# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 22 13:17:25 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)c4ccccc4[N+]([O-])=O
#
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
 A99  A99  5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine  ligand  62  42  .  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_A99
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
 A99  C'    C  CH1    0  -0.023   4.6143  -1.3917  -1.3004
 A99  N1    N  N      0  -0.476  -6.1526  -3.9038  -0.1159
 A99  C2    C  CR16   0   0.037  -6.6908  -2.8665  -0.7529
 A99  N3    N  N      0  -0.456  -6.2021  -1.6477  -0.8982
 A99  C4    C  CR56   0   0.481  -5.0143  -1.5180  -0.3094
 A99  C5    C  CR56   0  -0.014  -4.3291  -2.5028   0.3841
 A99  C6    C  CR6    0   0.448  -4.9585  -3.7569   0.4699
 A99  N6    N  NH2    0  -0.820  -4.4092  -4.7953   1.1047
 A99  N7    N  N      0  -0.467  -3.1296  -2.0275   0.8462
 A99  C8    C  CR15   0   0.105  -3.0867  -0.7901   0.4449
 A99  N9    N  NR5    0  -0.547  -4.2051  -0.4196  -0.2590
 A99  PA    P  P      0   1.391   0.2452   1.8358   0.4654
 A99  PB    P  P      0   1.377   0.9497  -0.6449  -0.8848
 A99  PG    P  P      0   1.357   2.6069  -1.8797  -2.9801
 A99  O'L   O  O     -1  -0.376   3.1975   0.2531   2.2911
 A99  O'M   O  O      0  -0.401   4.5001  -1.2442   1.5218
 A99  C1'   C  CR16   0  -0.222   4.0726   2.0136   0.4601
 A99  O1A   O  O      0  -0.798  -0.3754   0.9481   1.5030
 A99  C1B   C  CH1    0   0.225  -4.5351   0.8873  -0.7809
 A99  O1B   O  O      0  -0.787   1.6583  -1.3655   0.2159
 A99  O1G   O  OP    -1  -0.792   2.4911  -1.6740  -4.4573
 A99  C2'   C  CR6    0   0.193   4.1823   0.6427   0.2644
 A99  N2'   N  N      1   0.343   3.9249  -0.1813   1.4320
 A99  O2'   O  OH1    0  -0.653  -6.3732   1.7467   0.5021
 A99  O2A   O  OP    -1  -0.778   1.0735   3.0121   0.8765
 A99  C2B   C  CH1    0  -0.055  -4.9976   1.8746   0.2943
 A99  O2B   O  OP    -1  -0.770  -0.4411  -1.0090  -1.2869
 A99  O2G   O  O2     0  -0.621   4.1926  -1.5933  -2.6389
 A99  C3'   C  CR6    0   0.133   4.5388   0.0903  -0.9678
 A99  O3'   O  OH1    0  -0.670  -5.4590   3.6274  -1.3084
 A99  O3A   O  O2     0  -0.727   1.0709   0.9829  -0.6457
 A99  C3B   C  CH1    0  -0.025  -4.5606   3.2112  -0.3129
 A99  O3B   O  O2     0  -0.746   1.8930  -0.6067  -2.2440
 A99  O3G   O  O      0  -0.805   2.1724  -3.1617  -2.3421
 A99  C4'   C  CR16   0  -0.299   4.8307   0.9950  -1.9864
 A99  O4'   O  O2     0  -0.481  -3.4104   1.4562  -1.3754
 A99  C4B   C  CH1    0  -0.049  -3.2432   2.8139  -0.9606
 A99  C5'   C  CR16   0  -0.228   4.7715   2.3644  -1.7946
 A99  O5'   O  O2     0  -0.620  -0.9393   2.3717  -0.5589
 A99  C5B   C  CH2    0  -0.148  -2.0840   2.9492   0.0100
 A99  C6'   C  CR16   0  -0.274   4.3789   2.8802  -0.5685
 A99  CM'   C  CH3    0  -0.668   6.0455  -1.8958  -1.1903
 A99  H'    H  HCH1   0   0.243   3.9767  -1.9577  -0.6231
 A99  HN6   H  HNH2   0   0.401  -4.8918  -5.6754   1.1560
