# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 02:03:20 2020
#   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  47  31  .  2021-08-06  2021-08-06  
;
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   1.442  36.0738  12.1193  31.7164
 ATS  OG2   O   O      0  -0.841  35.3018  11.0201  32.7912
 ATS  OG3   O   O      0  -0.807  36.3241  11.0948  30.3079
 ATS  OG1   O   O      0  -0.783  37.5604  12.5983  32.1130
 ATS  PA    P   P      0   1.368  34.3224  14.5849  34.3385
 ATS  O5'   O   O2     0  -0.598  34.7732  16.1584  34.3541
 ATS  O11   O   OP    -1  -0.765  35.4855  13.7206  33.9528
 ATS  O13   O   O2     0  -0.743  33.2796  14.6115  33.0582
 ATS  O12   O   O      0  -0.767  33.5543  14.3753  35.5969
 ATS  C5'   C   CH2    0  -0.194  35.6292  16.6892  33.3657
 ATS  C4'   C   CH1    0  -0.083  34.8440  17.3730  32.2553
 ATS  O4'   O   O2     0  -0.486  33.9075  18.3185  32.7821
 ATS  C2'   C   CH1    0  -0.050  35.8261  19.5158  32.0695
 ATS  O2'   O   OH1    0  -0.669  36.0986  20.5941  31.2357
 ATS  C3'   C   CH1    0  -0.008  35.7287  18.1865  31.3100
 ATS  O3'   O   OH1    0  -0.654  35.2039  18.3072  30.0174
 ATS  C1'   C   CH1    0   0.193  34.4517  19.5950  32.7757
 ATS  N9    N   NR5    0  -0.547  34.5880  20.0810  34.1445
 ATS  C4    C   CR5    0   0.517  35.1444  21.2767  34.4733
 ATS  N3    N   N      0  -0.508  35.7077  22.1696  33.6556
 ATS  C2    C   C1     0   0.063  36.1535  23.2257  34.3169
 ATS  N1    N   N      0  -0.476  36.0974  23.4578  35.6232
 ATS  C6    C   C      0   0.462  35.5378  22.5482  36.4319
 ATS  N6    N   NH2    0  -0.814  35.4844  22.7880  37.7414
 ATS  C5    C   CR5    0   0.001  35.0204  21.3760  35.8487
 ATS  N7    N   N      0  -0.455  34.4034  20.2636  36.3573
 ATS  C8    C   CR15   0   0.110  34.1591  19.5204  35.3148
 ATS  PB    P   P      0   1.322  33.1313  13.3949  31.9661
 ATS  OB2   O   O      0  -0.760  32.0713  13.8247  31.0050
 ATS  C3B   C   CH2    0  -1.036  34.7571  13.3886  31.0946
 ATS  OB1   O   OP    -1  -0.798  32.9857  12.0794  32.7122
 ATS  HO2   H   H      0   0.478  34.3515  11.3428  32.9166
 ATS  HO3   H   H      0   0.467  35.5418  10.5823  30.0687
 ATS  H5'1  H   HCH2   0   0.239  36.2692  15.9196  32.9208
 ATS  H5'2  H   HCH2   0   0.236  36.2947  17.3991  33.8661
 ATS  H4'   H   HCH1   0   0.264  34.2641  16.6311  31.7029
 ATS  H2'   H   HCH1   0   0.243  36.5993  19.3953  32.8412
 ATS  HO2'  H   HOH1   0   0.458  36.1148  21.3804  31.8083
 ATS  H3'   H   HCH1   0   0.273  36.7144  17.7302  31.1939
 ATS  HO3'  H   HOH1   0   0.452  34.3457  18.7437  30.0420
 ATS  H1'   H   HCH1   0   0.276  33.7811  20.2843  32.2502
 ATS  H2    H   H      0   0.259  36.6254  23.9988  33.7209
 ATS  HN61  H   HNH2   0   0.405  35.9211  23.6095  38.1227
 ATS  HN62  H   HNH2   0   0.413  35.1388  22.0940  38.3811
 ATS  H8    H   HCR5   0   0.296  33.6837  18.5526  35.3387
