# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 05:05:26 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(2E)-3-(4-oxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)/C=C/C4=CCC(=O)C=C4)[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
 4UU  4UU  5'-O-[(R)-hydroxy{[(2E)-3-(4-oxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}phosphoryl]adenosine  ligand  54  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4UU
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
 4UU  C2   C  CR16  0   0.045   2.1155  25.3389  15.3362
 4UU  O34  O  O     0  -0.406  -1.1008  31.4378  14.5105
 4UU  CAR  C  C     0   0.591  -0.7015  32.2173  15.3318
 4UU  CAQ  C  C1    0  -0.422   0.6886  32.5341  15.6506
 4UU  CAP  C  C1    0  -0.185   1.6820  31.8419  15.0787
 4UU  CAK  C  CR6   0   0.163   3.1093  32.0374  15.3016
 4UU  CAJ  C  CR16  0  -0.231   4.0128  30.9841  14.8599
 4UU  CAD  C  CR16  0  -0.369   5.3474  31.0449  14.9999
 4UU  CAH  C  CR16  0  -0.271   3.6313  33.1426  15.8627
 4UU  CAS  C  C     0  -0.617   5.0860  33.3173  16.0772
 4UU  CAC  C  CR6   0   0.399   5.9902  32.1986  15.6171
 4UU  OBF  O  O     0  -0.437   7.1979  32.2725  15.7583
 4UU  O2P  O  O2    0  -0.610  -1.5501  32.9200  16.1325
 4UU  P    P  P     0   1.489  -3.1774  32.7185  16.0806
 4UU  O1P  O  OH1   0  -0.728  -3.5907  33.5864  17.3420
 4UU  O3P  O  O     0  -0.670  -3.8035  33.0221  14.7882
 4UU  C5'  C  CH2   0  -0.185  -2.8599  30.6602  17.7481
 4UU  C4'  C  CH1   0   0.002  -2.8096  29.1664  17.5640
 4UU  C3'  C  CH1   0  -0.035  -2.1753  28.4445  18.7508
 4UU  O3'  O  OH1   0  -0.654  -3.1174  28.2344  19.7609
 4UU  C2'  C  CH1   0  -0.046  -1.6762  27.1573  18.0827
 4UU  O2'  O  OH1   0  -0.662  -2.7307  26.2557  17.8908
 4UU  O4'  O  O2    0  -0.485  -1.9784  28.8433  16.4598
 4UU  C1'  C  CH1   0   0.169  -1.2519  27.6711  16.7036
 4UU  N9   N  NR5   0  -0.534   0.1661  27.9707  16.6230
 4UU  C4   C  CR56  0   0.493   1.1239  27.1109  16.1681
 4UU  N3   N  N     0  -0.457   0.9634  25.8759  15.6993
 4UU  C8   C  CR15  0   0.121   0.8234  29.1130  16.9897
 4UU  N7   N  N     0  -0.440   2.1092  29.0510  16.8067
 4UU  C5   C  CR56  0  -0.004   2.3204  27.7991  16.2920
 4UU  C6   C  CR6   0   0.458   3.4768  27.1140  15.8771
 4UU  N1   N  N     0  -0.472   3.3323  25.8737  15.3993
 4UU  N6   N  NH2   0  -0.818   4.6957  27.6589  15.9265
 4UU  H1   H  HCR6  0   0.254   2.0691  24.3313  14.9371
 4UU  H2   H  H     0   0.290   0.8702  33.3116  16.3818
 4UU  H3   H  H     0   0.283   1.4231  31.0450  14.3884
 4UU  H4   H  HCR6  0   0.277   3.5704  30.1125  14.3923
 4UU  H5   H  HCR6  0   0.273   5.9774  30.2369  14.6494
 4UU  H6   H  HCR6  0   0.281   2.9965  33.9634  16.1740
 4UU  H7   H  H     0   0.316   5.2663  33.4932  17.1453
 4UU  H8   H  H     0   0.314   5.4126  34.2490  15.5998
 4UU  H9   H  HOH1  0   0.510  -3.6529  34.5401  17.1898
 4UU  H10  H  HCH2  0   0.239  -1.8573  31.0547  17.9348
 4UU  H11  H  HCH2  0   0.273  -3.4829  30.8961  18.6129
 4UU  H12  H  HCH1  0   0.261  -3.8249  28.7853  17.3967
 4UU  H13  H  HCH1  0   0.248  -1.3139  29.0183  19.1173
 4UU  H14  H  HOH1  0   0.472  -2.6561  28.0978  20.5947
 4UU  H15  H  HCH1  0   0.265  -0.8374  26.6999  18.6211
