# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:17:42 2021
#   Inital geometry file: a 100 line input string
#   Ligand name: 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 WTA  WTA  5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine  ligand  43  25  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WTA
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
 WTA  C1'  C  CR15  0   0.175  -15.0653   6.6947  -26.3435
 WTA  C1P  C  CH2   0  -0.191  -13.1985   3.4283  -23.7373
 WTA  C2   C  CR16  0   0.040  -19.3713   6.7464  -26.6131
 WTA  C2'  C  CR15  0  -0.039  -14.9331   8.1730  -26.7006
 WTA  C2P  C  CH3   0  -0.686  -14.4238   2.7915  -23.1308
 WTA  C3'  C  CR15  0  -0.044  -13.9135   8.6366  -25.6537
 WTA  C4   C  CR56  0   0.488  -17.4441   6.5206  -25.5891
 WTA  C4'  C  CR15  0   0.009  -12.9955   7.4192  -25.5623
 WTA  C5   C  CR56  0  -0.003  -18.0497   6.2168  -24.3805
 WTA  C5'  C  CH2   0  -0.188  -12.3373   7.2852  -24.2134
 WTA  C6   C  CR6   0   0.458  -19.4573   6.2009  -24.3780
 WTA  C8   C  CR15  0   0.107  -15.9708   6.1452  -24.0207
 WTA  N1   N  N     0  -0.473  -20.0880   6.4740  -25.5257
 WTA  N3   N  N     0  -0.459  -18.0563   6.7943  -26.7396
 WTA  N6   N  NH2   0  -0.816  -20.1738   5.9164  -23.2899
 WTA  N7   N  N     0  -0.448  -17.1099   5.9845  -23.4122
 WTA  N9   N  NR5   0  -0.539  -16.1033   6.4763  -25.3414
 WTA  O1P  O  OH1   0  -0.736  -11.2642   5.9446  -21.6932
 WTA  O2'  O  OH1   0  -0.663  -14.3949   8.2459  -27.9910
 WTA  O2P  O  O     0  -0.699  -10.1874   4.1993  -23.3451
 WTA  O3'  O  OH1   0  -0.654  -13.1775   9.7624  -26.0363
 WTA  O3P  O  O2    0  -0.593  -12.7418   4.4741  -22.8531
 WTA  O4'  O  O     0  -0.492  -13.8322   6.2958  -25.8258
 WTA  O5'  O  O2    0  -0.588  -11.4260   6.1867  -24.2440
 WTA  P    P  P     0   1.480  -11.3015   5.1210  -23.0579
 WTA  H1   H  HCR5  0   0.290  -15.3256   6.0905  -27.2166
 WTA  H2   H  HCH2  0   0.241  -13.4221   3.8599  -24.7143
 WTA  H3   H  HCH2  0   0.244  -12.4091   2.6854  -23.8649
 WTA  H4   H  HCR6  0   0.253  -19.9460   6.9581  -27.5086
 WTA  H5   H  HCR5  0   0.265  -15.8877   8.7070  -26.6242
 WTA  H6   H  HCH3  0   0.242  -14.7701   1.9932  -23.7872
 WTA  H7   H  HCH3  0   0.240  -14.2031   2.3522  -22.1583
 WTA  H8   H  HCH3  0   0.234  -15.2408   3.5035  -23.0142
 WTA  H9   H  HCR5  0   0.251  -14.4263   8.8001  -24.6960
 WTA  H10  H  HCR5  0   0.262  -12.2225   7.4823  -26.3375
 WTA  H11  H  HCH2  0   0.266  -11.7771   8.1984  -24.0004
 WTA  H12  H  HCH2  0   0.237  -13.0923   7.1704  -23.4311
 WTA  H13  H  HCR5  0   0.285  -15.0085   6.0198  -23.5508
 WTA  H14  H  HNH2  0   0.404  -21.1771   5.9769  -23.3153
 WTA  H15  H  HNH2  0   0.412  -19.7296   5.7768  -22.3994
 WTA  H16  H  HOH1  0   0.504  -10.4305   6.4081  -21.5351
 WTA  H17  H  HOH1  0   0.453  -13.8847   9.0631  -28.0537
 WTA  H18  H  HOH1  0   0.471  -13.6834  10.5524  -25.8202

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
 WTA  O2'  C2'  single    1.400  0.020  1.400
 WTA  N3   C2   aromatic  1.322  0.020  1.322
 WTA  N3   C4   aromatic  1.332  0.020  1.332
 WTA  C2   N1   aromatic  1.331  0.020  1.331
 WTA  C1'  C2'  single    1.527  0.020  1.527
 WTA  C1'  O4'  single    1.396  0.020  1.396
 WTA  C1'  N9   single    1.459  0.020  1.459
 WTA  C2'  C3'  single    1.533  0.020  1.533
 WTA  O4'  C4'  single    1.425  0.020  1.425
 WTA  C4   N9   aromatic  1.364  0.020  1.364
