# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 17:44:10 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-[(S)-[(2,3-dihydroxybenzene-1-carbonyl)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)c4cccc(O)c4O)[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
 J2J  J2J  5'-O-[(S)-[(2,3-dihydroxybenzene-1-carbonyl)oxy](hydroxy)phosphoryl]adenosine  ligand  51  33  .  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_J2J
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
 J2J  C2    C  CR16  0   0.040  -37.8428   -7.0852  89.6381
 J2J  N3    N  N     0  -0.461  -37.9660   -7.6322  90.8349
 J2J  C4    C  CR56  0   0.489  -36.8730   -8.3114  91.1813
 J2J  C6    C  CR6   0   0.456  -35.7165   -7.8258  89.1663
 J2J  C8    C  CR15  0   0.101  -35.3567   -9.4854  92.2285
 J2J  C9    C  CR16  0  -0.331  -31.0055  -13.3181  90.4554
 J2J  C12   C  CR16  0  -0.254  -31.1536  -11.9903  90.8539
 J2J  C15   C  CR16  0  -0.282  -31.8086  -11.6934  92.0245
 J2J  C18   C  CR6   0  -0.203  -32.3388  -12.7181  92.8266
 J2J  C21   C  C     0   0.634  -33.0327  -12.2949  94.0497
 J2J  C3    C  CR6   0   0.255  -32.1957  -14.0537  92.4252
 J2J  C5    C  CR56  0  -0.004  -35.7193   -8.4531  90.4262
 J2J  N1    N  N     0  -0.473  -36.8082   -7.1436  88.8032
 J2J  N6    N  NH2   0  -0.816  -34.6720   -7.8800  88.3393
 J2J  O3    O  OH1   0  -0.628  -32.6382  -15.1361  93.0776
 J2J  C1'   C  CH1   0   0.168  -37.5161   -9.0603  93.5000
 J2J  C2'   C  CH1   0  -0.058  -38.8604   -9.7205  93.1700
 J2J  C3'   C  CH1   0  -0.002  -38.5088  -11.1904  93.3637
 J2J  C4'   C  CH1   0  -0.020  -37.5606  -11.1233  94.5713
 J2J  C5'   C  CH2   0  -0.189  -36.5434  -12.2343  94.5470
 J2J  C61   C  CR6   0   0.316  -31.5161  -14.3426  91.2260
 J2J  N7    N  N     0  -0.439  -34.7824   -9.1903  91.0994
 J2J  N9    N  NR5   0  -0.546  -36.6323   -8.9992  92.3359
 J2J  O17   O  O     0  -0.405  -33.1083  -11.1679  94.4528
 J2J  O1P   O  O     0  -0.663  -35.0680  -14.5328  96.3718
 J2J  O2'   O  OH1   0  -0.658  -39.8179   -9.3738  94.1292
 J2J  O2P   O  O2    0  -0.651  -33.6344  -13.3252  94.7073
 J2J  O3'   O  OH1   0  -0.653  -39.6381  -11.9811  93.5683
 J2J  O3P   O  OH1   0  -0.709  -33.7670  -12.3758  97.1169
 J2J  O4'   O  O2    0  -0.491  -36.9205   -9.8527  94.4810
 J2J  O5'   O  O2    0  -0.576  -35.6609  -12.0741  95.6650
 J2J  P     P  P     0   1.512  -34.5975  -13.1808  96.0456
 J2J  H2    H  HCR6  0   0.252  -38.6937   -6.5119  89.2859
 J2J  H8    H  HCR5  0   0.285  -34.8902  -10.0338  93.0294
 J2J  HC9   H  HCR6  0   0.279  -30.4889  -13.5612  89.5353