 4UU  H16  H  HOH1  0   0.454  -3.2752  26.2647  18.6877
 4UU  H17  H  HCH1  0   0.282  -1.4480  26.9176  15.9357
 4UU  H18  H  HCR5  0   0.280   0.3066  29.9762  17.3773
 4UU  H19  H  HNH2  0   0.404   5.5032  27.0951  15.7221
 4UU  H20  H  HNH2  0   0.411   4.8443  28.5318  16.4024
 4UU  O5'  O  O2    0  -0.579  -3.4347  31.2379  16.5709

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
 4UU  O3P  P    double    1.468  0.020  1.468
 4UU  O34  CAR  double    1.201  0.020  1.201
 4UU  CAJ  CAD  double    1.343  0.020  1.343
 4UU  CAJ  CAK  single    1.456  0.020  1.456
 4UU  CAD  CAC  single    1.458  0.020  1.458
 4UU  CAP  CAK  single    1.458  0.020  1.458
 4UU  CAP  CAQ  double    1.339  0.020  1.339
 4UU  CAK  CAH  double    1.345  0.020  1.345
 4UU  N6   C6   single    1.336  0.020  1.336
 4UU  N1   C6   aromatic  1.337  0.020  1.337
 4UU  N1   C2   aromatic  1.331  0.020  1.331
 4UU  CAR  CAQ  single    1.461  0.020  1.461
 4UU  CAR  O2P  single    1.362  0.020  1.362
 4UU  CAC  OBF  double    1.218  0.020  1.218
 4UU  CAC  CAS  single    1.510  0.020  1.510
 4UU  C6   C5   aromatic  1.407  0.020  1.407
 4UU  C2   N3   aromatic  1.322  0.020  1.322
 4UU  CAH  CAS  single    1.481  0.020  1.481
 4UU  C5   N7   aromatic  1.370  0.020  1.370
 4UU  C5   C4   aromatic  1.386  0.020  1.386
 4UU  N3   C4   aromatic  1.331  0.020  1.331
 4UU  N7   C8   aromatic  1.300  0.020  1.300
 4UU  C4   N9   aromatic  1.365  0.020  1.365
 4UU  O4'  C1'  single    1.400  0.020  1.400
 4UU  O4'  C4'  single    1.419  0.020  1.419
 4UU  C8   N9   aromatic  1.368  0.020  1.368
 4UU  N9   C1'  single    1.452  0.020  1.452
 4UU  P    O2P  single    1.641  0.020  1.641
 4UU  P    O5'  single    1.581  0.020  1.581
 4UU  P    O1P  single    1.586  0.020  1.586
 4UU  O5'  C5'  single    1.432  0.020  1.432
 4UU  C1'  C2'  single    1.532  0.020  1.532
 4UU  C4'  C5'  single    1.506  0.020  1.506
 4UU  C4'  C3'  single    1.527  0.020  1.527
 4UU  C2'  O2'  single    1.401  0.020  1.401
 4UU  C2'  C3'  single    1.534  0.020  1.534
 4UU  C3'  O3'  single    1.397  0.020  1.397
 4UU  C2   H1   single    0.930  0.020  1.080
 4UU  CAQ  H2   single    0.930  0.020  1.080
 4UU  CAP  H3   single    0.930  0.020  1.080
 4UU  CAJ  H4   single    0.930  0.020  1.080
 4UU  CAD  H5   single    0.930  0.020  1.080
 4UU  CAH  H6   single    0.930  0.020  1.080
 4UU  CAS  H7   single    0.970  0.020  1.090
 4UU  CAS  H8   single    0.970  0.020  1.090
 4UU  O1P  H9   single    0.850  0.020  0.980
 4UU  C5'  H10  single    0.970  0.020  1.090
 4UU  C5'  H11  single    0.970  0.020  1.090
 4UU  C4'  H12  single    0.970  0.020  1.090
 4UU  C3'  H13  single    0.970  0.020  1.090
 4UU  O3'  H14  single    0.850  0.020  0.980
 4UU  C2'  H15  single    0.970  0.020  1.090
 4UU  O2'  H16  single    0.850  0.020  0.980
 4UU  C1'  H17  single    0.970  0.020  1.090
 4UU  C8   H18  single    0.930  0.020  1.080
 4UU  N6   H19  single    0.860  0.020  1.020
 4UU  N6   H20  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
 4UU  H1   C2   N1   115.46  3.000
 4UU  H1   C2   N3   116.18  3.000
 4UU  N1   C2   N3   128.36  3.000
 4UU  O2P  CAR  CAQ  110.65  3.000
