# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 15:29:50 2020
#   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  56  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   1.362   0.5853   3.8276   1.9088
 AYL  N1    N  N      0  -0.475  -0.7134  -4.0417  -0.2556
 AYL  C2    C  C1     0   0.042  -1.0737  -3.3454  -1.3310
 AYL  N3    N  N      0  -0.455  -1.2825  -2.0449  -1.4348
 AYL  C4    C  CR5    0   0.488  -1.0799  -1.4180  -0.2782
 AYL  C5    C  CR5    0  -0.002  -0.6972  -2.0035   0.9185
 AYL  C6    C  C      0   0.449  -0.5097  -3.3962   0.8976
 AYL  N6    N  NH2    0  -0.819  -0.1101  -4.0865   1.9702
 AYL  N7    N  N      0  -0.456  -0.5539  -1.0569   1.8999
 AYL  C8    C  CR15   0   0.082  -0.8535   0.0688   1.3175
 AYL  N9    N  NR5    0  -0.544  -1.1827  -0.0848  -0.0043
 AYL  C1'   C  CH1    0   0.226  -1.6218   0.9351  -0.9227
 AYL  O1P   O  OP    -1  -0.790  -0.2730   2.9373   2.7628
 AYL  C2'   C  CH1    0  -0.043  -3.0418   1.4313  -0.6624
 AYL  O2'   O  OH1    0  -0.653  -3.9701   0.5468  -1.2134
 AYL  O2P   O  O2     0  -0.612   1.5639   2.9288   0.9545
 AYL  C3'   C  CH1    0  -0.041  -2.9843   2.8121  -1.3188
 AYL  O3'   O  OH1    0  -0.669  -3.0640   2.7080  -2.7174
 AYL  O3P   O  O      0  -0.789   1.3783   4.9316   2.5353
 AYL  C4'   C  CH1    0  -0.027  -1.5776   3.2592  -0.9308
 AYL  O4'   O  O2     0  -0.482  -0.8061   2.0605  -0.7951
 AYL  C5'   C  CH2    0  -0.163  -1.5887   4.0630   0.3579
 AYL  O5'   O  O2     0  -0.613  -0.3057   4.5203   0.7198
 AYL  CAC   C  CR6    0   0.336   3.8225  -3.4515  -1.8507
 AYL  CAD   C  CR16   0  -0.367   2.8921  -3.5182  -0.8182
 AYL  CAH   C  CR16   0  -0.299   4.6029  -1.3499  -0.9766
 AYL  CAJ   C  CR16   0  -0.296   2.8297  -2.4987   0.1215
 AYL  CAK   C  CR6    0   0.117   3.6749  -1.3964   0.0622
 AYL  CAP   C  CH2    0  -0.514   3.5341  -0.2647   1.0408
 AYL  CAQ   C  CH2    0  -0.452   2.6400   0.8471   0.4920
 AYL  CAR   C  CH2    0  -0.139   2.3775   1.9224   1.5274
 AYL  CAS   C  CR16   0  -0.325   4.6850  -2.3598  -1.9227
 AYL  HN6   H  HNH2   0   0.401  -0.0697  -5.0906   1.9327
 AYL  HN6A  H  HNH2   0   0.409  -0.0500  -3.6460   2.8715
 AYL  H8    H  HCR5   0   0.316  -0.8162   1.0439   1.7899
 AYL  H1'   H  HCH1   0   0.252  -1.5567   0.4911  -1.9233
 AYL  H2'   H  HCH1   0   0.247  -3.1890   1.5534   0.4188
 AYL  HO2'  H  HOH1   0   0.469  -4.8321   0.7153  -0.8198
 AYL  H3'   H  HCH1   0   0.250  -3.7522   3.4880  -0.9193
 AYL  HO3'  H  HOH1   0   0.449  -3.8015   2.1234  -2.9283
 AYL  H4'   H  HCH1   0   0.255  -1.1333   3.8666  -1.7258
 AYL  H5'   H  HCH2   0   0.232  -2.2156   4.9435   0.1886
 AYL  H5'A  H  HCH2   0   0.215  -2.0502   3.4901   1.1679
 AYL  HAD   H  HCR6   0   0.259   2.2069  -4.3563  -0.7491
 AYL  HAH   H  HCR6   0   0.245   5.2804  -0.5068  -1.0512
 AYL  HAJ   H  HCR6   0   0.243   2.1036  -2.5691   0.9221
 AYL  HAP   H  HCH2   0   0.235   3.1097  -0.6403   1.9765
 AYL  HAPA  H  HCH2   0   0.238   4.5165   0.1471   1.2892
 AYL  HAQ   H  HCH2   0   0.226   3.1085   1.2876  -0.3935
 AYL  HAQA  H  HCH2   0   0.238   1.6859   0.4258   0.1659
 AYL  HAR   H  HCH2   0   0.203   3.3265   2.3504   1.8745
 AYL  HARA  H  HCH2   0   0.200   1.8908   1.4705   2.3990
