# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 03:48:04 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: 3'-O-acetyl-5'-O-[(R)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)Oc2ccccc2)N3C=C(C)C(=O)NC3=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
 TPE  TPE  3'-O-acetyl-5'-O-[(R)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine  ligand  56  34  .  2021-08-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TPE
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
 TPE  C1B   C  CR6   0   0.350  23.4334  23.7489  17.4441
 TPE  C2B   C  CR16  0  -0.314  22.3219  23.5274  18.2412
 TPE  C3B   C  CR16  0  -0.256  22.3341  22.4649  19.1340
 TPE  C4B   C  CR16  0  -0.257  23.4520  21.6490  19.2432
 TPE  C5B   C  CR16  0  -0.249  24.5548  21.8848  18.4338
 TPE  C6B   C  CR16  0  -0.311  24.5503  22.9308  17.5208
 TPE  PA    P  P     0   1.529  22.5969  27.2974  18.4596
 TPE  O1A   O  O     0  -0.657  21.2378  26.7996  18.2201
 TPE  O2A   O  OH1   0  -0.719  22.6489  28.8433  18.7861
 TPE  O3A   O  O2    0  -0.699  23.6144  27.1976  17.2063
 TPE  PB    P  P     0   1.488  24.2747  26.0431  16.2955
 TPE  O1B   O  O     0  -0.649  24.3521  26.4383  14.8859
 TPE  O2B   O  OH1   0  -0.719  25.6162  25.8011  17.0996
 TPE  O3B   O  O2    0  -0.616  23.3519  24.7554  16.4975
 TPE  O5'   O  O2    0  -0.593  23.3116  26.5013  19.6325
 TPE  C5'   C  CH2   0  -0.228  24.5535  26.8801  20.2418
 TPE  C4'   C  CH1   0  -0.001  24.7512  26.0574  21.4904
 TPE  O4'   O  O2    0  -0.494  23.7835  26.4111  22.4659
 TPE  C3'   C  CH1   0  -0.033  24.6211  24.5370  21.2674
 TPE  O3'   O  O2    0  -0.465  25.6141  23.8199  22.0039
 TPE  CR    C  C     0   0.561  26.8522  23.7953  21.5039
 TPE  OR    O  O     0  -0.440  27.1610  24.3760  20.4949
 TPE  CHR   C  CH3   0  -0.772  27.7735  22.9832  22.3605
 TPE  C2'   C  CH2   0  -0.527  23.2735  24.2114  21.8749
 TPE  C1'   C  CH1   0   0.206  23.1232  25.2700  22.9584
 TPE  N1    N  NR6   0  -0.569  21.7469  25.6279  23.2533
 TPE  C2    C  CR6   0   0.736  21.2744  25.5167  24.5429
 TPE  O2    O  OC    0  -0.480  21.9386  25.1083  25.4729
 TPE  N3    N  NR16  0  -0.737  19.9687  25.9021  24.6975
 TPE  C4    C  CR6   0   0.564  19.0991  26.3888  23.7375
 TPE  O4    O  OC    0  -0.449  17.9572  26.6880  24.0310
 TPE  C5    C  CR6   0  -0.182  19.6751  26.5004  22.4106
 TPE  C5M   C  CH3   0  -0.717  18.8367  27.0255  21.2920
 TPE  C6    C  CR16  0   0.063  20.9532  26.1249  22.2494
 TPE  H2B   H  HCR6  0   0.281  21.4575  24.1723  18.1602
 TPE  H3B   H  HCR6  0   0.273  21.4665  22.2836  19.7548
 TPE  H4B   H  HCR6  0   0.265  23.4618  20.8308  19.9507
