# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:23:25 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  49  31  .  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_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   4.5498  -0.4013   0.5288
 TLO  C2    C  CR6    0   0.741   4.6777  -0.3658  -0.8403
 TLO  O2    O  O      0  -0.471   4.3292   0.5736  -1.5239
 TLO  N3    N  NR16   0  -0.734   5.2460  -1.4879  -1.3862
 TLO  C4    C  CR6    0   0.559   5.6848  -2.6264  -0.7351
 TLO  O4    O  O      0  -0.455   6.1792  -3.5467  -1.3606
 TLO  C5    C  CR6    0  -0.185   5.4956  -2.6025   0.7010
 TLO  C6    C  CR16   0   0.059   4.9401  -1.5050   1.2424
 TLO  PA    P  P      0   1.342  -1.3818   1.9778  -0.8390
 TLO  PB    P  P      0   1.327  -3.5618   0.0884  -0.7867
 TLO  CG    C  CR6    0   0.368  -5.3642  -1.0614   0.6911
 TLO  CZ    C  CR16   0  -0.271  -7.7434  -2.5049   0.7805
 TLO  C1'   C  CH1    0   0.220   3.9303   0.7191   1.2336
 TLO  O1A   O  OP    -1  -0.786  -1.8378   3.3192  -0.3609
 TLO  O1B   O  OP    -1  -0.772  -3.1639  -1.1501  -1.5196
 TLO  C2'   C  CH2    0  -0.561   4.5727   2.0920   1.0126
 TLO  O2A   O  O      0  -0.798  -1.2527   1.6943  -2.3020
 TLO  O2B   O  O      0  -0.780  -4.4581   1.1057  -1.4123
 TLO  C3'   C  CH1    0   0.023   3.5085   2.9098   0.2799
 TLO  O3'   O  OH1    0  -0.669   3.3915   4.2433   0.7084
 TLO  O3A   O  O2     0  -0.733  -2.2594   0.7986  -0.0989
 TLO  O3B   O  O2     0  -0.643  -4.2014  -0.3534   0.6931
 TLO  C4'   C  CH1    0   0.017   2.2192   2.1634   0.6240
 TLO  O4'   O  O2     0  -0.490   2.5873   0.8146   0.8529
 TLO  C5'   C  CH2    0  -0.161   1.1896   2.2346  -0.4753
 TLO  O5'   O  O2     0  -0.619   0.0124   1.5691  -0.0662
 TLO  C5M   C  CH3    0  -0.707   5.9198  -3.7858   1.5070
 TLO  CD1   C  CR16   0  -0.323  -5.3390  -2.4496   0.6001
 TLO  CD2   C  CR16   0  -0.328  -6.5789  -0.3945   0.8122
 TLO  CE1   C  CR16   0  -0.253  -6.5277  -3.1648   0.6515
 TLO  CE2   C  CR16   0  -0.252  -7.7625  -1.1184   0.8631
 TLO  HN3   H  HNR6   0   0.425   5.3526  -1.4694  -2.3932
 TLO  H6    H  HCR6   0   0.316   4.7736  -1.4363   2.3092
 TLO  HZ    H  HCR6   0   0.253  -8.6669  -3.0676   0.8202
 TLO  H1'   H  HCH1   0   0.253   4.0025   0.4439   2.2888
 TLO  H2'   H  HCH2   0   0.267   4.7654   2.5470   1.9858
 TLO  H2'A  H  HCH2   0   0.275   5.5225   2.0392   0.4830
 TLO  H3'   H  HCH1   0   0.233   3.6845   2.8669  -0.7988
 TLO  HO3'  H  HOH1   0   0.457   4.0987   4.7528   0.3024
 TLO  H4'   H  HCH1   0   0.227   1.8010   2.5957   1.5453
 TLO  H5'   H  HCH2   0   0.213   1.0055   3.2952  -0.6859
 TLO  H5'A  H  HCH2   0   0.216   1.5967   1.7816  -1.3860
 TLO  H5M   H  HCH3   0   0.247   6.9907  -3.9693   1.4098
 TLO  H5MA  H  HCH3   0   0.247   5.7001  -3.6366   2.5628
