# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:33:32 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5'-O-[(dithiophosphono)]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](S)(S)=O)[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
 ADS  ADS  5'-O-[(dithiophosphono)]adenosine  ligand  37  23  .  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_ADS
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
 ADS  P     P  P     0   0.974   0.7530  -0.1481   6.7239
 ADS  O1P   O  O     0  -0.639   0.5597  -1.0715   7.8599
 ADS  S2P   S  S2    0  -0.330   2.2502   1.2878   6.9693
 ADS  S3P   S  S2    0  -0.335  -0.8159   1.1604   6.2701
 ADS  O5'   O  O2    0  -0.555   1.0518  -0.9686   5.3866
 ADS  C5'   C  CH2   0  -0.180   1.4101  -0.3655   4.1417
 ADS  C4'   C  CR15  0  -0.032   0.6468  -1.0391   3.0328
 ADS  O4'   O  O     0  -0.493  -0.7468  -0.7645   3.1548
 ADS  C3'   C  CR15  0  -0.010   1.0269  -0.5233   1.6396
 ADS  O3'   O  OH1   0  -0.649   2.2001  -1.0551   1.1171
 ADS  C2'   C  CR15  0  -0.067  -0.2500  -0.8401   0.8500
 ADS  O2'   O  OH1   0  -0.654  -0.2634  -2.1672   0.3943
 ADS  C1'   C  CR15  0   0.151  -1.3320  -0.5543   1.8995
 ADS  N9    N  NR5   0  -0.533  -1.8179   0.8131   1.8265
 ADS  C8    C  CR15  0   0.108  -1.4262   1.9075   2.5494
 ADS  N7    N  N     0  -0.447  -2.0600   2.9946   2.2213
 ADS  C5    C  CR56  0  -0.002  -2.9162   2.6044   1.2258
 ADS  C6    C  CR6   0   0.458  -3.8772   3.2906   0.4598
 ADS  N6    N  NH2   0  -0.815  -4.1119   4.5961   0.5973
 ADS  N1    N  N     0  -0.473  -4.5673   2.5924  -0.4491
 ADS  C2    C  CR16  0   0.042  -4.3241   1.2926  -0.5937
 ADS  N3    N  N     0  -0.459  -3.4561   0.5416   0.0626
 ADS  C4    C  CR56  0   0.491  -2.7815   1.2504   0.9652
 ADS  HSP2  H  HSH1  0   0.283   3.0302   0.4953   7.7183
 ADS  HSP3  H  HSH1  0   0.278  -1.5745   0.2332   5.6657
 ADS  H5'1  H  HCH2  0   0.235   1.2109   0.7109   4.1451
 ADS  H5'2  H  HCH2  0   0.276   2.4805  -0.5067   3.9842
 ADS  H4'   H  HCR5  0   0.264   0.8168  -2.1232   3.0946
 ADS  H3'   H  HCR5  0   0.261   1.1603   0.5639   1.6764
 ADS  HO3'  H  HOH1  0   0.449   2.0222  -1.9527   0.8106
 ADS  H2'   H  HCR5  0   0.294  -0.3625  -0.2055  -0.0298
 ADS  HO2'  H  HOH1  0   0.464  -0.3916  -2.7858   1.1226
 ADS  H1'   H  HCR5  0   0.292  -2.1989  -1.2074   1.7634
 ADS  H8    H  HCR5  0   0.284  -0.6750   1.8458   3.3205
 ADS  HN61  H  HNH2  0   0.412  -3.6647   5.1279   1.3231
 ADS  HN62  H  HNH2  0   0.404  -4.8537   5.0335   0.0784
 ADS  H2    H  HCR6  0   0.254  -4.9169   0.7883  -1.3491

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
 ADS  P    O1P   double    1.477  0.020  1.477
 ADS  P    S2P   single    2.089  0.020  2.089
 ADS  P    S3P   single    2.093  0.020  2.093
 ADS  P    O5'   single    1.597  0.020  1.597
 ADS  S2P  HSP2  single    1.200  0.020  1.300
 ADS  S3P  HSP3  single    1.200  0.020  1.300
 ADS  O5'  C5'   single    1.429  0.020  1.429
 ADS  C5'  C4'   single    1.505  0.020  1.505
 ADS  C5'  H5'1  single    0.970  0.020  1.090
 ADS  C5'  H5'2  single    0.970  0.020  1.090
