# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 03:51:21 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)Oc3ccccc3)O2)C(=O)NC1=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
 TLO  TLO  5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine  ligand  51  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TLO
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
 TLO  N1    N  NR6   0  -0.567   4.4627  -0.3783   0.5547
 TLO  C2    C  CR6   0   0.744   4.5811  -0.2886  -0.8125
 TLO  O2    O  O     0  -0.474   4.2364   0.6823  -1.4534
 TLO  N3    N  NR16  0  -0.733   5.1324  -1.3926  -1.4083
 TLO  C4    C  CR6   0   0.559   5.5625  -2.5621  -0.8075
 TLO  O4    O  O     0  -0.454   6.0394  -3.4620  -1.4741
 TLO  C5    C  CR6   0  -0.184   5.3856  -2.5943   0.6304
 TLO  C6    C  CR16  0   0.059   4.8467  -1.5142   1.2208
 TLO  PA    P  P     0   1.485  -1.2878   1.8271  -0.9683
 TLO  PB    P  P     0   1.463  -3.5395   0.0516  -0.7560
 TLO  CG    C  CR6   0   0.344  -5.3510  -1.0562   0.7155
 TLO  CZ    C  CR16  0  -0.253  -7.7465  -2.4146   0.8967
 TLO  C1'   C  CH1   0   0.216   3.8679   0.7224   1.3088
 TLO  O1A   O  OH1   0  -0.720  -1.9297   3.2467  -0.6784
 TLO  O1B   O  OH1   0  -0.714  -3.0769  -1.2689  -1.4948
 TLO  C2'   C  CH2   0  -0.561   4.5370   2.0899   1.1464
 TLO  O2A   O  O     0  -0.686  -1.1508   1.5851  -2.4107
 TLO  O2B   O  O     0  -0.669  -4.3821   0.8900  -1.6162
 TLO  C3'   C  CH1   0   0.020   3.5048   2.9573   0.4249
 TLO  O3'   O  OH1   0  -0.666   3.3957   4.2714   0.9078
 TLO  O3A   O  O2    0  -0.673  -2.2082   0.7518  -0.1719
 TLO  O3B   O  O2    0  -0.603  -4.1414  -0.3772   0.6652
 TLO  C4'   C  CH1   0   0.016   2.1946   2.2188   0.7116
 TLO  O4'   O  O2    0  -0.488   2.5242   0.8636   0.9382
 TLO  C5'   C  CH2   0  -0.189   1.2263   2.3231  -0.4364
 TLO  O5'   O  O2    0  -0.577  -0.0006   1.6731  -0.0571
 TLO  C5M   C  CH3   0  -0.707   5.8032  -3.8141   1.3837
 TLO  CD1   C  CR16  0  -0.310  -5.3371  -2.4326   0.8684
 TLO  CD2   C  CR16  0  -0.301  -6.5376  -0.3443   0.6497
 TLO  CE1   C  CR16  0  -0.250  -6.5460  -3.1092   0.9613
 TLO  CE2   C  CR16  0  -0.251  -7.7385  -1.0344   0.7429
 TLO  HN3   H  HNR6  0   0.425   5.2320  -1.3343  -2.4146
 TLO  H6    H  HCR6  0   0.317   4.6898  -1.4870   2.2910
 TLO  HZ    H  HCR6  0   0.265  -8.6852  -2.9472   0.9707
 TLO  H1'   H  HCH1  0   0.259   3.9330   0.4001   2.3502
 TLO  HO1A  H  HOH1  0   0.507  -2.0387   3.4953   0.2505
 TLO  HO1B  H  HOH1  0   0.509  -2.4839  -1.8618  -1.0115
 TLO  H2'   H  HCH2  0   0.272   4.7197   2.5063   2.1384
 TLO  H2'A  H  HCH2  0   0.279   5.4948   2.0371   0.6318
 TLO  H3'   H  HCH1  0   0.240   3.7068   2.9587  -0.6497
 TLO  HO3'  H  HOH1  0   0.459   4.1137   4.7905   0.5339
 TLO  H4'   H  HCH1  0   0.244   1.7405   2.6502   1.6150
 TLO  H5'   H  HCH2  0   0.255   1.0502   3.3799  -0.6536
 TLO  H5'A  H  HCH2  0   0.258   1.6357   1.8419  -1.3262
