# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 14:49:28 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 8-({2-oxo-2-[(2-phenylethyl)amino]ethyl}sulfanyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4ccccc4)nc12
#
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
 5AQ  5AQ  8-({2-oxo-2-[(2-phenylethyl)amino]ethyl}sulfanyl)adenosine  ligand  56  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5AQ
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
 5AQ  C2   C  CR16  0   0.042    5.7161   2.6372  -0.0676
 5AQ  C4   C  CR56  0   0.492    3.9377   1.3531  -0.1385
 5AQ  C5   C  CR56  0   0.007    3.0828   2.4383  -0.1922
 5AQ  C6   C  CR6   0   0.449    3.6833   3.7087  -0.1707
 5AQ  N9   N  NR5   0  -0.587    3.1268   0.2483  -0.1693
 5AQ  CBA  C  CR16  0  -0.304   -7.7054   0.2950  -1.0507
 5AQ  CBB  C  CR16  0  -0.240   -8.9535  -0.3078  -0.9678
 5AQ  CBC  C  CR16  0  -0.270   -9.5312  -0.5463   0.2725
 5AQ  CBD  C  CR16  0  -0.240   -8.8534  -0.1750   1.4265
 5AQ  CBE  C  CR16  0  -0.305   -7.6055   0.4278   1.3386
 5AQ  CAZ  C  CR6   0   0.122   -7.0162   0.6709   0.1001
 5AQ  CAY  C  CH2   0  -0.562   -5.6448   1.2799   0.0090
 5AQ  CAX  C  CH2   0  -0.233   -4.5727   0.1961   0.0118
 5AQ  NAW  N  NH1   0  -0.644   -3.2516   0.7904  -0.0425
 5AQ  CAV  C  C     0   0.578   -2.1450   0.0658  -0.2243
 5AQ  OBF  O  O     0  -0.485   -2.1429  -1.1464  -0.3820
 5AQ  CAU  C  CH2   0  -0.679   -0.8541   0.8615  -0.2306
 5AQ  C8   C  CR5   0   0.336    1.8385   0.7283  -0.2468
 5AQ  N7   N  N     0  -0.461    1.7761   2.0275  -0.2648
 5AQ  N6   N  NH2   0  -0.819    2.9787   4.8411  -0.2196
 5AQ  N1   N  N     0  -0.472    5.0191   3.7680  -0.1061
 5AQ  N3   N  N     0  -0.457    5.2638   1.3937  -0.0769
 5AQ  C1'  C  CH1   0   0.209    3.5978  -1.1110  -0.0887
 5AQ  O4'  O  O2    0  -0.505    2.9373  -1.8916  -1.0417
 5AQ  C4'  C  CH1   0  -0.031    2.8187  -3.2436  -0.5659
 5AQ  C5'  C  CH2   0  -0.185    1.3546  -3.6517  -0.5086
 5AQ  O5'  O  OH1   0  -0.667    0.6879  -3.4650  -1.7307
 5AQ  C3'  C  CH1   0  -0.059    3.4888  -3.2738   0.8134
 5AQ  O3'  O  OH1   0  -0.666    4.8589  -3.5692   0.7498
 5AQ  C2'  C  CH1   0   0.004    3.3454  -1.8113   1.2436
 5AQ  O2'  O  OH1   0  -0.651    4.2439  -1.3488   2.1977
 5AQ  H1   H  HCR6  0   0.252    6.7935   2.7534  -0.0208
 5AQ  H3   H  HCR6  0   0.254   -9.4759  -0.5879  -1.8737
 5AQ  H4   H  HCR6  0   0.255  -10.5040  -1.0162   0.3396
 5AQ  H5   H  HCR6  0   0.255   -9.2975  -0.3524   2.3976
 5AQ  H6   H  HCR6  0   0.248   -7.0861   0.7164   2.2451
 5AQ  H7   H  HCH2  0   0.261   -5.5562   1.8757  -0.9030
 5AQ  H8   H  HCH2  0   0.259   -5.4820   1.9575   0.8516
 5AQ  H9   H  HCH2  0   0.244   -4.6722  -0.4220   0.9090
 5AQ  H10  H  HCH2  0   0.247   -4.7115  -0.4632  -0.8477