 TPE  H5B   H  HCR6  0   0.268  25.4260  21.2471  18.5014
 TPE  H6B   H  HCR6  0   0.274  25.3999  23.0807  16.8689
 TPE  HPA2  H  HOH1  0   0.510  23.4926  29.3094  18.7025
 TPE  HPB2  H  HOH1  0   0.516  26.3652  25.4790  16.5779
 TPE  H5'2  H  HCH2  0   0.266  25.3823  26.6923  19.5583
 TPE  H5'1  H  HCH2  0   0.272  24.5468  27.9410  20.5000
 TPE  H4'   H  HCH1  0   0.281  25.7487  26.3103  21.8641
 TPE  H3'   H  HCH1  0   0.293  24.6802  24.2622  20.2126
 TPE  HHR3  H  HCH3  0   0.265  28.7221  22.8277  21.8549
 TPE  HHR2  H  HCH3  0   0.279  27.9607  23.5075  23.2992
 TPE  HHR1  H  HCH3  0   0.272  27.3313  22.0196  22.6095
 TPE  H2'2  H  HCH2  0   0.275  22.5090  24.3173  21.1073
 TPE  H2'1  H  HCH2  0   0.293  23.2099  23.1974  22.2657
 TPE  H1'   H  HCH1  0   0.280  23.5682  24.9375  23.8968
 TPE  H3    H  HNR6  0   0.427  19.6056  25.8207  25.6395
 TPE  H5M3  H  HCH3  0   0.245  19.4073  27.0623  20.3649
 TPE  H5M2  H  HCH3  0   0.249  17.9629  26.3951  21.1220
 TPE  H5M1  H  HCH3  0   0.249  18.4732  28.0317  21.5038
 TPE  H6    H  HCR6  0   0.303  21.4251  26.2085  21.2818

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
 TPE  C1B  C2B   aromatic  1.386  0.020  1.386
 TPE  C1B  C6B   aromatic  1.387  0.020  1.387
 TPE  C1B  O3B   single    1.384  0.020  1.384
 TPE  C2B  C3B   aromatic  1.388  0.020  1.388
 TPE  C2B  H2B   single    0.930  0.020  1.080
 TPE  C3B  C4B   aromatic  1.388  0.020  1.388
 TPE  C3B  H3B   single    0.930  0.020  1.080
 TPE  C4B  C5B   aromatic  1.388  0.020  1.388
 TPE  C4B  H4B   single    0.930  0.020  1.080
 TPE  C5B  C6B   aromatic  1.388  0.020  1.388
 TPE  C5B  H5B   single    0.930  0.020  1.080
 TPE  C6B  H6B   single    0.930  0.020  1.080
 TPE  PA   O1A   double    1.467  0.020  1.467
 TPE  PA   O2A   single    1.581  0.020  1.581
 TPE  PA   O3A   single    1.617  0.020  1.617
 TPE  PA   O5'   single    1.588  0.020  1.588
 TPE  O2A  HPA2  single    0.850  0.020  0.980
 TPE  O3A  PB    single    1.612  0.020  1.612
 TPE  PB   O1B   double    1.466  0.020  1.466
 TPE  PB   O2B   single    1.583  0.020  1.583
 TPE  PB   O3B   single    1.597  0.020  1.597
 TPE  O2B  HPB2  single    0.850  0.020  0.980
 TPE  O5'  C5'   single    1.434  0.020  1.434
 TPE  C5'  C4'   single    1.508  0.020  1.508
 TPE  C5'  H5'2  single    0.970  0.020  1.090
 TPE  C5'  H5'1  single    0.970  0.020  1.090
 TPE  C4'  O4'   single    1.419  0.020  1.419
 TPE  C4'  C3'   single    1.542  0.020  1.542
 TPE  C4'  H4'   single    0.970  0.020  1.090
 TPE  O4'  C1'   single    1.407  0.020  1.407
 TPE  C3'  O3'   single    1.429  0.020  1.429
 TPE  C3'  C2'   single    1.514  0.020  1.514