 TLO  H5M   H  HCH3  0   0.248   6.8711  -4.0050   1.2692
 TLO  H5MA  H  HCH3  0   0.247   5.5952  -3.7050   2.4468
 TLO  H5MB  H  HCH3  0   0.247   5.2768  -4.7009   1.0283
 TLO  HD1   H  HCR6  0   0.278  -4.3990  -2.9694   0.9287
 TLO  HD2   H  HCR6  0   0.280  -6.5266   0.7319   0.5401
 TLO  HE1   H  HCR6  0   0.268  -6.5451  -4.1842   1.0823
 TLO  HE2   H  HCR6  0   0.268  -8.6702  -0.4867   0.6930

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
 TLO  C1'  N1    single    1.461  0.020  1.461
 TLO  N1   C6    single    1.372  0.020  1.372
 TLO  N1   C2    single    1.375  0.020  1.375
 TLO  O2   C2    double    1.213  0.020  1.213
 TLO  C2   N3    single    1.370  0.020  1.370
 TLO  N3   C4    single    1.383  0.020  1.383
 TLO  N3   HN3   single    0.860  0.020  1.020
 TLO  C5   C4    single    1.449  0.020  1.449
 TLO  C4   O4    double    1.217  0.020  1.217
 TLO  C6   C5    double    1.344  0.020  1.344
 TLO  C5   C5M   single    1.493  0.020  1.493
 TLO  C6   H6    single    0.930  0.020  1.080
 TLO  O3A  PA    single    1.624  0.020  1.624
 TLO  O2A  PA    double    1.469  0.020  1.469
 TLO  PA   O5'   single    1.585  0.020  1.585
 TLO  PA   O1A   single    1.585  0.020  1.585
 TLO  O3B  PB    single    1.602  0.020  1.602
 TLO  O2B  PB    double    1.467  0.020  1.467
 TLO  PB   O1B   single    1.582  0.020  1.582
 TLO  PB   O3A   single    1.614  0.020  1.614
 TLO  CD2  CG    aromatic  1.385  0.020  1.385
 TLO  CG   O3B   single    1.388  0.020  1.388
 TLO  CG   CD1   aromatic  1.385  0.020  1.385
 TLO  CE2  CZ    aromatic  1.389  0.020  1.389
 TLO  CZ   CE1   aromatic  1.388  0.020  1.388
 TLO  CZ   HZ    single    0.930  0.020  1.080
 TLO  C2'  C1'   single    1.531  0.020  1.531
 TLO  C1'  O4'   single    1.401  0.020  1.401
 TLO  C1'  H1'   single    0.970  0.020  1.090
 TLO  O1A  HO1A  single    0.850  0.020  0.980
 TLO  O1B  HO1B  single    0.850  0.020  0.980
 TLO  C3'  C2'   single    1.529  0.020  1.529
 TLO  C2'  H2'   single    0.970  0.020  1.090
 TLO  C2'  H2'A  single    0.970  0.020  1.090
 TLO  O3'  C3'   single    1.404  0.020  1.404
 TLO  C3'  C4'   single    1.531  0.020  1.531
 TLO  C3'  H3'   single    0.970  0.020  1.090
 TLO  O3'  HO3'  single    0.850  0.020  0.980
 TLO  C5'  C4'   single    1.505  0.020  1.505
 TLO  C4'  O4'   single    1.413  0.020  1.413
 TLO  C4'  H4'   single    0.970  0.020  1.090
 TLO  O5'  C5'   single    1.439  0.020  1.439
 TLO  C5'  H5'   single    0.970  0.020  1.090
 TLO  C5'  H5'A  single    0.970  0.020  1.090
 TLO  C5M  H5M   single    0.970  0.020  1.090
 TLO  C5M  H5MA  single    0.970  0.020  1.090
 TLO  C5M  H5MB  single    0.970  0.020  1.090
 TLO  CE1  CD1   aromatic  1.388  0.020  1.388
 TLO  CD1  HD1   single    0.930  0.020  1.080
 TLO  CE2  CD2   aromatic  1.388  0.020  1.388
 TLO  CD2  HD2   single    0.930  0.020  1.080
 TLO  CE1  HE1   single    0.930  0.020  1.080