 ATS  H3B1  H   HCH2   0   0.304  34.5597  13.1319  30.0511
 ATS  H3B2  H   HCH2   0   0.300  35.2100  14.3814  31.0901

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    1.720  0.020  1.720
 ATS  AS1  OG3   single    1.760  0.020  1.760
 ATS  AS1  OG1   double    1.611  0.020  1.611
 ATS  AS1  C3B   single    1.932  0.020  1.932
 ATS  OG2  HO2   single    0.850  0.020  0.980
 ATS  OG3  HO3   single    0.850  0.020  0.980
 ATS  PA   O5'   single    1.637  0.020  1.637
 ATS  PA   O11   deloc     1.500  0.020  1.500
 ATS  PA   O13   single    1.651  0.020  1.651
 ATS  PA   O12   deloc     1.489  0.020  1.489
 ATS  O5'  C5'   single    1.411  0.020  1.411
 ATS  O13  PB    single    1.641  0.020  1.641
 ATS  C5'  C4'   single    1.522  0.020  1.522
 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    1.431  0.020  1.431
 ATS  C4'  C3'   single    1.529  0.020  1.529
 ATS  C4'  H4'   single    0.970  0.020  1.090
 ATS  O4'  C1'   single    1.388  0.020  1.388
 ATS  C2'  O2'   single    1.390  0.020  1.390
 ATS  C2'  C3'   single    1.534  0.020  1.534
 ATS  C2'  C1'   single    1.547  0.020  1.547
 ATS  C2'  H2'   single    0.970  0.020  1.090
 ATS  O2'  HO2'  single    0.850  0.020  0.980
 ATS  C3'  O3'   single    1.400  0.020  1.400
 ATS  C3'  H3'   single    0.970  0.020  1.090
 ATS  O3'  HO3'  single    0.850  0.020  0.980
 ATS  C1'  N9    single    1.459  0.020  1.459
 ATS  C1'  H1'   single    0.970  0.020  1.090
 ATS  N9   C4    aromatic  1.359  0.020  1.359
 ATS  N9   C8    aromatic  1.367  0.020  1.367
 ATS  C4   N3    aromatic  1.335  0.020  1.335
 ATS  C4   C5    aromatic  1.385  0.020  1.385
 ATS  N3   C2    aromatic  1.323  0.020  1.323
 ATS  C2   N1    aromatic  1.328  0.020  1.328
 ATS  C2   H2    single    0.930  0.020  1.080
 ATS  N1   C6    aromatic  1.340  0.020  1.340
 ATS  C6   N6    single    1.332  0.020  1.332
 ATS  C6   C5    aromatic  1.408  0.020  1.408
 ATS  N6   HN61  single    0.860  0.020  1.020
 ATS  N6   HN62  single    0.860  0.020  1.020
 ATS  C5   N7    aromatic  1.370  0.020  1.370
 ATS  N7   C8    aromatic  1.303  0.020  1.303
 ATS  C8   H8    single    0.930  0.020  1.080
 ATS  PB   OB2   deloc     1.494  0.020  1.494
 ATS  PB   C3B   single    1.845  0.020  1.845
 ATS  PB   OB1   deloc     1.519  0.020  1.519
 ATS  C3B  H3B1  single    0.970  0.020  1.090
 ATS  C3B  H3B2  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
 ATS  C3B   AS1  OG1   120.84  3.000
 ATS  C3B   AS1  OG3   102.82  3.000
 ATS  OG1   AS1  OG3   103.82  3.000
 ATS  C3B   AS1  OG2   108.37  3.000
 ATS  OG1   AS1  OG2   116.75  3.000
 ATS  OG3   AS1  OG2   101.07  3.000
 ATS  HO2   OG2  AS1   107.18  3.000
 ATS  HO3   OG3  AS1   113.09  3.000
 ATS  O12   PA   O13   109.37  3.000
 ATS  O12   PA   O11   122.43  3.000
 ATS  O13   PA   O11   107.43  3.000
 ATS  O12   PA   O5'   105.62  3.000
 ATS  O13   PA   O5'    99.55  3.000
 ATS  O11   PA   O5'   110.05  3.000