 A99  HN6A  H  HNH2   0   0.409  -3.5235  -4.7075   1.5704
 A99  H1'   H  HCR6   0   0.270   3.7478   2.4031   1.4112
 A99  H1B   H  HCH1   0   0.254  -5.3376   0.7285  -1.5104
 A99  HO2'  H  HOH1   0   0.468  -6.5932   2.1183   1.3622
 A99  H2B   H  HCH1   0   0.250  -4.4355   1.6945   1.2191
 A99  HO3'  H  HOH1   0   0.448  -6.3533   3.5167  -0.9642
 A99  H3B   H  HCH1   0   0.247  -4.4217   3.9827   0.4566
 A99  H4'   H  HCR6   0   0.257   5.1012   0.6151  -2.9617
 A99  H4B   H  HCH1   0   0.257  -3.0423   3.4136  -1.8535
 A99  H5'   H  HCR6   0   0.259   5.0189   3.0294  -2.6121
 A99  H5B   H  HCH2   0   0.218  -1.9370   4.0175   0.2157
 A99  H5BA  H  HCH2   0   0.201  -2.3379   2.4738   0.9646
 A99  H6'   H  HCR6   0   0.259   4.3092   3.9479  -0.4126
 A99  HM'   H  HCH3   0   0.225   6.6948  -1.3850  -1.9036
 A99  HM'A  H  HCH3   0   0.235   6.4400  -1.7218  -0.1914
 A99  HM'B  H  HCH3   0   0.235   6.0910  -2.9669  -1.3919
 A99  H2    H  HCR6   0   0.247  -7.6577  -3.0514  -1.2095
 A99  H8    H  HCR5   0   0.324  -2.2543  -0.1191   0.6102

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
 A99  C'   O2G   single    1.418  0.020  1.418
 A99  C'   C3'   single    1.521  0.020  1.521
 A99  C'   CM'   single    1.521  0.020  1.521
 A99  N1   C2    aromatic  1.331  0.020  1.331
 A99  N1   C6    aromatic  1.338  0.020  1.338
 A99  C2   N3    aromatic  1.321  0.020  1.321
 A99  N3   C4    aromatic  1.332  0.020  1.332
 A99  C4   C5    aromatic  1.386  0.020  1.386
 A99  C4   N9    aromatic  1.365  0.020  1.365
 A99  C5   C6    aromatic  1.406  0.020  1.406
 A99  C5   N7    aromatic  1.371  0.020  1.371
 A99  C6   N6    single    1.335  0.020  1.335
 A99  N7   C8    aromatic  1.302  0.020  1.302
 A99  C8   N9    aromatic  1.372  0.020  1.372
 A99  N9   C1B   single    1.445  0.020  1.445
 A99  PA   O1A   deloc     1.500  0.020  1.500
 A99  PA   O2A   deloc     1.496  0.020  1.496
 A99  PA   O3A   single    1.626  0.020  1.626
 A99  PA   O5'   single    1.655  0.020  1.655
 A99  PB   O1B   deloc     1.494  0.020  1.494
 A99  PB   O2B   deloc     1.493  0.020  1.493
 A99  PB   O3A   single    1.650  0.020  1.650
 A99  PB   O3B   single    1.655  0.020  1.655
 A99  PG   O1G   deloc     1.496  0.020  1.496
 A99  PG   O2G   single    1.647  0.020  1.647
 A99  PG   O3B   single    1.635  0.020  1.635
 A99  PG   O3G   deloc     1.496  0.020  1.496
 A99  O'L  N2'   single    1.207  0.020  1.207
 A99  O'M  N2'   double    1.212  0.020  1.212
 A99  C1'  C2'   aromatic  1.389  0.020  1.389
 A99  C1'  C6'   aromatic  1.380  0.020  1.380
 A99  C1B  C2B   single    1.531  0.020  1.531
 A99  C1B  O4'   single    1.393  0.020  1.393
 A99  C2'  N2'   single    1.452  0.020  1.452
 A99  C2'  C3'   aromatic  1.397  0.020  1.397
 A99  O2'  C2B   single    1.397  0.020  1.397
 A99  C2B  C3B   single    1.532  0.020  1.532
 A99  C3'  C4'   aromatic  1.393  0.020  1.393
 A99  O3'  C3B   single    1.404  0.020  1.404
 A99  C3B  C4B   single    1.521  0.020  1.521
 A99  C4'  C5'   aromatic  1.384  0.020  1.384
