# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 08:00:32 2020
#   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  54  34  .  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_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  C      0   0.368  -1.1961   0.3100  -5.7981
 TPE  C2B   C  C1     0  -0.327  -1.9838  -0.5557  -6.5500
 TPE  C3B   C  C1     0  -0.253  -2.2485  -0.2666  -7.8817
 TPE  C4B   C  C1     0  -0.271  -1.7206   0.8741  -8.4733
 TPE  C5B   C  C1     0  -0.253  -0.9264   1.7294  -7.7201
 TPE  C6B   C  C1     0  -0.326  -0.6578   1.4497  -6.3870
 TPE  PA    P  P      0   1.347   0.6981  -1.7898  -1.3699
 TPE  O1A   O  O      0  -0.796   2.0506  -2.2360  -1.8251
 TPE  O2A   O  OP    -1  -0.786  -0.3254  -2.7825  -0.9207
 TPE  O3A   O  O2     0  -0.734   0.0186  -0.7801  -2.4750
 TPE  PB    P  P      0   1.328   0.3882  -0.8127  -4.0696
 TPE  O1B   O  O      0  -0.774   1.5869   0.0297  -4.3552
 TPE  O2B   O  OP    -1  -0.781   0.2602  -2.1946  -4.6200
 TPE  O3B   O  O2     0  -0.643  -0.9805   0.0552  -4.4780
 TPE  O5'   O  O2     0  -0.619   0.8603  -0.6163  -0.2248
 TPE  C5'   C  CH2    0  -0.156   1.4976  -0.9820   0.9792
 TPE  C4'   C  CH1    0   0.015   1.5513   0.2151   1.8964
 TPE  O4'   O  O2     0  -0.488   0.2464   0.5755   2.3081
 TPE  C3'   C  CH1    0   0.004   2.3359  -0.0613   3.1801
 TPE  O3'   O  O2     0  -0.463   3.6896   0.3128   2.9345
 TPE  CR    C  C      0   0.568   4.6097  -0.0339   3.8337
 TPE  OR    O  O      0  -0.449   4.3455  -0.6018   4.8628
 TPE  CHR   C  CH3    0  -0.771   5.9850   0.3594   3.3874
 TPE  C2'   C  CH2    0  -0.557   1.6304   0.7991   4.2196
 TPE  C1'   C  CH1    0   0.217   0.2409   1.0560   3.6214
 TPE  N1    N  NR6    0  -0.567  -0.8771   0.4597   4.3464
 TPE  C2    C  CR6    0   0.745  -0.9030  -0.8983   4.5635
 TPE  O2    O  OC     0  -0.473  -0.0183  -1.6501   4.2107
 TPE  N3    N  NR16   0  -0.734  -2.0160  -1.3461   5.2252
 TPE  C4    C  CR6    0   0.559  -3.0927  -0.6070   5.6810
 TPE  O4    O  OC     0  -0.454  -4.0167  -1.1504   6.2583
 TPE  C5    C  CR6    0  -0.185  -3.0036   0.8124   5.4031
 TPE  C5M   C  CH3    0  -0.707  -4.1153   1.7070   5.8431
 TPE  C6    C  CR16   0   0.061  -1.9151   1.2580   4.7532
 TPE  H2B   H  H      0   0.259  -2.3943  -1.4437  -6.0874
 TPE  H3B   H  H      0   0.255  -2.8680  -0.9399  -8.4602
 TPE  H4B   H  H      0   0.253  -1.9294   1.0959  -9.5116
 TPE  H5B   H  H      0   0.255  -0.5085   2.6201  -8.1715
 TPE  H6B   H  H      0   0.259  -0.0422   2.1174  -5.7988
 TPE  H5'2  H  HCH2   0   0.218   2.5259  -1.3163   0.7965
 TPE  H5'1  H  HCH2   0   0.217   0.9683  -1.7979   1.4850
 TPE  H4'   H  HCH1   0   0.241   2.0186   1.0580   1.3684
 TPE  H3'   H  HCH1   0   0.269   2.2932  -1.1173   3.4479
 TPE  HHR3  H  HCH3   0   0.263   6.7004   0.2157   4.1918
 TPE  HHR2  H  HCH3   0   0.278   6.2869  -0.2546   2.5374
 TPE  HHR1  H  HCH3   0   0.271   6.0091   1.3983   3.0608
 TPE  H2'2  H  HCH2   0   0.288   1.5918   0.3397   5.2040
 TPE  H2'1  H  HCH2   0   0.281   2.1474   1.7546   4.3231
 TPE  H1'   H  HCH1   0   0.260   0.0304   2.1280   3.6289
 TPE  H3    H  HNR6   0   0.426  -2.0434  -2.3441   5.3956
