# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 13:59:55 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2~{R})-3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-2-azanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
#
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
 5X8  5X8  '(2~{R})-3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-2-azanyl-propanoic acid'  L-peptide  42  25  .  2022-07-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_5X8
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
 5X8  N1   N  N      0  -0.474  -5.2545  -1.7510  -0.2448
 5X8  C5   C  CR56   0  -0.009  -2.9112  -1.6242  -0.0919
 5X8  C8   C  CR15   0   0.112  -0.9612  -0.8149  -0.0540
 5X8  C2   C  CR16   0   0.042  -5.2499  -0.4316  -0.4196
 5X8  C6   C  CR6    0   0.453  -4.0914  -2.3893  -0.0773
 5X8  N3   N  N      0  -0.453  -4.2160   0.3907  -0.4447
 5X8  C4   C  CR56   0   0.489  -3.0663  -0.2584  -0.2742
 5X8  C    C  C      0   0.412   5.4024  -2.0173   0.3477
 5X8  O    O  O     -1  -0.597   5.2315  -2.9783   1.1193
 5X8  CA   C  CH1    0  -0.221   4.1730  -1.5273  -0.4613
 5X8  N    N  NH2    0  -0.787   3.1147  -2.5159  -0.4628
 5X8  CB   C  CH2    0  -0.545   3.7684  -0.1563   0.1018
 5X8  SG   S  S2     0  -0.030   2.4474   0.5767  -0.9115
 5X8  C4'  C  CR15   0  -0.009   0.6828   2.6041  -0.3765
 5X8  O4'  O  O      0  -0.490  -0.2578   1.7758  -1.0662
 5X8  C3'  C  CR15   0  -0.011  -0.1402   3.3645   0.6540
 5X8  O3'  O  OH1    0  -0.667  -0.7445   4.4623   0.0242
 5X8  C2'  C  CR15   0  -0.054  -1.1824   2.3044   1.0237
 5X8  O2'  O  OH1    0  -0.651  -2.3756   2.8098   1.5422
 5X8  C1'  C  CR15   0   0.223  -1.4417   1.6490  -0.3367
 5X8  N9   N  NR5    0  -0.541  -1.8002   0.2504  -0.2460
 5X8  N7   N  N      0  -0.451  -1.5869  -1.9512   0.0399
 5X8  N6   N  NH2    0  -0.816  -4.0900  -3.7154   0.0807
 5X8  H1   H  HCR5   0   0.285   0.1133  -0.6957  -0.0267
 5X8  H2   H  HCR6   0   0.251  -6.2255   0.0231  -0.5558
 5X8  H4   H  HCH1   0   0.224   4.5044  -1.3751  -1.4954
 5X8  H5   H  HNH2   0   0.330   2.9267  -2.7993   0.4905
 5X8  H6   H  HNH2   0   0.329   2.2599  -2.1154  -0.8304
 5X8  H8   H  HCH2   0   0.256   3.3929  -0.2710   1.1229
 5X8  H9   H  HCH2   0   0.263   4.6233   0.5189   0.1229
 5X8  H10  H  HCH2   0   0.265   1.4300   1.2488   1.1607
 5X8  H11  H  HCH2   0   0.291   2.5788   2.4548   0.5920
 5X8  H12  H  HCR5   0   0.275   1.1297   3.2795  -1.1104
 5X8  H13  H  HCR5   0   0.254   0.4645   3.6683   1.5189
 5X8  H14  H  HOH1   0   0.450  -1.5133   4.7202   0.5466
 5X8  H15  H  HCR5   0   0.252  -0.7275   1.5730   1.7026
 5X8  H16  H  HOH1   0   0.469  -2.2762   2.9275   2.4922
 5X8  H17  H  HCR5   0   0.265  -2.2758   2.1471  -0.8425
 5X8  H18  H  HNH2   0   0.402  -4.9602  -4.2054   0.1983
 5X8  H19  H  HNH2   0   0.410  -3.2426  -4.2020   0.3157
 5X8  C5'  C  CH2    0  -0.580   1.7836   1.7786   0.2721
 5X8  OXT  O  OC     0  -0.615   6.4553  -1.3744   0.1695

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
 5X8  N    CA   single    1.458  0.019  1.458
 5X8  O    C    deloc     1.231  0.020  1.231
 5X8  C    CA   single    1.525  0.021  1.525
 5X8  C    OXT  deloc     1.247  0.020  1.247
 5X8  CA   CB   single    1.521  0.033  1.521
 5X8  SG   CB   single    1.819  0.020  1.819
 5X8  SG   C5'  single    1.813  0.020  1.813