 5AQ  H11  H  HNH1  0   0.411   -3.1661   1.7816   0.1202
 5AQ  H12  H  HCH2  0   0.323   -0.8184   1.5345  -1.0885
 5AQ  H13  H  HCH2  0   0.317   -0.7566   1.4654   0.6722
 5AQ  H14  H  HNH2  0   0.403    3.4427   5.7314  -0.1665
 5AQ  H15  H  HNH2  0   0.410    1.9743   4.8270  -0.2260
 5AQ  H16  H  HCH1  0   0.264    4.6769  -1.0579  -0.2752
 5AQ  H17  H  HCH1  0   0.254    3.3461  -3.8983  -1.2682
 5AQ  H18  H  HCH2  0   0.243    1.3147  -4.7184  -0.2754
 5AQ  H19  H  HCH2  0   0.206    0.8478  -3.1288   0.3129
 5AQ  H20  H  HOH1  0   0.447    0.5545  -2.5193  -1.8575
 5AQ  H21  H  HCH1  0   0.254    2.9611  -3.9544   1.4946
 5AQ  H22  H  HOH1  0   0.457    4.9604  -4.4735   0.4370
 5AQ  H23  H  HCH1  0   0.239    2.3027  -1.6447   1.5495
 5AQ  H24  H  HOH1  0   0.464    3.9779  -1.6802   3.0609
 5AQ  SAT  S  S2    0   0.067    0.4785  -0.3544  -0.3295
 5AQ  H2   H  HCR6  0   0.249   -7.2631   0.4801  -2.0227

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
 5AQ  CAX  CAY  single    1.525  0.020  1.525
 5AQ  CAX  NAW  single    1.450  0.020  1.450
 5AQ  CAY  CAZ  single    1.503  0.020  1.503
 5AQ  CBE  CAZ  aromatic  1.393  0.020  1.393
 5AQ  CBE  CBD  aromatic  1.389  0.020  1.389
 5AQ  CAZ  CBA  aromatic  1.393  0.020  1.393
 5AQ  NAW  CAV  single    1.335  0.020  1.335
 5AQ  OBF  CAV  double    1.222  0.020  1.222
 5AQ  CBD  CBC  aromatic  1.389  0.020  1.389
 5AQ  N6   C6   single    1.335  0.020  1.335
 5AQ  CAV  CAU  single    1.516  0.020  1.516
 5AQ  CBA  CBB  aromatic  1.389  0.020  1.389
 5AQ  CBC  CBB  aromatic  1.389  0.020  1.389
 5AQ  C6   N1   aromatic  1.339  0.020  1.339
 5AQ  C6   C5   aromatic  1.405  0.020  1.405
 5AQ  CAU  SAT  single    1.807  0.020  1.807
 5AQ  N7   C5   aromatic  1.372  0.020  1.372
 5AQ  N7   C8   aromatic  1.301  0.020  1.301
 5AQ  N1   C2   aromatic  1.329  0.020  1.329
 5AQ  C5   C4   aromatic  1.383  0.020  1.383
 5AQ  C8   SAT  single    1.740  0.020  1.740
 5AQ  C8   N9   aromatic  1.377  0.020  1.377
 5AQ  C2   N3   aromatic  1.323  0.020  1.323
 5AQ  C4   N9   aromatic  1.371  0.020  1.371
 5AQ  C4   N3   aromatic  1.328  0.020  1.328
 5AQ  N9   C1'  single    1.441  0.020  1.441
 5AQ  O4'  C1'  single    1.398  0.020  1.398
 5AQ  O4'  C4'  single    1.438  0.020  1.438
 5AQ  C1'  C2'  single    1.526  0.020  1.526
 5AQ  C5'  C4'  single    1.521  0.020  1.521
 5AQ  C5'  O5'  single    1.405  0.020  1.405
 5AQ  C2'  C3'  single    1.531  0.020  1.531
 5AQ  C2'  O2'  single    1.390  0.020  1.390
 5AQ  C4'  C3'  single    1.534  0.020  1.534
 5AQ  C3'  O3'  single    1.403  0.020  1.403
 5AQ  C2   H1   single    0.930  0.020  1.080
 5AQ  CBA  H2   single    0.930  0.020  1.080
 5AQ  CBB  H3   single    0.930  0.020  1.080
 5AQ  CBC  H4   single    0.930  0.020  1.080