 TPE  H5M3  H  HCH3   0   0.248  -5.0663   1.4067   5.4015
 TPE  H5M2  H  HCH3   0   0.247  -4.2405   1.6814   6.9264
 TPE  H5M1  H  HCH3   0   0.247  -3.9224   2.7385   5.5531
 TPE  H6    H  HCR6   0   0.318  -1.8012   2.3074   4.5164

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  1.391  0.020  1.391
 TPE  C1B  C6B   aromatic  1.391  0.020  1.391
 TPE  C1B  O3B   single    1.362  0.020  1.362
 TPE  C2B  C3B   aromatic  1.388  0.020  1.388
 TPE  C2B  H2B   single    0.930  0.020  1.080
 TPE  C3B  C4B   aromatic  1.389  0.020  1.389
 TPE  C3B  H3B   single    0.930  0.020  1.080
 TPE  C4B  C5B   aromatic  1.389  0.020  1.389
 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   deloc     1.495  0.020  1.495
 TPE  PA   O2A   deloc     1.495  0.020  1.495
 TPE  PA   O3A   single    1.644  0.020  1.644
 TPE  PA   O5'   single    1.648  0.020  1.648
 TPE  O3A  PB    single    1.637  0.020  1.637
 TPE  PB   O1B   deloc     1.493  0.020  1.493
 TPE  PB   O2B   deloc     1.493  0.020  1.493
 TPE  PB   O3B   single    1.671  0.020  1.671
 TPE  O5'  C5'   single    1.410  0.020  1.410
 TPE  C5'  C4'   single    1.509  0.020  1.509
 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    1.415  0.020  1.415
 TPE  C4'  C3'   single    1.530  0.020  1.530
 TPE  C4'  H4'   single    0.970  0.020  1.090
 TPE  O4'  C1'   single    1.398  0.020  1.398
 TPE  C3'  O3'   single    1.426  0.020  1.426
 TPE  C3'  C2'   single    1.523  0.020  1.523
 TPE  C3'  H3'   single    0.970  0.020  1.090
 TPE  O3'  CR    single    1.332  0.020  1.332
 TPE  CR   OR    double    1.205  0.020  1.205
 TPE  CR   CHR   single    1.498  0.020  1.498
 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    1.534  0.020  1.534
 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    1.460  0.020  1.460
 TPE  C1'  H1'   single    0.970  0.020  1.090
 TPE  N1   C2    aromatic  1.376  0.020  1.376
 TPE  N1   C6    aromatic  1.371  0.020  1.371
 TPE  C2   O2    double    1.213  0.020  1.213
 TPE  C2   N3    aromatic  1.370  0.020  1.370
 TPE  N3   C4    aromatic  1.383  0.020  1.383
 TPE  N3   H3    single    0.860  0.020  1.020
 TPE  C4   O4    double    1.217  0.020  1.217
 TPE  C4   C5    aromatic  1.449  0.020  1.449
 TPE  C5   C5M   single    1.493  0.020  1.493
 TPE  C5   C6    aromatic  1.344  0.020  1.344
 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   120.16  3.000
 TPE  O3B   C1B  C2B   119.82  3.000
 TPE  C6B   C1B  C2B   120.00  3.000
 TPE  H2B   C2B  C3B   120.58  3.000
 TPE  H2B   C2B  C1B   119.62  3.000
 TPE  C3B   C2B  C1B   119.80  3.000
 TPE  H3B   C3B  C4B   120.04  3.000
 TPE  H3B   C3B  C2B   119.49  3.000
 TPE  C4B   C3B  C2B   120.47  3.000
 TPE  H4B   C4B  C5B   120.29  3.000
 TPE  H4B   C4B  C3B   120.24  3.000
 TPE  C5B   C4B  C3B   119.47  3.000
 TPE  H5B   C5B  C6B   119.44  3.000
 TPE  H5B   C5B  C4B   120.08  3.000
 TPE  C6B   C5B  C4B   120.48  3.000
 TPE  H6B   C6B  C5B   120.52  3.000
 TPE  H6B   C6B  C1B   119.70  3.000
 TPE  C5B   C6B  C1B   119.78  3.000
 TPE  O5'   PA   O3A    94.04  3.000
 TPE  O5'   PA   O2A   109.36  3.000
 TPE  O3A   PA   O2A   109.08  3.000
 TPE  O5'   PA   O1A   109.58  3.000
 TPE  O3A   PA   O1A   110.64  3.000