 J2J  HC12  H  HCR6  0   0.265  -30.7536  -11.1978  90.2370
 J2J  HC15  H  HCR6  0   0.267  -31.9277  -10.6648  92.3331
 J2J  HN61  H  HNH2  0   0.404  -34.7174   -7.4449  87.4341
 J2J  HN62  H  HNH2  0   0.411  -33.8571   -8.4212  88.5688
 J2J  HO3   H  HOH1  0   0.495  -33.1189  -14.8931  93.8812
 J2J  HO6   H  HOH1  0   0.477  -31.7564  -16.2271  91.4479
 J2J  H1'   H  HCH1  0   0.292  -37.6418   -8.0405  93.8747
 J2J  H2'   H  HCH1  0   0.275  -39.1951   -9.4999  92.1517
 J2J  H3'   H  HCH1  0   0.253  -37.9460  -11.5184  92.4793
 J2J  H4'   H  HCH1  0   0.265  -38.1370  -11.1712  95.5017
 J2J  H5'2  H  HCH2  0   0.271  -37.0640  -13.1939  94.6019
 J2J  H5'1  H  HCH2  0   0.240  -35.9738  -12.2102  93.6134
 J2J  HO2'  H  HOH1  0   0.463  -40.0888   -8.4621  93.9806
 J2J  HO3'  H  HOH1  0   0.464  -39.4483  -12.8751  93.2707
 J2J  H1    H  HOH1  0   0.515  -33.2794  -12.9289  97.7442
 J2J  O6    O  OH1   0  -0.630  -31.3586  -15.6153  90.8165

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
 J2J  N6   C6    single    1.333  0.020  1.333
 J2J  N1   C6    aromatic  1.338  0.020  1.338
 J2J  N1   C2    aromatic  1.331  0.020  1.331
 J2J  C6   C5    aromatic  1.407  0.020  1.407
 J2J  C2   N3    aromatic  1.322  0.020  1.322
 J2J  C5   N7    aromatic  1.369  0.020  1.369
 J2J  C5   C4    aromatic  1.386  0.020  1.386
 J2J  C9   C12   aromatic  1.394  0.020  1.394
 J2J  C9   C61   aromatic  1.380  0.020  1.380
 J2J  C12  C15   aromatic  1.374  0.020  1.374
 J2J  N7   C8    aromatic  1.301  0.020  1.301
 J2J  N3   C4    aromatic  1.333  0.020  1.333
 J2J  O6   C61   single    1.346  0.020  1.346
 J2J  C4   N9    aromatic  1.365  0.020  1.365
 J2J  C61  C3    aromatic  1.408  0.020  1.408
 J2J  C15  C18   aromatic  1.405  0.020  1.405
 J2J  C8   N9    aromatic  1.369  0.020  1.369
 J2J  N9   C1'   single    1.463  0.020  1.463
 J2J  C3   C18   aromatic  1.402  0.020  1.402
 J2J  C3   O3    single    1.339  0.020  1.339
 J2J  C18  C21   single    1.469  0.020  1.469
 J2J  C2'  C3'   single    1.524  0.020  1.524
 J2J  C2'  C1'   single    1.534  0.020  1.534
 J2J  C2'  O2'   single    1.399  0.020  1.399
 J2J  C3'  O3'   single    1.394  0.020  1.394
 J2J  C3'  C4'   single    1.537  0.020  1.537
 J2J  C1'  O4'   single    1.395  0.020  1.395
 J2J  C21  O17   double    1.199  0.020  1.199
 J2J  C21  O2P   single    1.362  0.020  1.362
 J2J  O4'  C4'   single    1.426  0.020  1.426
 J2J  C4'  C5'   single    1.507  0.020  1.507
 J2J  O2P  P     single    1.655  0.020  1.655
 J2J  C5'  O5'   single    1.433  0.020  1.433
 J2J  O5'  P     single    1.581  0.020  1.581
 J2J  P    O1P   double    1.468  0.020  1.468