 ATS  C5'   O5'  PA    121.47  3.000
 ATS  PB    O13  PA    124.12  3.000
 ATS  H5'2  C5'  H5'1  106.63  3.000
 ATS  H5'2  C5'  C4'   110.85  3.000
 ATS  H5'1  C5'  C4'   108.70  3.000
 ATS  H5'2  C5'  O5'   107.02  3.000
 ATS  H5'1  C5'  O5'   112.00  3.000
 ATS  C4'   C5'  O5'   111.53  3.000
 ATS  H4'   C4'  C3'   110.86  3.000
 ATS  H4'   C4'  O4'   106.72  3.000
 ATS  C3'   C4'  O4'   104.75  3.000
 ATS  H4'   C4'  C5'   109.74  3.000
 ATS  C3'   C4'  C5'   113.05  3.000
 ATS  O4'   C4'  C5'   111.45  3.000
 ATS  C1'   O4'  C4'   110.45  3.000
 ATS  H2'   C2'  C1'   108.06  3.000
 ATS  H2'   C2'  C3'   107.30  3.000
 ATS  C1'   C2'  C3'   102.35  3.000
 ATS  H2'   C2'  O2'   111.62  3.000
 ATS  C1'   C2'  O2'   114.09  3.000
 ATS  C3'   C2'  O2'   112.81  3.000
 ATS  HO2'  O2'  C2'   106.09  3.000
 ATS  H3'   C3'  O3'   106.02  3.000
 ATS  H3'   C3'  C2'   110.93  3.000
 ATS  O3'   C3'  C2'   113.97  3.000
 ATS  H3'   C3'  C4'   111.44  3.000
 ATS  O3'   C3'  C4'   113.56  3.000
 ATS  C2'   C3'  C4'   101.05  3.000
 ATS  HO3'  O3'  C3'   110.45  3.000
 ATS  H1'   C1'  N9    107.31  3.000
 ATS  H1'   C1'  C2'   110.91  3.000
 ATS  N9    C1'  C2'   111.24  3.000
 ATS  H1'   C1'  O4'   109.92  3.000
 ATS  N9    C1'  O4'   109.80  3.000
 ATS  C2'   C1'  O4'   107.66  3.000
 ATS  C8    N9   C4    106.39  3.000
 ATS  C8    N9   C1'   129.61  3.000
 ATS  C4    N9   C1'   123.93  3.000
 ATS  C5    C4   N3    126.73  3.000
 ATS  C5    C4   N9    105.47  3.000
 ATS  N3    C4   N9    127.79  3.000
 ATS  C2    N3   C4    111.70  3.000
 ATS  H2    C2   N1    115.75  3.000
 ATS  H2    C2   N3    116.16  3.000
 ATS  N1    C2   N3    128.08  3.000
 ATS  C6    N1   C2    119.53  3.000
 ATS  C5    C6   N6    122.84  3.000
 ATS  C5    C6   N1    117.95  3.000
 ATS  N6    C6   N1    119.20  3.000
 ATS  HN62  N6   HN61  118.17  3.000
 ATS  HN62  N6   C6    121.00  3.000
 ATS  HN61  N6   C6    120.16  3.000
 ATS  N7    C5   C6    133.46  3.000
 ATS  N7    C5   C4    110.54  3.000
 ATS  C6    C5   C4    116.00  3.000
 ATS  C8    N7   C5    104.51  3.000
 ATS  H8    C8   N7    125.21  3.000
 ATS  H8    C8   N9    121.69  3.000
 ATS  N7    C8   N9    113.09  3.000
 ATS  OB1   PB   C3B   108.27  3.000
 ATS  OB1   PB   OB2   119.80  3.000
 ATS  C3B   PB   OB2   108.81  3.000
 ATS  OB1   PB   O13   108.89  3.000
 ATS  C3B   PB   O13   103.72  3.000
 ATS  OB2   PB   O13   106.19  3.000
 ATS  H3B2  C3B  H3B1  106.54  3.000
 ATS  H3B2  C3B  PB    111.39  3.000
 ATS  H3B1  C3B  PB    107.03  3.000
 ATS  H3B2  C3B  AS1   108.44  3.000
 ATS  H3B1  C3B  AS1   106.03  3.000
 ATS  PB    C3B  AS1   116.80  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    96.60  30.0  3
 ATS  Var_02    O13   PB   C3B  AS1   96.91  30.0  1
 ATS  Var_03    PB    C3B  AS1  OG2   11.33  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

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