 A99  O4'  C4B   single    1.429  0.020  1.429
 A99  C4B  C5B   single    1.518  0.020  1.518
 A99  C5'  C6'   aromatic  1.387  0.020  1.387
 A99  O5'  C5B   single    1.403  0.020  1.403
 A99  C'   H'    single    0.970  0.020  1.090
 A99  C2   H2    single    0.930  0.020  1.080
 A99  N6   HN6   single    0.860  0.020  1.020
 A99  N6   HN6A  single    0.860  0.020  1.020
 A99  C8   H8    single    0.930  0.020  1.080
 A99  C1'  H1'   single    0.930  0.020  1.080
 A99  C1B  H1B   single    0.970  0.020  1.090
 A99  O2'  HO2'  single    0.850  0.020  0.980
 A99  C2B  H2B   single    0.970  0.020  1.090
 A99  O3'  HO3'  single    0.850  0.020  0.980
 A99  C3B  H3B   single    0.970  0.020  1.090
 A99  C4'  H4'   single    0.930  0.020  1.080
 A99  C4B  H4B   single    0.970  0.020  1.090
 A99  C5'  H5'   single    0.930  0.020  1.080
 A99  C5B  H5B   single    0.970  0.020  1.090
 A99  C5B  H5BA  single    0.970  0.020  1.090
 A99  C6'  H6'   single    0.930  0.020  1.080
 A99  CM'  HM'   single    0.970  0.020  1.090
 A99  CM'  HM'A  single    0.970  0.020  1.090
 A99  CM'  HM'B  single    0.970  0.020  1.090

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
 A99  H'    C'   CM'   109.48  3.000
 A99  H'    C'   C3'   109.97  3.000
 A99  CM'   C'   C3'   110.72  3.000
 A99  H'    C'   O2G   109.83  3.000
 A99  CM'   C'   O2G   107.52  3.000
 A99  C3'   C'   O2G   109.29  3.000
 A99  C6    N1   C2    119.00  3.000
 A99  H2    C2   N3    116.14  3.000
 A99  H2    C2   N1    115.40  3.000
 A99  N3    C2   N1    128.47  3.000
 A99  C4    N3   C2    111.78  3.000
 A99  N9    C4   C5    105.09  3.000
 A99  N9    C4   N3    128.55  3.000
 A99  C5    C4   N3    126.37  3.000
 A99  N7    C5   C6    132.90  3.000
 A99  N7    C5   C4    110.79  3.000
 A99  C6    C5   C4    116.31  3.000
 A99  N6    C6   C5    122.59  3.000
 A99  N6    C6   N1    119.33  3.000
 A99  C5    C6   N1    118.08  3.000
 A99  HN6A  N6   HN6   118.45  3.000
 A99  HN6A  N6   C6    121.00  3.000
 A99  HN6   N6   C6    120.51  3.000
 A99  C8    N7   C5    104.75  3.000
 A99  H8    C8   N9    122.54  3.000
 A99  H8    C8   N7    124.60  3.000
 A99  N9    C8   N7    112.82  3.000
 A99  C1B   N9   C8    127.97  3.000
 A99  C1B   N9   C4    125.37  3.000
 A99  C8    N9   C4    106.54  3.000
 A99  O5'   PA   O3A    96.33  3.000
 A99  O5'   PA   O2A   108.16  3.000
 A99  O3A   PA   O2A   108.60  3.000
 A99  O5'   PA   O1A   108.88  3.000
 A99  O3A   PA   O1A   111.86  3.000
 A99  O2A   PA   O1A   120.28  3.000
 A99  O3B   PB   O3A    93.12  3.000
 A99  O3B   PB   O2B   108.39  3.000
 A99  O3A   PB   O2B   110.37  3.000
 A99  O3B   PB   O1B   110.23  3.000
 A99  O3A   PB   O1B   109.53  3.000
 A99  O2B   PB   O1B   121.50  3.000
 A99  O3G   PG   O3B   110.39  3.000
 A99  O3G   PG   O2G   109.89  3.000
 A99  O3B   PG   O2G   101.06  3.000
 A99  O3G   PG   O1G   121.09  3.000
 A99  O3B   PG   O1G   107.68  3.000
 A99  O2G   PG   O1G   104.79  3.000
 A99  H1'   C1'  C6'   119.86  3.000
 A99  H1'   C1'  C2'   120.31  3.000