 5AQ  CBD  H5   single    0.930  0.020  1.080
 5AQ  CBE  H6   single    0.930  0.020  1.080
 5AQ  CAY  H7   single    0.970  0.020  1.090
 5AQ  CAY  H8   single    0.970  0.020  1.090
 5AQ  CAX  H9   single    0.970  0.020  1.090
 5AQ  CAX  H10  single    0.970  0.020  1.090
 5AQ  NAW  H11  single    0.860  0.020  1.020
 5AQ  CAU  H12  single    0.970  0.020  1.090
 5AQ  CAU  H13  single    0.970  0.020  1.090
 5AQ  N6   H14  single    0.860  0.020  1.020
 5AQ  N6   H15  single    0.860  0.020  1.020
 5AQ  C1'  H16  single    0.970  0.020  1.090
 5AQ  C4'  H17  single    0.970  0.020  1.090
 5AQ  C5'  H18  single    0.970  0.020  1.090
 5AQ  C5'  H19  single    0.970  0.020  1.090
 5AQ  O5'  H20  single    0.850  0.020  0.980
 5AQ  C3'  H21  single    0.970  0.020  1.090
 5AQ  O3'  H22  single    0.850  0.020  0.980
 5AQ  C2'  H23  single    0.970  0.020  1.090
 5AQ  O2'  H24  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
 5AQ  H1   C2   N3   116.13  3.000
 5AQ  H1   C2   N1   115.54  3.000
 5AQ  N3   C2   N1   128.33  3.000
 5AQ  N3   C4   N9   128.05  3.000
 5AQ  N3   C4   C5   126.53  3.000
 5AQ  N9   C4   C5   105.43  3.000
 5AQ  N7   C5   C6   132.73  3.000
 5AQ  N7   C5   C4   110.86  3.000
 5AQ  C6   C5   C4   116.41  3.000
 5AQ  N1   C6   N6   119.40  3.000
 5AQ  N1   C6   C5   117.85  3.000
 5AQ  N6   C6   C5   122.74  3.000
 5AQ  C1'  N9   C8   129.63  3.000
 5AQ  C1'  N9   C4   124.46  3.000
 5AQ  C8   N9   C4   105.89  3.000
 5AQ  H2   CBA  CAZ  119.53  3.000
 5AQ  H2   CBA  CBB  119.63  3.000
 5AQ  CAZ  CBA  CBB  120.83  3.000
 5AQ  H3   CBB  CBC  120.14  3.000
 5AQ  H3   CBB  CBA  119.74  3.000
 5AQ  CBC  CBB  CBA  120.11  3.000
 5AQ  H4   CBC  CBD  120.21  3.000
 5AQ  H4   CBC  CBB  120.25  3.000
 5AQ  CBD  CBC  CBB  119.55  3.000
 5AQ  H5   CBD  CBE  119.78  3.000
 5AQ  H5   CBD  CBC  120.09  3.000
 5AQ  CBE  CBD  CBC  120.13  3.000
 5AQ  H6   CBE  CAZ  119.64  3.000
 5AQ  H6   CBE  CBD  119.55  3.000
 5AQ  CAZ  CBE  CBD  120.81  3.000
 5AQ  CAY  CAZ  CBE  120.70  3.000
 5AQ  CBE  CAZ  CBA  118.56  3.000
 5AQ  CAY  CAZ  CBA  120.70  3.000
 5AQ  H8   CAY  H7   107.05  3.000
 5AQ  H8   CAY  CAX  109.54  3.000
 5AQ  H7   CAY  CAX  109.39  3.000
 5AQ  H8   CAY  CAZ  109.89  3.000
 5AQ  H7   CAY  CAZ  110.20  3.000
 5AQ  CAX  CAY  CAZ  110.69  3.000
 5AQ  H10  CAX  H9   107.03  3.000
 5AQ  H10  CAX  NAW  109.50  3.000
 5AQ  H9   CAX  NAW  110.20  3.000
 5AQ  H10  CAX  CAY  109.78  3.000
 5AQ  H9   CAX  CAY  109.83  3.000
 5AQ  NAW  CAX  CAY  110.45  3.000
 5AQ  H11  NAW  CAV  119.03  3.000
 5AQ  H11  NAW  CAX  118.32  3.000
 5AQ  CAV  NAW  CAX  122.54  3.000
 5AQ  CAU  CAV  OBF  121.22  3.000
 5AQ  CAU  CAV  NAW  114.92  3.000
 5AQ  OBF  CAV  NAW  123.86  3.000
 5AQ  H13  CAU  H12  107.85  3.000
 5AQ  H13  CAU  SAT  110.61  3.000
 5AQ  H12  CAU  SAT  110.37  3.000
