# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 17:01:52 2021
#   Inital geometry file: a 141 line input string
#   Ligand name: 5'-O-[(R)-{[(2E)-3-(3,4-dioxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}(hydroxy)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=CC(=O)C(=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
 4UV  4UV  5'-O-[(R)-{[(2E)-3-(3,4-dioxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  53  35  .  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_4UV
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
 4UV  O1P  O  OH1   0  -0.726  -3.1792  33.7568  17.4018
 4UV  P    P  P     0   1.483  -3.0266  32.7605  16.1776
 4UV  O3P  O  O     0  -0.667  -3.6206  33.1378  14.8901
 4UV  O2P  O  O2    0  -0.610  -1.3946  32.5822  16.1788
 4UV  CAR  C  C     0   0.620  -0.6965  31.8791  15.2526
 4UV  CAQ  C  C1    0  -0.408   0.7394  31.9267  15.5680
 4UV  CAP  C  C1    0  -0.202   1.6338  31.3637  14.7483
 4UV  CAK  C  CR6   0   0.167   3.0774  31.3956  14.9263
 4UV  CAH  C  CR16  0  -0.224   3.6724  32.0737  16.0815
 4UV  CAS  C  CR16  0  -0.342   4.9929  32.1483  16.2747
 4UV  CAC  C  CR6   0   0.313   5.9221  31.5390  15.3237
 4UV  OBF  O  O     0  -0.358   7.1237  31.6097  15.4255
 4UV  CAD  C  CR6   0   0.324   5.3103  30.8001  14.1213
 4UV  O35  O  O     0  -0.360   6.0427  30.2751  13.3143
 4UV  CAJ  C  CR16  0  -0.424   3.8577  30.7973  14.0007
 4UV  O34  O  O     0  -0.397  -1.2070  31.3363  14.3158
 4UV  O5'  O  O2    0  -0.578  -3.5896  31.4048  16.7600
 4UV  C5'  C  CH2   0  -0.196  -3.0947  30.7647  17.9463
 4UV  C4'  C  CH1   0   0.020  -2.7099  29.3509  17.6039
 4UV  O4'  O  O2    0  -0.492  -1.6255  29.3684  16.6925
 4UV  C1'  C  CH1   0   0.175  -0.8222  28.2270  16.8563
 4UV  C2'  C  CH1   0  -0.054  -1.3600  27.4710  18.0813
 4UV  O2'  O  OH1   0  -0.662  -2.1900  26.4451  17.6119
 4UV  C3'  C  CH1   0  -0.031  -2.1862  28.5539  18.7940
 4UV  O3'  O  OH1   0  -0.654  -3.2443  28.0510  19.5539
 4UV  N9   N  NR5   0  -0.532   0.5567  28.6361  16.9819
 4UV  C8   C  CR15  0   0.110   1.1114  29.4896  17.8993
 4UV  N7   N  N     0  -0.435   2.4012  29.5994  17.7919
 4UV  C5   C  CR56  0   0.010   2.7280  28.7778  16.7443
 4UV  C4   C  CR56  0   0.507   1.5914  28.1744  16.2215
 4UV  C6   C  CR6   0   0.452   3.9425  28.4370  16.1299
 4UV  N6   N  NH2   0  -0.819   5.1231  28.9725  16.4984
 4UV  N1   N  N     0  -0.458   3.9158  27.5846  15.1054
 4UV  C2   C  CR16  0   0.044   2.7477  27.0941  14.6995
 4UV  N3   N  N     0  -0.448   1.5463  27.3296  15.1979
 4UV  H1   H  HOH1  0   0.510  -3.0037  34.6878  17.2042
 4UV  H2   H  H     0   0.304   1.0228  32.4572  16.4669
 4UV  H3   H  H     0   0.293   1.2835  30.8502  13.8592
 4UV  H4   H  HCR6  0   0.283   3.0182  32.5362  16.8060
 4UV  H5   H  HCR6  0   0.295   5.4056  32.6594  17.1349
 4UV  H6   H  HCR6  0   0.294   3.4244  30.2970  13.1432
 4UV  H7   H  HCH2  0   0.247  -2.2431  31.3001  18.3729
 4UV  H8   H  HCH2  0   0.276  -3.8968  30.7607  18.6844
 4UV  H9   H  HCH1  0   0.258  -3.5739  28.8322  17.1673
 4UV  H10  H  HCH1  0   0.281  -0.8619  27.5840  15.9729