 WTA  C4   C5   aromatic  1.386  0.020  1.386
 WTA  N1   C6   aromatic  1.338  0.020  1.338
 WTA  N9   C8   aromatic  1.368  0.020  1.368
 WTA  C4'  C3'  single    1.527  0.020  1.527
 WTA  C4'  C5'  single    1.507  0.020  1.507
 WTA  C3'  O3'  single    1.398  0.020  1.398
 WTA  C6   C5   aromatic  1.408  0.020  1.408
 WTA  C6   N6   single    1.334  0.020  1.334
 WTA  C5   N7   aromatic  1.369  0.020  1.369
 WTA  O5'  C5'  single    1.428  0.020  1.428
 WTA  O5'  P    single    1.599  0.020  1.599
 WTA  C8   N7   aromatic  1.301  0.020  1.301
 WTA  O2P  P    double    1.474  0.020  1.474
 WTA  P    O1P  single    1.594  0.020  1.594
 WTA  P    O3P  single    1.592  0.020  1.592
 WTA  C1P  O3P  single    1.444  0.020  1.444
 WTA  C1P  C2P  single    1.508  0.020  1.508
 WTA  C1'  H1   single    0.970  0.020  1.090
 WTA  C1P  H2   single    0.970  0.020  1.090
 WTA  C1P  H3   single    0.970  0.020  1.090
 WTA  C2   H4   single    0.930  0.020  1.080
 WTA  C2'  H5   single    0.970  0.020  1.090
 WTA  C2P  H6   single    0.970  0.020  1.090
 WTA  C2P  H7   single    0.970  0.020  1.090
 WTA  C2P  H8   single    0.970  0.020  1.090
 WTA  C3'  H9   single    0.970  0.020  1.090
 WTA  C4'  H10  single    0.970  0.020  1.090
 WTA  C5'  H11  single    0.970  0.020  1.090
 WTA  C5'  H12  single    0.970  0.020  1.090
 WTA  C8   H13  single    0.930  0.020  1.080
 WTA  N6   H14  single    0.860  0.020  1.020
 WTA  N6   H15  single    0.860  0.020  1.020
 WTA  O1P  H16  single    0.850  0.020  0.980
 WTA  O2'  H17  single    0.850  0.020  0.980
 WTA  O3'  H18  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
 WTA  H1   C1'  O4'  110.41  3.000
 WTA  H1   C1'  N9   107.24  3.000
 WTA  O4'  C1'  N9   109.33  3.000
 WTA  H1   C1'  C2'  111.65  3.000
 WTA  N9   C1'  C2'  111.54  3.000
 WTA  O4'  C1'  C2'  106.68  3.000
 WTA  H3   C1P  H2   108.23  3.000
 WTA  H3   C1P  O3P  109.62  3.000
 WTA  H2   C1P  O3P  109.07  3.000
 WTA  H3   C1P  C2P  110.31  3.000
 WTA  H2   C1P  C2P  111.14  3.000
 WTA  O3P  C1P  C2P  108.46  3.000
 WTA  H4   C2   N3   116.16  3.000
 WTA  H4   C2   N1   115.41  3.000
 WTA  N3   C2   N1   128.42  3.000
 WTA  H5   C2'  O2'  111.94  3.000
 WTA  H5   C2'  C3'  112.59  3.000
 WTA  O2'  C2'  C3'  110.98  3.000
 WTA  H5   C2'  C1'  112.33  3.000
 WTA  C3'  C2'  C1'  100.99  3.000
 WTA  O2'  C2'  C1'  107.42  3.000
 WTA  H8   C2P  H7   108.64  3.000
 WTA  H8   C2P  H6   107.74  3.000
 WTA  H7   C2P  H6   107.85  3.000
 WTA  H8   C2P  C1P  112.10  3.000
 WTA  H7   C2P  C1P  111.38  3.000
 WTA  H6   C2P  C1P  108.98  3.000
 WTA  H9   C3'  O3'  111.37  3.000
 WTA  H9   C3'  C4'  110.30  3.000
 WTA  O3'  C3'  C4'  109.98  3.000
 WTA  H9   C3'  C2'  109.26  3.000
 WTA  O3'  C3'  C2'  113.99  3.000
 WTA  C4'  C3'  C2'  101.51  3.000
 WTA  N9   C4   N3   127.98  3.000
 WTA  N9   C4   C5   105.31  3.000
 WTA  N3   C4   C5   126.71  3.000
 WTA  H10  C4'  O4'  109.17  3.000
 WTA  H10  C4'  C5'  109.27  3.000
 WTA  O4'  C4'  C5'  110.60  3.000
 WTA  H10  C4'  C3'  109.60  3.000
 WTA  C5'  C4'  C3'  112.76  3.000
 WTA  O4'  C4'  C3'  105.33  3.000
 WTA  N7   C5   C6   133.09  3.000
 WTA  N7   C5   C4   110.73  3.000
 WTA  C6   C5   C4   116.17  3.000
 WTA  H12  C5'  H11  107.61  3.000
 WTA  H12  C5'  O5'  112.04  3.000
 WTA  H11  C5'  O5'  108.67  3.000
 WTA  H12  C5'  C4'  110.38  3.000
 WTA  H11  C5'  C4'  108.92  3.000
 WTA  O5'  C5'  C4'  109.15  3.000
 WTA  N6   C6   N1   119.36  3.000