 J2J  P    O3P   single    1.577  0.020  1.577
 J2J  C2   H2    single    0.930  0.020  1.080
 J2J  C8   H8    single    0.930  0.020  1.080
 J2J  C9   HC9   single    0.930  0.020  1.080
 J2J  C12  HC12  single    0.930  0.020  1.080
 J2J  C15  HC15  single    0.930  0.020  1.080
 J2J  N6   HN61  single    0.860  0.020  1.020
 J2J  N6   HN62  single    0.860  0.020  1.020
 J2J  O3   HO3   single    0.850  0.020  0.980
 J2J  O6   HO6   single    0.850  0.020  0.980
 J2J  C1'  H1'   single    0.970  0.020  1.090
 J2J  C2'  H2'   single    0.970  0.020  1.090
 J2J  C3'  H3'   single    0.970  0.020  1.090
 J2J  C4'  H4'   single    0.970  0.020  1.090
 J2J  C5'  H5'2  single    0.970  0.020  1.090
 J2J  C5'  H5'1  single    0.970  0.020  1.090
 J2J  O2'  HO2'  single    0.850  0.020  0.980
 J2J  O3'  HO3'  single    0.850  0.020  0.980
 J2J  O3P  H1    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
 J2J  H2    C2   N1    115.43  3.000
 J2J  H2    C2   N3    116.08  3.000
 J2J  N1    C2   N3    128.50  3.000
 J2J  C4    N3   C2    111.71  3.000
 J2J  N9    C4   C5    105.21  3.000
 J2J  N9    C4   N3    128.40  3.000
 J2J  C5    C4   N3    126.38  3.000
 J2J  N6    C6   N1    119.45  3.000
 J2J  N1    C6   C5    117.95  3.000
 J2J  N6    C6   C5    122.59  3.000
 J2J  H8    C8   N9    121.73  3.000
 J2J  H8    C8   N7    124.74  3.000
 J2J  N9    C8   N7    113.50  3.000
 J2J  HC9   C9   C61   118.97  3.000
 J2J  HC9   C9   C12   120.49  3.000
 J2J  C61   C9   C12   120.54  3.000
 J2J  HC12  C12  C15   120.28  3.000
 J2J  HC12  C12  C9    119.73  3.000
 J2J  C15   C12  C9    120.00  3.000
 J2J  HC15  C15  C18   119.32  3.000
 J2J  HC15  C15  C12   120.11  3.000
 J2J  C18   C15  C12   120.58  3.000
 J2J  C3    C18  C21   124.14  3.000
 J2J  C21   C18  C15   116.33  3.000
 J2J  C3    C18  C15   119.52  3.000
 J2J  O2P   C21  O17   121.37  3.000
 J2J  O2P   C21  C18   113.13  3.000
 J2J  O17   C21  C18   125.49  3.000
 J2J  C61   C3   O3    114.11  3.000
 J2J  O3    C3   C18   126.65  3.000
 J2J  C61   C3   C18   119.24  3.000
 J2J  N7    C5   C6    132.75  3.000
 J2J  N7    C5   C4    110.90  3.000
 J2J  C6    C5   C4    116.34  3.000
 J2J  C6    N1   C2    119.12  3.000
 J2J  HN62  N6   HN61  118.39  3.000
 J2J  HN62  N6   C6    121.03  3.000
 J2J  HN61  N6   C6    120.36  3.000
 J2J  HO3   O3   C3    111.46  3.000
 J2J  H1'   C1'  O4'   109.75  3.000
 J2J  H1'   C1'  N9    107.65  3.000
 J2J  O4'   C1'  N9    109.00  3.000
 J2J  H1'   C1'  C2'   111.99  3.000
 J2J  O4'   C1'  C2'   106.32  3.000
 J2J  N9    C1'  C2'   112.11  3.000
 J2J  H2'   C2'  O2'   112.25  3.000