 TPE  O2A   PA   O1A   120.84  3.000
 TPE  PB    O3A  PA    123.31  3.000
 TPE  O3B   PB   O2B   108.69  3.000
 TPE  O3B   PB   O1B   108.53  3.000
 TPE  O2B   PB   O1B   121.38  3.000
 TPE  O3B   PB   O3A    92.45  3.000
 TPE  O2B   PB   O3A   110.99  3.000
 TPE  O1B   PB   O3A   110.88  3.000
 TPE  PB    O3B  C1B   117.63  3.000
 TPE  C5'   O5'  PA    116.94  3.000
 TPE  H5'1  C5'  H5'2  107.62  3.000
 TPE  H5'1  C5'  C4'   109.10  3.000
 TPE  H5'2  C5'  C4'   108.05  3.000
 TPE  H5'1  C5'  O5'   111.63  3.000
 TPE  H5'2  C5'  O5'   111.13  3.000
 TPE  C4'   C5'  O5'   109.22  3.000
 TPE  H4'   C4'  C3'   108.89  3.000
 TPE  H4'   C4'  O4'   109.67  3.000
 TPE  C3'   C4'  O4'   105.96  3.000
 TPE  H4'   C4'  C5'   109.36  3.000
 TPE  C3'   C4'  C5'   112.64  3.000
 TPE  O4'   C4'  C5'   110.25  3.000
 TPE  C1'   O4'  C4'   111.37  3.000
 TPE  H3'   C3'  C2'   111.19  3.000
 TPE  H3'   C3'  O3'   109.49  3.000
 TPE  C2'   C3'  O3'   114.16  3.000
 TPE  H3'   C3'  C4'   111.17  3.000
 TPE  C2'   C3'  C4'   103.48  3.000
 TPE  O3'   C3'  C4'   107.16  3.000
 TPE  CR    O3'  C3'   118.10  3.000
 TPE  CHR   CR   OR    125.41  3.000
 TPE  CHR   CR   O3'   111.38  3.000
 TPE  OR    CR   O3'   123.21  3.000
 TPE  HHR1  CHR  HHR2  107.27  3.000
 TPE  HHR1  CHR  HHR3  109.50  3.000
 TPE  HHR2  CHR  HHR3  108.67  3.000
 TPE  HHR1  CHR  CR    111.10  3.000
 TPE  HHR2  CHR  CR    109.77  3.000
 TPE  HHR3  CHR  CR    110.45  3.000
 TPE  H2'1  C2'  H2'2  107.52  3.000
 TPE  H2'1  C2'  C1'   108.62  3.000
 TPE  H2'2  C2'  C1'   113.05  3.000
 TPE  H2'1  C2'  C3'   109.88  3.000
 TPE  H2'2  C2'  C3'   113.32  3.000
 TPE  C1'   C2'  C3'   104.36  3.000
 TPE  H1'   C1'  N1    104.47  3.000
 TPE  H1'   C1'  C2'   109.64  3.000
 TPE  N1    C1'  C2'   115.57  3.000
 TPE  H1'   C1'  O4'   110.14  3.000
 TPE  N1    C1'  O4'   109.21  3.000
 TPE  C2'   C1'  O4'   107.76  3.000
 TPE  C6    N1   C2    120.91  3.000
 TPE  C6    N1   C1'   119.30  3.000
 TPE  C2    N1   C1'   119.74  3.000
 TPE  N3    C2   O2    122.02  3.000
 TPE  N3    C2   N1    114.48  3.000
 TPE  O2    C2   N1    123.50  3.000
 TPE  H3    N3   C4    116.74  3.000
 TPE  H3    N3   C2    115.18  3.000
 TPE  C4    N3   C2    128.08  3.000
 TPE  C5    C4   O4    125.09  3.000
 TPE  C5    C4   N3    114.35  3.000
 TPE  O4    C4   N3    120.56  3.000
 TPE  C6    C5   C5M   123.15  3.000
 TPE  C6    C5   C4    117.86  3.000
 TPE  C5M   C5   C4    118.98  3.000
 TPE  H5M1  C5M  H5M2  107.88  3.000
 TPE  H5M1  C5M  H5M3  107.90  3.000
 TPE  H5M2  C5M  H5M3  107.19  3.000
 TPE  H5M1  C5M  C5    110.93  3.000
 TPE  H5M2  C5M  C5    111.35  3.000
 TPE  H5M3  C5M  C5    111.40  3.000
 TPE  H6    C6   C5    120.85  3.000
 TPE  H6    C6   N1    114.84  3.000
 TPE  C5    C6   N1    124.31  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    -58.76  30.0  2
 TPE  Var_02    O3A   PB   O3B  C1B  -178.76  30.0  1
 TPE  Var_03    C4'   C5'  O5'  PA   -179.96  30.0  3
 TPE  Var_04    OR    CR   O3'  C3'    -2.85  30.0  3
 TPE  Var_05    O5'   PA   O3A  PB    139.12  30.0  1
 TPE  Var_06    HHR3  CHR  CR   O3'   171.01  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

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

