# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 13:50:31 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: 5'-O-[(S)-{[(R)-(arsonomethyl)(hydroxy)phosphoryl]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)O[P@@](O)(=O)C[As](O)(O)=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
 ATS  ATS  5'-O-[(S)-{[(R)-(arsonomethyl)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine  ligand  49  31  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ATS
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
 ATS  AS1   AS  AS    0   1.511  35.1565  12.8056  30.6907
 ATS  OG2   O   O     0  -0.755  34.8483  11.1752  30.2429
 ATS  OG3   O   O     0  -0.751  36.0357  13.5526  29.4176
 ATS  OG1   O   O     0  -0.778  36.0637  12.9820  32.0293
 ATS  PA    P   P     0   1.482  34.2114  14.0292  34.7076
 ATS  O5'   O   O2    0  -0.569  34.9281  15.4354  34.9177
 ATS  O11   O   OH1   0  -0.775  35.3001  12.9429  34.4158
 ATS  O13   O   O2    0  -0.724  33.4868  14.2877  33.2596
 ATS  O12   O   O     0  -0.676  33.2818  13.7277  35.8037
 ATS  C5'   C   CH2   0  -0.214  35.9531  15.9286  34.0506
 ATS  C4'   C   CR15  0  -0.030  35.3991  16.9205  33.0499
 ATS  O4'   O   O     0  -0.487  34.8343  18.0357  33.7385
 ATS  C2'   C   CR15  0  -0.022  36.7876  18.8288  32.7405
 ATS  O2'   O   OH1   0  -0.645  37.3208  19.7259  31.8216
 ATS  C3'   C   CR15  0  -0.047  36.4941  17.4639  32.1132
 ATS  O3'   O   OH1   0  -0.649  36.1032  17.5235  30.7716
 ATS  C1'   C   CR15  0   0.172  35.4068  19.2268  33.2761
 ATS  N9    N   NR5   0  -0.543  35.4446  20.1708  34.3597
 ATS  C4    C   CR56  0   0.487  35.0435  21.4763  34.3183
 ATS  N3    N   N     0  -0.456  34.5206  22.1465  33.2951
 ATS  C2    C   CR16  0   0.047  34.2561  23.4008  33.6182
 ATS  N1    N   N     0  -0.474  34.4518  24.0138  34.7825
 ATS  C6    C   CR6   0   0.461  34.9783  23.3256  35.8020
 ATS  N6    N   NH2   0  -0.815  35.1671  23.9344  36.9731
 ATS  C5    C   CR56  0  -0.009  35.3028  21.9735  35.5852
 ATS  N7    N   N     0  -0.448  35.8437  21.0033  36.3895
 ATS  C8    C   CR15  0   0.111  35.9145  19.9531  35.6287
 ATS  PB    P   P     0   1.417  32.5332  13.4025  32.3072
 ATS  OB2   O   O     0  -0.649  31.1281  13.8392  32.2679
 ATS  C3B   C   CH2   0  -1.022  33.3898  13.5497  30.7211
 ATS  OB1   O   OH1   0  -0.740  32.8485  11.9367  32.8500
 ATS  HO2   H   H     0   0.503  35.6371  10.6124  30.2809
 ATS  HO3   H   H     0   0.502  35.6172  13.4757  28.5470
 ATS  HOB   H   HOH1  0   0.502  35.6436  12.8876  33.4538
 ATS  H5'1  H   HCH2  0   0.247  36.4509  15.1200  33.5116
 ATS  H5'2  H   HCH2  0   0.265  36.7009  16.3999  34.6909
 ATS  H4'   H   HCR5  0   0.260  34.6183  16.4446  32.4485
 ATS  H2'   H   HCR5  0   0.250  37.4613  18.6704  33.5946
 ATS  HO2'  H   HOH1  0   0.465  37.7135  20.4632  32.2990
 ATS  H3'   H   HCR5  0   0.281  37.3815  16.8272  32.1338
