# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:25:56 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(methyl)phosphoryl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 M33  M33  5'-O-[(S)-hydroxy{[(S)-hydroxy(methyl)phosphoryl]oxy}phosphoryl]adenosine  ligand  42  27  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M33
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
 M33  PB    P  P      0   1.265   5.3955   1.4928   0.3897
 M33  O1B   O  O      0  -0.812   6.3663   0.7514  -0.4881
 M33  O2B   O  OP    -1  -0.806   5.0220   2.9129   0.0647
 M33  C3B   C  CH3    0  -0.950   5.9138   1.3867   2.1316
 M33  PA    P  P      0   1.338   3.3702  -0.3049  -0.6946
 M33  O1A   O  OP    -1  -0.799   3.9317  -1.6927  -0.6712
 M33  O2A   O  O      0  -0.807   3.3182   0.4624  -1.9800
 M33  O3A   O  O2     0  -0.750   3.9920   0.5985   0.5120
 M33  O5'   O  O2     0  -0.620   1.8570  -0.3372  -0.0228
 M33  C5'   C  CH2    0  -0.151   0.8636  -1.0526  -0.7160
 M33  C4'   C  CH1    0   0.007  -0.1601  -1.5724   0.2625
 M33  O4'   O  O2     0  -0.495  -0.8217  -0.4925   0.9232
 M33  C3'   C  CH1    0  -0.045  -1.2830  -2.3655  -0.4006
 M33  O3'   O  OH1    0  -0.656  -0.8973  -3.6980  -0.5831
 M33  C2'   C  CH1    0  -0.040  -2.4222  -2.1835   0.6081
 M33  O2'   O  OH1    0  -0.664  -2.2343  -3.0043   1.7274
 M33  C1'   C  CH1    0   0.172  -2.1887  -0.7391   1.0470
 M33  N9    N  NR5    0  -0.534  -2.9248   0.1996   0.2064
 M33  C8    C  CR15   0   0.100  -2.4639   0.9892  -0.8107
 M33  N7    N  N      0  -0.451  -3.3928   1.7179  -1.3593
 M33  C5    C  CR56   0  -0.003  -4.5308   1.3956  -0.6691
 M33  C6    C  CR6    0   0.457  -5.8660   1.8314  -0.7596
 M33  N6    N  NH2    0  -0.817  -6.2721   2.7315  -1.6557
 M33  N1    N  N      0  -0.474  -6.7545   1.3088   0.0931
 M33  C2    C  CR16   0   0.039  -6.3483   0.4075   0.9840
 M33  N3    N  N      0  -0.458  -5.1327  -0.0786   1.1651
 M33  C4    C  CR56   0   0.486  -4.2604   0.4534   0.3103
 M33  H3B1  H  HCH3   0   0.241   6.8230   1.9726   2.2751
 M33  H3B2  H  HCH3   0   0.240   5.1540   1.7855   2.8043
 M33  H3B3  H  HCH3   0   0.239   6.1285   0.3600   2.4280
 M33  H5'1  H  HCH2   0   0.209   0.3764  -0.4191  -1.4675
 M33  H5'2  H  HCH2   0   0.220   1.2727  -1.9220  -1.2453
 M33  H4'   H  HCH1   0   0.244   0.3449  -2.1989   1.0084
 M33  H3'   H  HCH1   0   0.245  -1.5598  -1.8928  -1.3526
 M33  HO3'  H  HOH1   0   0.469  -1.4695  -4.0992  -1.2454
 M33  H2'   H  HCH1   0   0.260  -3.4136  -2.3248   0.1613
 M33  HO2'  H  HOH1   0   0.452  -1.8920  -3.8516   1.4162
 M33  H1'   H  HCH1   0   0.283  -2.5207  -0.5739   2.0757
 M33  H8    H  HCR5   0   0.298  -1.4261   0.9999  -1.1032
 M33  HN61  H  HNH2   0   0.411  -5.6228   3.1652  -2.2878
 M33  HN62  H  HNH2   0   0.403  -7.2265   3.0475  -1.6614
 M33  H2    H  HCR6   0   0.252  -7.1195   0.0262   1.6449

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
 M33  N6   C6    single    1.333  0.020  1.333
 M33  O2A  PA    deloc     1.498  0.020  1.498
 M33  C6   C5    aromatic  1.407  0.020  1.407
 M33  C6   N1    aromatic  1.338  0.020  1.338
 M33  N7   C5    aromatic  1.369  0.020  1.369
 M33  N7   C8    aromatic  1.302  0.020  1.302
 M33  O1A  PA    deloc     1.497  0.020  1.497
 M33  C5'  O5'   single    1.407  0.020  1.407
 M33  C5'  C4'   single    1.508  0.020  1.508
 M33  C5   C4    aromatic  1.386  0.020  1.386
 M33  N1   C2    aromatic  1.331  0.020  1.331