 J2J  H2'   C2'  C3'   112.54  3.000
 J2J  O2'   C2'  C3'   108.05  3.000
 J2J  H2'   C2'  C1'   112.43  3.000
 J2J  O2'   C2'  C1'   110.23  3.000
 J2J  C3'   C2'  C1'   100.70  3.000
 J2J  H3'   C3'  O3'   111.34  3.000
 J2J  H3'   C3'  C4'   109.24  3.000
 J2J  O3'   C3'  C4'   114.16  3.000
 J2J  H3'   C3'  C2'   107.70  3.000
 J2J  C4'   C3'  C2'   101.54  3.000
 J2J  O3'   C3'  C2'   112.27  3.000
 J2J  H4'   C4'  O4'   109.20  3.000
 J2J  H4'   C4'  C5'   109.68  3.000
 J2J  O4'   C4'  C5'   110.68  3.000
 J2J  H4'   C4'  C3'   109.93  3.000
 J2J  C5'   C4'  C3'   111.82  3.000
 J2J  O4'   C4'  C3'   105.44  3.000
 J2J  H5'1  C5'  H5'2  108.07  3.000
 J2J  H5'1  C5'  O5'   110.04  3.000
 J2J  H5'2  C5'  O5'   110.62  3.000
 J2J  H5'1  C5'  C4'   110.43  3.000
 J2J  H5'2  C5'  C4'   108.97  3.000
 J2J  O5'   C5'  C4'   108.70  3.000
 J2J  O6    C61  C3    120.62  3.000
 J2J  C3    C61  C9    120.12  3.000
 J2J  O6    C61  C9    119.26  3.000
 J2J  C5    N7   C8    104.30  3.000
 J2J  C1'   N9   C8    127.62  3.000
 J2J  C1'   N9   C4    125.97  3.000
 J2J  C8    N9   C4    106.07  3.000
 J2J  HO2'  O2'  C2'   108.76  3.000
 J2J  P     O2P  C21   125.54  3.000
 J2J  HO3'  O3'  C3'   108.80  3.000
 J2J  H1    O3P  P     114.45  3.000
 J2J  C4'   O4'  C1'   111.05  3.000
 J2J  P     O5'  C5'   121.57  3.000
 J2J  O5'   P    O3P    99.23  3.000
 J2J  O3P   P    O2P   106.71  3.000
 J2J  O5'   P    O2P   104.94  3.000
 J2J  O3P   P    O1P   119.21  3.000
 J2J  O5'   P    O1P   118.85  3.000
 J2J  O2P   P    O1P   106.60  3.000
 J2J  HO6   O6   C61   110.62  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
 J2J  CONST_01  C5    C6   N1   C2     0.00   0.0  0
 J2J  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 J2J  CONST_03  N9    C4   N3   C2   180.00   0.0  0
 J2J  CONST_04  C6    N1   C2   N3     0.00   0.0  0
 J2J  CONST_05  C6    C5   C4   N3     0.00   0.0  0
 J2J  CONST_06  N7    C5   C4   N3   180.00   0.0  0
 J2J  CONST_07  C8    N9   C4   N3   180.00   0.0  0
 J2J  CONST_08  N1    C6   C5   C4     0.00   0.0  0
 J2J  CONST_09  C8    N7   C5   C4     0.00   0.0  0
 J2J  CONST_10  N1    C2   N3   C4     0.00   0.0  0
 J2J  CONST_11  N7    C8   N9   C4     0.00   0.0  0
 J2J  CONST_12  C8    N7   C5   C6   180.00   0.0  0
 J2J  CONST_13  N9    C4   C5   C6   180.00   0.0  0
 J2J  CONST_14  C5    C4   N9   C8     0.00   0.0  0
 J2J  CONST_15  C18   C15  C12  C9     0.00   0.0  0
 J2J  CONST_16  C18   C3   C61  C9     0.00   0.0  0
 J2J  CONST_17  C3    C61  C9   C12    0.00   0.0  0
 J2J  CONST_18  C3    C18  C15  C12    0.00   0.0  0
