# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 18:24:20 2020
#   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  44  29  .  2021-08-23  2021-08-23  
;
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  -0.567   0.0214   0.4408  -4.5452
 TTE  C2    C  CR6    0   0.744   0.1089  -0.9293  -4.6280
 TTE  O2    O  O      0  -0.472  -0.7484  -1.6846  -4.2212
 TTE  N3    N  NR16   0  -0.733   1.2543  -1.3903  -5.2252
 TTE  C4    C  CR6    0   0.558   2.3081  -0.6544  -5.7345
 TTE  O4    O  O      0  -0.457   3.2622  -1.2109  -6.2478
 TTE  C5    C  CR6    0  -0.185   2.1575   0.7791  -5.5920
 TTE  C5M   C  CH3    0  -0.707   3.2412   1.6749  -6.0956
 TTE  C6    C  CR16   0   0.060   1.0374   1.2369  -5.0066
 TTE  C1'   C  CR15   0   0.218  -1.1289   1.0666  -3.8910
 TTE  C2'   C  CH2    0  -0.561  -2.5076   0.6871  -4.4391
 TTE  C3'   C  CR15   0   0.022  -3.1787  -0.0952  -3.3101
 TTE  O3'   O  OH1    0  -0.670  -4.5400   0.2017  -3.1185
 TTE  C4'   C  CR15   0   0.017  -2.3976   0.3562  -2.0755
 TTE  O4'   O  O      0  -0.484  -1.1144   0.7529  -2.5303
 TTE  C5'   C  CH2    0  -0.149  -2.2583  -0.7260  -1.0322
 TTE  O5'   O  O2     0  -0.628  -1.6747  -0.1926   0.1336
 TTE  PA    P  P      0   1.328  -0.6851  -1.1907   1.0130
 TTE  O1A   O  O      0  -0.807   0.5382  -1.4893   0.1999
 TTE  O2A   O  OP    -1  -0.821  -1.5043  -2.3275   1.5520
 TTE  O3A   O  O2     0  -0.760  -0.3881  -0.0683   2.1455
 TTE  PB    P  P      0   1.272   0.2290  -0.4173   3.6859
 TTE  O1B   O  O      0  -0.827   1.1423  -1.6049   3.5252
 TTE  O2B   O  OP    -1  -0.817  -0.9575  -0.5175   4.6061
 TTE  CC    C  CH2    0  -0.996   1.1486   1.1183   3.9511
 TTE  PG    P  P      0   1.162   1.7075   1.4271   5.7136
 TTE  O1G   O  O      0  -0.909   2.2782   0.0887   6.1962
 TTE  O2G   O  OP    -1  -0.922   2.7692   2.5303   5.5764
 TTE  O3G   O  OP    -1  -0.911   0.4610   1.8858   6.4766
 TTE  HN3   H  HNR6   0   0.424   1.3254  -2.3979  -5.2979
 TTE  H5M1  H  HCH3   0   0.246   3.3688   1.5770  -7.1747
 TTE  H5M2  H  HCH3   0   0.247   3.0160   2.7177  -5.8784
 TTE  H5M3  H  HCH3   0   0.247   4.2003   1.4357  -5.6347
 TTE  H6    H  HCR6   0   0.315   0.8780   2.2985  -4.8721
 TTE  H1'   H  HCR5   0   0.251  -0.9609   2.1372  -4.0323
 TTE  H2'1  H  HCH2   0   0.266  -3.0705   1.6050  -4.6191
 TTE  H2'2  H  HCH2   0   0.274  -2.4607   0.1435  -5.3812
 TTE  H3'   H  HCR5   0   0.230  -3.0389  -1.1683  -3.4674
 TTE  HO'3  H  HOH1   0   0.456  -5.0427  -0.2334  -3.8132
 TTE  H4'   H  HCR5   0   0.222  -2.9164   1.2234  -1.6398
 TTE  H5'1  H  HCH2   0   0.206  -3.2571  -1.1241  -0.8153
 TTE  H5'2  H  HCH2   0   0.209  -1.6637  -1.5416  -1.4588
 TTE  HCC1  H  HCH2   0   0.204   2.0228   1.0984   3.2920
 TTE  HCC2  H  HCH2   0   0.207   0.5405   1.9670   3.6216

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  1.375  0.020  1.375
 TTE  N1   C6    single  1.371  0.020  1.371
 TTE  N1   C1'   single  1.464  0.020  1.464
 TTE  C2   O2    double  1.213  0.020  1.213
