# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 16:08:31 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: [[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Cn1cnc2c(N)ncnc12)OC[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O
#
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
 EOI  EOI  '[[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  40  27  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EOI
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
 EOI  C     C  CH3    0  -0.672  -3.1630   4.3480   0.2974
 EOI  N     N  NR5    0  -0.481  -3.8540   0.6878  -0.4376
 EOI  O     O  O2     0  -0.482  -1.9971   2.3267   0.9435
 EOI  P     P  P      0   1.127   0.0282   1.1031  -0.3365
 EOI  S     S  S2     0  -0.351  -0.1429  -0.5842   0.7195
 EOI  C1    C  CH1    0  -0.037  -2.8371   2.9008  -0.0364
 EOI  N1    N  N      0  -0.417  -3.3574  -1.0746  -1.7126
 EOI  O1    O  O      0  -0.602  -0.5707   1.1488  -1.7124
 EOI  P1    P  P      0   1.341   2.9130   0.8432  -0.9652
 EOI  C2    C  CH2    0  -0.317  -4.1082   2.0660  -0.0900
 EOI  N2    N  N      0  -0.475  -3.8128  -0.3789   1.7404
 EOI  O2    O  O2     0  -0.697   1.5879   1.6267  -0.3572
 EOI  P2    P  P      0   1.214   3.8265  -1.4819   0.6472
 EOI  C3    C  CR15   0   0.082  -3.6287   0.1946  -1.6892
 EOI  N3    N  N      0  -0.287  -3.2677  -2.6996   1.5880
 EOI  O3    O  O      0  -0.718   2.4893  -0.1408  -2.0027
 EOI  C4    C  CR56   0   0.054  -3.3875  -1.4445  -0.3936
 EOI  O4    O  OP    -1  -0.918   3.9059   1.9240  -1.2731
 EOI  C5    C  CR56   0   0.433  -3.6872  -0.3598   0.4162
 EOI  O5    O  O2     0  -0.740   3.3908   0.0962   0.4090
 EOI  C6    C  CR16   0  -0.009  -3.5806  -1.5791   2.2367
 EOI  O6    O  OP    -1  -0.950   4.0453  -1.5880   2.1277
 EOI  C7    C  CR6    0   0.382  -3.1595  -2.6641   0.2576
 EOI  O7    O  OP    -1  -0.940   2.4899  -2.2915   0.2059
 EOI  C8    C  CH2    0  -0.427  -0.6185   2.4786   0.7095
 EOI  O8    O  O      0  -0.957   4.9224  -1.8651  -0.2990
 EOI  H     H  HCH3   0   0.256  -2.2548   4.9497   0.3511
 EOI  HA    H  HCH3   0   0.215  -3.8002   4.7893  -0.4699
 EOI  HB    H  HCH3   0   0.260  -3.6792   4.4256   1.2559
 EOI  HS    H  HSH1   0   0.276   1.6621  -1.7736   0.3261
 EOI  H1    H  HCH1   0   0.315  -2.3552   2.8571  -1.0199
 EOI  H2    H  HCH2   0   0.279  -4.7948   2.4926  -0.8223
 EOI  H2A   H  HCH2   0   0.282  -4.6146   2.0807   0.8762
 EOI  H3    H  HCR5   0   0.283  -3.6946   0.8347  -2.5565
 EOI  HN4   H  HNH2   0   0.372  -2.8394  -4.6622   0.0872
 EOI  HN4A  H  HNH2   0   0.384  -2.9028  -3.8159  -1.4013
 EOI  H6    H  HCR6   0   0.247  -3.6612  -1.6752   3.3150
 EOI  H8    H  HCH2   0   0.292  -0.3811   3.4402   0.2341
 EOI  H8A   H  HCH2   0   0.272  -0.1085   2.4660   1.6756
 EOI  N4    N  NH2    0  -0.891  -2.8149  -3.7829  -0.4006

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
 EOI  C   C1    single    1.521  0.020  1.521
 EOI  C   H     single    0.970  0.020  1.090
 EOI  C   HA    single    0.970  0.020  1.090
 EOI  C   HB    single    0.970  0.020  1.090
 EOI  C2  N     single    1.444  0.020  1.444
 EOI  N   C3    aromatic  1.364  0.020  1.364