 TLO  H5MB  H  HCH3   0   0.247   5.4066  -4.6923   1.1832
 TLO  HD1   H  HCR6   0   0.259  -4.3926  -2.9645   0.5005
 TLO  HD2   H  HCR6   0   0.259  -6.5927   0.6858   0.8772
 TLO  HE1   H  HCR6   0   0.255  -6.5021  -4.2450   0.5870
 TLO  HE2   H  HCR6   0   0.255  -8.7040  -0.5937   0.9644

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    1.371  0.020  1.371
 TLO  N1   C2    single    1.376  0.020  1.376
 TLO  O2   C2    double    1.213  0.020  1.213
 TLO  C2   N3    single    1.371  0.020  1.371
 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    1.218  0.020  1.218
 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    1.646  0.020  1.646
 TLO  O2A  PA    deloc     1.496  0.020  1.496
 TLO  PA   O5'   single    1.646  0.020  1.646
 TLO  PA   O1A   deloc     1.495  0.020  1.495
 TLO  O3B  PB    single    1.672  0.020  1.672
 TLO  O2B  PB    deloc     1.493  0.020  1.493
 TLO  PB   O1B   deloc     1.493  0.020  1.493
 TLO  PB   O3A   single    1.635  0.020  1.635
 TLO  CD2  CG    aromatic  1.391  0.020  1.391
 TLO  CG   O3B   single    1.361  0.020  1.361
 TLO  CG   CD1   aromatic  1.391  0.020  1.391
 TLO  CE2  CZ    aromatic  1.389  0.020  1.389
 TLO  CZ   CE1   aromatic  1.389  0.020  1.389
 TLO  CZ   HZ    single    0.930  0.020  1.080
 TLO  C2'  C1'   single    1.532  0.020  1.532
 TLO  C1'  O4'   single    1.399  0.020  1.399
 TLO  C1'  H1'   single    0.970  0.020  1.090
 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    1.406  0.020  1.406
 TLO  C3'  C4'   single    1.529  0.020  1.529
 TLO  C3'  H3'   single    0.970  0.020  1.090
 TLO  O3'  HO3'  single    0.850  0.020  0.980
 TLO  C5'  C4'   single    1.508  0.020  1.508
 TLO  C4'  O4'   single    1.417  0.020  1.417
 TLO  C4'  H4'   single    0.970  0.020  1.090
 TLO  O5'  C5'   single    1.413  0.020  1.413
 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    119.13  3.000
 TLO  C6    N1   C2    120.82  3.000
 TLO  C1'   N1   C2    119.98  3.000
 TLO  N3    C2   O2    121.91  3.000
 TLO  N3    C2   N1    114.43  3.000
 TLO  O2    C2   N1    123.66  3.000
 TLO  HN3   N3   C4    116.73  3.000
 TLO  HN3   N3   C2    115.12  3.000
 TLO  C4    N3   C2    128.16  3.000
 TLO  C5    C4   O4    125.08  3.000
 TLO  O4    C4   N3    120.61  3.000
 TLO  C5    C4   N3    114.31  3.000
 TLO  C5M   C5   C6    123.17  3.000
 TLO  C5M   C5   C4    119.01  3.000
 TLO  C6    C5   C4    117.82  3.000
 TLO  H6    C6   C5    120.84  3.000
 TLO  H6    C6   N1    114.73  3.000
 TLO  C5    C6   N1    124.43  3.000
 TLO  O5'   PA   O3A    93.59  3.000
 TLO  O5'   PA   O2A   109.82  3.000
 TLO  O3A   PA   O2A   110.49  3.000
 TLO  O5'   PA   O1A   109.33  3.000
 TLO  O2A   PA   O1A   120.60  3.000
 TLO  O3A   PA   O1A   109.66  3.000
