# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 11:03:35 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 5'-O-(phosphonoacetyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COC(=O)C[P](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
 SON  SON  5'-O-(phosphonoacetyl)adenosine  ligand  42  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SON
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
 SON  PB    P  P     0   1.370  -3.3837   2.0296  -0.0246
 SON  O1B   O  O     0  -0.698  -3.7366   2.4812   1.3382
 SON  O2B   O  OH1   0  -0.739  -1.7928   1.8475  -0.1360
 SON  O3B   O  OH1   0  -0.736  -3.8564   2.9596  -1.2379
 SON  CB    C  CH2   0  -0.855  -4.0922   0.4374  -0.5323
 SON  CA    C  C     0   0.573  -3.4973  -0.6547   0.3127
 SON  OA    O  O     0  -0.430  -3.8660  -0.9329   1.4234
 SON  O5'   O  O2    0  -0.440  -2.4853  -1.2437  -0.3052
 SON  C5'   C  CH2   0  -0.181  -1.7325  -2.2123   0.4232
 SON  C4'   C  CH1   0  -0.048  -0.5956  -2.6512  -0.4748
 SON  O4'   O  O2    0  -0.486   0.1691  -1.5212  -0.9002
 SON  C1'   C  CH1   0   0.212   1.4589  -1.5640  -0.3531
 SON  N9    N  NR5   0  -0.541   1.8573  -0.2370   0.0334
 SON  C4    C  CR56  0   0.492   2.9701   0.4324  -0.3910
 SON  N3    N  N     0  -0.457   3.9163   0.0138  -1.2270
 SON  C2    C  CR16  0   0.047   4.8450   0.9356  -1.4148
 SON  N1    N  N     0  -0.474   4.9204   2.1532  -0.8846
 SON  C6    C  CR6   0   0.458   3.9621   2.5590  -0.0437
 SON  N6    N  NH2   0  -0.816   4.0408   3.7746   0.5001
 SON  C5    C  CR56  0  -0.012   2.9116   1.6660   0.2371
 SON  N7    N  N     0  -0.448   1.7905   1.7609   1.0221
 SON  C8    C  CR15  0   0.118   1.1937   0.6175   0.8736
 SON  C2'   C  CH1   0  -0.048   1.3805  -2.5544   0.8074
 SON  O2'   O  OH1   0  -0.651   2.6494  -3.0622   1.0822
 SON  C3'   C  CH1   0  -0.035   0.3765  -3.5703   0.2561
 SON  O3'   O  OH1   0  -0.665   0.9819  -4.4176  -0.6834
 SON  H2B   H  HOH1  0   0.492  -1.4566   1.5298  -0.9844
 SON  H3B   H  HOH1  0   0.501  -3.7866   3.9089  -1.0627
 SON  HB1   H  HCH2  0   0.327  -3.9021   0.2743  -1.5938
 SON  HB2   H  HCH2  0   0.333  -5.1701   0.4817  -0.3717
 SON  H5'1  H  HCH2  0   0.265  -2.3543  -3.0756   0.6713
 SON  H5'2  H  HCH2  0   0.242  -1.3700  -1.7767   1.3592
 SON  H4'   H  HCH1  0   0.276  -1.0066  -3.1477  -1.3591
 SON  H1'   H  HCH1  0   0.264   2.1969  -1.9023  -1.0884
 SON  H2    H  HCR6  0   0.253   5.6532   0.6699  -2.0880
 SON  HN61  H  HNH2  0   0.404   4.7573   4.4143   0.2027
 SON  HN62  H  HNH2  0   0.411   3.2966   4.1324   1.0726
 SON  H8    H  HCR5  0   0.290   0.2622   0.3427   1.3449
 SON  H2'   H  HCH1  0   0.250   0.9428  -2.0612   1.6857
 SON  H3    H  HOH1  0   0.471   2.6403  -3.4741   1.9526
 SON  H3'   H  HCH1  0   0.260  -0.1157  -4.1369   1.0577
 SON  H1    H  HOH1  0   0.451   1.8058  -4.7433  -0.3021

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
 SON  PB   O1B   double    1.479  0.020  1.479
 SON  PB   O2B   single    1.605  0.020  1.605
 SON  PB   O3B   single    1.600  0.020  1.600
 SON  PB   CB    single    1.815  0.020  1.815
 SON  O2B  H2B   single    0.850  0.020  0.980
 SON  O3B  H3B   single    0.850  0.020  0.980
 SON  CB   CA    single    1.504  0.020  1.504
 SON  CB   HB1   single    0.970  0.020  1.090
 SON  CB   HB2   single    0.970  0.020  1.090
 SON  CA   OA    double    1.203  0.020  1.203
 SON  CA   O5'   single    1.324  0.020  1.324