 EOI  N   C5    aromatic  1.362  0.020  1.362
 EOI  C8  O     single    1.407  0.020  1.407
 EOI  O   C1    single    1.413  0.020  1.413
 EOI  C8  P     single    1.845  0.020  1.845
 EOI  S   P     single    1.998  0.020  1.998
 EOI  P   O2    single    1.645  0.020  1.645
 EOI  P   O1    double    1.501  0.020  1.501
 EOI  S   HS    single    1.200  0.020  1.300
 EOI  C1  C2    single    1.522  0.020  1.522
 EOI  C1  H1    single    0.970  0.020  1.090
 EOI  C3  N1    aromatic  1.298  0.020  1.298
 EOI  N1  C4    aromatic  1.370  0.020  1.370
 EOI  O5  P1    single    1.635  0.020  1.635
 EOI  O3  P1    deloc     1.491  0.020  1.491
 EOI  O2  P1    single    1.655  0.020  1.655
 EOI  P1  O4    deloc     1.500  0.020  1.500
 EOI  C2  H2    single    0.970  0.020  1.090
 EOI  C2  H2A   single    0.970  0.020  1.090
 EOI  N2  C5    aromatic  1.330  0.020  1.330
 EOI  N2  C6    aromatic  1.319  0.020  1.319
 EOI  O8  P2    deloc     1.498  0.020  1.498
 EOI  O6  P2    deloc     1.500  0.020  1.500
 EOI  P2  O7    deloc     1.624  0.020  1.624
 EOI  P2  O5    single    1.654  0.020  1.654
 EOI  C3  H3    single    0.930  0.020  1.080
 EOI  C6  N3    aromatic  1.332  0.020  1.332
 EOI  N3  C7    aromatic  1.335  0.020  1.335
 EOI  C5  C4    aromatic  1.386  0.020  1.386
 EOI  C4  C7    aromatic  1.401  0.020  1.401
 EOI  C7  N4    single    1.343  0.020  1.343
 EOI  N4  HN4   single    0.890  0.020  1.040
 EOI  N4  HN4A  single    0.890  0.020  1.040
 EOI  C6  H6    single    0.930  0.020  1.080
 EOI  C8  H8    single    0.970  0.020  1.090
 EOI  C8  H8A   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
 EOI  HB    C   HA   108.22  3.000
 EOI  HB    C   H    108.14  3.000
 EOI  HA    C   H    107.33  3.000
 EOI  HB    C   C1   111.21  3.000
 EOI  HA    C   C1   110.85  3.000
 EOI  H     C   C1   110.94  3.000
 EOI  C5    N   C3   106.08  3.000
 EOI  C5    N   C2   127.22  3.000
 EOI  C3    N   C2   126.52  3.000
 EOI  C8    O   C1   115.06  3.000
 EOI  C8    P   O2    95.86  3.000
 EOI  O2    P   O1   110.91  3.000
 EOI  C8    P   O1   110.92  3.000
 EOI  O1    P   S    118.42  3.000
 EOI  O2    P   S    110.89  3.000
 EOI  C8    P   S    107.45  3.000
 EOI  HS    S   P    106.99  3.000
 EOI  H1    C1  C2   108.29  3.000
 EOI  H1    C1  O    110.17  3.000
 EOI  C2    C1  O    107.35  3.000
 EOI  H1    C1  C    109.21  3.000
 EOI  C2    C1  C    110.54  3.000
 EOI  O     C1  C    111.22  3.000
 EOI  C4    N1  C3   104.01  3.000
 EOI  O5    P1  O4   107.96  3.000
 EOI  O4    P1  O3   121.38  3.000
 EOI  O5    P1  O3   111.48  3.000
 EOI  O4    P1  O2   105.32  3.000
 EOI  O3    P1  O2   109.90  3.000
 EOI  O5    P1  O2    98.13  3.000
 EOI  H2A   C2  H2   107.29  3.000
 EOI  H2A   C2  C1   110.44  3.000
 EOI  H2    C2  C1   109.57  3.000
 EOI  H2A   C2  N    107.92  3.000
 EOI  H2    C2  N    108.81  3.000
 EOI  C1    C2  N    112.65  3.000
 EOI  C6    N2  C5   111.77  3.000
 EOI  P1    O2  P    127.80  3.000
 EOI  O8    P2  O7   107.64  3.000
 EOI  O7    P2  O6   110.67  3.000
 EOI  O8    P2  O6   119.91  3.000
 EOI  O7    P2  O5   102.69  3.000
 EOI  O6    P2  O5   104.35  3.000
 EOI  O8    P2  O5   110.23  3.000
