# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 01:27:12 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H](O)[C@H]3OC
#
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
 TV8  TV8  "(2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol"
  ligand  38  21  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TV8
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
 TV8  C10  C  CH3   0  -0.433  -36.3474   5.1350   -7.3077
 TV8  C15  C  CR56  0   0.485  -33.2089   1.0717   -7.2978
 TV8  C17  C  CR16  0   0.044  -34.2571  -0.8501   -7.1316
 TV8  C01  C  CH1   0   0.168  -33.9012   3.4093   -7.8828
 TV8  C03  C  CH1   0  -0.008  -33.6002   5.4002   -9.0334
 TV8  C04  C  CH2   0  -0.154  -32.6178   6.0385   -9.9882
 TV8  C06  C  CH1   0  -0.019  -33.4229   5.7621   -7.5654
 TV8  C08  C  CH1   0  -0.056  -34.0545   4.5547   -6.8430
 TV8  C12  C  CR15  0   0.103  -31.6019   2.5563   -7.2920
 TV8  C14  C  CR56  0  -0.005  -31.9877   0.5037   -6.9768
 TV8  C19  C  CR6   0   0.496  -31.9929  -0.8827   -6.7208
 TV8  N11  N  NR5   0  -0.534  -32.9468   2.3983   -7.4938
 TV8  N13  N  N     0  -0.448  -30.9951   1.4490   -6.9809
 TV8  N16  N  N     0  -0.457  -34.3782   0.4397   -7.3879
 TV8  N18  N  N     0  -0.488  -33.1593  -1.5314   -6.8109
 TV8  N20  N  NH1   0  -0.643  -30.8885  -1.5562   -6.3953
 TV8  O02  O  O2    0  -0.489  -33.4761   3.9816   -9.0855
 TV8  O05  O  OH1   0  -0.666  -33.0265   5.7313  -11.3009
 TV8  O07  O  OH1   0  -0.659  -32.0451   5.8446   -7.2907
 TV8  O09  O  O2    0  -0.473  -35.3668   4.7128   -6.3844
 TV8  H1   H  HCH3  0   0.253  -37.3031   5.1043   -6.7871
 TV8  H2   H  HCH3  0   0.220  -36.1884   6.1601   -7.6558
 TV8  H3   H  HCH3  0   0.220  -36.4230   4.4815   -8.1829
 TV8  H5   H  HCH3  0   0.252  -29.8421  -3.2605   -5.9067
 TV8  H6   H  HCH3  0   0.238  -31.4998  -3.2478   -5.2991
 TV8  H7   H  HCH3  0   0.237  -31.1893  -3.5486   -7.0114
 TV8  H8   H  HCH1  0   0.267  -34.8526   2.8802   -8.0023
 TV8  H9   H  HCH1  0   0.242  -34.6105   5.6951   -9.3455
 TV8  H10  H  HCH2  0   0.208  -31.6042   5.6784   -9.7833
 TV8  H11  H  HCH2  0   0.205  -32.6242   7.1206   -9.8034
 TV8  H12  H  HCH1  0   0.259  -33.9344   6.7001   -7.3205
 TV8  H13  H  HCH1  0   0.284  -33.4805   4.3197   -5.9432
 TV8  H14  H  HCR5  0   0.294  -31.1293   3.5219   -7.3868
 TV8  H15  H  HNH1  0   0.406  -30.0235  -1.0440   -6.3518
 TV8  H16  H  HOH1  0   0.455  -32.3832   6.1052  -11.9096
 TV8  H17  H  HOH1  0   0.461  -31.9263   6.0917   -6.3675
 TV8  H4   H  HCR6  0   0.248  -35.1687  -1.4359   -7.1875
 TV8  C21  C  CH3   0  -0.513  -30.8635  -2.9761   -6.1421

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
 TV8  O05  C04  single    1.409  0.020  1.409
 TV8  C04  C03  single    1.511  0.020  1.511
 TV8  C03  O02  single    1.425  0.020  1.425
 TV8  C03  C06  single    1.522  0.020  1.522
 TV8  O02  C01  single    1.398  0.020  1.398
 TV8  C06  O07  single    1.407  0.020  1.407
 TV8  C06  C08  single    1.542  0.020  1.542
 TV8  N16  C17  aromatic  1.321  0.020  1.321
 TV8  N16  C15  aromatic  1.332  0.020  1.332
 TV8  C17  N18  aromatic  1.331  0.020  1.331
 TV8  C01  N11  single    1.444  0.020  1.444
 TV8  C01  C08  single    1.555  0.020  1.555