 SON  O5'  C5'   single    1.427  0.020  1.427
 SON  C5'  C4'   single    1.514  0.020  1.514
 SON  C5'  H5'1  single    0.970  0.020  1.090
 SON  C5'  H5'2  single    0.970  0.020  1.090
 SON  C4'  O4'   single    1.429  0.020  1.429
 SON  C4'  C3'   single    1.524  0.020  1.524
 SON  C4'  H4'   single    0.970  0.020  1.090
 SON  O4'  C1'   single    1.402  0.020  1.402
 SON  C1'  N9    single    1.438  0.020  1.438
 SON  C1'  C2'   single    1.528  0.020  1.528
 SON  C1'  H1'   single    0.970  0.020  1.090
 SON  N9   C4    aromatic  1.366  0.020  1.366
 SON  N9   C8    aromatic  1.370  0.020  1.370
 SON  C4   N3    aromatic  1.330  0.020  1.330
 SON  C4   C5    aromatic  1.386  0.020  1.386
 SON  N3   C2    aromatic  1.322  0.020  1.322
 SON  C2   N1    aromatic  1.330  0.020  1.330
 SON  C2   H2    single    0.930  0.020  1.080
 SON  N1   C6    aromatic  1.338  0.020  1.338
 SON  C6   N6    single    1.334  0.020  1.334
 SON  C6   C5    aromatic  1.407  0.020  1.407
 SON  N6   HN61  single    0.860  0.020  1.020
 SON  N6   HN62  single    0.860  0.020  1.020
 SON  C5   N7    aromatic  1.372  0.020  1.372
 SON  N7   C8    aromatic  1.298  0.020  1.298
 SON  C8   H8    single    0.930  0.020  1.080
 SON  C2'  O2'   single    1.394  0.020  1.394
 SON  C2'  C3'   single    1.531  0.020  1.531
 SON  C2'  H2'   single    0.970  0.020  1.090
 SON  O2'  H3    single    0.850  0.020  0.980
 SON  C3'  O3'   single    1.403  0.020  1.403
 SON  C3'  H3'   single    0.970  0.020  1.090
 SON  O3'  H1    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
 SON  CB    PB   O3B   100.51  3.000
 SON  CB    PB   O2B   105.55  3.000
 SON  O3B   PB   O2B   107.82  3.000
 SON  CB    PB   O1B   115.63  3.000
 SON  O3B   PB   O1B   116.80  3.000
 SON  O2B   PB   O1B   109.58  3.000
 SON  H2B   O2B  PB    116.30  3.000
 SON  H3B   O3B  PB    114.30  3.000
 SON  HB2   CB   HB1   108.77  3.000
 SON  HB2   CB   CA    109.74  3.000
 SON  HB1   CB   CA    111.67  3.000
 SON  HB2   CB   PB    108.00  3.000
 SON  HB1   CB   PB    109.59  3.000
 SON  CA    CB   PB    109.00  3.000
 SON  O5'   CA   OA    124.22  3.000
 SON  O5'   CA   CB    111.30  3.000
 SON  OA    CA   CB    124.44  3.000
 SON  C5'   O5'  CA    117.85  3.000
 SON  H5'2  C5'  H5'1  108.00  3.000
 SON  H5'2  C5'  C4'   111.96  3.000
 SON  H5'1  C5'  C4'   109.46  3.000
 SON  H5'2  C5'  O5'   109.95  3.000
 SON  H5'1  C5'  O5'   110.62  3.000
 SON  C4'   C5'  O5'   106.87  3.000
 SON  H4'   C4'  C3'   110.70  3.000
 SON  H4'   C4'  O4'   108.61  3.000
 SON  C3'   C4'  O4'   106.16  3.000
 SON  H4'   C4'  C5'   109.19  3.000
 SON  C3'   C4'  C5'   111.67  3.000
 SON  O4'   C4'  C5'   110.44  3.000
 SON  C1'   O4'  C4'   110.61  3.000
 SON  H1'   C1'  C2'   110.14  3.000
 SON  H1'   C1'  N9    106.18  3.000
 SON  C2'   C1'  N9    114.09  3.000
 SON  H1'   C1'  O4'   111.55  3.000
 SON  C2'   C1'  O4'   105.61  3.000
 SON  N9    C1'  O4'   109.36  3.000
 SON  C8    N9   C4    106.23  3.000
 SON  C8    N9   C1'   127.31  3.000
 SON  C4    N9   C1'   126.45  3.000
 SON  C5    C4   N3    126.53  3.000
 SON  C5    C4   N9    105.13  3.000
 SON  N3    C4   N9    128.34  3.000
 SON  C2    N3   C4    111.68  3.000
 SON  H2    C2   N1    115.42  3.000
 SON  H2    C2   N3    116.15  3.000
 SON  N1    C2   N3    128.43  3.000
 SON  C6    N1   C2    119.18  3.000
 SON  C5    C6   N6    122.76  3.000
 SON  C5    C6   N1    117.89  3.000
 SON  N6    C6   N1    119.36  3.000