 TLO  CE2  HE2   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
 TLO  C1'   N1   C6    119.16  3.000
 TLO  C6    N1   C2    120.85  3.000
 TLO  C1'   N1   C2    119.94  3.000
 TLO  N3    C2   O2    121.96  3.000
 TLO  N3    C2   N1    114.48  3.000
 TLO  O2    C2   N1    123.56  3.000
 TLO  HN3   N3   C4    116.72  3.000
 TLO  HN3   N3   C2    115.16  3.000
 TLO  C4    N3   C2    128.12  3.000
 TLO  C5    C4   O4    125.09  3.000
 TLO  O4    C4   N3    120.59  3.000
 TLO  C5    C4   N3    114.32  3.000
 TLO  C5M   C5   C6    123.17  3.000
 TLO  C5M   C5   C4    118.98  3.000
 TLO  C6    C5   C4    117.84  3.000
 TLO  H6    C6   C5    120.86  3.000
 TLO  H6    C6   N1    114.77  3.000
 TLO  C5    C6   N1    124.37  3.000
 TLO  O5'   PA   O3A    96.55  3.000
 TLO  O5'   PA   O2A   118.22  3.000
 TLO  O3A   PA   O2A   115.16  3.000
 TLO  O5'   PA   O1A   108.12  3.000
 TLO  O2A   PA   O1A   111.41  3.000
 TLO  O3A   PA   O1A   105.90  3.000
 TLO  O3B   PB   O3A    96.03  3.000
 TLO  O3A   PB   O2B   115.98  3.000
 TLO  O3B   PB   O2B   117.22  3.000
 TLO  O3A   PB   O1B   106.85  3.000
 TLO  O2B   PB   O1B   111.77  3.000
 TLO  O3B   PB   O1B   107.50  3.000
 TLO  CD2   CG   CD1   121.64  3.000
 TLO  CD1   CG   O3B   118.77  3.000
 TLO  CD2   CG   O3B   119.56  3.000
 TLO  HZ    CZ   CE2   120.12  3.000
 TLO  HZ    CZ   CE1   120.05  3.000
 TLO  CE2   CZ   CE1   119.83  3.000
 TLO  H1'   C1'  O4'   109.83  3.000
 TLO  H1'   C1'  C2'   109.79  3.000
 TLO  O4'   C1'  C2'   107.52  3.000
 TLO  H1'   C1'  N1    104.22  3.000
 TLO  O4'   C1'  N1    109.27  3.000
 TLO  C2'   C1'  N1    116.12  3.000
 TLO  HO1A  O1A  PA    116.82  3.000
 TLO  HO1B  O1B  PB    117.20  3.000
 TLO  H2'A  C2'  H2'   107.51  3.000
 TLO  H2'A  C2'  C3'   113.48  3.000
 TLO  H2'   C2'  C3'   108.99  3.000
 TLO  H2'A  C2'  C1'   113.03  3.000
 TLO  H2'   C2'  C1'   108.52  3.000
 TLO  C3'   C2'  C1'   105.17  3.000
 TLO  H3'   C3'  C4'   110.05  3.000
 TLO  H3'   C3'  O3'   110.56  3.000
 TLO  C4'   C3'  O3'   108.69  3.000
 TLO  H3'   C3'  C2'   109.86  3.000
 TLO  C4'   C3'  C2'   102.46  3.000
 TLO  O3'   C3'  C2'   114.90  3.000
 TLO  HO3'  O3'  C3'   108.26  3.000
 TLO  PB    O3A  PA    125.27  3.000
 TLO  CG    O3B  PB    119.37  3.000
 TLO  H4'   C4'  C5'   109.50  3.000
 TLO  H4'   C4'  O4'   109.93  3.000
 TLO  C5'   C4'  O4'   109.80  3.000
 TLO  H4'   C4'  C3'   108.55  3.000
 TLO  O4'   C4'  C3'   107.04  3.000
 TLO  C5'   C4'  C3'   111.97  3.000
 TLO  C4'   O4'  C1'   111.27  3.000
 TLO  H5'A  C5'  H5'   108.95  3.000
 TLO  H5'A  C5'  O5'   109.61  3.000
 TLO  H5'   C5'  O5'   110.59  3.000
 TLO  H5'A  C5'  C4'   110.48  3.000
 TLO  H5'   C5'  C4'   108.79  3.000
 TLO  O5'   C5'  C4'   108.42  3.000
 TLO  C5'   O5'  PA    119.80  3.000
 TLO  H5MB  C5M  H5MA  107.91  3.000
 TLO  H5MB  C5M  H5M   107.21  3.000
 TLO  H5MA  C5M  H5M   107.88  3.000
 TLO  H5MB  C5M  C5    111.39  3.000
 TLO  H5MA  C5M  C5    110.93  3.000