 ATS  HO3'  H   HOH1  0   0.453  35.3237  18.0802  30.6701
 ATS  H1'   H   HCR5  0   0.264  34.8114  19.6943  32.4808
 ATS  H2    H   HCR6  0   0.253  33.8254  24.0152  32.8348
 ATS  HN61  H   HNH2  0   0.404  34.9778  24.9173  37.0686
 ATS  HN62  H   HNH2  0   0.411  35.6189  23.4618  37.7360
 ATS  H8    H   HCR5  0   0.299  36.2861  18.9882  35.9394
 ATS  H3B1  H   HCH2  0   0.364  32.7969  13.0496  29.9499
 ATS  H3B2  H   HCH2  0   0.353  33.4494  14.6057  30.4438
 ATS  HB1   H   HOH1  0   0.513  32.2102  11.2546  32.5945

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
 ATS  AS1  OG2   single    1.719  0.020  1.719
 ATS  AS1  OG3   single    1.718  0.020  1.718
 ATS  AS1  OG1   double    1.627  0.020  1.627
 ATS  AS1  C3B   single    1.917  0.020  1.917
 ATS  OG2  HO2   single    0.850  0.020  0.980
 ATS  OG3  HO3   single    0.850  0.020  0.980
 ATS  PA   O5'   single    1.592  0.020  1.592
 ATS  PA   O11   single    1.565  0.020  1.565
 ATS  PA   O13   single    1.640  0.020  1.640
 ATS  PA   O12   double    1.469  0.020  1.469
 ATS  O5'  C5'   single    1.430  0.020  1.430
 ATS  O11  HOB   single    0.850  0.020  0.980
 ATS  O13  PB    single    1.612  0.020  1.612
 ATS  C5'  C4'   single    1.514  0.020  1.514
 ATS  C5'  H5'1  single    0.970  0.020  1.090
 ATS  C5'  H5'2  single    0.970  0.020  1.090
 ATS  C4'  O4'   single    1.427  0.020  1.427
 ATS  C4'  C3'   single    1.540  0.020  1.540
 ATS  C4'  H4'   single    0.970  0.020  1.090
 ATS  O4'  C1'   single    1.400  0.020  1.400
 ATS  C2'  O2'   single    1.391  0.020  1.391
 ATS  C2'  C3'   single    1.531  0.020  1.531
 ATS  C2'  C1'   single    1.534  0.020  1.534
 ATS  C2'  H2'   single    0.970  0.020  1.090
 ATS  O2'  HO2'  single    0.850  0.020  0.980
 ATS  C3'  O3'   single    1.399  0.020  1.399
 ATS  C3'  H3'   single    0.970  0.020  1.090
 ATS  O3'  HO3'  single    0.850  0.020  0.980
 ATS  C1'  N9    single    1.438  0.020  1.438
 ATS  C1'  H1'   single    0.970  0.020  1.090
 ATS  N9   C4    aromatic  1.366  0.020  1.366
 ATS  N9   C8    aromatic  1.371  0.020  1.371
 ATS  C4   N3    aromatic  1.330  0.020  1.330
 ATS  C4   C5    aromatic  1.385  0.020  1.385
 ATS  N3   C2    aromatic  1.322  0.020  1.322
 ATS  C2   N1    aromatic  1.330  0.020  1.330
 ATS  C2   H2    single    0.930  0.020  1.080
 ATS  N1   C6    aromatic  1.338  0.020  1.338
 ATS  C6   N6    single    1.333  0.020  1.333
 ATS  C6   C5    aromatic  1.407  0.020  1.407
 ATS  N6   HN61  single    0.860  0.020  1.020
 ATS  N6   HN62  single    0.860  0.020  1.020
 ATS  C5   N7    aromatic  1.371  0.020  1.371
 ATS  N7   C8    aromatic  1.299  0.020  1.299
 ATS  C8   H8    single    0.930  0.020  1.080
 ATS  PB   OB2   double    1.472  0.020  1.472
 ATS  PB   C3B   single    1.809  0.020  1.809
 ATS  PB   OB1   single    1.595  0.020  1.595
 ATS  C3B  H3B1  single    0.970  0.020  1.090
