# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 21:03:46 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)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)C[P](O)(O)=O)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
 TTE  TTE  5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]thymidine  ligand  48  29  .  2021-08-23  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TTE
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
 TTE  N1    N  NR6   0  -0.559  -22.1895  34.6487  58.9495
 TTE  C2    C  CR6   0   0.731  -21.9380  33.6011  58.0980
 TTE  O2    O  O     0  -0.487  -22.8193  32.9723  57.5446
 TTE  N3    N  NR16  0  -0.732  -20.6106  33.3127  57.9227
 TTE  C4    C  CR6   0   0.561  -19.5237  33.9044  58.5427
 TTE  O4    O  O     0  -0.456  -18.3920  33.5205  58.3084
 TTE  C5    C  CR6   0  -0.183  -19.8696  34.9784  59.4496
 TTE  C5M   C  CH3   0  -0.713  -18.7817  35.6921  60.1829
 TTE  C6    C  CR16  0   0.043  -21.1699  35.2935  59.5935
 TTE  C1'   C  CH1   0   0.185  -23.6105  34.9335  59.2514
 TTE  C2'   C  CH2   0  -0.531  -24.1400  34.0480  60.3778
 TTE  C3'   C  CH1   0  -0.001  -23.8857  34.9275  61.5972
 TTE  O3'   O  OH1   0  -0.680  -24.6321  34.6297  62.7384
 TTE  C4'   C  CH1   0   0.023  -24.2540  36.2910  61.0165
 TTE  O4'   O  O2    0  -0.496  -23.7281  36.2582  59.6931
 TTE  C5'   C  CH2   0  -0.221  -23.8087  37.5306  61.7501
 TTE  O5'   O  O2    0  -0.579  -22.3878  37.5890  61.9375
 TTE  PA    P  P     0   1.482  -21.7149  37.4974  63.3778
 TTE  O1A   O  O     0  -0.680  -22.5410  37.9704  64.4989
 TTE  O2A   O  OH1   0  -0.758  -20.3131  38.1488  63.1327
 TTE  O3A   O  O2    0  -0.723  -21.3536  35.9078  63.4504
 TTE  PB    P  P     0   1.445  -21.2520  34.7387  64.5458
 TTE  O1B   O  O     0  -0.667  -22.3695  33.7711  64.4679
 TTE  O2B   O  OH1   0  -0.726  -21.0845  35.5674  65.8911
 TTE  CC    C  CH2   0  -1.040  -19.6392  34.0401  64.1368
 TTE  PG    P  P     0   1.432  -18.2480  35.1791  64.3016
 TTE  O1G   O  O     0  -0.722  -18.4479  36.5655  63.7767
 TTE  O2G   O  OH1   0  -0.723  -17.9360  35.1257  65.8624
 TTE  O3G   O  OH1   0  -0.722  -17.1062  34.3645  63.5470
 TTE  HN3   H  HNR6  0   0.425  -20.4147  32.5459  57.2908
 TTE  H5M1  H  HCH3  0   0.235  -19.1948  36.4552  60.8397
 TTE  H5M2  H  HCH3  0   0.241  -18.1983  35.0048  60.7971
 TTE  H5M3  H  HCH3  0   0.252  -18.0877  36.1815  59.4984
 TTE  H6    H  HCR6  0   0.312  -21.4624  36.1131  60.2317
 TTE  H1'   H  HCH1  0   0.281  -24.1583  34.8036  58.3193
 TTE  H2'1  H  HCH2  0   0.267  -25.2130  33.8882  60.2472
 TTE  H2'2  H  HCH2  0   0.280  -23.6518  33.0755  60.4192
 TTE  H3'   H  HCH1  0   0.226  -22.8147  34.9003  61.8147
 TTE  HO'3  H  HOH1  0   0.458  -24.0410  34.2295  63.3906
 TTE  H4'   H  HCH1  0   0.253  -25.3513  36.3634  60.9760
 TTE  H5'1  H  HCH2  0   0.277  -24.0902  38.4194  61.1845
 TTE  H5'2  H  HCH2  0   0.257  -24.3385  37.5694  62.7036
 TTE  HOA2  H  HOH1  0   0.506  -19.5274  37.5657  63.3930
 TTE  HOB2  H  HOH1  0   0.512  -21.2044  35.0605  66.7071
 TTE  HCC1  H  HCH2  0   0.358  -19.4650  33.1644  64.7676
 TTE  HCC2  H  HCH2  0   0.344  -19.6881  33.6763  63.1069
 TTE  HOG2  H  HOH1  0   0.506  -17.5423  35.9317  66.2258
 TTE  HOG3  H  HOH1  0   0.507  -16.2840  34.8546  63.3988

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
 TTE  N1   C2    single  1.373  0.020  1.373
 TTE  N1   C6    single  1.367  0.020  1.367
