# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:13:48 2021
#   Inital geometry file: a 134 line input string
#   Ligand name: 5'-O-{(S)-hydroxy[3-(4-hydroxyphenyl)propoxy]phosphoryl}adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OCCCc4ccc(O)cc4)[C@@H](O)[C@H]3O
#
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
 AYL  AYL  5'-O-{(S)-hydroxy[3-(4-hydroxyphenyl)propoxy]phosphoryl}adenosine  ligand  57  33  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AYL
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
 AYL  P     P  P     0   1.486   -9.3757  15.1137  -23.2233
 AYL  N1    N  N     0  -0.473   -4.8549  14.9877  -28.6785
 AYL  C2    C  CR16  0   0.037   -6.1770  15.0132  -28.8264
 AYL  N3    N  N     0  -0.456   -7.0620  14.1073  -28.4482
 AYL  C4    C  CR56  0   0.503   -6.4788  13.0683  -27.8565
 AYL  C5    C  CR56  0   0.012   -5.1222  12.8977  -27.6357
 AYL  C6    C  CR6   0   0.460   -4.2828  13.9339  -28.0863
 AYL  N6    N  NH2   0  -0.811   -2.9524  13.8939  -27.9731
 AYL  N7    N  N     0  -0.451   -4.8830  11.7057  -27.0014
 AYL  C8    C  CR15  0   0.105   -6.0599  11.1799  -26.8392
 AYL  N9    N  NR5   0  -0.547   -7.0759  11.9508  -27.3419
 AYL  C1'   C  CH1   0   0.178   -8.5097  11.7286  -27.3628
 AYL  O1P   O  OH1   0  -0.736   -9.2910  14.6038  -21.7156
 AYL  C2'   C  CH1   0  -0.059   -8.9144  10.3152  -26.9543
 AYL  O2'   O  OH1   0  -0.663  -10.1317  10.0432  -27.5902
 AYL  O2P   O  O2    0  -0.592   -7.8096  15.2080  -23.4833
 AYL  C3'   C  CH1   0  -0.046   -9.1172  10.4789  -25.4406
 AYL  O3'   O  OH1   0  -0.654  -10.0132   9.5564  -24.8926
 AYL  O3P   O  O     0  -0.696  -10.1834  16.3161  -23.4947
 AYL  C4'   C  CH1   0   0.015   -9.6934  11.8908  -25.3569
 AYL  O4'   O  O2    0  -0.481   -9.1430  12.5956  -26.4594
 AYL  C5'   C  CH2   0  -0.183   -9.3407  12.5903  -24.0683
 AYL  O5'   O  O2    0  -0.593   -9.9145  13.8967  -24.1092
 AYL  CAC   C  CR6   0   0.335   -0.8147  14.3176  -24.1105
 AYL  CAD   C  CR16  0  -0.322   -1.5303  15.3944  -23.5914
 AYL  CAH   C  CR16  0  -0.331   -2.8991  13.2219  -24.6109
 AYL  CAJ   C  CR16  0  -0.296   -2.9152  15.3708  -23.5911
 AYL  CAK   C  CR6   0   0.122   -3.6319  14.2907  -24.1068
 AYL  CAP   C  CH2   0  -0.501   -5.1384  14.2683  -24.0907
 AYL  CAQ   C  CH2   0  -0.472   -5.7731  15.5148  -24.7069
 AYL  CAR   C  CH2   0  -0.198   -7.2808  15.4444  -24.8006
 AYL  CAS   C  CR16  0  -0.373   -1.5099  13.2254  -24.6177
 AYL  H2    H  HCR6  0   0.255   -6.5746  15.8951  -29.3169
 AYL  HN6   H  HNH2  0   0.401   -2.4162  14.7159  -28.1948
 AYL  HN6A  H  HNH2  0   0.410   -2.5177  13.2106  -27.3774
 AYL  H8    H  HCR5  0   0.302   -6.2386  10.2237  -26.3713
 AYL  H1'   H  HCH1  0   0.284   -8.8464  11.9598  -28.3753
 AYL  HO1P  H  HOH1  0   0.503  -10.1248  14.6664  -21.2307
 AYL  H2'   H  HCH1  0   0.265   -8.1586   9.5607  -27.2023
