# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:55:46 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(N(CC=C)C(=O)N2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C(=O)N1
#
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
 SDL  SDL  2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione  ligand  41  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SDL
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
 SDL  O5   O  O     0  -0.501  -0.8300  -1.9866  -0.0575
 SDL  C5   C  CR5   0   0.712   0.0228  -1.1237   0.0578
 SDL  N1   N  NR5   0  -0.579   1.3288  -1.2960   0.4027
 SDL  C10  C  CH2   0  -0.377   1.9598  -2.5961   0.5230
 SDL  C11  C  C1    0  -0.174   2.5564  -3.0427  -0.7775
 SDL  C12  C  C2    0  -0.508   3.8537  -3.2447  -0.9633
 SDL  C6   C  CR56  0   0.083   1.9762  -0.0636   0.3813
 SDL  C9   C  CR56  0   0.506   1.0433   0.8869   0.0571
 SDL  N4   N  N     0  -0.514   1.2269   2.2045  -0.0327
 SDL  C8   C  CR6   0   0.699   2.4562   2.5899   0.2261
 SDL  N3   N  NH2   0  -0.828   2.7831   3.8841   0.1239
 SDL  N2   N  NR16  0  -0.725   3.4389   1.7159   0.5675
 SDL  C7   C  CR6   0   0.530   3.2956   0.3259   0.7019
 SDL  O4   O  O     0  -0.480   4.2434  -0.3613   1.0559
 SDL  N    N  NR5   0  -0.625  -0.1494   0.2422  -0.1504
 SDL  C4   C  CH1   0   0.180  -1.4063   0.9000  -0.4133
 SDL  C3   C  CH1   0  -0.045  -2.1663   0.4035  -1.6516
 SDL  O2   O  OH1   0  -0.673  -2.6537   1.5321  -2.3304
 SDL  C2   C  CH1   0  -0.043  -3.3277  -0.4060  -1.0535
 SDL  O1   O  OH1   0  -0.663  -4.5061  -0.3124  -1.8129
 SDL  O3   O  O2    0  -0.495  -2.2564   0.7466   0.6938
 SDL  C1   C  CH1   0   0.022  -3.5295   0.2511   0.3103
 SDL  C    C  CH2   0  -0.160  -4.0402  -0.7197   1.3466
 SDL  O    O  OH1   0  -0.671  -4.2863  -0.0317   2.5496
 SDL  H1   H  HCH2  0   0.276   2.7169  -2.5460   1.3027
 SDL  H2   H  HCH2  0   0.275   1.1932  -3.2972   0.8538
 SDL  H3   H  H     0   0.253   1.8572  -3.1982  -1.5936
 SDL  H4   H  H     0   0.240   4.5723  -3.0854  -0.1690
 SDL  H5   H  H     0   0.243   4.2440  -3.5754  -1.9166
 SDL  H7   H  HNH2  0   0.415   2.0340   4.5462   0.0124
 SDL  H8   H  HNH2  0   0.417   3.6368   4.2367   0.5223
 SDL  H9   H  HCH1  0   0.269  -1.1488   1.9526  -0.5575
 SDL  H10  H  HCH1  0   0.247  -1.5291  -0.2055  -2.3034
 SDL  H11  H  HOH1  0   0.448  -3.5249   1.2966  -2.6773
 SDL  H12  H  HCH1  0   0.259  -3.0160  -1.4449  -0.9288
 SDL  H13  H  HOH1  0   0.469  -4.5175  -1.0295  -2.4546
 SDL  H14  H  HCH1  0   0.231  -4.2396   1.0842   0.2089
 SDL  H15  H  HCH2  0   0.203  -4.9530  -1.1824   0.9483
 SDL  H16  H  HCH2  0   0.202  -3.2990  -1.5190   1.4724
 SDL  H17  H  HOH1  0   0.457  -4.5852  -0.6714   3.2020
 SDL  H6   H  HNR6  0   0.428   4.3631   2.0776   0.7670

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
 SDL  O1   C2   single  1.405  0.020  1.405
 SDL  C2   C3   single  1.537  0.020  1.537
 SDL  C2   C1   single  1.527  0.020  1.527
 SDL  O2   C3   single  1.404  0.020  1.404
 SDL  O    C    single  1.408  0.020  1.408
 SDL  C    C1   single  1.509  0.020  1.509
 SDL  C3   C4   single  1.535  0.020  1.535
 SDL  C1   O3   single  1.419  0.020  1.419
 SDL  N3   C8   single  1.339  0.020  1.339