 A99  C6'   C1'  C2'   119.83  3.000
 A99  H1B   C1B  O4'   111.48  3.000
 A99  H1B   C1B  C2B   109.85  3.000
 A99  O4'   C1B  C2B   106.27  3.000
 A99  H1B   C1B  N9    106.05  3.000
 A99  O4'   C1B  N9    109.81  3.000
 A99  C2B   C1B  N9    113.48  3.000
 A99  C3'   C2'  N2'   122.02  3.000
 A99  C3'   C2'  C1'   122.33  3.000
 A99  N2'   C2'  C1'   115.64  3.000
 A99  C2'   N2'  O'M   118.24  3.000
 A99  C2'   N2'  O'L   118.37  3.000
 A99  O'M   N2'  O'L   123.31  3.000
 A99  HO2'  O2'  C2B   108.83  3.000
 A99  H2B   C2B  C3B   109.34  3.000
 A99  H2B   C2B  O2'   111.35  3.000
 A99  C3B   C2B  O2'   114.82  3.000
 A99  H2B   C2B  C1B   109.35  3.000
 A99  C3B   C2B  C1B   101.43  3.000
 A99  O2'   C2B  C1B   110.05  3.000
 A99  PG    O2G  C'    120.44  3.000
 A99  C4'   C3'  C2'   116.21  3.000
 A99  C4'   C3'  C'    117.55  3.000
 A99  C2'   C3'  C'    126.23  3.000
 A99  HO3'  O3'  C3B   107.83  3.000
 A99  PB    O3A  PA    125.40  3.000
 A99  H3B   C3B  C4B   111.86  3.000
 A99  H3B   C3B  O3'   111.68  3.000
 A99  C4B   C3B  O3'   109.25  3.000
 A99  H3B   C3B  C2B   111.79  3.000
 A99  C4B   C3B  C2B   100.84  3.000
 A99  O3'   C3B  C2B   110.92  3.000
 A99  PG    O3B  PB    126.93  3.000
 A99  H4'   C4'  C5'   118.91  3.000
 A99  H4'   C4'  C3'   118.94  3.000
 A99  C5'   C4'  C3'   122.15  3.000
 A99  C4B   O4'  C1B   111.00  3.000
 A99  H4B   C4B  C5B   109.43  3.000
 A99  H4B   C4B  O4'   107.78  3.000
 A99  C5B   C4B  O4'   111.07  3.000
 A99  H4B   C4B  C3B   111.31  3.000
 A99  C5B   C4B  C3B   111.46  3.000
 A99  O4'   C4B  C3B   105.69  3.000
 A99  H5'   C5'  C6'   120.25  3.000
 A99  H5'   C5'  C4'   119.57  3.000
 A99  C6'   C5'  C4'   120.17  3.000
 A99  C5B   O5'  PA    117.79  3.000
 A99  H5BA  C5B  H5B   106.85  3.000
 A99  H5BA  C5B  O5'   111.33  3.000
 A99  H5B   C5B  O5'   111.55  3.000
 A99  H5BA  C5B  C4B   109.96  3.000
 A99  H5B   C5B  C4B   107.98  3.000
 A99  O5'   C5B  C4B   109.10  3.000
 A99  H6'   C6'  C5'   120.86  3.000
 A99  H6'   C6'  C1'   119.90  3.000
 A99  C5'   C6'  C1'   119.23  3.000
 A99  HM'B  CM'  HM'A  108.16  3.000
 A99  HM'B  CM'  HM'   108.30  3.000
 A99  HM'A  CM'  HM'   108.03  3.000
 A99  HM'B  CM'  C'    110.56  3.000
 A99  HM'A  CM'  C'    110.76  3.000
 A99  HM'   CM'  C'    110.93  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
 A99  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 A99  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 A99  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 A99  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 A99  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 A99  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 A99  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 A99  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 A99  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 A99  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 A99  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 A99  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 A99  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 A99  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 A99  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 A99  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 A99  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 A99  CONST_18  C4'   C3'  C2'  C1'     0.00   0.0  0