 AYL  HO2'  H  HOH1  0   0.454  -10.6302   9.4378  -27.0270
 AYL  H3'   H  HCH1  0   0.249   -8.1455  10.4389  -24.9303
 AYL  HO3'  H  HOH1  0   0.471   -9.5374   8.7455  -24.6851
 AYL  H4'   H  HCH1  0   0.255  -10.7849  11.8482  -25.4583
 AYL  H5'   H  HCH2  0   0.262   -9.7519  12.0281  -23.2261
 AYL  H5'A  H  HCH2  0   0.233   -8.2533  12.6339  -23.9476
 AYL  HAD   H  HCR6  0   0.259   -1.0002  16.2472  -23.1854
 AYL  HAH   H  HCR6  0   0.266   -3.4185  12.3640  -25.0209
 AYL  HAJ   H  HCR6  0   0.246   -3.4421  16.2199  -23.1724
 AYL  HAP   H  HCH2  0   0.232   -5.4914  13.3784  -24.6216
 AYL  HAPA  H  HCH2  0   0.251   -5.4837  14.1601  -23.0591
 AYL  HAQ   H  HCH2  0   0.243   -5.4864  16.4078  -24.1461
 AYL  HAQA  H  HCH2  0   0.244   -5.4002  15.6605  -25.7244
 AYL  HAR   H  HCH2  0   0.235   -7.5869  14.6369  -25.4706
 AYL  HARA  H  HCH2  0   0.258   -7.6797  16.3804  -25.1988
 AYL  HAS   H  HCR6  0   0.268   -0.9737  12.3729  -25.0208
 AYL  HOBF  H  HOH1  0   0.472    0.9144  13.5855  -24.4706
 AYL  OBF   O  OH1   0  -0.636    0.5337  14.3863  -24.0935

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
 AYL  P    O1P   single    1.594  0.020  1.594
 AYL  P    O2P   single    1.590  0.020  1.590
 AYL  P    O3P   double    1.474  0.020  1.474
 AYL  P    O5'   single    1.599  0.020  1.599
 AYL  N1   C2    aromatic  1.331  0.020  1.331
 AYL  N1   C6    aromatic  1.337  0.020  1.337
 AYL  C2   N3    aromatic  1.322  0.020  1.322
 AYL  N3   C4    aromatic  1.330  0.020  1.330
 AYL  C4   C5    aromatic  1.385  0.020  1.385
 AYL  C4   N9    aromatic  1.367  0.020  1.367
 AYL  C5   C6    aromatic  1.408  0.020  1.408
 AYL  C5   N7    aromatic  1.371  0.020  1.371
 AYL  C6   N6    single    1.336  0.020  1.336
 AYL  N7   C8    aromatic  1.299  0.020  1.299
 AYL  C8   N9    aromatic  1.371  0.020  1.371
 AYL  N9   C1'   single    1.451  0.020  1.451
 AYL  C1'  C2'   single    1.526  0.020  1.526
 AYL  C1'  O4'   single    1.403  0.020  1.403
 AYL  C2'  O2'   single    1.400  0.020  1.400
 AYL  C2'  C3'   single    1.536  0.020  1.536
 AYL  O2P  CAR   single    1.439  0.020  1.439
 AYL  C3'  O3'   single    1.398  0.020  1.398
 AYL  C3'  C4'   single    1.527  0.020  1.527
 AYL  C4'  O4'   single    1.420  0.020  1.420
 AYL  C4'  C5'   single    1.508  0.020  1.508
 AYL  C5'  O5'   single    1.427  0.020  1.427
 AYL  CAC  CAD   aromatic  1.393  0.020  1.393
 AYL  CAC  CAS   aromatic  1.390  0.020  1.390
 AYL  CAC  OBF   single    1.350  0.020  1.350
 AYL  CAD  CAJ   aromatic  1.385  0.020  1.385
 AYL  CAH  CAK   aromatic  1.390  0.020  1.390
 AYL  CAH  CAS   aromatic  1.389  0.020  1.389
 AYL  CAJ  CAK   aromatic  1.395  0.020  1.395
 AYL  CAK  CAP   single    1.507  0.020  1.507
 AYL  CAP  CAQ   single    1.528  0.020  1.528
 AYL  CAQ  CAR   single    1.512  0.020  1.512