 TV8  N18  C19  aromatic  1.338  0.020  1.338
 TV8  C15  N11  aromatic  1.366  0.020  1.366
 TV8  C15  C14  aromatic  1.385  0.020  1.385
 TV8  N11  C12  aromatic  1.369  0.020  1.369
 TV8  C08  O09  single    1.399  0.020  1.399
 TV8  C10  O09  single    1.411  0.020  1.411
 TV8  C19  C14  aromatic  1.410  0.020  1.410
 TV8  C19  N20  single    1.334  0.020  1.334
 TV8  C14  N13  aromatic  1.371  0.020  1.371
 TV8  C21  N20  single    1.443  0.020  1.443
 TV8  C12  N13  aromatic  1.300  0.020  1.300
 TV8  C10  H1   single    0.970  0.020  1.090
 TV8  C10  H2   single    0.970  0.020  1.090
 TV8  C10  H3   single    0.970  0.020  1.090
 TV8  C17  H4   single    0.930  0.020  1.080
 TV8  C21  H5   single    0.970  0.020  1.090
 TV8  C21  H6   single    0.970  0.020  1.090
 TV8  C21  H7   single    0.970  0.020  1.090
 TV8  C01  H8   single    0.970  0.020  1.090
 TV8  C03  H9   single    0.970  0.020  1.090
 TV8  C04  H10  single    0.970  0.020  1.090
 TV8  C04  H11  single    0.970  0.020  1.090
 TV8  C06  H12  single    0.970  0.020  1.090
 TV8  C08  H13  single    0.970  0.020  1.090
 TV8  C12  H14  single    0.930  0.020  1.080
 TV8  N20  H15  single    0.860  0.020  1.020
 TV8  O05  H16  single    0.850  0.020  0.980
 TV8  O07  H17  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
 TV8  H3   C10  H2   108.35  3.000
 TV8  H3   C10  H1   107.74  3.000
 TV8  H2   C10  H1   107.82  3.000
 TV8  H3   C10  O09  113.11  3.000
 TV8  H2   C10  O09  112.79  3.000
 TV8  H1   C10  O09  106.78  3.000
 TV8  N16  C15  N11  128.26  3.000
 TV8  N11  C15  C14  105.21  3.000
 TV8  N16  C15  C14  126.53  3.000
 TV8  H4   C17  N18  115.40  3.000
 TV8  H4   C17  N16  116.12  3.000
 TV8  N18  C17  N16  128.48  3.000
 TV8  H8   C01  O02  111.60  3.000
 TV8  H8   C01  N11  105.39  3.000
 TV8  O02  C01  N11  108.51  3.000
 TV8  H8   C01  C08  110.08  3.000
 TV8  N11  C01  C08  113.63  3.000
 TV8  O02  C01  C08  107.68  3.000
 TV8  H9   C03  O02  109.71  3.000
 TV8  H9   C03  C06  108.51  3.000
 TV8  O02  C03  C06  105.17  3.000
 TV8  H9   C03  C04  107.77  3.000
 TV8  C06  C03  C04  115.67  3.000
 TV8  O02  C03  C04  109.92  3.000
 TV8  H11  C04  H10  107.34  3.000
 TV8  H11  C04  O05  111.72  3.000
 TV8  H10  C04  O05  111.79  3.000
 TV8  H11  C04  C03  107.82  3.000
 TV8  H10  C04  C03  110.16  3.000
 TV8  O05  C04  C03  107.94  3.000
 TV8  H12  C06  O07  111.29  3.000
 TV8  H12  C06  C08  111.97  3.000
 TV8  O07  C06  C08  110.82  3.000
 TV8  H12  C06  C03  111.38  3.000
 TV8  C08  C06  C03  102.59  3.000
 TV8  O07  C06  C03  108.43  3.000
 TV8  H13  C08  O09  104.31  3.000
 TV8  H13  C08  C06  109.81  3.000
 TV8  O09  C08  C06  116.69  3.000
 TV8  H13  C08  C01  109.91  3.000
 TV8  O09  C08  C01  113.27  3.000
 TV8  C06  C08  C01  102.89  3.000
 TV8  H14  C12  N13  125.34  3.000
 TV8  H14  C12  N11  121.37  3.000
 TV8  N13  C12  N11  113.29  3.000
 TV8  N13  C14  C19  132.95  3.000
 TV8  N13  C14  C15  110.80  3.000
 TV8  C19  C14  C15  116.25  3.000
 TV8  N20  C19  N18  119.58  3.000
 TV8  N20  C19  C14  122.53  3.000
 TV8  N18  C19  C14  117.89  3.000
 TV8  C12  N11  C01  127.46  3.000
 TV8  C12  N11  C15  106.23  3.000
 TV8  C01  N11  C15  126.28  3.000
 TV8  C14  N13  C12  104.48  3.000