 AYL  HAS   H  HCR6   0   0.258   5.4159  -2.3045  -2.7202
 AYL  HOBF  H  HOH1   0   0.471   3.2936  -5.1119  -2.6353
 AYL  OBF   O  OH1    0  -0.637   3.9313  -4.4085  -2.7985
 AYL  H2    H  H      0   0.249  -1.2156  -3.9263  -2.2363

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   deloc     1.503  0.020  1.503
 AYL  P    O2P   single    1.636  0.020  1.636
 AYL  P    O3P   deloc     1.497  0.020  1.497
 AYL  P    O5'   single    1.639  0.020  1.639
 AYL  N1   C2    aromatic  1.331  0.020  1.331
 AYL  N1   C6    aromatic  1.337  0.020  1.337
 AYL  C2   N3    aromatic  1.321  0.020  1.321
 AYL  N3   C4    aromatic  1.331  0.020  1.331
 AYL  C4   C5    aromatic  1.386  0.020  1.386
 AYL  C4   N9    aromatic  1.365  0.020  1.365
 AYL  C5   C6    aromatic  1.405  0.020  1.405
 AYL  C5   N7    aromatic  1.371  0.020  1.371
 AYL  C6   N6    single    1.337  0.020  1.337
 AYL  N7   C8    aromatic  1.302  0.020  1.302
 AYL  C8   N9    aromatic  1.371  0.020  1.371
 AYL  N9   C1'   single    1.441  0.020  1.441
 AYL  C1'  C2'   single    1.527  0.020  1.527
 AYL  C1'  O4'   single    1.396  0.020  1.396
 AYL  C2'  O2'   single    1.396  0.020  1.396
 AYL  C2'  C3'   single    1.530  0.020  1.530
 AYL  O2P  CAR   single    1.415  0.020  1.415
 AYL  C3'  O3'   single    1.405  0.020  1.405
 AYL  C3'  C4'   single    1.526  0.020  1.526
 AYL  C4'  O4'   single    1.432  0.020  1.432
 AYL  C4'  C5'   single    1.519  0.020  1.519
 AYL  C5'  O5'   single    1.409  0.020  1.409
 AYL  CAC  CAD   aromatic  1.391  0.020  1.391
 AYL  CAC  CAS   aromatic  1.393  0.020  1.393
 AYL  CAC  OBF   single    1.351  0.020  1.351
 AYL  CAD  CAJ   aromatic  1.388  0.020  1.388
 AYL  CAH  CAK   aromatic  1.394  0.020  1.394
 AYL  CAH  CAS   aromatic  1.386  0.020  1.386
 AYL  CAJ  CAK   aromatic  1.390  0.020  1.390
 AYL  CAK  CAP   single    1.503  0.020  1.503
 AYL  CAP  CAQ   single    1.529  0.020  1.529
 AYL  CAQ  CAR   single    1.516  0.020  1.516
 AYL  C2   H2    single    0.930  0.020  1.080
 AYL  N6   HN6   single    0.860  0.020  1.020
 AYL  N6   HN6A  single    0.860  0.020  1.020
 AYL  C8   H8    single    0.930  0.020  1.080
 AYL  C1'  H1'   single    0.970  0.020  1.090
 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  106.25  3.000
 AYL  O5'   P    O2P   97.71  3.000
 AYL  O3P   P    O2P  109.42  3.000
 AYL  O5'   P    O1P  110.61  3.000
 AYL  O3P   P    O1P  120.12  3.000
 AYL  O2P   P    O1P  110.34  3.000
 AYL  C6    N1   C2   119.05  3.000
 AYL  H2    C2   N3   116.16  3.000
 AYL  H2    C2   N1   115.43  3.000
 AYL  N3    C2   N1   128.41  3.000
 AYL  C4    N3   C2   111.79  3.000
 AYL  N9    C4   C5   105.08  3.000
 AYL  N9    C4   N3   128.53  3.000
 AYL  C5    C4   N3   126.39  3.000
 AYL  N7    C5   C6   132.91  3.000
 AYL  N7    C5   C4   110.81  3.000
 AYL  C6    C5   C4   116.27  3.000
 AYL  N6    C6   C5   122.67  3.000
 AYL  N6    C6   N1   119.23  3.000
 AYL  C5    C6   N1   118.09  3.000
 AYL  HN6A  N6   HN6  117.95  3.000
 AYL  HN6A  N6   C6   120.74  3.000
 AYL  HN6   N6   C6   119.86  3.000
 AYL  C8    N7   C5   104.63  3.000
 AYL  H8    C8   N9   121.95  3.000
 AYL  H8    C8   N7   125.07  3.000
 AYL  N9    C8   N7   112.93  3.000