 ATS  C3B  H3B2  single    0.970  0.020  1.090
 ATS  OB1  HB1   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
 ATS  C3B   AS1  OG1   117.31  3.000
 ATS  C3B   AS1  OG3   108.33  3.000
 ATS  OG1   AS1  OG3   106.10  3.000
 ATS  C3B   AS1  OG2   101.95  3.000
 ATS  OG1   AS1  OG2   114.66  3.000
 ATS  OG3   AS1  OG2   108.13  3.000
 ATS  HO2   OG2  AS1   113.23  3.000
 ATS  HO3   OG3  AS1   114.22  3.000
 ATS  O12   PA   O13   114.31  3.000
 ATS  O12   PA   O11   115.91  3.000
 ATS  O13   PA   O11   104.60  3.000
 ATS  O12   PA   O5'   111.58  3.000
 ATS  O13   PA   O5'   100.15  3.000
 ATS  O11   PA   O5'   108.93  3.000
 ATS  C5'   O5'  PA    123.17  3.000
 ATS  HOB   O11  PA    116.51  3.000
 ATS  PB    O13  PA    134.14  3.000
 ATS  H5'2  C5'  H5'1  107.28  3.000
 ATS  H5'2  C5'  C4'   110.83  3.000
 ATS  H5'1  C5'  C4'   109.01  3.000
 ATS  H5'2  C5'  O5'   106.51  3.000
 ATS  H5'1  C5'  O5'   111.75  3.000
 ATS  C4'   C5'  O5'   111.37  3.000
 ATS  H4'   C4'  C3'   109.05  3.000
 ATS  H4'   C4'  O4'   108.82  3.000
 ATS  C3'   C4'  O4'   107.40  3.000
 ATS  H4'   C4'  C5'   109.84  3.000
 ATS  C3'   C4'  C5'   111.90  3.000
 ATS  O4'   C4'  C5'   109.75  3.000
 ATS  C1'   O4'  C4'   110.10  3.000
 ATS  H2'   C2'  C1'   108.53  3.000
 ATS  H2'   C2'  C3'   107.91  3.000
 ATS  C1'   C2'  C3'   101.65  3.000
 ATS  H2'   C2'  O2'   111.80  3.000
 ATS  C1'   C2'  O2'   114.12  3.000
 ATS  C3'   C2'  O2'   112.21  3.000
 ATS  HO2'  O2'  C2'   108.85  3.000
 ATS  H3'   C3'  O3'   105.66  3.000
 ATS  H3'   C3'  C2'   110.87  3.000
 ATS  O3'   C3'  C2'   114.12  3.000
 ATS  H3'   C3'  C4'   111.13  3.000
 ATS  O3'   C3'  C4'   113.56  3.000
 ATS  C2'   C3'  C4'   101.64  3.000
 ATS  HO3'  O3'  C3'   110.61  3.000
 ATS  H1'   C1'  N9    106.30  3.000
 ATS  H1'   C1'  C2'   110.23  3.000
 ATS  N9    C1'  C2'   114.20  3.000
 ATS  H1'   C1'  O4'   112.31  3.000
 ATS  N9    C1'  O4'   108.69  3.000
 ATS  C2'   C1'  O4'   105.23  3.000
 ATS  C8    N9   C4    106.28  3.000
 ATS  C8    N9   C1'   127.05  3.000
 ATS  C4    N9   C1'   126.65  3.000
 ATS  C5    C4   N3    126.59  3.000
 ATS  C5    C4   N9    105.09  3.000
 ATS  N3    C4   N9    128.32  3.000
 ATS  C2    N3   C4    111.63  3.000
 ATS  H2    C2   N1    115.44  3.000
 ATS  H2    C2   N3    116.12  3.000
 ATS  N1    C2   N3    128.44  3.000
 ATS  C6    N1   C2    119.19  3.000
 ATS  C5    C6   N6    122.78  3.000
 ATS  C5    C6   N1    117.87  3.000
 ATS  N6    C6   N1    119.35  3.000
 ATS  HN62  N6   HN61  118.19  3.000
 ATS  HN62  N6   C6    121.05  3.000
 ATS  HN61  N6   C6    120.21  3.000
 ATS  N7    C5   C6    132.86  3.000
 ATS  N7    C5   C4    110.87  3.000
 ATS  C6    C5   C4    116.27  3.000
 ATS  C8    N7   C5    104.47  3.000
 ATS  H8    C8   N7    124.95  3.000
 ATS  H8    C8   N9    121.76  3.000
 ATS  N7    C8   N9    113.28  3.000
 ATS  OB1   PB   C3B   106.24  3.000