 AYL  C2   H2    single    0.930  0.020  1.080
 AYL  N6   HN6   single    0.890  0.020  1.040
 AYL  N6   HN6A  single    0.890  0.020  1.040
 AYL  C8   H8    single    0.930  0.020  1.080
 AYL  C1'  H1'   single    0.970  0.020  1.090
 AYL  O1P  HO1P  single    0.850  0.020  0.980
 AYL  C2'  H2'   single    0.970  0.020  1.090
 AYL  O2'  HO2'  single    0.850  0.020  0.980
 AYL  C3'  H3'   single    0.970  0.020  1.090
 AYL  O3'  HO3'  single    0.850  0.020  0.980
 AYL  C4'  H4'   single    0.970  0.020  1.090
 AYL  C5'  H5'   single    0.970  0.020  1.090
 AYL  C5'  H5'A  single    0.970  0.020  1.090
 AYL  CAD  HAD   single    0.930  0.020  1.080
 AYL  CAH  HAH   single    0.930  0.020  1.080
 AYL  CAJ  HAJ   single    0.930  0.020  1.080
 AYL  CAP  HAP   single    0.970  0.020  1.090
 AYL  CAP  HAPA  single    0.970  0.020  1.090
 AYL  CAQ  HAQ   single    0.970  0.020  1.090
 AYL  CAQ  HAQA  single    0.970  0.020  1.090
 AYL  CAR  HAR   single    0.970  0.020  1.090
 AYL  CAR  HARA  single    0.970  0.020  1.090
 AYL  CAS  HAS   single    0.930  0.020  1.080
 AYL  OBF  HOBF  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
 AYL  O5'   P    O3P  109.53  3.000
 AYL  O5'   P    O2P  106.65  3.000
 AYL  O3P   P    O2P  117.46  3.000
 AYL  O5'   P    O1P  107.37  3.000
 AYL  O3P   P    O1P  117.67  3.000
 AYL  O2P   P    O1P   96.97  3.000
 AYL  C6    N1   C2   119.30  3.000
 AYL  H2    C2   N3   116.19  3.000
 AYL  H2    C2   N1   115.47  3.000
 AYL  N3    C2   N1   128.34  3.000
 AYL  C4    N3   C2   111.66  3.000
 AYL  N9    C4   C5   105.49  3.000
 AYL  N9    C4   N3   127.90  3.000
 AYL  C5    C4   N3   126.62  3.000
 AYL  N7    C5   C6   133.15  3.000
 AYL  N7    C5   C4   110.59  3.000
 AYL  C6    C5   C4   116.26  3.000
 AYL  N6    C6   C5   123.01  3.000
 AYL  N6    C6   N1   119.16  3.000
 AYL  C5    C6   N1   117.82  3.000
 AYL  HN6A  N6   HN6  117.09  3.000
 AYL  HN6A  N6   C6   120.08  3.000
 AYL  HN6   N6   C6   119.18  3.000
 AYL  C8    N7   C5   104.57  3.000
 AYL  H8    C8   N9   122.31  3.000
 AYL  H8    C8   N7   124.24  3.000
 AYL  N9    C8   N7   113.45  3.000
 AYL  C1'   N9   C8   130.65  3.000
 AYL  C1'   N9   C4   123.45  3.000
 AYL  C8    N9   C4   105.90  3.000
 AYL  H1'   C1'  O4'  109.08  3.000
 AYL  H1'   C1'  C2'  111.27  3.000
 AYL  O4'   C1'  C2'  106.28  3.000
 AYL  H1'   C1'  N9   106.60  3.000
 AYL  O4'   C1'  N9   110.00  3.000
 AYL  C2'   C1'  N9   113.58  3.000
 AYL  HO1P  O1P  P    114.08  3.000
 AYL  H2'   C2'  C3'  112.79  3.000
 AYL  H2'   C2'  O2'  111.28  3.000
 AYL  C3'   C2'  O2'  110.70  3.000
 AYL  H2'   C2'  C1'  113.21  3.000
 AYL  C3'   C2'  C1'  101.55  3.000
 AYL  O2'   C2'  C1'  106.79  3.000
 AYL  HO2'  O2'  C2'  107.80  3.000
 AYL  CAR   O2P  P    121.42  3.000
 AYL  H3'   C3'  C4'  110.00  3.000
 AYL  H3'   C3'  O3'  111.16  3.000