 TLO  O3B   PB   O3A    92.71  3.000
 TLO  O3A   PB   O2B   111.01  3.000
 TLO  O3B   PB   O2B   108.74  3.000
 TLO  O3A   PB   O1B   110.76  3.000
 TLO  O2B   PB   O1B   121.29  3.000
 TLO  O3B   PB   O1B   108.50  3.000
 TLO  CD2   CG   CD1   119.98  3.000
 TLO  CD1   CG   O3B   120.24  3.000
 TLO  CD2   CG   O3B   119.76  3.000
 TLO  HZ    CZ   CE2   120.34  3.000
 TLO  HZ    CZ   CE1   120.22  3.000
 TLO  CE2   CZ   CE1   119.45  3.000
 TLO  H1'   C1'  O4'   110.08  3.000
 TLO  H1'   C1'  C2'   109.71  3.000
 TLO  O4'   C1'  C2'   107.58  3.000
 TLO  H1'   C1'  N1    104.16  3.000
 TLO  O4'   C1'  N1    109.15  3.000
 TLO  C2'   C1'  N1    116.09  3.000
 TLO  H2'A  C2'  H2'   107.46  3.000
 TLO  H2'A  C2'  C3'   113.58  3.000
 TLO  H2'   C2'  C3'   109.10  3.000
 TLO  H2'A  C2'  C1'   113.11  3.000
 TLO  H2'   C2'  C1'   108.60  3.000
 TLO  C3'   C2'  C1'   104.87  3.000
 TLO  H3'   C3'  C4'   109.79  3.000
 TLO  H3'   C3'  O3'   110.56  3.000
 TLO  C4'   C3'  O3'   108.93  3.000
 TLO  H3'   C3'  C2'   109.85  3.000
 TLO  C4'   C3'  C2'   102.59  3.000
 TLO  O3'   C3'  C2'   114.78  3.000
 TLO  HO3'  O3'  C3'   108.23  3.000
 TLO  PB    O3A  PA    123.15  3.000
 TLO  CG    O3B  PB    117.58  3.000
 TLO  H4'   C4'  C5'   109.41  3.000
 TLO  H4'   C4'  O4'   109.73  3.000
 TLO  C5'   C4'  O4'   109.89  3.000
 TLO  H4'   C4'  C3'   108.49  3.000
 TLO  O4'   C4'  C3'   106.38  3.000
 TLO  C5'   C4'  C3'   112.87  3.000
 TLO  C4'   O4'  C1'   111.00  3.000
 TLO  H5'A  C5'  H5'   107.61  3.000
 TLO  H5'A  C5'  O5'   110.83  3.000
 TLO  H5'   C5'  O5'   111.79  3.000
 TLO  H5'A  C5'  C4'   109.44  3.000
 TLO  H5'   C5'  C4'   107.47  3.000
 TLO  O5'   C5'  C4'   109.61  3.000
 TLO  C5'   O5'  PA    116.93  3.000
 TLO  H5MB  C5M  H5MA  107.87  3.000
 TLO  H5MB  C5M  H5M   107.20  3.000
 TLO  H5MA  C5M  H5M   107.90  3.000
 TLO  H5MB  C5M  C5    111.39  3.000
 TLO  H5MA  C5M  C5    110.95  3.000
 TLO  H5M   C5M  C5    111.35  3.000
 TLO  HD1   CD1  CE1   120.48  3.000
 TLO  HD1   CD1  CG    119.78  3.000
 TLO  CE1   CD1  CG    119.75  3.000
 TLO  HD2   CD2  CE2   120.49  3.000
 TLO  HD2   CD2  CG    119.66  3.000
 TLO  CE2   CD2  CG    119.85  3.000
 TLO  HE1   CE1  CD1   119.45  3.000
 TLO  HE1   CE1  CZ    120.01  3.000
 TLO  CD1   CE1  CZ    120.53  3.000
 TLO  HE2   CE2  CD2   119.48  3.000
 TLO  HE2   CE2  CZ    120.09  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    -94.08  30.0  2
 TLO  Var_02    H5M  C5M  C5   C4     60.93  30.0  3
 TLO  Var_03    C4'  C5'  O5'  PA    158.35  30.0  3
 TLO  Var_04    O2B  PB   O3B  CG     68.49  30.0  3
 TLO  Var_05    O3B  PB   O3A  PA   -156.29  30.0  2
 TLO  Var_06    O2A  PA   O3A  PB    -38.20  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

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