 5AQ  H13  CAU  CAV  111.30  3.000
 5AQ  H12  CAU  CAV  110.78  3.000
 5AQ  SAT  CAU  CAV  105.96  3.000
 5AQ  N7   C8   SAT  125.68  3.000
 5AQ  SAT  C8   N9   121.13  3.000
 5AQ  N7   C8   N9   113.19  3.000
 5AQ  C8   N7   C5   104.64  3.000
 5AQ  H15  N6   H14  118.30  3.000
 5AQ  H15  N6   C6   121.08  3.000
 5AQ  H14  N6   C6   120.39  3.000
 5AQ  C6   N1   C2   119.15  3.000
 5AQ  C4   N3   C2   111.73  3.000
 5AQ  H16  C1'  C2'  109.48  3.000
 5AQ  H16  C1'  O4'  112.09  3.000
 5AQ  C2'  C1'  O4'  105.12  3.000
 5AQ  H16  C1'  N9   105.45  3.000
 5AQ  C2'  C1'  N9   115.32  3.000
 5AQ  O4'  C1'  N9   109.53  3.000
 5AQ  C4'  O4'  C1'  109.78  3.000
 5AQ  H17  C4'  C3'  110.77  3.000
 5AQ  H17  C4'  C5'  109.10  3.000
 5AQ  C3'  C4'  C5'  112.42  3.000
 5AQ  H17  C4'  O4'  108.06  3.000
 5AQ  C3'  C4'  O4'  106.26  3.000
 5AQ  C5'  C4'  O4'  110.12  3.000
 5AQ  H19  C5'  H18  106.76  3.000
 5AQ  H19  C5'  O5'  111.63  3.000
 5AQ  H18  C5'  O5'  107.35  3.000
 5AQ  H19  C5'  C4'  110.17  3.000
 5AQ  H18  C5'  C4'  107.77  3.000
 5AQ  O5'  C5'  C4'  112.86  3.000
 5AQ  H20  O5'  C5'  108.10  3.000
 5AQ  H21  C3'  C2'  111.89  3.000
 5AQ  H21  C3'  O3'  111.52  3.000
 5AQ  C2'  C3'  O3'  107.77  3.000
 5AQ  H21  C3'  C4'  111.11  3.000
 5AQ  O3'  C3'  C4'  112.95  3.000
 5AQ  C2'  C3'  C4'  101.13  3.000
 5AQ  H22  O3'  C3'  108.40  3.000
 5AQ  H23  C2'  O2'  111.82  3.000
 5AQ  H23  C2'  C3'  108.16  3.000
 5AQ  O2'  C2'  C3'  116.76  3.000
 5AQ  H23  C2'  C1'  109.28  3.000
 5AQ  O2'  C2'  C1'  109.86  3.000
 5AQ  C3'  C2'  C1'  100.23  3.000
 5AQ  H24  O2'  C2'  108.82  3.000
 5AQ  C8   SAT  CAU   98.92  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
 5AQ  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 5AQ  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 5AQ  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 5AQ  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 5AQ  CONST_05  C8   N7   C5   C4      0.00   0.0  0
 5AQ  CONST_06  N7   C8   N9   C4      0.00   0.0  0
 5AQ  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 5AQ  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 5AQ  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 5AQ  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 5AQ  CONST_11  C8   N7   C5   C6    180.00   0.0  0
 5AQ  CONST_12  N9   C4   C5   C6    180.00   0.0  0
 5AQ  CONST_13  N3   C4   C5   C6      0.00   0.0  0
 5AQ  CONST_14  N7   C5   C4   N9      0.00   0.0  0
 5AQ  CONST_15  CBD  CBE  CAZ  CBA     0.00   0.0  0
 5AQ  CONST_16  CBD  CBC  CBB  CBA     0.00   0.0  0
 5AQ  CONST_17  CBE  CAZ  CBA  CBB     0.00   0.0  0
 5AQ  CONST_18  CBE  CBD  CBC  CBB     0.00   0.0  0
 5AQ  CONST_19  CAZ  CBE  CBD  CBC     0.00   0.0  0
 5AQ  CONST_20  CAZ  CBA  CBB  CBC     0.00   0.0  0