 TV8  C17  N16  C15  111.70  3.000
 TV8  C19  N18  C17  119.15  3.000
 TV8  H15  N20  C19  117.73  3.000
 TV8  H15  N20  C21  118.59  3.000
 TV8  C19  N20  C21  123.65  3.000
 TV8  C03  O02  C01  110.46  3.000
 TV8  H16  O05  C04  108.12  3.000
 TV8  H17  O07  C06  108.84  3.000
 TV8  C08  O09  C10  118.10  3.000
 TV8  H7   C21  H6   108.12  3.000
 TV8  H7   C21  H5   108.43  3.000
 TV8  H6   C21  H5   108.42  3.000
 TV8  H7   C21  N20  111.82  3.000
 TV8  H6   C21  N20  111.77  3.000
 TV8  H5   C21  N20  108.18  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
 TV8  CONST_01  N18  C17  N16  C15    0.00   0.0  0
 TV8  CONST_02  N13  C12  N11  C15    0.00   0.0  0
 TV8  CONST_03  N18  C19  C14  C15    0.00   0.0  0
 TV8  CONST_04  C12  N13  C14  C15    0.00   0.0  0
 TV8  CONST_05  N11  C15  N16  C17  180.00   0.0  0
 TV8  CONST_06  C14  C15  N16  C17    0.00   0.0  0
 TV8  CONST_07  C14  C19  N18  C17    0.00   0.0  0
 TV8  CONST_08  N16  C15  N11  C12  180.00   0.0  0
 TV8  CONST_09  C14  C15  N11  C12    0.00   0.0  0
 TV8  CONST_10  C19  C14  N13  C12  180.00   0.0  0
 TV8  CONST_11  N11  C12  N13  C14    0.00   0.0  0
 TV8  CONST_12  N16  C17  N18  C19    0.00   0.0  0
 TV8  CONST_13  N16  C15  C14  C19    0.00   0.0  0
 TV8  CONST_14  N11  C15  C14  C19  180.00   0.0  0
 TV8  CONST_15  N13  C14  C15  N11    0.00   0.0  0
 TV8  CONST_16  N16  C15  C14  N13  180.00   0.0  0
 TV8  CONST_17  N18  C19  C14  N13  180.00   0.0  0
 TV8  CONST_18  N16  C15  N11  C01    0.00   0.0  0
 TV8  CONST_19  C14  C15  N11  C01  180.00   0.0  0
 TV8  CONST_20  N13  C12  N11  C01  180.00   0.0  0
 TV8  CONST_21  N20  C19  C14  C15  180.00   0.0  0
 TV8  CONST_22  N20  C19  N18  C17  180.00   0.0  0
 TV8  CONST_23  N20  C19  C14  N13    0.00   0.0  0
 TV8  CONST_24  H4   C17  N16  C15  180.00   0.0  0
 TV8  CONST_25  H14  C12  N11  C15  180.00   0.0  0
 TV8  CONST_26  H14  C12  N11  C01    0.00   0.0  0
 TV8  CONST_27  H14  C12  N13  C14  180.00   0.0  0
 TV8  CONST_28  H4   C17  N18  C19  180.00   0.0  0
 TV8  CONST_29  N18  C19  N20  C21    0.00   0.0  0
 TV8  CONST_30  C14  C19  N20  C21  180.00   0.0  0
 TV8  CONST_31  H15  N20  C19  C14    0.00   0.0  0
 TV8  CONST_32  H15  N20  C19  N18  180.00   0.0  0
 TV8  Var_01    H1   C10  O09  C08  174.69  30.0  3
 TV8  Var_02    H2   C10  O09  C08  -67.05  30.0  3
 TV8  Var_03    H3   C10  O09  C08   56.35  30.0  3
 TV8  Var_04    H5   C21  N20  C19  179.65  30.0  3
 TV8  Var_05    H6   C21  N20  C19  -61.06  30.0  3
 TV8  Var_06    H7   C21  N20  C19   60.32  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
 TV8  chir_01  C01  O02  N11  C08  negativ
 TV8  chir_02  C03  O02  C06  C04  negativ
 TV8  chir_03  C06  O07  C08  C03  positiv
 TV8  chir_04  C08  O09  C01  C06  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
 TV8  plan-1  C15  0.020
 TV8  plan-1  C17  0.020
 TV8  plan-1  C01  0.020
 TV8  plan-1  C12  0.020
 TV8  plan-1  C14  0.020
 TV8  plan-1  C19  0.020
 TV8  plan-1  N11  0.020
 TV8  plan-1  N13  0.020
 TV8  plan-1  N16  0.020
 TV8  plan-1  N18  0.020
 TV8  plan-1  N20  0.020
 TV8  plan-1  H14  0.020
 TV8  plan-1  H4   0.020
 TV8  plan-2  C19  0.020
 TV8  plan-2  N20  0.020
 TV8  plan-2  H15  0.020
 TV8  plan-2  C21  0.020