 TTE  N1   C1'   single  1.480  0.020  1.480
 TTE  C2   O2    double  1.216  0.020  1.216
 TTE  C2   N3    single  1.370  0.020  1.370
 TTE  N3   C4    single  1.384  0.020  1.384
 TTE  N3   HN3   single  0.860  0.020  1.020
 TTE  C4   O4    double  1.218  0.020  1.218
 TTE  C4   C5    single  1.448  0.020  1.448
 TTE  C5   C5M   single  1.494  0.020  1.494
 TTE  C5   C6    double  1.346  0.020  1.346
 TTE  C5M  H5M1  single  0.970  0.020  1.090
 TTE  C5M  H5M2  single  0.970  0.020  1.090
 TTE  C5M  H5M3  single  0.970  0.020  1.090
 TTE  C6   H6    single  0.930  0.020  1.080
 TTE  C1'  C2'   single  1.527  0.020  1.527
 TTE  C1'  O4'   single  1.401  0.020  1.401
 TTE  C1'  H1'   single  0.970  0.020  1.090
 TTE  C2'  C3'   single  1.525  0.020  1.525
 TTE  C2'  H2'1  single  0.970  0.020  1.090
 TTE  C2'  H2'2  single  0.970  0.020  1.090
 TTE  C3'  O3'   single  1.396  0.020  1.396
 TTE  C3'  C4'   single  1.527  0.020  1.527
 TTE  C3'  H3'   single  0.970  0.020  1.090
 TTE  O3'  HO'3  single  0.850  0.020  0.980
 TTE  C4'  O4'   single  1.425  0.020  1.425
 TTE  C4'  C5'   single  1.508  0.020  1.508
 TTE  C4'  H4'   single  0.970  0.020  1.090
 TTE  C5'  O5'   single  1.434  0.020  1.434
 TTE  C5'  H5'1  single  0.970  0.020  1.090
 TTE  C5'  H5'2  single  0.970  0.020  1.090
 TTE  O5'  PA    single  1.592  0.020  1.592
 TTE  PA   O1A   double  1.471  0.020  1.471
 TTE  PA   O2A   single  1.565  0.020  1.565
 TTE  PA   O3A   single  1.632  0.020  1.632
 TTE  O2A  HOA2  single  0.850  0.020  0.980
 TTE  O3A  PB    single  1.605  0.020  1.605
 TTE  PB   O1B   double  1.480  0.020  1.480
 TTE  PB   O2B   single  1.589  0.020  1.589
 TTE  PB   CC    single  1.805  0.020  1.805
 TTE  O2B  HOB2  single  0.850  0.020  0.980
 TTE  CC   PG    single  1.806  0.020  1.806
 TTE  CC   HCC1  single  0.970  0.020  1.090
 TTE  CC   HCC2  single  0.970  0.020  1.090
 TTE  PG   O1G   double  1.496  0.020  1.496
 TTE  PG   O2G   single  1.593  0.020  1.593
 TTE  PG   O3G   single  1.593  0.020  1.593
 TTE  O2G  HOG2  single  0.850  0.020  0.980
 TTE  O3G  HOG3  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
 TTE  C1'   N1   C6    121.93  3.000
 TTE  C1'   N1   C2    116.68  3.000
 TTE  C6    N1   C2    121.01  3.000
 TTE  N3    C2   O2    122.37  3.000
 TTE  N3    C2   N1    114.67  3.000
 TTE  O2    C2   N1    122.95  3.000
 TTE  HN3   N3   C4    116.82  3.000
 TTE  HN3   N3   C2    115.26  3.000
 TTE  C4    N3   C2    127.86  3.000
 TTE  C5    C4   O4    125.20  3.000
 TTE  C5    C4   N3    114.21  3.000
 TTE  O4    C4   N3    120.59  3.000
 TTE  C6    C5   C5M   122.65  3.000
 TTE  C6    C5   C4    118.14  3.000
 TTE  C5M   C5   C4    119.22  3.000
 TTE  H5M3  C5M  H5M2  107.20  3.000
 TTE  H5M3  C5M  H5M1  107.80  3.000
 TTE  H5M2  C5M  H5M1  107.75  3.000
 TTE  H5M3  C5M  C5    111.70  3.000
 TTE  H5M2  C5M  C5    111.40  3.000
 TTE  H5M1  C5M  C5    110.79  3.000
 TTE  H6    C6   C5    120.20  3.000
 TTE  H6    C6   N1    115.76  3.000
 TTE  C5    C6   N1    124.03  3.000
 TTE  H1'   C1'  O4'   109.90  3.000
 TTE  H1'   C1'  C2'   112.80  3.000
 TTE  O4'   C1'  C2'   106.65  3.000
 TTE  H1'   C1'  N1    106.58  3.000
 TTE  O4'   C1'  N1    109.07  3.000
 TTE  C2'   C1'  N1    111.82  3.000
 TTE  H2'2  C2'  H2'1  108.31  3.000
 TTE  H2'2  C2'  C3'   114.20  3.000
 TTE  H2'1  C2'  C3'   110.10  3.000
 TTE  H2'2  C2'  C1'   112.97  3.000