 4UV  H11  H  HCH1  0   0.265  -0.5467  27.0811  18.7051
 4UV  H12  H  HOH1  0   0.453  -2.8575  26.2737  18.2882
 4UV  H13  H  HCH1  0   0.246  -1.5211  29.1846  19.3988
 4UV  H14  H  HOH1  0   0.472  -2.9211  27.8225  20.4317
 4UV  H15  H  HCR5  0   0.297   0.5122  30.0089  18.6321
 4UV  H16  H  HNH2  0   0.405   5.9584  28.4969  16.1934
 4UV  H17  H  HNH2  0   0.410   5.1847  29.4016  17.4078
 4UV  H18  H  HCR6  0   0.259   2.7925  26.4119  13.8581

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
 4UV  O35  CAD  double    1.210  0.020  1.210
 4UV  O3P  P    double    1.467  0.020  1.467
 4UV  O34  CAR  double    1.197  0.020  1.197
 4UV  CAD  CAJ  single    1.458  0.020  1.458
 4UV  CAD  CAC  single    1.538  0.020  1.538
 4UV  CAJ  CAK  double    1.350  0.020  1.350
 4UV  N6   C6   single    1.348  0.020  1.348
 4UV  OBF  CAC  double    1.208  0.020  1.208
 4UV  CAP  CAK  single    1.455  0.020  1.455
 4UV  CAP  CAQ  double    1.338  0.020  1.338
 4UV  CAC  CAS  single    1.463  0.020  1.463
 4UV  CAK  CAH  single    1.466  0.020  1.466
 4UV  N1   C6   aromatic  1.333  0.020  1.333
 4UV  N1   C2   aromatic  1.330  0.020  1.330
 4UV  CAR  CAQ  single    1.471  0.020  1.471
 4UV  CAR  O2P  single    1.356  0.020  1.356
 4UV  C6   C5   aromatic  1.403  0.020  1.403
 4UV  C2   N3   aromatic  1.322  0.020  1.322
 4UV  C5   N7   aromatic  1.371  0.020  1.371
 4UV  C5   C4   aromatic  1.389  0.020  1.389
 4UV  CAS  CAH  double    1.337  0.020  1.337
 4UV  N7   C8   aromatic  1.299  0.020  1.299
 4UV  N3   C4   aromatic  1.328  0.020  1.328
 4UV  C4   N9   aromatic  1.365  0.020  1.365
 4UV  C8   N9   aromatic  1.370  0.020  1.370
 4UV  O4'  C1'  single    1.405  0.020  1.405
 4UV  O4'  C4'  single    1.417  0.020  1.417
 4UV  N9   C1'  single    1.444  0.020  1.444
 4UV  P    O2P  single    1.642  0.020  1.642
 4UV  P    O5'  single    1.579  0.020  1.579
 4UV  P    O1P  single    1.586  0.020  1.586
 4UV  O5'  C5'  single    1.436  0.020  1.436
 4UV  C1'  C2'  single    1.537  0.020  1.537
 4UV  C4'  C5'  single    1.505  0.020  1.505
 4UV  C4'  C3'  single    1.525  0.020  1.525
 4UV  C2'  O2'  single    1.401  0.020  1.401
 4UV  C2'  C3'  single    1.537  0.020  1.537
 4UV  C3'  O3'  single    1.396  0.020  1.396
 4UV  O1P  H1   single    0.850  0.020  0.980
 4UV  CAQ  H2   single    0.930  0.020  1.080
 4UV  CAP  H3   single    0.930  0.020  1.080
 4UV  CAH  H4   single    0.930  0.020  1.080
 4UV  CAS  H5   single    0.930  0.020  1.080
 4UV  CAJ  H6   single    0.930  0.020  1.080
 4UV  C5'  H7   single    0.970  0.020  1.090
 4UV  C5'  H8   single    0.970  0.020  1.090
 4UV  C4'  H9   single    0.970  0.020  1.090
 4UV  C1'  H10  single    0.970  0.020  1.090
 4UV  C2'  H11  single    0.970  0.020  1.090
 4UV  O2'  H12  single    0.850  0.020  0.980
 4UV  C3'  H13  single    0.970  0.020  1.090
 4UV  O3'  H14  single    0.850  0.020  0.980
 4UV  C8   H15  single    0.930  0.020  1.080
 4UV  N6   H16  single    0.890  0.020  1.040
 4UV  N6   H17  single    0.890  0.020  1.040
 4UV  C2   H18  single    0.930  0.020  1.080

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