 J2J  CONST_19  C61   C9   C12  C15    0.00   0.0  0
 J2J  CONST_20  C61   C3   C18  C15    0.00   0.0  0
 J2J  CONST_21  N9    C8   N7   C5     0.00   0.0  0
 J2J  CONST_22  N7    C5   C6   N1   180.00   0.0  0
 J2J  CONST_23  N9    C4   C5   N7     0.00   0.0  0
 J2J  CONST_24  C1'   N9   C4   N3     0.00   0.0  0
 J2J  CONST_25  C1'   N9   C4   C5   180.00   0.0  0
 J2J  CONST_26  N7    C8   N9   C1'  180.00   0.0  0
 J2J  CONST_27  N6    C6   N1   C2   180.00   0.0  0
 J2J  CONST_28  N6    C6   C5   C4   180.00   0.0  0
 J2J  CONST_29  O3    C3   C61  C9   180.00   0.0  0
 J2J  CONST_30  O6    C61  C9   C12  180.00   0.0  0
 J2J  CONST_31  C21   C18  C15  C12  180.00   0.0  0
 J2J  CONST_32  O3    C3   C18  C15  180.00   0.0  0
 J2J  CONST_33  O6    C61  C3   C18  180.00   0.0  0
 J2J  CONST_34  C61   C3   C18  C21  180.00   0.0  0
 J2J  CONST_35  N7    C5   C6   N6     0.00   0.0  0
 J2J  CONST_36  H2    C2   N3   C4   180.00   0.0  0
 J2J  CONST_37  H8    C8   N9   C4   180.00   0.0  0
 J2J  CONST_38  HC15  C15  C12  C9   180.00   0.0  0
 J2J  CONST_39  HC9   C9   C12  C15  180.00   0.0  0
 J2J  CONST_40  HC12  C12  C15  C18  180.00   0.0  0
 J2J  CONST_41  HN61  N6   C6   C5   180.00   0.0  0
 J2J  CONST_42  HN62  N6   C6   C5     0.00   0.0  0
 J2J  Var_01    O17   C21  C18  C15   -4.86  30.0  2
 J2J  Var_02    O5'   P    O2P  C21   50.67  30.0  3
 J2J  Var_03    O2P   P    O5'  C5'   59.55  30.0  3
 J2J  Var_04    H5'2  C5'  O5'  P     52.03  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
 J2J  chir_01  C1'  N9   C2'  O4'  negativ
 J2J  chir_02  C2'  O2'  C3'  C1'  positiv
 J2J  chir_03  C3'  O3'  C4'  C2'  positiv
 J2J  chir_04  C4'  O4'  C3'  C5'  negativ
 J2J  chir_05  P    O5'  O1P  O3P  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
 J2J  plan-1  C9    0.020
 J2J  plan-1  C12   0.020
 J2J  plan-1  C15   0.020
 J2J  plan-1  C18   0.020
 J2J  plan-1  C21   0.020
 J2J  plan-1  C3    0.020
 J2J  plan-1  O3    0.020
 J2J  plan-1  C61   0.020
 J2J  plan-1  HC9   0.020
 J2J  plan-1  HC12  0.020
 J2J  plan-1  HC15  0.020
 J2J  plan-1  O6    0.020
 J2J  plan-2  C2    0.020
 J2J  plan-2  N3    0.020
 J2J  plan-2  C4    0.020
 J2J  plan-2  C6    0.020
 J2J  plan-2  C8    0.020
 J2J  plan-2  C5    0.020
 J2J  plan-2  N1    0.020
 J2J  plan-2  N6    0.020
 J2J  plan-2  C1'   0.020
 J2J  plan-2  N7    0.020
 J2J  plan-2  N9    0.020
 J2J  plan-2  H2    0.020
 J2J  plan-2  H8    0.020
 J2J  plan-3  C6    0.020
 J2J  plan-3  N6    0.020
 J2J  plan-3  HN61  0.020
 J2J  plan-3  HN62  0.020
 J2J  plan-4  C18   0.020
 J2J  plan-4  C21   0.020
 J2J  plan-4  O17   0.020
 J2J  plan-4  O2P   0.020