 TLO  H5M   C5M  C5    111.33  3.000
 TLO  HD1   CD1  CE1   120.61  3.000
 TLO  HD1   CD1  CG    120.51  3.000
 TLO  CE1   CD1  CG    118.88  3.000
 TLO  HD2   CD2  CE2   120.67  3.000
 TLO  HD2   CD2  CG    120.49  3.000
 TLO  CE2   CD2  CG    118.84  3.000
 TLO  HE1   CE1  CD1   119.41  3.000
 TLO  HE1   CE1  CZ    120.20  3.000
 TLO  CD1   CE1  CZ    120.39  3.000
 TLO  HE2   CE2  CD2   119.36  3.000
 TLO  HE2   CE2  CZ    120.22  3.000
 TLO  CD2   CE2  CZ    120.43  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
 TLO  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 TLO  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 TLO  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 TLO  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 TLO  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 TLO  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 TLO  CONST_07  C4   N3   C2   N1      0.00   0.0  0
 TLO  CONST_08  C5   C4   N3   C2      0.00   0.0  0
 TLO  CONST_09  C1'  N1   C2   N3    180.00   0.0  0
 TLO  CONST_10  C6   N1   C2   N3      0.00   0.0  0
 TLO  CONST_11  CE2  CD2  CG   O3B   180.00   0.0  0
 TLO  CONST_12  CE1  CD1  CG   O3B   180.00   0.0  0
 TLO  CONST_13  O4   C4   N3   C2    180.00   0.0  0
 TLO  CONST_14  C1'  N1   C2   O2      0.00   0.0  0
 TLO  CONST_15  C6   N1   C2   O2    180.00   0.0  0
 TLO  CONST_16  C4   N3   C2   O2    180.00   0.0  0
 TLO  CONST_17  HE2  CE2  CD2  CG    180.00   0.0  0
 TLO  CONST_18  HE1  CE1  CD1  CG    180.00   0.0  0
 TLO  CONST_19  HD2  CD2  CE2  CZ    180.00   0.0  0
 TLO  CONST_20  HD1  CD1  CE1  CZ    180.00   0.0  0
 TLO  CONST_21  HZ   CZ   CE1  CD1   180.00   0.0  0
 TLO  CONST_22  HN3  N3   C2   N1    180.00   0.0  0
 TLO  Var_01    CD2  CG   O3B  PB    -82.43  30.0  2
 TLO  Var_02    H5M  C5M  C5   C4     60.92  30.0  3
 TLO  Var_03    C4'  C5'  O5'  PA    169.95  30.0  3
 TLO  Var_04    O2B  PB   O3B  CG     56.83  30.0  3
 TLO  Var_05    O3B  PB   O3A  PA   -160.33  30.0  2
 TLO  Var_06    O2A  PA   O3A  PB    -36.31  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
 TLO  chir_03  C1'  N1   C2'  O4'  negativ
 TLO  chir_04  C3'  O3'  C4'  C2'  positiv
 TLO  chir_05  C4'  O4'  C3'  C5'  negativ
 TLO  chir_06  PA   O2A  O5'  O1A  both
 TLO  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
 TLO  plan-1  N1   0.020
 TLO  plan-1  C2   0.020
 TLO  plan-1  O2   0.020
 TLO  plan-1  N3   0.020
 TLO  plan-1  C4   0.020
 TLO  plan-1  O4   0.020
 TLO  plan-1  C5   0.020
 TLO  plan-1  C6   0.020
 TLO  plan-1  C1'  0.020
 TLO  plan-1  C5M  0.020
 TLO  plan-1  HN3  0.020
 TLO  plan-1  H6   0.020
 TLO  plan-2  CG   0.020
 TLO  plan-2  CZ   0.020
 TLO  plan-2  O3B  0.020
 TLO  plan-2  CD1  0.020
 TLO  plan-2  CD2  0.020
 TLO  plan-2  CE1  0.020
 TLO  plan-2  CE2  0.020
 TLO  plan-2  HZ   0.020
 TLO  plan-2  HD1  0.020
 TLO  plan-2  HD2  0.020
 TLO  plan-2  HE1  0.020
 TLO  plan-2  HE2  0.020