 SON  HN62  N6   HN61  118.01  3.000
 SON  HN62  N6   C6    120.87  3.000
 SON  HN61  N6   C6    120.08  3.000
 SON  N7    C5   C6    132.88  3.000
 SON  N7    C5   C4    110.82  3.000
 SON  C6    C5   C4    116.30  3.000
 SON  C8    N7   C5    104.44  3.000
 SON  H8    C8   N7    124.81  3.000
 SON  H8    C8   N9    121.80  3.000
 SON  N7    C8   N9    113.38  3.000
 SON  H2'   C2'  C3'   108.94  3.000
 SON  H2'   C2'  O2'   111.63  3.000
 SON  C3'   C2'  O2'   115.22  3.000
 SON  H2'   C2'  C1'   109.69  3.000
 SON  C3'   C2'  C1'   100.97  3.000
 SON  O2'   C2'  C1'   109.83  3.000
 SON  H3    O2'  C2'   108.99  3.000
 SON  H3'   C3'  O3'   111.76  3.000
 SON  H3'   C3'  C2'   111.93  3.000
 SON  O3'   C3'  C2'   111.04  3.000
 SON  H3'   C3'  C4'   112.04  3.000
 SON  O3'   C3'  C4'   108.56  3.000
 SON  C2'   C3'  C4'   100.99  3.000
 SON  H1    O3'  C3'   107.93  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
 SON  CONST_01  C2    N3   C4   N9    180.00   0.0  0
 SON  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 SON  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 SON  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 SON  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 SON  CONST_06  N1    C2   N3   C4      0.00   0.0  0
 SON  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 SON  CONST_08  C8    N7   C5   C4      0.00   0.0  0
 SON  CONST_09  C8    N9   C4   N3    180.00   0.0  0
 SON  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 SON  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 SON  CONST_12  C6    N1   C2   N3      0.00   0.0  0
 SON  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 SON  CONST_14  C5    C6   N1   C2      0.00   0.0  0
 SON  CONST_15  N7    C5   C6   N1    180.00   0.0  0
 SON  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 SON  CONST_17  C8    N9   C4   C5      0.00   0.0  0
 SON  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 SON  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 SON  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 SON  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 SON  CONST_22  N6    C6   N1   C2    180.00   0.0  0
 SON  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 SON  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 SON  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 SON  CONST_26  HN61  N6   C6   N1      0.00   0.0  0
 SON  CONST_27  HN62  N6   C6   N1    180.00   0.0  0
 SON  Var_01    C4'   C5'  O5'  CA   -176.24  30.0  3
 SON  Var_02    OA    CA   CB   PB     81.16  30.0  3
 SON  Var_03    CA    CB   PB   O1B   -66.31  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
 SON  chir_01  C4'  C5'  O4'  C3'  negativ
 SON  chir_02  C1'  O4'  N9   C2'  negativ
 SON  chir_03  C2'  O2'  C1'  C3'  negativ
 SON  chir_04  C3'  O3'  C2'  C4'  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
 SON  plan-1  C1'   0.020
 SON  plan-1  N9    0.020
 SON  plan-1  C4    0.020
 SON  plan-1  N3    0.020
 SON  plan-1  C2    0.020
 SON  plan-1  N1    0.020
 SON  plan-1  C6    0.020
 SON  plan-1  N6    0.020
 SON  plan-1  C5    0.020
 SON  plan-1  N7    0.020
 SON  plan-1  C8    0.020
 SON  plan-1  H2    0.020
 SON  plan-1  H8    0.020
 SON  plan-2  C6    0.020
 SON  plan-2  N6    0.020
 SON  plan-2  HN61  0.020
 SON  plan-2  HN62  0.020
 SON  plan-3  CB    0.020
 SON  plan-3  CA    0.020
 SON  plan-3  OA    0.020
 SON  plan-3  O5'   0.020