 TPE  C3'  H3'   single    0.970  0.020  1.090
 TPE  O3'  CR    single    1.335  0.020  1.335
 TPE  CR   OR    double    1.204  0.020  1.204
 TPE  CR   CHR   single    1.497  0.020  1.497
 TPE  CHR  HHR3  single    0.970  0.020  1.090
 TPE  CHR  HHR2  single    0.970  0.020  1.090
 TPE  CHR  HHR1  single    0.970  0.020  1.090
 TPE  C2'  C1'   single    1.522  0.020  1.522
 TPE  C2'  H2'2  single    0.970  0.020  1.090
 TPE  C2'  H2'1  single    0.970  0.020  1.090
 TPE  C1'  N1    single    1.452  0.020  1.452
 TPE  C1'  H1'   single    0.970  0.020  1.090
 TPE  N1   C2    aromatic  1.378  0.020  1.378
 TPE  N1   C6    aromatic  1.373  0.020  1.373
 TPE  C2   O2    double    1.214  0.020  1.214
 TPE  C2   N3    aromatic  1.370  0.020  1.370
 TPE  N3   C4    aromatic  1.384  0.020  1.384
 TPE  N3   H3    single    0.860  0.020  1.020
 TPE  C4   O4    double    1.216  0.020  1.216
 TPE  C4   C5    aromatic  1.451  0.020  1.451
 TPE  C5   C5M   single    1.493  0.020  1.493
 TPE  C5   C6    aromatic  1.342  0.020  1.342
 TPE  C5M  H5M3  single    0.970  0.020  1.090
 TPE  C5M  H5M2  single    0.970  0.020  1.090
 TPE  C5M  H5M1  single    0.970  0.020  1.090
 TPE  C6   H6    single    0.930  0.020  1.080

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
 TPE  O3B   C1B  C6B   120.95  3.000
 TPE  O3B   C1B  C2B   117.55  3.000
 TPE  C6B   C1B  C2B   121.33  3.000
 TPE  H2B   C2B  C3B   120.78  3.000
 TPE  H2B   C2B  C1B   120.18  3.000
 TPE  C3B   C2B  C1B   119.04  3.000
 TPE  H3B   C3B  C4B   120.13  3.000
 TPE  H3B   C3B  C2B   119.36  3.000
 TPE  C4B   C3B  C2B   120.51  3.000
 TPE  H4B   C4B  C5B   120.17  3.000
 TPE  H4B   C4B  C3B   120.22  3.000
 TPE  C5B   C4B  C3B   119.60  3.000
 TPE  H5B   C5B  C6B   119.20  3.000
 TPE  H5B   C5B  C4B   120.22  3.000
 TPE  C6B   C5B  C4B   120.58  3.000
 TPE  H6B   C6B  C5B   119.89  3.000
 TPE  H6B   C6B  C1B   121.18  3.000
 TPE  C5B   C6B  C1B   118.91  3.000
 TPE  O5'   PA   O3A   104.97  3.000
 TPE  O5'   PA   O2A   108.84  3.000
 TPE  O3A   PA   O2A   101.52  3.000
 TPE  O5'   PA   O1A   111.56  3.000
 TPE  O3A   PA   O1A   115.81  3.000
 TPE  O2A   PA   O1A   113.33  3.000
 TPE  HPA2  O2A  PA    118.81  3.000
 TPE  PB    O3A  PA    137.71  3.000
 TPE  O3B   PB   O2B   107.59  3.000
 TPE  O3B   PB   O1B   111.69  3.000
 TPE  O2B   PB   O1B   119.01  3.000
 TPE  O3B   PB   O3A   105.63  3.000
 TPE  O2B   PB   O3A    99.77  3.000
 TPE  O1B   PB   O3A   111.83  3.000
 TPE  HPB2  O2B  PB    115.65  3.000
 TPE  PB    O3B  C1B   129.70  3.000
 TPE  C5'   O5'  PA    124.84  3.000
 TPE  H5'1  C5'  H5'2  108.67  3.000
 TPE  H5'1  C5'  C4'   109.57  3.000