 ADS  C4'  O4'   single    1.426  0.020  1.426
 ADS  C4'  C3'   single    1.534  0.020  1.534
 ADS  C4'  H4'   single    0.970  0.020  1.090
 ADS  O4'  C1'   single    1.401  0.020  1.401
 ADS  C3'  O3'   single    1.390  0.020  1.390
 ADS  C3'  C2'   single    1.534  0.020  1.534
 ADS  C3'  H3'   single    0.970  0.020  1.090
 ADS  O3'  HO3'  single    0.850  0.020  0.980
 ADS  C2'  O2'   single    1.403  0.020  1.403
 ADS  C2'  C1'   single    1.534  0.020  1.534
 ADS  C2'  H2'   single    0.970  0.020  1.090
 ADS  O2'  HO2'  single    0.850  0.020  0.980
 ADS  C1'  N9    single    1.453  0.020  1.453
 ADS  C1'  H1'   single    0.970  0.020  1.090
 ADS  N9   C8    aromatic  1.369  0.020  1.369
 ADS  N9   C4    aromatic  1.364  0.020  1.364
 ADS  C8   N7    aromatic  1.300  0.020  1.300
 ADS  C8   H8    single    0.930  0.020  1.080
 ADS  N7   C5    aromatic  1.370  0.020  1.370
 ADS  C5   C6    aromatic  1.408  0.020  1.408
 ADS  C5   C4    aromatic  1.385  0.020  1.385
 ADS  C6   N6    single    1.333  0.020  1.333
 ADS  C6   N1    aromatic  1.338  0.020  1.338
 ADS  N6   HN61  single    0.860  0.020  1.020
 ADS  N6   HN62  single    0.860  0.020  1.020
 ADS  N1   C2    aromatic  1.330  0.020  1.330
 ADS  C2   N3    aromatic  1.322  0.020  1.322
 ADS  C2   H2    single    0.930  0.020  1.080
 ADS  N3   C4    aromatic  1.331  0.020  1.331

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
 ADS  O5'   P    S3P   106.25  3.000
 ADS  O5'   P    S2P   108.51  3.000
 ADS  S3P   P    S2P    97.65  3.000
 ADS  O5'   P    O1P   110.32  3.000
 ADS  S3P   P    O1P   117.36  3.000
 ADS  S2P   P    O1P   115.68  3.000
 ADS  HSP2  S2P  P      94.37  3.000
 ADS  HSP3  S3P  P      95.14  3.000
 ADS  C5'   O5'  P     124.02  3.000
 ADS  H5'2  C5'  H5'1  107.82  3.000
 ADS  H5'2  C5'  C4'   109.47  3.000
 ADS  H5'1  C5'  C4'   110.49  3.000
 ADS  H5'2  C5'  O5'   108.49  3.000
 ADS  H5'1  C5'  O5'   111.51  3.000
 ADS  C4'   C5'  O5'   109.01  3.000
 ADS  H4'   C4'  C3'   110.15  3.000
 ADS  H4'   C4'  O4'   109.66  3.000
 ADS  C3'   C4'  O4'   104.79  3.000
 ADS  H4'   C4'  C5'   108.76  3.000
 ADS  C3'   C4'  C5'   113.14  3.000
 ADS  O4'   C4'  C5'   110.27  3.000
 ADS  C1'   O4'  C4'   111.13  3.000
 ADS  H3'   C3'  C2'   108.87  3.000
 ADS  H3'   C3'  O3'   106.83  3.000
 ADS  C2'   C3'  O3'   115.47  3.000
 ADS  H3'   C3'  C4'   109.47  3.000
 ADS  C2'   C3'  C4'   101.06  3.000
 ADS  O3'   C3'  C4'   114.96  3.000
 ADS  HO3'  O3'  C3'   108.64  3.000
 ADS  H2'   C2'  C1'   111.75  3.000
 ADS  H2'   C2'  O2'   106.70  3.000
 ADS  C1'   C2'  O2'   113.06  3.000
 ADS  H2'   C2'  C3'   112.38  3.000
 ADS  C1'   C2'  C3'   101.33  3.000
 ADS  O2'   C2'  C3'   111.73  3.000
 ADS  HO2'  O2'  C2'   111.27  3.000
 ADS  H1'   C1'  N9    106.90  3.000
 ADS  H1'   C1'  C2'   111.26  3.000
 ADS  N9    C1'  C2'   112.14  3.000
 ADS  H1'   C1'  O4'   110.66  3.000
 ADS  N9    C1'  O4'   109.02  3.000
 ADS  C2'   C1'  O4'   106.88  3.000
 ADS  C4    N9   C8    106.21  3.000
 ADS  C4    N9   C1'   124.72  3.000
 ADS  C8    N9   C1'   129.07  3.000
 ADS  H8    C8   N7    124.60  3.000