 ATS  OB1   PB   OB2   118.07  3.000
 ATS  C3B   PB   OB2   113.86  3.000
 ATS  OB1   PB   O13   100.76  3.000
 ATS  C3B   PB   O13   101.14  3.000
 ATS  OB2   PB   O13   114.67  3.000
 ATS  H3B2  C3B  H3B1  106.99  3.000
 ATS  H3B2  C3B  PB    109.08  3.000
 ATS  H3B1  C3B  PB    108.93  3.000
 ATS  H3B2  C3B  AS1   108.70  3.000
 ATS  H3B1  C3B  AS1   108.11  3.000
 ATS  PB    C3B  AS1   114.76  3.000
 ATS  HB1   OB1  PB    115.30  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
 ATS  CONST_01  C2    N3   C4   N9   180.00   0.0  0
 ATS  CONST_02  C6    C5   C4   N9   180.00   0.0  0
 ATS  CONST_03  N7    C5   C4   N9     0.00   0.0  0
 ATS  CONST_04  C5    N7   C8   N9     0.00   0.0  0
 ATS  CONST_05  N7    C8   N9   C4     0.00   0.0  0
 ATS  CONST_06  N1    C2   N3   C4     0.00   0.0  0
 ATS  CONST_07  N1    C6   C5   C4     0.00   0.0  0
 ATS  CONST_08  C8    N7   C5   C4     0.00   0.0  0
 ATS  CONST_09  C8    N9   C4   N3   180.00   0.0  0
 ATS  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 ATS  CONST_11  N7    C5   C4   N3   180.00   0.0  0
 ATS  CONST_12  C6    N1   C2   N3     0.00   0.0  0
 ATS  CONST_13  C5    C4   N3   C2     0.00   0.0  0
 ATS  CONST_14  C5    C6   N1   C2     0.00   0.0  0
 ATS  CONST_15  N7    C5   C6   N1   180.00   0.0  0
 ATS  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 ATS  CONST_17  C8    N9   C4   C5     0.00   0.0  0
 ATS  CONST_18  N3    C4   N9   C1'    0.00   0.0  0
 ATS  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 ATS  CONST_20  N7    C8   N9   C1'  180.00   0.0  0
 ATS  CONST_21  N6    C6   C5   C4   180.00   0.0  0
 ATS  CONST_22  N6    C6   N1   C2   180.00   0.0  0
 ATS  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 ATS  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 ATS  CONST_25  H2    C2   N3   C4   180.00   0.0  0
 ATS  CONST_26  HN61  N6   C6   N1     0.00   0.0  0
 ATS  CONST_27  HN62  N6   C6   N1   180.00   0.0  0
 ATS  Var_01    C4'   C5'  O5'  PA    99.40  30.0  3
 ATS  Var_02    O13   PB   C3B  AS1   63.08  30.0  1
 ATS  Var_03    PB    C3B  AS1  OG2   88.69  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
 ATS  chir_02  C4'  C5'  O4'  C3'  negativ
 ATS  chir_03  C2'  O2'  C3'  C1'  positiv
 ATS  chir_04  C3'  O3'  C2'  C4'  negativ
 ATS  chir_05  C1'  O4'  N9   C2'  negativ
 ATS  chir_06  PA   O11  O13  O12  both
 ATS  chir_07  PB   OB2  OB1  C3B  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
 ATS  plan-1  C1'   0.020
 ATS  plan-1  N9    0.020
 ATS  plan-1  C4    0.020
 ATS  plan-1  N3    0.020
 ATS  plan-1  C2    0.020
 ATS  plan-1  N1    0.020
 ATS  plan-1  C6    0.020
 ATS  plan-1  N6    0.020
 ATS  plan-1  C5    0.020
 ATS  plan-1  N7    0.020
 ATS  plan-1  C8    0.020
 ATS  plan-1  H2    0.020
 ATS  plan-1  H8    0.020
 ATS  plan-2  C6    0.020
 ATS  plan-2  N6    0.020
 ATS  plan-2  HN61  0.020
 ATS  plan-2  HN62  0.020