 4UU  O2P  CAR  O34  122.00  3.000
 4UU  CAQ  CAR  O34  127.34  3.000
 4UU  H2   CAQ  CAP  122.36  3.000
 4UU  H2   CAQ  CAR  117.56  3.000
 4UU  CAP  CAQ  CAR  120.04  3.000
 4UU  H3   CAP  CAK  115.41  3.000
 4UU  H3   CAP  CAQ  118.30  3.000
 4UU  CAK  CAP  CAQ  126.28  3.000
 4UU  CAH  CAK  CAJ  118.69  3.000
 4UU  CAH  CAK  CAP  123.64  3.000
 4UU  CAJ  CAK  CAP  117.65  3.000
 4UU  H4   CAJ  CAD  119.14  3.000
 4UU  H4   CAJ  CAK  117.35  3.000
 4UU  CAD  CAJ  CAK  123.51  3.000
 4UU  H5   CAD  CAC  118.10  3.000
 4UU  H5   CAD  CAJ  120.70  3.000
 4UU  CAC  CAD  CAJ  121.20  3.000
 4UU  H6   CAH  CAS  116.40  3.000
 4UU  H6   CAH  CAK  121.01  3.000
 4UU  CAS  CAH  CAK  122.59  3.000
 4UU  H8   CAS  H7   103.80  3.000
 4UU  H8   CAS  CAC  108.57  3.000
 4UU  H7   CAS  CAC  108.47  3.000
 4UU  H8   CAS  CAH  109.26  3.000
 4UU  H7   CAS  CAH  108.74  3.000
 4UU  CAC  CAS  CAH  117.17  3.000
 4UU  OBF  CAC  CAS  120.88  3.000
 4UU  CAS  CAC  CAD  116.82  3.000
 4UU  OBF  CAC  CAD  122.29  3.000
 4UU  P    O2P  CAR  122.41  3.000
 4UU  O5'  P    O3P  113.41  3.000
 4UU  O5'  P    O1P  102.91  3.000
 4UU  O3P  P    O1P  118.42  3.000
 4UU  O1P  P    O2P   99.56  3.000
 4UU  O5'  P    O2P  105.47  3.000
 4UU  O3P  P    O2P  115.19  3.000
 4UU  H9   O1P  P    115.53  3.000
 4UU  H11  C5'  H10  108.06  3.000
 4UU  H11  C5'  C4'  109.28  3.000
 4UU  H10  C5'  C4'  110.37  3.000
 4UU  H11  C5'  O5'  109.58  3.000
 4UU  H10  C5'  O5'  111.28  3.000
 4UU  C4'  C5'  O5'  108.25  3.000
 4UU  H12  C4'  O4'  110.13  3.000
 4UU  H12  C4'  C3'  109.79  3.000
 4UU  O4'  C4'  C3'  104.70  3.000
 4UU  H12  C4'  C5'  109.40  3.000
 4UU  C3'  C4'  C5'  112.82  3.000
 4UU  O4'  C4'  C5'  109.91  3.000
 4UU  H13  C3'  C2'  109.19  3.000
 4UU  H13  C3'  O3'  111.49  3.000
 4UU  C2'  C3'  O3'  114.09  3.000
 4UU  H13  C3'  C4'  109.77  3.000
 4UU  O3'  C3'  C4'  110.66  3.000
 4UU  C2'  C3'  C4'  101.15  3.000
 4UU  H14  O3'  C3'  108.93  3.000
 4UU  H15  C2'  C1'  111.72  3.000
 4UU  H15  C2'  O2'  112.00  3.000
 4UU  C1'  C2'  O2'  107.53  3.000
 4UU  H15  C2'  C3'  112.65  3.000
 4UU  O2'  C2'  C3'  110.79  3.000
 4UU  C1'  C2'  C3'  101.59  3.000
 4UU  H16  O2'  C2'  107.79  3.000
 4UU  C1'  O4'  C4'  111.03  3.000
 4UU  H17  C1'  N9   106.16  3.000
 4UU  H17  C1'  O4'  111.19  3.000
 4UU  N9   C1'  O4'  108.93  3.000
 4UU  H17  C1'  C2'  110.58  3.000
 4UU  N9   C1'  C2'  112.94  3.000
 4UU  O4'  C1'  C2'  107.09  3.000
 4UU  C8   N9   C4   106.14  3.000
 4UU  C8   N9   C1'  128.82  3.000
 4UU  C4   N9   C1'  125.03  3.000
 4UU  C5   C4   N3   126.62  3.000
 4UU  N3   C4   N9   128.12  3.000
 4UU  C5   C4   N9   105.26  3.000
 4UU  C4   N3   C2   111.63  3.000
 4UU  H18  C8   N7   124.25  3.000
 4UU  H18  C8   N9   122.32  3.000
 4UU  N7   C8   N9   113.43  3.000
 4UU  C5   N7   C8   104.41  3.000
 4UU  C6   C5   N7   133.05  3.000
 4UU  N7   C5   C4   110.75  3.000
 4UU  C6   C5   C4   116.20  3.000
 4UU  N6   C6   N1   119.35  3.000
 4UU  N1   C6   C5   117.93  3.000
 4UU  N6   C6   C5   122.71  3.000
 4UU  C6   N1   C2   119.25  3.000
 4UU  H20  N6   H19  117.66  3.000
 4UU  H20  N6   C6   120.43  3.000
 4UU  H19  N6   C6   119.75  3.000