 4UV  H1   O1P  P    115.43  3.000
 4UV  O5'  P    O2P  105.12  3.000
 4UV  O5'  P    O3P  113.58  3.000
 4UV  O2P  P    O3P  115.53  3.000
 4UV  O5'  P    O1P  102.73  3.000
 4UV  O2P  P    O1P   99.40  3.000
 4UV  O3P  P    O1P  118.48  3.000
 4UV  CAR  O2P  P    124.58  3.000
 4UV  O34  CAR  CAQ  126.79  3.000
 4UV  CAQ  CAR  O2P  109.83  3.000
 4UV  O34  CAR  O2P  123.36  3.000
 4UV  H2   CAQ  CAP  122.72  3.000
 4UV  H2   CAQ  CAR  116.74  3.000
 4UV  CAP  CAQ  CAR  120.52  3.000
 4UV  H3   CAP  CAK  115.54  3.000
 4UV  H3   CAP  CAQ  119.05  3.000
 4UV  CAK  CAP  CAQ  125.41  3.000
 4UV  CAJ  CAK  CAH  120.70  3.000
 4UV  CAH  CAK  CAP  120.62  3.000
 4UV  CAJ  CAK  CAP  118.67  3.000
 4UV  H4   CAH  CAS  118.52  3.000
 4UV  H4   CAH  CAK  118.74  3.000
 4UV  CAS  CAH  CAK  122.74  3.000
 4UV  H5   CAS  CAC  118.12  3.000
 4UV  H5   CAS  CAH  121.19  3.000
 4UV  CAC  CAS  CAH  120.69  3.000
 4UV  CAD  CAC  OBF  119.32  3.000
 4UV  OBF  CAC  CAS  123.55  3.000
 4UV  CAD  CAC  CAS  117.11  3.000
 4UV  CAJ  CAD  O35  123.19  3.000
 4UV  CAJ  CAD  CAC  117.51  3.000
 4UV  O35  CAD  CAC  119.28  3.000
 4UV  H6   CAJ  CAD  117.71  3.000
 4UV  H6   CAJ  CAK  121.07  3.000
 4UV  CAD  CAJ  CAK  121.22  3.000
 4UV  C5'  O5'  P    124.36  3.000
 4UV  H8   C5'  H7   108.12  3.000
 4UV  H8   C5'  C4'  109.80  3.000
 4UV  H7   C5'  C4'  110.48  3.000
 4UV  H8   C5'  O5'  107.91  3.000
 4UV  H7   C5'  O5'  111.89  3.000
 4UV  C4'  C5'  O5'  108.60  3.000
 4UV  H9   C4'  C3'  109.49  3.000
 4UV  H9   C4'  O4'  110.63  3.000
 4UV  C3'  C4'  O4'  104.22  3.000
 4UV  H9   C4'  C5'  109.45  3.000
 4UV  C3'  C4'  C5'  113.66  3.000
 4UV  O4'  C4'  C5'  109.30  3.000
 4UV  C1'  O4'  C4'  110.64  3.000
 4UV  H10  C1'  N9   105.76  3.000
 4UV  H10  C1'  C2'  110.01  3.000
 4UV  N9   C1'  C2'  113.85  3.000
 4UV  H10  C1'  O4'  111.26  3.000
 4UV  C2'  C1'  O4'  107.01  3.000
 4UV  N9   C1'  O4'  109.02  3.000
 4UV  H11  C2'  C3'  112.67  3.000
 4UV  H11  C2'  O2'  111.70  3.000
 4UV  C3'  C2'  O2'  110.66  3.000
 4UV  H11  C2'  C1'  111.64  3.000
 4UV  C3'  C2'  C1'  102.19  3.000
 4UV  O2'  C2'  C1'  107.49  3.000
 4UV  H12  O2'  C2'  107.76  3.000
 4UV  H13  C3'  O3'  111.47  3.000
 4UV  H13  C3'  C2'  109.54  3.000
 4UV  O3'  C3'  C2'  113.95  3.000
 4UV  H13  C3'  C4'  109.73  3.000
 4UV  O3'  C3'  C4'  110.65  3.000
 4UV  C2'  C3'  C4'  101.01  3.000
 4UV  H14  O3'  C3'  109.10  3.000
 4UV  C4   N9   C8   106.07  3.000
 4UV  C8   N9   C1'  128.41  3.000
 4UV  C4   N9   C1'  125.45  3.000
 4UV  H15  C8   N7   124.51  3.000
 4UV  H15  C8   N9   121.96  3.000
 4UV  N7   C8   N9   113.53  3.000
 4UV  C5   N7   C8   104.43  3.000
 4UV  C6   C5   C4   115.98  3.000
 4UV  C4   C5   N7   110.67  3.000
 4UV  C6   C5   N7   133.36  3.000
 4UV  N3   C4   C5   126.46  3.000
 4UV  N3   C4   N9   128.24  3.000
 4UV  C5   C4   N9   105.30  3.000
 4UV  N1   C6   N6   118.80  3.000
 4UV  N1   C6   C5   118.33  3.000
 4UV  N6   C6   C5   122.82  3.000
 4UV  H17  N6   H16  115.04  3.000
 4UV  H17  N6   C6   118.01  3.000
 4UV  H16  N6   C6   117.10  3.000
 4UV  C2   N1   C6   119.20  3.000
 4UV  H18  C2   N3   116.25  3.000