 5X8  C5'  C4'  single    1.521  0.020  1.521
 5X8  C4'  O4'  single    1.431  0.020  1.431
 5X8  C4'  C3'  single    1.522  0.020  1.522
 5X8  O2'  C2'  single    1.396  0.020  1.396
 5X8  O4'  C1'  single    1.396  0.020  1.396
 5X8  N3   C2   aromatic  1.321  0.020  1.321
 5X8  N3   C4   aromatic  1.331  0.020  1.331
 5X8  O3'  C3'  single    1.402  0.020  1.402
 5X8  C2   N1   aromatic  1.331  0.020  1.331
 5X8  C1'  C2'  single    1.532  0.020  1.532
 5X8  C1'  N9   single    1.447  0.020  1.447
 5X8  C3'  C2'  single    1.532  0.020  1.532
 5X8  C4   N9   aromatic  1.365  0.020  1.365
 5X8  C4   C5   aromatic  1.387  0.020  1.387
 5X8  N9   C8   aromatic  1.370  0.020  1.370
 5X8  N1   C6   aromatic  1.337  0.020  1.337
 5X8  C5   C6   aromatic  1.407  0.020  1.407
 5X8  C5   N7   aromatic  1.370  0.020  1.370
 5X8  C6   N6   single    1.335  0.020  1.335
 5X8  C8   N7   aromatic  1.301  0.020  1.301
 5X8  C8   H1   single    0.930  0.020  1.080
 5X8  C2   H2   single    0.930  0.020  1.080
 5X8  CA   H4   single    0.970  0.020  1.090
 5X8  N    H5   single    0.890  0.020  1.040
 5X8  N    H6   single    0.890  0.020  1.040
 5X8  CB   H8   single    0.970  0.020  1.090
 5X8  CB   H9   single    0.970  0.020  1.090
 5X8  C5'  H10  single    0.970  0.020  1.090
 5X8  C5'  H11  single    0.970  0.020  1.090
 5X8  C4'  H12  single    0.970  0.020  1.090
 5X8  C3'  H13  single    0.970  0.020  1.090
 5X8  O3'  H14  single    0.850  0.020  0.980
 5X8  C2'  H15  single    0.970  0.020  1.090
 5X8  O2'  H16  single    0.850  0.020  0.980
 5X8  C1'  H17  single    0.970  0.020  1.090
 5X8  N6   H18  single    0.860  0.020  1.020
 5X8  N6   H19  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
 5X8  C6   N1   C2   119.12  3.000
 5X8  N7   C5   C4   110.84  3.000
 5X8  N7   C5   C6   132.85  3.000
 5X8  C4   C5   C6   116.31  3.000
 5X8  H1   C8   N7   124.92  3.000
 5X8  H1   C8   N9   121.77  3.000
 5X8  N7   C8   N9   113.27  3.000
 5X8  H2   C2   N3   116.13  3.000
 5X8  H2   C2   N1   115.40  3.000
 5X8  N3   C2   N1   128.47  3.000
 5X8  N6   C6   C5   122.71  3.000
 5X8  N6   C6   N1   119.32  3.000
 5X8  C5   C6   N1   117.96  3.000
 5X8  C4   N3   C2   111.71  3.000
 5X8  N9   C4   N3   128.47  3.000
 5X8  N9   C4   C5   105.12  3.000
 5X8  N3   C4   C5   126.42  3.000
 5X8  CA   C    O    120.80  1.700
 5X8  CA   C    OXT  120.80  1.700
 5X8  O    C    OXT  127.09  3.000
 5X8  H4   CA   CB   107.55  3.000
 5X8  H4   CA   N    108.34  3.000
 5X8  CB   CA   N    110.40  1.500
 5X8  H4   CA   C    107.23  3.000
 5X8  CB   CA   C    110.50  1.500
 5X8  N    CA   C    111.00  2.800
 5X8  H6   N    H5   107.20  3.000
 5X8  H6   N    CA   110.31  3.000
 5X8  H5   N    CA   109.02  3.000
 5X8  H9   CB   H8   108.43  3.000
 5X8  H9   CB   SG   109.32  3.000
 5X8  H8   CB   SG   108.23  3.000
 5X8  H9   CB   CA   110.70  3.000
 5X8  H8   CB   CA   109.82  3.000
 5X8  SG   CB   CA   110.28  3.000
 5X8  C5'  SG   CB    99.75  3.000
 5X8  H12  C4'  C3'  111.52  3.000
 5X8  H12  C4'  O4'  107.63  3.000
 5X8  C3'  C4'  O4'  105.08  3.000
 5X8  H12  C4'  C5'  109.01  3.000
 5X8  C3'  C4'  C5'  111.94  3.000
 5X8  O4'  C4'  C5'  111.54  3.000
 5X8  C1'  O4'  C4'  110.99  3.000
 5X8  H13  C3'  C2'  112.08  3.000
 5X8  H13  C3'  O3'  111.98  3.000
 5X8  C2'  C3'  O3'  110.91  3.000
 5X8  H13  C3'  C4'  111.94  3.000