 EOI  H3    C3  N1   125.30  3.000
 EOI  H3    C3  N    120.83  3.000
 EOI  N1    C3  N    113.86  3.000
 EOI  C7    N3  C6   118.81  3.000
 EOI  C7    C4  C5   116.40  3.000
 EOI  C7    C4  N1   132.75  3.000
 EOI  C5    C4  N1   110.85  3.000
 EOI  C4    C5  N2   126.21  3.000
 EOI  C4    C5  N    105.19  3.000
 EOI  N2    C5  N    128.58  3.000
 EOI  P2    O5  P1   129.32  3.000
 EOI  H6    C6  N3   115.26  3.000
 EOI  H6    C6  N2   116.17  3.000
 EOI  N3    C6  N2   128.57  3.000
 EOI  N4    C7  C4   122.61  3.000
 EOI  N4    C7  N3   119.14  3.000
 EOI  C4    C7  N3   118.23  3.000
 EOI  H8A   C8  H8   106.97  3.000
 EOI  H8A   C8  P    109.22  3.000
 EOI  H8    C8  P    109.35  3.000
 EOI  H8A   C8  O    108.01  3.000
 EOI  H8    C8  O    112.23  3.000
 EOI  P     C8  O    110.94  3.000
 EOI  HN4A  N4  HN4  116.87  3.000
 EOI  HN4A  N4  C7   119.53  3.000
 EOI  HN4   N4  C7   118.97  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
 EOI  CONST_01  C4    N1  C3  N     0.00   0.0  0
 EOI  CONST_02  C6    N2  C5  N   180.00   0.0  0
 EOI  CONST_03  N1    C4  C5  N     0.00   0.0  0
 EOI  CONST_04  C7    C4  C5  N   180.00   0.0  0
 EOI  CONST_05  C5    N   C3  N1    0.00   0.0  0
 EOI  CONST_06  N2    C5  C4  N1  180.00   0.0  0
 EOI  CONST_07  N3    C7  C4  N1  180.00   0.0  0
 EOI  CONST_08  C3    N   C5  N2  180.00   0.0  0
 EOI  CONST_09  C7    C4  C5  N2    0.00   0.0  0
 EOI  CONST_10  C7    N3  C6  N2    0.00   0.0  0
 EOI  CONST_11  C4    C5  N   C3    0.00   0.0  0
 EOI  CONST_12  C5    C4  N1  C3    0.00   0.0  0
 EOI  CONST_13  C7    C4  N1  C3  180.00   0.0  0
 EOI  CONST_14  C5    N2  C6  N3    0.00   0.0  0
 EOI  CONST_15  C5    C4  C7  N3    0.00   0.0  0
 EOI  CONST_16  C6    N2  C5  C4    0.00   0.0  0
 EOI  CONST_17  C6    N3  C7  C4    0.00   0.0  0
 EOI  CONST_18  C2    N   C3  N1  180.00   0.0  0
 EOI  CONST_19  N4    C7  C4  N1    0.00   0.0  0
 EOI  CONST_20  N2    C5  N   C2    0.00   0.0  0
 EOI  CONST_21  C4    C5  N   C2  180.00   0.0  0
 EOI  CONST_22  C6    N3  C7  N4  180.00   0.0  0
 EOI  CONST_23  C5    C4  C7  N4  180.00   0.0  0
 EOI  CONST_24  H3    C3  N1  C4  180.00   0.0  0
 EOI  CONST_25  H6    C6  N2  C5  180.00   0.0  0
 EOI  CONST_26  HN4   N4  C7  N3    0.00   0.0  0
 EOI  CONST_27  HN4A  N4  C7  N3  180.00   0.0  0
 EOI  Var_01    C3    N   C2  C1  -79.40  30.0  2
 EOI  Var_02    S     P   C8  O   -65.45  30.0  3
 EOI  Var_03    O5    P1  O2  P   -92.51  30.0  3
 EOI  Var_04    O8    P2  O5  P1   54.72  30.0  3
 EOI  Var_05    C8    P   O2  P1  172.42  30.0  1

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
 EOI  chir_02  C1  C  O   C2  negativ
 EOI  chir_03  P   S  O2  O1  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
 EOI  plan-1  N     0.020
 EOI  plan-1  N1    0.020
 EOI  plan-1  C2    0.020
 EOI  plan-1  N2    0.020
 EOI  plan-1  C3    0.020
 EOI  plan-1  N3    0.020
 EOI  plan-1  C4    0.020
 EOI  plan-1  C5    0.020
 EOI  plan-1  C6    0.020
 EOI  plan-1  C7    0.020
 EOI  plan-1  H3    0.020
 EOI  plan-1  H6    0.020
 EOI  plan-1  N4    0.020
 EOI  plan-2  C7    0.020
 EOI  plan-2  HN4   0.020
 EOI  plan-2  HN4A  0.020
 EOI  plan-2  N4    0.020