 5AQ  CONST_21  N3   C4   N9   C8    180.00   0.0  0
 5AQ  CONST_22  N1   C6   C5   N7    180.00   0.0  0
 5AQ  CONST_23  N3   C4   C5   N7    180.00   0.0  0
 5AQ  CONST_24  C1'  N9   C4   C5    180.00   0.0  0
 5AQ  CONST_25  C1'  N9   C8   N7    180.00   0.0  0
 5AQ  CONST_26  C1'  N9   C4   N3      0.00   0.0  0
 5AQ  CONST_27  N6   C6   N1   C2    180.00   0.0  0
 5AQ  CONST_28  N6   C6   C5   C4    180.00   0.0  0
 5AQ  CONST_29  SAT  C8   N9   C4    180.00   0.0  0
 5AQ  CONST_30  SAT  C8   N7   C5    180.00   0.0  0
 5AQ  CONST_31  CAY  CAZ  CBA  CBB   180.00   0.0  0
 5AQ  CONST_32  CAY  CAZ  CBE  CBD   180.00   0.0  0
 5AQ  CONST_33  C1'  N9   C8   SAT     0.00   0.0  0
 5AQ  CONST_34  N6   C6   C5   N7      0.00   0.0  0
 5AQ  CONST_35  H1   C2   N3   C4    180.00   0.0  0
 5AQ  CONST_36  H6   CBE  CAZ  CBA   180.00   0.0  0
 5AQ  CONST_37  H4   CBC  CBB  CBA   180.00   0.0  0
 5AQ  CONST_38  H5   CBD  CBC  CBB   180.00   0.0  0
 5AQ  CONST_39  H2   CBA  CBB  CBC   180.00   0.0  0
 5AQ  CONST_40  H3   CBB  CBC  CBD   180.00   0.0  0
 5AQ  CONST_41  H14  N6   C6   C5    180.00   0.0  0
 5AQ  CONST_42  H15  N6   C6   C5      0.00   0.0  0
 5AQ  CONST_43  OBF  CAV  NAW  CAX     0.00   0.0  0
 5AQ  CONST_44  CAU  CAV  NAW  CAX   180.00   0.0  0
 5AQ  CONST_45  H11  NAW  CAV  OBF   180.00   0.0  0
 5AQ  Var_01    CAX  CAY  CAZ  CBA   -88.38  30.0  2
 5AQ  Var_02    N7   C8   SAT  CAU    -6.53  30.0  2
 5AQ  Var_03    NAW  CAX  CAY  CAZ  -178.58  30.0  1
 5AQ  Var_04    H12  CAU  SAT  C8     62.61  30.0  2
 5AQ  Var_05    CAV  NAW  CAX  CAY  -171.17  30.0  3
 5AQ  Var_06    SAT  CAU  CAV  NAW   174.67  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
 5AQ  chir_01  C1'  N9   O4'  C2'  positiv
 5AQ  chir_02  C4'  O4'  C3'  C5'  negativ
 5AQ  chir_03  C3'  O3'  C4'  C2'  positiv
 5AQ  chir_04  C2'  O2'  C3'  C1'  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
 5AQ  plan-1  CBA  0.020
 5AQ  plan-1  CBB  0.020
 5AQ  plan-1  CBC  0.020
 5AQ  plan-1  CBD  0.020
 5AQ  plan-1  CBE  0.020
 5AQ  plan-1  CAZ  0.020
 5AQ  plan-1  CAY  0.020
 5AQ  plan-1  H3   0.020
 5AQ  plan-1  H4   0.020
 5AQ  plan-1  H5   0.020
 5AQ  plan-1  H6   0.020
 5AQ  plan-1  H2   0.020
 5AQ  plan-2  C2   0.020
 5AQ  plan-2  C4   0.020
 5AQ  plan-2  C5   0.020
 5AQ  plan-2  C6   0.020
 5AQ  plan-2  N9   0.020
 5AQ  plan-2  C8   0.020
 5AQ  plan-2  N7   0.020
 5AQ  plan-2  N6   0.020
 5AQ  plan-2  N1   0.020
 5AQ  plan-2  N3   0.020
 5AQ  plan-2  C1'  0.020
 5AQ  plan-2  H1   0.020
 5AQ  plan-2  SAT  0.020
 5AQ  plan-3  C6   0.020
 5AQ  plan-3  N6   0.020
 5AQ  plan-3  H14  0.020
 5AQ  plan-3  H15  0.020
 5AQ  plan-4  CAX  0.020
 5AQ  plan-4  NAW  0.020
 5AQ  plan-4  CAV  0.020
 5AQ  plan-4  OBF  0.020
 5AQ  plan-4  CAU  0.020
 5AQ  plan-4  H11  0.020