 M33  O4'  C4'   single    1.428  0.020  1.428
 M33  O4'  C1'   single    1.395  0.020  1.395
 M33  C8   N9    aromatic  1.368  0.020  1.368
 M33  PA   O5'   single    1.656  0.020  1.656
 M33  PA   O3A   single    1.631  0.020  1.631
 M33  C2   N3    aromatic  1.322  0.020  1.322
 M33  C4   N9    aromatic  1.363  0.020  1.363
 M33  C4   N3    aromatic  1.332  0.020  1.332
 M33  C4'  C3'   single    1.526  0.020  1.526
 M33  N9   C1'   single    1.459  0.020  1.459
 M33  C1'  C2'   single    1.528  0.020  1.528
 M33  O1B  PB    deloc     1.504  0.020  1.504
 M33  O3A  PB    single    1.669  0.020  1.669
 M33  C3'  C2'   single    1.532  0.020  1.532
 M33  C3'  O3'   single    1.399  0.020  1.399
 M33  C2'  O2'   single    1.401  0.020  1.401
 M33  O2B  PB    deloc     1.504  0.020  1.504
 M33  PB   C3B   single    1.820  0.020  1.820
 M33  C3B  H3B1  single    0.970  0.020  1.090
 M33  C3B  H3B2  single    0.970  0.020  1.090
 M33  C3B  H3B3  single    0.970  0.020  1.090
 M33  C5'  H5'1  single    0.970  0.020  1.090
 M33  C5'  H5'2  single    0.970  0.020  1.090
 M33  C4'  H4'   single    0.970  0.020  1.090
 M33  C3'  H3'   single    0.970  0.020  1.090
 M33  O3'  HO3'  single    0.850  0.020  0.980
 M33  C2'  H2'   single    0.970  0.020  1.090
 M33  O2'  HO2'  single    0.850  0.020  0.980
 M33  C1'  H1'   single    0.970  0.020  1.090
 M33  C8   H8    single    0.930  0.020  1.080
 M33  N6   HN61  single    0.860  0.020  1.020
 M33  N6   HN62  single    0.860  0.020  1.020
 M33  C2   H2    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
 M33  O3A   PB   C3B    97.94  3.000
 M33  C3B   PB   O2B   109.42  3.000
 M33  O3A   PB   O2B   108.24  3.000
 M33  C3B   PB   O1B   110.24  3.000
 M33  O2B   PB   O1B   119.97  3.000
 M33  O3A   PB   O1B   108.75  3.000
 M33  H3B3  C3B  H3B2  108.31  3.000
 M33  H3B3  C3B  H3B1  107.81  3.000
 M33  H3B2  C3B  H3B1  107.64  3.000
 M33  H3B3  C3B  PB    111.79  3.000
 M33  H3B2  C3B  PB    111.75  3.000
 M33  H3B1  C3B  PB    109.37  3.000
 M33  O5'   PA   O3A    93.39  3.000
 M33  O3A   PA   O2A   111.38  3.000
 M33  O5'   PA   O2A   109.05  3.000
 M33  O3A   PA   O1A   111.03  3.000
 M33  O5'   PA   O1A   108.56  3.000
 M33  O2A   PA   O1A   120.08  3.000
 M33  PA    O3A  PB    124.29  3.000
 M33  C5'   O5'  PA    117.08  3.000
 M33  H5'2  C5'  H5'1  107.02  3.000
 M33  H5'2  C5'  C4'   107.04  3.000
 M33  H5'1  C5'  C4'   110.00  3.000
 M33  H5'2  C5'  O5'   112.17  3.000
 M33  H5'1  C5'  O5'   110.94  3.000
 M33  C4'   C5'  O5'   109.56  3.000
 M33  H4'   C4'  C3'   109.71  3.000
 M33  H4'   C4'  O4'   109.29  3.000
 M33  C3'   C4'  O4'   104.65  3.000
 M33  H4'   C4'  C5'   108.99  3.000
 M33  C3'   C4'  C5'   113.36  3.000
 M33  O4'   C4'  C5'   110.73  3.000
 M33  C1'   O4'  C4'   111.19  3.000
 M33  H3'   C3'  C2'   109.40  3.000
 M33  H3'   C3'  O3'   111.49  3.000
 M33  C2'   C3'  O3'   113.82  3.000
 M33  H3'   C3'  C4'   109.77  3.000
 M33  O3'   C3'  C4'   110.41  3.000
 M33  C2'   C3'  C4'   101.49  3.000
 M33  HO3'  O3'  C3'   108.83  3.000
 M33  H2'   C2'  C1'   112.15  3.000
 M33  H2'   C2'  O2'   111.80  3.000
 M33  C1'   C2'  O2'   107.70  3.000
 M33  H2'   C2'  C3'   112.87  3.000
 M33  O2'   C2'  C3'   110.90  3.000
 M33  C1'   C2'  C3'   100.83  3.000
 M33  HO2'  O2'  C2'   107.72  3.000
 M33  H1'   C1'  N9    106.95  3.000
 M33  H1'   C1'  C2'   111.52  3.000
 M33  N9    C1'  C2'   111.45  3.000