 A99  CONST_19  C4'   C5'  C6'  C1'     0.00   0.0  0
 A99  CONST_20  C5'   C6'  C1'  C2'     0.00   0.0  0
 A99  CONST_21  C5'   C4'  C3'  C2'     0.00   0.0  0
 A99  CONST_22  C6'   C1'  C2'  C3'     0.00   0.0  0
 A99  CONST_23  C6'   C5'  C4'  C3'     0.00   0.0  0
 A99  CONST_24  C1B   N9   C4   N3      0.00   0.0  0
 A99  CONST_25  C1B   N9   C4   C5    180.00   0.0  0
 A99  CONST_26  C1B   N9   C8   N7    180.00   0.0  0
 A99  CONST_27  C1'   C2'  C3'  C'    180.00   0.0  0
 A99  CONST_28  C5'   C4'  C3'  C'    180.00   0.0  0
 A99  CONST_29  N6    C6   N1   C2    180.00   0.0  0
 A99  CONST_30  N6    C6   C5   C4    180.00   0.0  0
 A99  CONST_31  N7    C5   C6   N6      0.00   0.0  0
 A99  CONST_32  C6'   C1'  C2'  N2'   180.00   0.0  0
 A99  CONST_33  C4'   C3'  C2'  N2'   180.00   0.0  0
 A99  CONST_34  H2    C2   N3   C4    180.00   0.0  0
 A99  CONST_35  H8    C8   N9   C4    180.00   0.0  0
 A99  CONST_36  H5'   C5'  C6'  C1'   180.00   0.0  0
 A99  CONST_37  H6'   C6'  C1'  C2'   180.00   0.0  0
 A99  CONST_38  H4'   C4'  C3'  C2'   180.00   0.0  0
 A99  CONST_39  H1'   C1'  C2'  C3'   180.00   0.0  0
 A99  CONST_44  HN6   N6   C6   N1      0.00   0.0  0
 A99  CONST_45  HN6A  N6   C6   N1    180.00   0.0  0
 A99  Var_01    C4B   C5B  O5'  PA   -155.53  30.0  3
 A99  Var_02    O1G   PG   O2G  C'    165.33  30.0  1
 A99  Var_03    O1B   PB   O3A  PA    -74.66  30.0  1
 A99  Var_04    O1A   PA   O3A  PB     15.25  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
 A99  chir_01  C'   O2G  C3'  CM'  positiv
 A99  chir_05  C1B  N9   C2B  O4'  negativ
 A99  chir_06  C2B  O2'  C3B  C1B  positiv
 A99  chir_07  C3B  O3'  C4B  C2B  positiv
 A99  chir_08  C4B  O4'  C3B  C5B  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
 A99  plan-1  C'    0.020
 A99  plan-1  C1'   0.020
 A99  plan-1  C2'   0.020
 A99  plan-1  N2'   0.020
 A99  plan-1  C3'   0.020
 A99  plan-1  C4'   0.020
 A99  plan-1  C5'   0.020
 A99  plan-1  C6'   0.020
 A99  plan-1  H1'   0.020
 A99  plan-1  H4'   0.020
 A99  plan-1  H5'   0.020
 A99  plan-1  H6'   0.020
 A99  plan-2  N1    0.020
 A99  plan-2  C2    0.020
 A99  plan-2  N3    0.020
 A99  plan-2  C4    0.020
 A99  plan-2  C5    0.020
 A99  plan-2  C6    0.020
 A99  plan-2  N6    0.020
 A99  plan-2  N7    0.020
 A99  plan-2  C8    0.020
 A99  plan-2  N9    0.020
 A99  plan-2  C1B   0.020
 A99  plan-2  H2    0.020
 A99  plan-2  H8    0.020
 A99  plan-3  C6    0.020
 A99  plan-3  N6    0.020
 A99  plan-3  HN6   0.020
 A99  plan-3  HN6A  0.020
 A99  plan-4  O'L   0.020
 A99  plan-4  O'M   0.020
 A99  plan-4  C2'   0.020
 A99  plan-4  N2'   0.020