 AYL  C4'   C3'  O3'  110.29  3.000
 AYL  H3'   C3'  C2'  109.71  3.000
 AYL  C4'   C3'  C2'  101.68  3.000
 AYL  O3'   C3'  C2'  113.62  3.000
 AYL  HO3'  O3'  C3'  108.87  3.000
 AYL  H4'   C4'  C5'  109.25  3.000
 AYL  H4'   C4'  O4'  109.47  3.000
 AYL  C5'   C4'  O4'  110.04  3.000
 AYL  H4'   C4'  C3'  109.54  3.000
 AYL  C5'   C4'  C3'  112.79  3.000
 AYL  O4'   C4'  C3'  105.67  3.000
 AYL  C4'   O4'  C1'  111.61  3.000
 AYL  H5'A  C5'  H5'  108.02  3.000
 AYL  H5'A  C5'  O5'  111.47  3.000
 AYL  H5'   C5'  O5'  109.97  3.000
 AYL  H5'A  C5'  C4'  110.18  3.000
 AYL  H5'   C5'  C4'  109.38  3.000
 AYL  O5'   C5'  C4'  107.82  3.000
 AYL  C5'   O5'  P    123.04  3.000
 AYL  OBF   CAC  CAS  122.94  3.000
 AYL  OBF   CAC  CAD  117.97  3.000
 AYL  CAS   CAC  CAD  119.09  3.000
 AYL  HAD   CAD  CAJ  120.17  3.000
 AYL  HAD   CAD  CAC  119.79  3.000
 AYL  CAJ   CAD  CAC  120.03  3.000
 AYL  HAH   CAH  CAS  118.66  3.000
 AYL  HAH   CAH  CAK  119.55  3.000
 AYL  CAS   CAH  CAK  121.79  3.000
 AYL  HAJ   CAJ  CAK  119.98  3.000
 AYL  HAJ   CAJ  CAD  118.23  3.000
 AYL  CAK   CAJ  CAD  121.79  3.000
 AYL  CAP   CAK  CAJ  121.41  3.000
 AYL  CAP   CAK  CAH  121.29  3.000
 AYL  CAJ   CAK  CAH  117.29  3.000
 AYL  HAPA  CAP  HAP  105.98  3.000
 AYL  HAPA  CAP  CAQ  109.27  3.000
 AYL  HAP   CAP  CAQ  109.49  3.000
 AYL  HAPA  CAP  CAK  109.10  3.000
 AYL  HAP   CAP  CAK  109.23  3.000
 AYL  CAQ   CAP  CAK  113.50  3.000
 AYL  HAQA  CAQ  HAQ  106.21  3.000
 AYL  HAQA  CAQ  CAR  106.77  3.000
 AYL  HAQ   CAQ  CAR  109.35  3.000
 AYL  HAQA  CAQ  CAP  110.01  3.000
 AYL  HAQ   CAQ  CAP  110.53  3.000
 AYL  CAR   CAQ  CAP  113.64  3.000
 AYL  HARA  CAR  HAR  107.89  3.000
 AYL  HARA  CAR  CAQ  110.29  3.000
 AYL  HAR   CAR  CAQ  110.58  3.000
 AYL  HARA  CAR  O2P  109.89  3.000
 AYL  HAR   CAR  O2P  109.69  3.000
 AYL  CAQ   CAR  O2P  108.50  3.000
 AYL  HAS   CAS  CAH  119.61  3.000
 AYL  HAS   CAS  CAC  120.38  3.000
 AYL  CAH   CAS  CAC  120.01  3.000
 AYL  HOBF  OBF  CAC  110.33  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
 AYL  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 AYL  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 AYL  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 AYL  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 AYL  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 AYL  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 AYL  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 AYL  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 AYL  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 AYL  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 AYL  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 AYL  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 AYL  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 AYL  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 AYL  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 AYL  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 AYL  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 AYL  CONST_18  CAK   CAJ  CAD  CAC     0.00   0.0  0