 SDL  C4   O3   single  1.404  0.020  1.404
 SDL  C4   N    single  1.443  0.020  1.443
 SDL  N4   C8   double  1.314  0.020  1.314
 SDL  N4   C9   single  1.333  0.020  1.333
 SDL  C8   N2   single  1.359  0.020  1.359
 SDL  C9   N    single  1.372  0.020  1.372
 SDL  C9   C6   double  1.371  0.020  1.371
 SDL  N    C5   single  1.392  0.020  1.392
 SDL  N2   C7   single  1.404  0.020  1.404
 SDL  C5   O5   double  1.219  0.020  1.219
 SDL  C5   N1   single  1.362  0.020  1.362
 SDL  C6   C7   single  1.413  0.020  1.413
 SDL  C6   N1   single  1.392  0.020  1.392
 SDL  C7   O4   double  1.223  0.020  1.223
 SDL  N1   C10  single  1.450  0.020  1.450
 SDL  C12  C11  double  1.326  0.020  1.326
 SDL  C11  C10  single  1.499  0.020  1.499
 SDL  C10  H1   single  0.970  0.020  1.090
 SDL  C10  H2   single  0.970  0.020  1.090
 SDL  C11  H3   single  0.930  0.020  1.080
 SDL  C12  H4   single  0.930  0.020  1.080
 SDL  C12  H5   single  0.930  0.020  1.080
 SDL  N3   H7   single  0.890  0.020  1.040
 SDL  N3   H8   single  0.890  0.020  1.040
 SDL  C4   H9   single  0.970  0.020  1.090
 SDL  C3   H10  single  0.970  0.020  1.090
 SDL  O2   H11  single  0.850  0.020  0.980
 SDL  C2   H12  single  0.970  0.020  1.090
 SDL  O1   H13  single  0.850  0.020  0.980
 SDL  C1   H14  single  0.970  0.020  1.090
 SDL  C    H15  single  0.970  0.020  1.090
 SDL  C    H16  single  0.970  0.020  1.090
 SDL  O    H17  single  0.850  0.020  0.980
 SDL  N2   H6   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
 SDL  N    C5   N1   106.30  3.000
 SDL  N1   C5   O5   127.27  3.000
 SDL  N    C5   O5   126.43  3.000
 SDL  C6   N1   C10  126.33  3.000
 SDL  C10  N1   C5   123.49  3.000
 SDL  C6   N1   C5   109.28  3.000
 SDL  H2   C10  H1   107.54  3.000
 SDL  H2   C10  C11  110.58  3.000
 SDL  H1   C10  C11  111.01  3.000
 SDL  H2   C10  N1   107.20  3.000
 SDL  H1   C10  N1   108.72  3.000
 SDL  C11  C10  N1   111.61  3.000
 SDL  H3   C11  C12  120.19  3.000
 SDL  H3   C11  C10  116.00  3.000
 SDL  C12  C11  C10  123.81  3.000
 SDL  H5   C12  H4   116.86  3.000
 SDL  H5   C12  C11  121.53  3.000
 SDL  H4   C12  C11  121.61  3.000
 SDL  C7   C6   C9   119.88  3.000
 SDL  C7   C6   N1   132.45  3.000
 SDL  C9   C6   N1   107.51  3.000
 SDL  N    C9   N4   125.03  3.000
 SDL  N    C9   C6   107.56  3.000
 SDL  N4   C9   C6   127.41  3.000
 SDL  C8   N4   C9   113.91  3.000
 SDL  N2   C8   N3   117.67  3.000
 SDL  N2   C8   N4   122.51  3.000
 SDL  N3   C8   N4   119.80  3.000
 SDL  H8   N3   H7   116.44  3.000
 SDL  H8   N3   C8   121.06  3.000
 SDL  H7   N3   C8   117.57  3.000
 SDL  H6   N2   C7   115.34  3.000
 SDL  H6   N2   C8   118.69  3.000
 SDL  C7   N2   C8   125.96  3.000
 SDL  O4   C7   N2   120.33  3.000
 SDL  O4   C7   C6   129.39  3.000
 SDL  N2   C7   C6   110.28  3.000
 SDL  C4   N    C9   124.81  3.000
 SDL  C9   N    C5   109.32  3.000
 SDL  C4   N    C5   125.61  3.000
 SDL  H9   C4   O3   110.59  3.000
 SDL  H9   C4   C3   108.76  3.000
 SDL  O3   C4   C3   107.51  3.000
 SDL  H9   C4   N    104.94  3.000
 SDL  O3   C4   N    109.50  3.000
 SDL  C3   C4   N    115.52  3.000
 SDL  H10  C3   C2   112.21  3.000
 SDL  H10  C3   O2   111.15  3.000
 SDL  C2   C3   O2   110.43  3.000
 SDL  H10  C3   C4   111.80  3.000
