  Var_02    H1   C24  C28  C31   119.37  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
 QVR  chir_01  C36  C31  O37  C40  negativ
 QVR  chir_02  C38  O37  N47  C39  negativ
 QVR  chir_03  C39  O41  C38  C40  negativ
 QVR  chir_04  C40  O42  C39  C36  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
 QVR  plan-1  C38  0.020
 QVR  plan-1  C49  0.020
 QVR  plan-1  C50  0.020
 QVR  plan-1  C51  0.020
 QVR  plan-1  C53  0.020
 QVR  plan-1  C55  0.020
 QVR  plan-1  N47  0.020
 QVR  plan-1  N48  0.020
 QVR  plan-1  N52  0.020
 QVR  plan-1  N54  0.020
 QVR  plan-1  N57  0.020
 QVR  plan-1  H58  0.020
 QVR  plan-1  H56  0.020
 QVR  plan-2  C55  0.020
 QVR  plan-2  N57  0.020
 QVR  plan-2  H59  0.020
 QVR  plan-2  H60  0.020
 QVR  plan-3  C24  0.020
 QVR  plan-3  C28  0.020
 QVR  plan-3  C31  0.020
 QVR  plan-3  C36  0.020
 QVR  plan-3  H28  0.020
 QVR  plan-3  H31  0.020