 ADS  H8    C8   N9    122.09  3.000
 ADS  N7    C8   N9    113.31  3.000
 ADS  C5    N7   C8    104.47  3.000
 ADS  C4    C5   C6    116.14  3.000
 ADS  C4    C5   N7    110.75  3.000
 ADS  C6    C5   N7    133.11  3.000
 ADS  N1    C6   N6    119.35  3.000
 ADS  N1    C6   C5    117.87  3.000
 ADS  N6    C6   C5    122.78  3.000
 ADS  HN62  N6   HN61  118.09  3.000
 ADS  HN62  N6   C6    120.17  3.000
 ADS  HN61  N6   C6    120.95  3.000
 ADS  C2    N1   C6    119.30  3.000
 ADS  H2    C2   N3    116.13  3.000
 ADS  H2    C2   N1    115.47  3.000
 ADS  N3    C2   N1    128.40  3.000
 ADS  C4    N3   C2    111.52  3.000
 ADS  N3    C4   C5    126.77  3.000
 ADS  N3    C4   N9    127.97  3.000
 ADS  C5    C4   N9    105.26  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
 ADS  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 ADS  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 ADS  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 ADS  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 ADS  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 ADS  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 ADS  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 ADS  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 ADS  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 ADS  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 ADS  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 ADS  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 ADS  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 ADS  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 ADS  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 ADS  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 ADS  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 ADS  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 ADS  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 ADS  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 ADS  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 ADS  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 ADS  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 ADS  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 ADS  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 ADS  CONST_26  HN61  N6   C6   C5      0.00   0.0  0
 ADS  CONST_27  HN62  N6   C6   C5    180.00   0.0  0
 ADS  Var_01    C4'   C5'  O5'  P    -136.62  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
 ADS  chir_01  C4'  C5'  O4'  C3'  negativ
 ADS  chir_02  C3'  O3'  C4'  C2'  positiv
 ADS  chir_03  C2'  O2'  C3'  C1'  positiv
 ADS  chir_04  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
 ADS  plan-1  C1'   0.020
 ADS  plan-1  N9    0.020
 ADS  plan-1  C8    0.020
 ADS  plan-1  N7    0.020
 ADS  plan-1  C5    0.020
 ADS  plan-1  C6    0.020
 ADS  plan-1  N6    0.020
 ADS  plan-1  N1    0.020
 ADS  plan-1  C2    0.020
 ADS  plan-1  N3    0.020
 ADS  plan-1  C4    0.020
 ADS  plan-1  H8    0.020
 ADS  plan-1  H2    0.020
 ADS  plan-2  C6    0.020
 ADS  plan-2  N6    0.020
 ADS  plan-2  HN61  0.020
 ADS  plan-2  HN62  0.020