 AYL  CONST_19  CAK   CAH  CAS  CAC     0.00   0.0  0
 AYL  CONST_20  CAH   CAS  CAC  CAD     0.00   0.0  0
 AYL  CONST_21  CAH   CAK  CAJ  CAD     0.00   0.0  0
 AYL  CONST_22  CAS   CAC  CAD  CAJ     0.00   0.0  0
 AYL  CONST_23  CAS   CAH  CAK  CAJ     0.00   0.0  0
 AYL  CONST_24  C1'   N9   C4   N3      0.00   0.0  0
 AYL  CONST_25  C1'   N9   C4   C5    180.00   0.0  0
 AYL  CONST_26  C1'   N9   C8   N7    180.00   0.0  0
 AYL  CONST_27  N6    C6   N1   C2    180.00   0.0  0
 AYL  CONST_28  N6    C6   C5   C4    180.00   0.0  0
 AYL  CONST_29  N7    C5   C6   N6      0.00   0.0  0
 AYL  CONST_30  CAP   CAK  CAJ  CAD   180.00   0.0  0
 AYL  CONST_31  OBF   CAC  CAS  CAH   180.00   0.0  0
 AYL  CONST_32  OBF   CAC  CAD  CAJ   180.00   0.0  0
 AYL  CONST_33  CAS   CAH  CAK  CAP   180.00   0.0  0
 AYL  CONST_34  H2    C2   N3   C4    180.00   0.0  0
 AYL  CONST_35  H8    C8   N9   C4    180.00   0.0  0
 AYL  CONST_36  HAJ   CAJ  CAD  CAC   180.00   0.0  0
 AYL  CONST_37  HAH   CAH  CAS  CAC   180.00   0.0  0
 AYL  CONST_38  HAS   CAS  CAC  CAD   180.00   0.0  0
 AYL  CONST_39  HAD   CAD  CAJ  CAK   180.00   0.0  0
 AYL  CONST_40  HN6   N6   C6   N1      0.00   0.0  0
 AYL  CONST_41  HN6A  N6   C6   N1    180.00   0.0  0
 AYL  Var_01    CAQ   CAP  CAK  CAH  -128.92  30.0  2
 AYL  Var_02    C4'   C5'  O5'  P    -157.73  30.0  2
 AYL  Var_03    CAR   CAQ  CAP  CAK   175.05  30.0  3
 AYL  Var_04    CAQ   CAR  O2P  P     178.55  30.0  3
 AYL  Var_05    CAP   CAQ  CAR  O2P    56.64  30.0  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
 AYL  chir_02  C1'  N9   C2'  O4'  negativ
 AYL  chir_03  C2'  O2'  C3'  C1'  positiv
 AYL  chir_04  C3'  O3'  C4'  C2'  positiv
 AYL  chir_05  C4'  O4'  C3'  C5'  negativ
 AYL  chir_06  P    O2P  O3P  O5'  both

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
 AYL  plan-1  CAC   0.020
 AYL  plan-1  CAD   0.020
 AYL  plan-1  CAH   0.020
 AYL  plan-1  CAJ   0.020
 AYL  plan-1  CAK   0.020
 AYL  plan-1  CAP   0.020
 AYL  plan-1  CAS   0.020
 AYL  plan-1  HAD   0.020
 AYL  plan-1  HAH   0.020
 AYL  plan-1  HAJ   0.020
 AYL  plan-1  HAS   0.020
 AYL  plan-1  OBF   0.020
 AYL  plan-2  N1    0.020
 AYL  plan-2  C2    0.020
 AYL  plan-2  N3    0.020
 AYL  plan-2  C4    0.020
 AYL  plan-2  C5    0.020
 AYL  plan-2  C6    0.020
 AYL  plan-2  N6    0.020
 AYL  plan-2  N7    0.020
 AYL  plan-2  C8    0.020
 AYL  plan-2  N9    0.020
 AYL  plan-2  C1'   0.020
 AYL  plan-2  H2    0.020
 AYL  plan-2  H8    0.020
 AYL  plan-3  C6    0.020
 AYL  plan-3  N6    0.020
 AYL  plan-3  HN6   0.020
 AYL  plan-3  HN6A  0.020