 AYL  C1'   N9   C8   127.48  3.000
 AYL  C1'   N9   C4   125.90  3.000
 AYL  C8    N9   C4   106.55  3.000
 AYL  H1'   C1'  O4'  112.03  3.000
 AYL  H1'   C1'  C2'  110.03  3.000
 AYL  O4'   C1'  C2'  105.42  3.000
 AYL  H1'   C1'  N9   106.08  3.000
 AYL  O4'   C1'  N9   109.53  3.000
 AYL  C2'   C1'  N9   113.88  3.000
 AYL  H2'   C2'  C3'  109.09  3.000
 AYL  H2'   C2'  O2'  111.72  3.000
 AYL  C3'   C2'  O2'  115.32  3.000
 AYL  H2'   C2'  C1'  109.19  3.000
 AYL  C3'   C2'  C1'  100.67  3.000
 AYL  O2'   C2'  C1'  110.21  3.000
 AYL  HO2'  O2'  C2'  108.87  3.000
 AYL  CAR   O2P  P    119.90  3.000
 AYL  H3'   C3'  C4'  111.82  3.000
 AYL  H3'   C3'  O3'  111.60  3.000
 AYL  C4'   C3'  O3'  109.10  3.000
 AYL  H3'   C3'  C2'  111.90  3.000
 AYL  C4'   C3'  C2'  100.95  3.000
 AYL  O3'   C3'  C2'  110.98  3.000
 AYL  HO3'  O3'  C3'  107.83  3.000
 AYL  H4'   C4'  C5'  109.00  3.000
 AYL  H4'   C4'  O4'  108.34  3.000
 AYL  C5'   C4'  O4'  111.50  3.000
 AYL  H4'   C4'  C3'  110.61  3.000
 AYL  C5'   C4'  C3'  111.34  3.000
 AYL  O4'   C4'  C3'  105.99  3.000
 AYL  C4'   O4'  C1'  110.57  3.000
 AYL  H5'A  C5'  H5'  107.12  3.000
 AYL  H5'A  C5'  O5'  111.33  3.000
 AYL  H5'   C5'  O5'  107.47  3.000
 AYL  H5'A  C5'  C4'  110.74  3.000
 AYL  H5'   C5'  C4'  107.39  3.000
 AYL  O5'   C5'  C4'  112.51  3.000
 AYL  C5'   O5'  P    122.95  3.000
 AYL  OBF   CAC  CAS  117.96  3.000
 AYL  OBF   CAC  CAD  122.71  3.000
 AYL  CAS   CAC  CAD  119.33  3.000
 AYL  HAD   CAD  CAJ  119.73  3.000
 AYL  HAD   CAD  CAC  120.45  3.000
 AYL  CAJ   CAD  CAC  119.82  3.000
 AYL  HAH   CAH  CAS  118.85  3.000
 AYL  HAH   CAH  CAK  119.56  3.000
 AYL  CAS   CAH  CAK  121.59  3.000
 AYL  HAJ   CAJ  CAK  119.38  3.000
 AYL  HAJ   CAJ  CAD  118.88  3.000
 AYL  CAK   CAJ  CAD  121.74  3.000
 AYL  CAP   CAK  CAJ  120.82  3.000
 AYL  CAP   CAK  CAH  121.51  3.000
 AYL  CAJ   CAK  CAH  117.58  3.000
 AYL  HAPA  CAP  HAP  106.47  3.000
 AYL  HAPA  CAP  CAQ  109.46  3.000
 AYL  HAP   CAP  CAQ  109.26  3.000
 AYL  HAPA  CAP  CAK  110.32  3.000
 AYL  HAP   CAP  CAK  109.56  3.000
 AYL  CAQ   CAP  CAK  111.64  3.000
 AYL  HAQA  CAQ  HAQ  106.71  3.000
 AYL  HAQA  CAQ  CAR  109.04  3.000
 AYL  HAQ   CAQ  CAR  109.96  3.000
 AYL  HAQA  CAQ  CAP  109.72  3.000
 AYL  HAQ   CAQ  CAP  109.44  3.000
 AYL  CAR   CAQ  CAP  111.84  3.000
 AYL  HARA  CAR  HAR  107.07  3.000
 AYL  HARA  CAR  CAQ  109.13  3.000
 AYL  HAR   CAR  CAQ  110.06  3.000
 AYL  HARA  CAR  O2P  111.09  3.000
 AYL  HAR   CAR  O2P  110.35  3.000
 AYL  CAQ   CAR  O2P  109.12  3.000
 AYL  HAS   CAS  CAH  120.35  3.000
 AYL  HAS   CAS  CAC  119.72  3.000
 AYL  CAH   CAS  CAC  119.93  3.000
 AYL  HOBF  OBF  CAC  110.18  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
 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    83.11  30.0  2
 AYL  Var_02    C4'   C5'  O5'  P    -103.39  30.0  2
 AYL  Var_03    CAR   CAQ  CAP  CAK   174.07  30.0  3
 AYL  Var_04    CAQ   CAR  O2P  P     152.82  30.0  3
 AYL  Var_05    CAP   CAQ  CAR  O2P   179.13  30.0  1

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

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  H8    0.020
 AYL  plan-2  H2    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