 WTA  N6   C6   C5   122.76  3.000
 WTA  N1   C6   C5   117.88  3.000
 WTA  H13  C8   N9   122.37  3.000
 WTA  H13  C8   N7   124.26  3.000
 WTA  N9   C8   N7   113.36  3.000
 WTA  C6   N1   C2   119.27  3.000
 WTA  C4   N3   C2   111.54  3.000
 WTA  H15  N6   H14  118.16  3.000
 WTA  H15  N6   C6   121.01  3.000
 WTA  H14  N6   C6   120.18  3.000
 WTA  C8   N7   C5   104.43  3.000
 WTA  C8   N9   C4   106.17  3.000
 WTA  C8   N9   C1'  129.07  3.000
 WTA  C4   N9   C1'  124.72  3.000
 WTA  H16  O1P  P    114.06  3.000
 WTA  H17  O2'  C2'  107.89  3.000
 WTA  H18  O3'  C3'  108.82  3.000
 WTA  P    O3P  C1P  120.12  3.000
 WTA  C4'  O4'  C1'  111.22  3.000
 WTA  P    O5'  C5'  123.13  3.000
 WTA  O5'  P    O3P  107.20  3.000
 WTA  O3P  P    O2P  117.05  3.000
 WTA  O5'  P    O2P  109.33  3.000
 WTA  O3P  P    O1P   96.95  3.000
 WTA  O2P  P    O1P  118.16  3.000
 WTA  O5'  P    O1P  107.00  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
 WTA  CONST_01  N9   C4   N3   C2    180.00   0.0  0
 WTA  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 WTA  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 WTA  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 WTA  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 WTA  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 WTA  CONST_07  C8   N7   C5   C4      0.00   0.0  0
 WTA  CONST_08  C8   N9   C4   C5      0.00   0.0  0
 WTA  CONST_09  N9   C8   N7   C5      0.00   0.0  0
 WTA  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 WTA  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 WTA  CONST_12  N9   C4   C5   C6    180.00   0.0  0
 WTA  CONST_13  C8   N7   C5   C6    180.00   0.0  0
 WTA  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 WTA  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 WTA  CONST_16  N7   C5   C4   N3    180.00   0.0  0
 WTA  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 WTA  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 WTA  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 WTA  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 WTA  CONST_21  N6   C6   N1   C2    180.00   0.0  0
 WTA  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 WTA  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 WTA  CONST_24  H13  C8   N9   C1'     0.00   0.0  0
 WTA  CONST_25  H4   C2   N3   C4    180.00   0.0  0
 WTA  CONST_26  H14  N6   C6   C5    180.00   0.0  0
 WTA  CONST_27  H15  N6   C6   C5      0.00   0.0  0
 WTA  Var_01    O5'  P    O3P  C1P    79.93  30.0  1
 WTA  Var_02    H6   C2P  C1P  O3P  -179.43  30.0  3
 WTA  Var_03    H11  C5'  O5'  P     104.42  30.0  3
 WTA  Var_04    H2   C1P  O3P  P     -71.87  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
 WTA  chir_01  C1'  C2'  O4'  N9   negativ
 WTA  chir_02  C2'  O2'  C3'  C1'  positiv
 WTA  chir_03  C3'  O3'  C4'  C2'  positiv
 WTA  chir_04  C4'  O4'  C3'  C5'  negativ
 WTA  chir_05  P    O2P  O1P  O3P  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
 WTA  plan-1  C1'  0.020
 WTA  plan-1  C2   0.020
 WTA  plan-1  C4   0.020
 WTA  plan-1  C5   0.020
 WTA  plan-1  C6   0.020
 WTA  plan-1  C8   0.020
 WTA  plan-1  N1   0.020
 WTA  plan-1  N3   0.020
 WTA  plan-1  N6   0.020
 WTA  plan-1  N7   0.020
 WTA  plan-1  N9   0.020
 WTA  plan-1  H4   0.020
 WTA  plan-1  H13  0.020
 WTA  plan-2  C6   0.020
 WTA  plan-2  N6   0.020
 WTA  plan-2  H14  0.020
 WTA  plan-2  H15  0.020