 TPE  H5'2  C5'  C4'   108.98  3.000
 TPE  H5'1  C5'  O5'   110.60  3.000
 TPE  H5'2  C5'  O5'   110.26  3.000
 TPE  C4'   C5'  O5'   108.73  3.000
 TPE  H4'   C4'  C3'   110.73  3.000
 TPE  H4'   C4'  O4'   109.22  3.000
 TPE  C3'   C4'  O4'   106.72  3.000
 TPE  H4'   C4'  C5'   106.02  3.000
 TPE  C3'   C4'  C5'   114.01  3.000
 TPE  O4'   C4'  C5'   110.11  3.000
 TPE  C1'   O4'  C4'   111.01  3.000
 TPE  H3'   C3'  C2'   112.45  3.000
 TPE  H3'   C3'  O3'   109.51  3.000
 TPE  C2'   C3'  O3'   107.69  3.000
 TPE  H3'   C3'  C4'   112.55  3.000
 TPE  C2'   C3'  C4'   103.25  3.000
 TPE  O3'   C3'  C4'   111.19  3.000
 TPE  CR    O3'  C3'   117.42  3.000
 TPE  CHR   CR   OR    125.66  3.000
 TPE  CHR   CR   O3'   111.48  3.000
 TPE  OR    CR   O3'   122.85  3.000
 TPE  HHR1  CHR  HHR2  107.34  3.000
 TPE  HHR1  CHR  HHR3  109.54  3.000
 TPE  HHR2  CHR  HHR3  108.63  3.000
 TPE  HHR1  CHR  CR    111.15  3.000
 TPE  HHR2  CHR  CR    109.69  3.000
 TPE  HHR3  CHR  CR    110.41  3.000
 TPE  H2'1  C2'  H2'2  107.62  3.000
 TPE  H2'1  C2'  C1'   112.74  3.000
 TPE  H2'2  C2'  C1'   111.40  3.000
 TPE  H2'1  C2'  C3'   113.36  3.000
 TPE  H2'2  C2'  C3'   108.74  3.000
 TPE  C1'   C2'  C3'   102.95  3.000
 TPE  H1'   C1'  N1    106.69  3.000
 TPE  H1'   C1'  C2'   111.11  3.000
 TPE  N1    C1'  C2'   114.18  3.000
 TPE  H1'   C1'  O4'   110.91  3.000
 TPE  N1    C1'  O4'   108.41  3.000
 TPE  C2'   C1'  O4'   105.57  3.000
 TPE  C6    N1   C2    121.02  3.000
 TPE  C6    N1   C1'   119.25  3.000
 TPE  C2    N1   C1'   119.68  3.000
 TPE  N3    C2   O2    121.99  3.000
 TPE  N3    C2   N1    114.19  3.000
 TPE  O2    C2   N1    123.82  3.000
 TPE  H3    N3   C4    116.63  3.000
 TPE  H3    N3   C2    115.09  3.000
 TPE  C4    N3   C2    128.28  3.000
 TPE  C5    C4   O4    125.06  3.000
 TPE  C5    C4   N3    114.34  3.000
 TPE  O4    C4   N3    120.60  3.000
 TPE  C6    C5   C5M   122.90  3.000
 TPE  C6    C5   C4    117.80  3.000
 TPE  C5M   C5   C4    119.29  3.000
 TPE  H5M1  C5M  H5M2  107.25  3.000
 TPE  H5M1  C5M  H5M3  107.98  3.000
 TPE  H5M2  C5M  H5M3  107.85  3.000
 TPE  H5M1  C5M  C5    111.47  3.000
 TPE  H5M2  C5M  C5    111.30  3.000
 TPE  H5M3  C5M  C5    110.81  3.000
 TPE  H6    C6   C5    120.15  3.000
 TPE  H6    C6   N1    115.50  3.000
 TPE  C5    C6   N1    124.35  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
 TPE  CONST_01  C4B   C3B  C2B  C1B    0.00   0.0  0
 TPE  CONST_02  C4B   C5B  C6B  C1B    0.00   0.0  0
 TPE  CONST_03  C5B   C6B  C1B  C2B    0.00   0.0  0
 TPE  CONST_04  C5B   C4B  C3B  C2B    0.00   0.0  0
 TPE  CONST_05  C6B   C1B  C2B  C3B    0.00   0.0  0