 SDL  O2   C3   C4   107.56  3.000
 SDL  C2   C3   C4   103.33  3.000
 SDL  H11  O2   C3   106.89  3.000
 SDL  H12  C2   C1   110.19  3.000
 SDL  H12  C2   O1   111.38  3.000
 SDL  C1   C2   O1   110.07  3.000
 SDL  H12  C2   C3   109.27  3.000
 SDL  C1   C2   C3   102.75  3.000
 SDL  O1   C2   C3   112.85  3.000
 SDL  H13  O1   C2   108.70  3.000
 SDL  C1   O3   C4   111.61  3.000
 SDL  H14  C1   C    109.41  3.000
 SDL  H14  C1   O3   109.87  3.000
 SDL  C    C1   O3   110.04  3.000
 SDL  H14  C1   C2   109.21  3.000
 SDL  O3   C1   C2   105.84  3.000
 SDL  C    C1   C2   112.41  3.000
 SDL  H16  C    H15  107.23  3.000
 SDL  H16  C    O    112.10  3.000
 SDL  H15  C    O    111.75  3.000
 SDL  H16  C    C1   108.59  3.000
 SDL  H15  C    C1   107.66  3.000
 SDL  O    C    C1   109.37  3.000
 SDL  H17  O    C    108.00  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
 SDL  CONST_01  N4   C9   N    C5   180.00   0.0  0
 SDL  CONST_02  C6   C9   N    C5     0.00   0.0  0
 SDL  CONST_03  C9   C6   N1   C5     0.00   0.0  0
 SDL  CONST_04  C4   N    C5   N1   180.00   0.0  0
 SDL  CONST_05  C9   N    C5   N1     0.00   0.0  0
 SDL  CONST_06  N    C9   C6   N1     0.00   0.0  0
 SDL  CONST_07  C8   N4   C9   C6     0.00   0.0  0
 SDL  CONST_08  C4   N    C9   C6   180.00   0.0  0
 SDL  CONST_09  C8   N2   C7   C6     0.00   0.0  0
 SDL  CONST_10  N    C5   N1   C6     0.00   0.0  0
 SDL  CONST_11  N2   C8   N4   C9     0.00   0.0  0
 SDL  CONST_12  C7   N2   C8   N4     0.00   0.0  0
 SDL  CONST_13  C4   N    C9   N4     0.00   0.0  0
 SDL  CONST_14  N    C9   N4   C8   180.00   0.0  0
 SDL  CONST_15  C4   N    C5   O5     0.00   0.0  0
 SDL  CONST_16  C9   N    C5   O5   180.00   0.0  0
 SDL  CONST_17  C6   N1   C5   O5   180.00   0.0  0
 SDL  CONST_18  N    C5   N1   C10  180.00   0.0  0
 SDL  CONST_19  C9   C6   N1   C10  180.00   0.0  0
 SDL  CONST_20  N3   C8   N4   C9   180.00   0.0  0
 SDL  CONST_21  O4   C7   N2   C8   180.00   0.0  0
 SDL  CONST_22  C7   N2   C8   N3   180.00   0.0  0
 SDL  CONST_23  H6   N2   C7   C6   180.00   0.0  0
 SDL  CONST_24  C10  N1   C5   O5     0.00   0.0  0
 SDL  CONST_25  H7   N3   C8   N4     0.00   0.0  0
 SDL  CONST_26  H8   N3   C8   N4   180.00   0.0  0
 SDL  Var_01    C11  C10  N1   C5    89.74  30.0  3
 SDL  Var_02    C12  C11  C10  N1   116.58  30.0  2
 SDL  Var_03    H4   C12  C11  C10   -0.59   0.0  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
 SDL  chir_01  C4  C3  O3  N   negativ
 SDL  chir_02  C3  O2  C2  C4  positiv
 SDL  chir_03  C2  O1  C1  C3  positiv
 SDL  chir_04  C1  O3  C2  C   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
 SDL  plan-1  C10  0.020
 SDL  plan-1  C11  0.020
 SDL  plan-1  C12  0.020
 SDL  plan-1  H3   0.020
 SDL  plan-1  H4   0.020
 SDL  plan-1  H5   0.020
 SDL  plan-2  O5   0.020
 SDL  plan-2  C5   0.020
 SDL  plan-2  N1   0.020
 SDL  plan-2  C10  0.020
 SDL  plan-2  C6   0.020
 SDL  plan-2  C9   0.020
 SDL  plan-2  N4   0.020
 SDL  plan-2  C8   0.020
 SDL  plan-2  N3   0.020
 SDL  plan-2  N2   0.020
 SDL  plan-2  C7   0.020
 SDL  plan-2  O4   0.020
 SDL  plan-2  N    0.020
 SDL  plan-2  C4   0.020
 SDL  plan-2  H7   0.020
 SDL  plan-2  H8   0.020
 SDL  plan-2  H6   0.020