 5X8  C2'  C3'  C4'  100.69  3.000
 5X8  O3'  C3'  C4'  108.66  3.000
 5X8  H14  O3'  C3'  108.03  3.000
 5X8  H15  C2'  C1'  109.55  3.000
 5X8  H15  C2'  O2'  111.48  3.000
 5X8  C1'  C2'  O2'  109.88  3.000
 5X8  H15  C2'  C3'  109.19  3.000
 5X8  C1'  C2'  C3'  101.35  3.000
 5X8  O2'  C2'  C3'  114.88  3.000
 5X8  H16  O2'  C2'  108.83  3.000
 5X8  H17  C1'  N9   106.26  3.000
 5X8  H17  C1'  C2'  110.14  3.000
 5X8  N9   C1'  C2'  113.57  3.000
 5X8  H17  C1'  O4'  111.29  3.000
 5X8  N9   C1'  O4'  109.31  3.000
 5X8  C2'  C1'  O4'  106.35  3.000
 5X8  C1'  N9   C4   126.09  3.000
 5X8  C4   N9   C8   106.33  3.000
 5X8  C1'  N9   C8   127.52  3.000
 5X8  C8   N7   C5   104.45  3.000
 5X8  H19  N6   H18  117.80  3.000
 5X8  H19  N6   C6   120.62  3.000
 5X8  H18  N6   C6   119.79  3.000
 5X8  H11  C5'  H10  107.32  3.000
 5X8  H11  C5'  C4'  108.41  3.000
 5X8  H10  C5'  C4'  112.05  3.000
 5X8  H11  C5'  SG   109.59  3.000
 5X8  H10  C5'  SG   109.13  3.000
 5X8  C4'  C5'  SG   110.27  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
 5X8  CONST_01  C4   N3   C2  N1     0.00   0.0  0
 5X8  CONST_02  C4   C5   C6  N1     0.00   0.0  0
 5X8  CONST_03  N7   C5   C6  N1   180.00   0.0  0
 5X8  CONST_04  C2   N3   C4  C5     0.00   0.0  0
 5X8  CONST_05  C8   N9   C4  C5     0.00   0.0  0
 5X8  CONST_06  C2   N1   C6  C5     0.00   0.0  0
 5X8  CONST_07  N9   C8   N7  C5     0.00   0.0  0
 5X8  CONST_08  N3   C4   N9  C8   180.00   0.0  0
 5X8  CONST_09  C4   C5   N7  C8     0.00   0.0  0
 5X8  CONST_10  C6   C5   N7  C8   180.00   0.0  0
 5X8  CONST_11  N9   C4   N3  C2   180.00   0.0  0
 5X8  CONST_12  N3   C2   N1  C6     0.00   0.0  0
 5X8  CONST_13  N3   C4   C5  C6     0.00   0.0  0
 5X8  CONST_14  N9   C4   C5  C6   180.00   0.0  0
 5X8  CONST_15  N7   C5   C4  N3   180.00   0.0  0
 5X8  CONST_16  N7   C8   N9  C4     0.00   0.0  0
 5X8  CONST_17  N7   C5   C4  N9     0.00   0.0  0
 5X8  CONST_18  C1'  N9   C4  C5   180.00   0.0  0
 5X8  CONST_19  C1'  N9   C4  N3     0.00   0.0  0
 5X8  CONST_20  N7   C8   N9  C1'  180.00   0.0  0
 5X8  CONST_21  N6   C6   N1  C2   180.00   0.0  0
 5X8  CONST_22  N6   C6   C5  C4   180.00   0.0  0
 5X8  CONST_23  N6   C6   C5  N7     0.00   0.0  0
 5X8  CONST_24  H1   C8   N7  C5   180.00   0.0  0
 5X8  CONST_25  H2   C2   N1  C6   180.00   0.0  0
 5X8  CONST_26  H18  N6   C6  N1     0.00   0.0  0
 5X8  CONST_27  H19  N6   C6  N1   180.00   0.0  0
 5X8  Var_01    C4'  C5'  SG  CB   176.73  30.0  3
 5X8  Var_02    H8   CB   SG  C5'   39.85  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
 5X8  chir_01  CA   N    C    CB   positiv
 5X8  chir_02  C4'  O4'  C5'  C3'  positiv
 5X8  chir_03  C3'  O3'  C4'  C2'  positiv
 5X8  chir_04  C2'  O2'  C3'  C1'  positiv
 5X8  chir_05  C1'  O4'  N9   C2'  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
 5X8  plan-1  N1   0.020
 5X8  plan-1  C5   0.020
 5X8  plan-1  C8   0.020
 5X8  plan-1  C2   0.020
 5X8  plan-1  C6   0.020
 5X8  plan-1  N3   0.020
 5X8  plan-1  C4   0.020
 5X8  plan-1  C1'  0.020
 5X8  plan-1  N9   0.020
 5X8  plan-1  N7   0.020
 5X8  plan-1  N6   0.020
 5X8  plan-1  H1   0.020
 5X8  plan-1  H2   0.020
 5X8  plan-2  C6   0.020
 5X8  plan-2  N6   0.020
 5X8  plan-2  H18  0.020
 5X8  plan-2  H19  0.020
 5X8  plan-3  C    0.020
 5X8  plan-3  O    0.020
 5X8  plan-3  CA   0.020
 5X8  plan-3  OXT  0.020