 M33  H1'   C1'  O4'   110.76  3.000
 M33  C2'   C1'  O4'   106.95  3.000
 M33  N9    C1'  O4'   109.24  3.000
 M33  C4    N9   C8    106.22  3.000
 M33  C4    N9   C1'   124.75  3.000
 M33  C8    N9   C1'   129.03  3.000
 M33  H8    C8   N7    124.53  3.000
 M33  H8    C8   N9    122.13  3.000
 M33  N7    C8   N9    113.34  3.000
 M33  C5    N7   C8    104.41  3.000
 M33  C4    C5   C6    116.17  3.000
 M33  C4    C5   N7    110.73  3.000
 M33  C6    C5   N7    133.09  3.000
 M33  N1    C6   N6    119.32  3.000
 M33  N1    C6   C5    117.91  3.000
 M33  N6    C6   C5    122.76  3.000
 M33  HN62  N6   HN61  118.31  3.000
 M33  HN62  N6   C6    120.34  3.000
 M33  HN61  N6   C6    121.15  3.000
 M33  C2    N1   C6    119.25  3.000
 M33  H2    C2   N3    116.17  3.000
 M33  H2    C2   N1    115.40  3.000
 M33  N3    C2   N1    128.43  3.000
 M33  C4    N3   C2    111.55  3.000
 M33  N3    C4   C5    126.68  3.000
 M33  N3    C4   N9    128.02  3.000
 M33  C5    C4   N9    105.30  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
 M33  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 M33  CONST_02  C6    C5   C4   N9   180.00   0.0  0
 M33  CONST_03  N7    C5   C4   N9     0.00   0.0  0
 M33  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 M33  CONST_05  C6    C5   N7   C8   180.00   0.0  0
 M33  CONST_06  C4    C5   N7   C8     0.00   0.0  0
 M33  CONST_07  C5    C4   N9   C8     0.00   0.0  0
 M33  CONST_08  N3    C4   N9   C8   180.00   0.0  0
 M33  CONST_09  N1    C6   C5   N7   180.00   0.0  0
 M33  CONST_10  N3    C4   C5   N7   180.00   0.0  0
 M33  CONST_11  C4    N9   C8   N7     0.00   0.0  0
 M33  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 M33  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 M33  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 M33  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 M33  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 M33  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 M33  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 M33  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 M33  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 M33  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 M33  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 M33  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 M33  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 M33  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 M33  CONST_26  HN61  N6   C6   C5     0.00   0.0  0
 M33  CONST_27  HN62  N6   C6   C5   180.00   0.0  0
 M33  Var_01    C4'   C5'  O5'  PA   151.54  30.0  1
 M33  Var_02    O2A   PA   O3A  PB   -48.12  30.0  2
 M33  Var_03    H3B1  C3B  PB   O1B   69.42  30.0  3

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
 M33  chir_03  C4'  C5'  O4'  C3'  negativ
 M33  chir_04  C3'  O3'  C4'  C2'  positiv
 M33  chir_05  C2'  O2'  C3'  C1'  positiv
 M33  chir_06  C1'  O4'  N9   C2'  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
 M33  plan-1  C1'   0.020
 M33  plan-1  N9    0.020
 M33  plan-1  C8    0.020
 M33  plan-1  N7    0.020
 M33  plan-1  C5    0.020
 M33  plan-1  C6    0.020
 M33  plan-1  N6    0.020
 M33  plan-1  N1    0.020
 M33  plan-1  C2    0.020
 M33  plan-1  N3    0.020
 M33  plan-1  C4    0.020
 M33  plan-1  H8    0.020
 M33  plan-1  H2    0.020
 M33  plan-2  C6    0.020
 M33  plan-2  N6    0.020
 M33  plan-2  HN61  0.020
 M33  plan-2  HN62  0.020