 4UV  H18  C2   N1   115.63  3.000
 4UV  N3   C2   N1   128.11  3.000
 4UV  C2   N3   C4   111.91  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
 4UV  CONST_01  C6   C5   C4   N9    180.00   0.0  0
 4UV  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 4UV  CONST_03  C2   N3   C4   N9    180.00   0.0  0
 4UV  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 4UV  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 4UV  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 4UV  CONST_07  C5   C4   N9   C8      0.00   0.0  0
 4UV  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 4UV  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 4UV  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 4UV  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 4UV  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 4UV  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 4UV  CONST_14  N1   C6   C5   C4      0.00   0.0  0
 4UV  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 4UV  CONST_16  N3   C2   N1   C6      0.00   0.0  0
 4UV  CONST_17  N3   C4   C5   C6      0.00   0.0  0
 4UV  CONST_18  C5   C4   N9   C1'   180.00   0.0  0
 4UV  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 4UV  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 4UV  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 4UV  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 4UV  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 4UV  CONST_24  H15  C8   N9   C1'     0.00   0.0  0
 4UV  CONST_25  H18  C2   N3   C4    180.00   0.0  0
 4UV  Var_01    CAJ  CAK  CAP  CAQ  -178.99  30.0  2
 4UV  Var_02    CAK  CAP  CAQ  CAR   177.29   0.0  2
 4UV  Var_03    C4'  C5'  O5'  P    -125.25  30.0  3
 4UV  Var_04    O34  CAR  O2P  P       1.65  30.0  1
 4UV  Var_05    CAP  CAQ  CAR  O2P  -176.26  30.0  2
 4UV  Var_06    O5'  P    O2P  CAR    78.55  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
 4UV  chir_02  C4'  O4'  C5'  C3'  positiv
 4UV  chir_03  C1'  O4'  N9   C2'  negativ
 4UV  chir_04  C2'  O2'  C1'  C3'  negativ
 4UV  chir_05  C3'  O3'  C4'  C2'  positiv
 4UV  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
 4UV  plan-1  O2P  0.020
 4UV  plan-1  CAR  0.020
 4UV  plan-1  CAQ  0.020
 4UV  plan-1  O34  0.020
 4UV  plan-2  CAR  0.020
 4UV  plan-2  CAQ  0.020
 4UV  plan-2  CAP  0.020
 4UV  plan-2  CAK  0.020
 4UV  plan-2  H2   0.020
 4UV  plan-2  H3   0.020
 4UV  plan-3  CAP  0.020
 4UV  plan-3  CAK  0.020
 4UV  plan-3  CAH  0.020
 4UV  plan-3  CAS  0.020
 4UV  plan-3  CAC  0.020
 4UV  plan-3  OBF  0.020
 4UV  plan-3  CAD  0.020
 4UV  plan-3  O35  0.020
 4UV  plan-3  CAJ  0.020
 4UV  plan-3  H4   0.020
 4UV  plan-3  H5   0.020
 4UV  plan-3  H6   0.020
 4UV  plan-4  C1'  0.020
 4UV  plan-4  N9   0.020
 4UV  plan-4  C8   0.020
 4UV  plan-4  N7   0.020
 4UV  plan-4  C5   0.020
 4UV  plan-4  C4   0.020
 4UV  plan-4  C6   0.020
 4UV  plan-4  N6   0.020
 4UV  plan-4  N1   0.020
 4UV  plan-4  C2   0.020
 4UV  plan-4  N3   0.020
 4UV  plan-4  H15  0.020
 4UV  plan-4  H18  0.020
 4UV  plan-5  C6   0.020
 4UV  plan-5  N6   0.020
 4UV  plan-5  H16  0.020
 4UV  plan-5  H17  0.020