 TPE  CONST_06  C6B   C5B  C4B  C3B    0.00   0.0  0
 TPE  CONST_07  C4    N3   C2   N1     0.00   0.0  0
 TPE  CONST_08  C4    C5   C6   N1     0.00   0.0  0
 TPE  CONST_09  C5    C6   N1   C2     0.00   0.0  0
 TPE  CONST_10  C5    C4   N3   C2     0.00   0.0  0
 TPE  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 TPE  CONST_12  C6    C5   C4   N3     0.00   0.0  0
 TPE  CONST_13  N3    C2   N1   C1'  180.00   0.0  0
 TPE  CONST_14  C5    C6   N1   C1'  180.00   0.0  0
 TPE  CONST_15  O3B   C1B  C2B  C3B  180.00   0.0  0
 TPE  CONST_16  O3B   C1B  C6B  C5B  180.00   0.0  0
 TPE  CONST_17  O2    C2   N1   C1'    0.00   0.0  0
 TPE  CONST_18  C5M   C5   C6   N1   180.00   0.0  0
 TPE  CONST_19  O4    C4   N3   C2   180.00   0.0  0
 TPE  CONST_20  C6    N1   C2   O2   180.00   0.0  0
 TPE  CONST_21  C4    N3   C2   O2   180.00   0.0  0
 TPE  CONST_22  C5M   C5   C4   N3   180.00   0.0  0
 TPE  CONST_23  C6    C5   C4   O4   180.00   0.0  0
 TPE  CONST_24  H3B   C3B  C2B  C1B  180.00   0.0  0
 TPE  CONST_25  H5B   C5B  C6B  C1B  180.00   0.0  0
 TPE  CONST_26  H6B   C6B  C1B  C2B  180.00   0.0  0
 TPE  CONST_27  H4B   C4B  C3B  C2B  180.00   0.0  0
 TPE  CONST_28  H2B   C2B  C3B  C4B  180.00   0.0  0
 TPE  CONST_29  H6    C6   N1   C1'    0.00   0.0  0
 TPE  CONST_30  H3    N3   C2   N1   180.00   0.0  0
 TPE  Var_01    H5M3  C5M  C5   C4   179.29  30.0  2
 TPE  Var_02    O3A   PB   O3B  C1B  -88.95  30.0  2
 TPE  Var_03    C4'   C5'  O5'  PA   168.14  30.0  3
 TPE  Var_04    OR    CR   O3'  C3'    2.10  30.0  3
 TPE  Var_05    O5'   PA   O3A  PB    60.79  30.0  1
 TPE  Var_06    HHR3  CHR  CR   O3'  170.02  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
 TPE  chir_03  C4'  C5'  O4'  C3'  negativ
 TPE  chir_04  C3'  O3'  C2'  C4'  negativ
 TPE  chir_05  C1'  O4'  N1   C2'  negativ
 TPE  chir_06  PA   O2A  O3A  O5'  both
 TPE  chir_07  PB   O1B  O2B  O3B  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
 TPE  plan-1  O3'  0.020
 TPE  plan-1  CR   0.020
 TPE  plan-1  OR   0.020
 TPE  plan-1  CHR  0.020
 TPE  plan-2  C1B  0.020
 TPE  plan-2  C2B  0.020
 TPE  plan-2  C3B  0.020
 TPE  plan-2  C4B  0.020
 TPE  plan-2  C5B  0.020
 TPE  plan-2  C6B  0.020
 TPE  plan-2  O3B  0.020
 TPE  plan-2  H2B  0.020
 TPE  plan-2  H3B  0.020
 TPE  plan-2  H4B  0.020
 TPE  plan-2  H5B  0.020
 TPE  plan-2  H6B  0.020
 TPE  plan-3  C1'  0.020
 TPE  plan-3  N1   0.020
 TPE  plan-3  C2   0.020
 TPE  plan-3  O2   0.020
 TPE  plan-3  N3   0.020
 TPE  plan-3  C4   0.020
 TPE  plan-3  O4   0.020
 TPE  plan-3  C5   0.020
 TPE  plan-3  C5M  0.020
 TPE  plan-3  C6   0.020
 TPE  plan-3  H3   0.020
 TPE  plan-3  H6   0.020