 4UU  C5'  O5'  P    124.58  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
 4UU  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 4UU  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 4UU  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 4UU  CONST_04  C6   C5   C4   N9    180.00   0.0  0
 4UU  CONST_05  N7   C5   C4   N9      0.00   0.0  0
 4UU  CONST_06  C5   N7   C8   N9      0.00   0.0  0
 4UU  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 4UU  CONST_08  C8   N7   C5   C4      0.00   0.0  0
 4UU  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 4UU  CONST_10  N7   C8   N9   C4      0.00   0.0  0
 4UU  CONST_11  C6   N1   C2   N3      0.00   0.0  0
 4UU  CONST_12  C6   C5   C4   N3      0.00   0.0  0
 4UU  CONST_13  N7   C5   C4   N3    180.00   0.0  0
 4UU  CONST_14  C8   N9   C4   N3    180.00   0.0  0
 4UU  CONST_15  C6   C5   N7   C8    180.00   0.0  0
 4UU  CONST_16  C5   C4   N9   C8      0.00   0.0  0
 4UU  CONST_17  N1   C6   C5   N7    180.00   0.0  0
 4UU  CONST_18  C5   C4   N9   C1'   180.00   0.0  0
 4UU  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 4UU  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 4UU  CONST_21  N6   C6   N1   C2    180.00   0.0  0
 4UU  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 4UU  CONST_23  N6   C6   C5   N7      0.00   0.0  0
 4UU  CONST_24  H18  C8   N9   C1'     0.00   0.0  0
 4UU  CONST_25  H1   C2   N3   C4    180.00   0.0  0
 4UU  CONST_26  H19  N6   C6   C5    180.00   0.0  0
 4UU  CONST_27  H20  N6   C6   C5      0.00   0.0  0
 4UU  Var_01    CAC  CAD  CAJ  CAK    -0.05  30.0  1
 4UU  Var_02    CAC  CAS  CAH  CAK     0.91  30.0  1
 4UU  Var_03    CAS  CAC  CAD  CAJ    -0.47  30.0  1
 4UU  Var_04    CAS  CAH  CAK  CAJ    -1.43  30.0  1
 4UU  Var_05    CAH  CAK  CAJ  CAD     1.02  30.0  1
 4UU  Var_06    CAH  CAS  CAC  CAD     0.08  30.0  1
 4UU  Var_07    CAJ  CAK  CAP  CAQ   164.79  30.0  2
 4UU  Var_08    CAK  CAP  CAQ  CAR  -179.68   0.0  2
 4UU  Var_09    C4'  C5'  O5'  P    -154.89  30.0  3
 4UU  Var_10    CAP  CAQ  CAR  O34    -5.92  30.0  2
 4UU  Var_11    O3P  P    O2P  CAR   -60.75  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
 4UU  chir_02  C4'  O4'  C5'  C3'  positiv
 4UU  chir_03  C3'  O3'  C4'  C2'  positiv
 4UU  chir_04  C2'  O2'  C3'  C1'  positiv
 4UU  chir_05  C1'  O4'  N9   C2'  negativ
 4UU  chir_06  P    O2P  O5'  O1P  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
 4UU  plan-1  C6   0.020
 4UU  plan-1  N6   0.020
 4UU  plan-1  H19  0.020
 4UU  plan-1  H20  0.020
 4UU  plan-2  C2   0.020
 4UU  plan-2  C1'  0.020
 4UU  plan-2  N9   0.020
 4UU  plan-2  C4   0.020
 4UU  plan-2  N3   0.020
 4UU  plan-2  C8   0.020
 4UU  plan-2  N7   0.020
 4UU  plan-2  C5   0.020
 4UU  plan-2  C6   0.020
 4UU  plan-2  N1   0.020
 4UU  plan-2  N6   0.020
 4UU  plan-2  H1   0.020
 4UU  plan-2  H18  0.020
 4UU  plan-3  CAD  0.020
 4UU  plan-3  CAS  0.020
 4UU  plan-3  CAC  0.020
 4UU  plan-3  OBF  0.020
 4UU  plan-4  O34  0.020
 4UU  plan-4  CAR  0.020
 4UU  plan-4  CAQ  0.020
 4UU  plan-4  O2P  0.020
 4UU  plan-5  CAR  0.020
 4UU  plan-5  CAQ  0.020
 4UU  plan-5  CAP  0.020
 4UU  plan-5  CAK  0.020
 4UU  plan-5  H2   0.020
 4UU  plan-5  H3   0.020