 TTE  H2'1  C2'  C1'   109.70  3.000
 TTE  C3'   C2'  C1'   101.39  3.000
 TTE  H3'   C3'  C4'   109.52  3.000
 TTE  H3'   C3'  O3'   110.85  3.000
 TTE  C4'   C3'  O3'   111.87  3.000
 TTE  H3'   C3'  C2'   107.95  3.000
 TTE  C4'   C3'  C2'    99.83  3.000
 TTE  O3'   C3'  C2'   116.21  3.000
 TTE  HO'3  O3'  C3'   108.23  3.000
 TTE  H4'   C4'  C5'   104.97  3.000
 TTE  H4'   C4'  O4'   109.60  3.000
 TTE  C5'   C4'  O4'   111.22  3.000
 TTE  H4'   C4'  C3'   108.26  3.000
 TTE  C5'   C4'  C3'   118.55  3.000
 TTE  O4'   C4'  C3'   104.10  3.000
 TTE  C4'   O4'  C1'   110.22  3.000
 TTE  H5'2  C5'  H5'1  107.39  3.000
 TTE  H5'2  C5'  O5'   111.43  3.000
 TTE  H5'1  C5'  O5'   106.88  3.000
 TTE  H5'2  C5'  C4'   108.11  3.000
 TTE  H5'1  C5'  C4'   109.97  3.000
 TTE  O5'   C5'  C4'   112.93  3.000
 TTE  PA    O5'  C5'   122.30  3.000
 TTE  O3A   PA   O2A   102.36  3.000
 TTE  O3A   PA   O1A   113.81  3.000
 TTE  O2A   PA   O1A   119.25  3.000
 TTE  O3A   PA   O5'   100.94  3.000
 TTE  O2A   PA   O5'   102.30  3.000
 TTE  O1A   PA   O5'   115.70  3.000
 TTE  HOA2  O2A  PA    114.53  3.000
 TTE  PB    O3A  PA    138.92  3.000
 TTE  CC    PB   O2B   107.43  3.000
 TTE  CC    PB   O1B   114.19  3.000
 TTE  O2B   PB   O1B   117.72  3.000
 TTE  CC    PB   O3A   100.60  3.000
 TTE  O2B   PB   O3A   101.80  3.000
 TTE  O1B   PB   O3A   113.10  3.000
 TTE  HOB2  O2B  PB    115.31  3.000
 TTE  HCC2  CC   HCC1  106.51  3.000
 TTE  HCC2  CC   PG    109.28  3.000
 TTE  HCC1  CC   PG    109.26  3.000
 TTE  HCC2  CC   PB    107.60  3.000
 TTE  HCC1  CC   PB    108.77  3.000
 TTE  PG    CC   PB    115.07  3.000
 TTE  O3G   PG   O2G   107.86  3.000
 TTE  O3G   PG   O1G   113.80  3.000
 TTE  O2G   PG   O1G   113.65  3.000
 TTE  O3G   PG   CC    100.75  3.000
 TTE  O2G   PG   CC    102.66  3.000
 TTE  O1G   PG   CC    116.73  3.000
 TTE  HOG2  O2G  PG    114.82  3.000
 TTE  HOG3  O3G  PG    114.97  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
 TTE  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 TTE  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 TTE  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 TTE  CONST_04  C1'   N1   C2   N3    180.00   0.0  0
 TTE  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 TTE  CONST_06  C6    N1   C2   O2    180.00   0.0  0
 TTE  CONST_07  C1'   N1   C2   O2      0.00   0.0  0
 TTE  CONST_08  C4    N3   C2   O2    180.00   0.0  0
 TTE  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 TTE  Var_01    H5M1  C5M  C5   C4   -178.77  30.0  3
 TTE  Var_02    O1A   PA   O5'  C5'   -27.51  30.0  3
 TTE  Var_03    O1B   PB   O3A  PA    106.49  30.0  3
 TTE  Var_04    PG    CC   PB   O3A    61.39  30.0  3
 TTE  Var_05    O1G   PG   CC   PB    -43.25  30.0  3
 TTE  Var_06    H5'1  C5'  O5'  PA    125.52  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
 TTE  chir_01  C1'  N1   C2'  O4'  negativ
 TTE  chir_02  C3'  O3'  C4'  C2'  positiv
 TTE  chir_03  C4'  O4'  C3'  C5'  negativ
 TTE  chir_04  PA   O1A  O2A  O3A  both
 TTE  chir_05  PB   O1B  O3A  CC   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
 TTE  plan-1  N1   0.020
 TTE  plan-1  C2   0.020
 TTE  plan-1  O2   0.020
 TTE  plan-1  N3   0.020
 TTE  plan-1  C4   0.020
 TTE  plan-1  O4   0.020
 TTE  plan-1  C5   0.020
 TTE  plan-1  C5M  0.020
 TTE  plan-1  C6   0.020
 TTE  plan-1  C1'  0.020
 TTE  plan-1  HN3  0.020
 TTE  plan-1  H6   0.020