 TTE  C2   N3    single  1.372  0.020  1.372
 TTE  N3   C4    single  1.383  0.020  1.383
 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  1.493  0.020  1.493
 TTE  C5   C6    double  1.344  0.020  1.344
 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  1.531  0.020  1.531
 TTE  C1'  O4'   single  1.396  0.020  1.396
 TTE  C1'  H1'   single  0.970  0.020  1.090
 TTE  C2'  C3'   single  1.529  0.020  1.529
 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  1.406  0.020  1.406
 TTE  C3'  C4'   single  1.529  0.020  1.529
 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  1.418  0.020  1.418
 TTE  C4'  C5'   single  1.510  0.020  1.510
 TTE  C4'  H4'   single  0.970  0.020  1.090
 TTE  C5'  O5'   single  1.409  0.020  1.409
 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  1.658  0.020  1.658
 TTE  PA   O1A   deloc   1.499  0.020  1.499
 TTE  PA   O2A   deloc   1.501  0.020  1.501
 TTE  PA   O3A   single  1.622  0.020  1.622
 TTE  O3A  PB    single  1.696  0.020  1.696
 TTE  PB   O1B   deloc   1.507  0.020  1.507
 TTE  PB   O2B   deloc   1.505  0.020  1.505
 TTE  PB   CC    single  1.809  0.020  1.809
 TTE  CC   PG    single  1.875  0.020  1.875
 TTE  CC   HCC1  single  0.970  0.020  1.090
 TTE  CC   HCC2  single  0.970  0.020  1.090
 TTE  PG   O1G   deloc   1.533  0.020  1.533
 TTE  PG   O2G   deloc   1.537  0.020  1.537
 TTE  PG   O3G   deloc   1.532  0.020  1.532

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    118.98  3.000
 TTE  C1'   N1   C2    120.18  3.000
 TTE  C6    N1   C2    120.74  3.000
 TTE  N3    C2   O2    121.81  3.000
 TTE  N3    C2   N1    114.46  3.000
 TTE  O2    C2   N1    123.73  3.000
 TTE  HN3   N3   C4    116.72  3.000
 TTE  HN3   N3   C2    115.11  3.000
 TTE  C4    N3   C2    128.17  3.000
 TTE  C5    C4   O4    125.11  3.000
 TTE  C5    C4   N3    114.29  3.000
 TTE  O4    C4   N3    120.60  3.000
 TTE  C6    C5   C5M   123.18  3.000
 TTE  C6    C5   C4    117.81  3.000
 TTE  C5M   C5   C4    119.01  3.000
 TTE  H5M3  C5M  H5M2  107.91  3.000
 TTE  H5M3  C5M  H5M1  107.18  3.000
 TTE  H5M2  C5M  H5M1  107.91  3.000
 TTE  H5M3  C5M  C5    111.35  3.000
 TTE  H5M2  C5M  C5    110.92  3.000
 TTE  H5M1  C5M  C5    111.38  3.000
 TTE  H6    C6   C5    120.74  3.000
 TTE  H6    C6   N1    114.76  3.000
 TTE  C5    C6   N1    124.50  3.000
 TTE  H1'   C1'  O4'   110.15  3.000
 TTE  H1'   C1'  C2'   109.57  3.000
 TTE  O4'   C1'  C2'   107.60  3.000
 TTE  H1'   C1'  N1    103.90  3.000
 TTE  O4'   C1'  N1    109.35  3.000
 TTE  C2'   C1'  N1    116.20  3.000
 TTE  H2'2  C2'  H2'1  107.42  3.000
 TTE  H2'2  C2'  C3'   113.73  3.000
 TTE  H2'1  C2'  C3'   109.01  3.000
 TTE  H2'2  C2'  C1'   113.24  3.000
 TTE  H2'1  C2'  C1'   108.35  3.000
 TTE  C3'   C2'  C1'   104.94  3.000
 TTE  H3'   C3'  C4'   109.91  3.000
 TTE  H3'   C3'  O3'   110.52  3.000
 TTE  C4'   C3'  O3'   108.79  3.000
 TTE  H3'   C3'  C2'   109.87  3.000
 TTE  C4'   C3'  C2'   102.76  3.000
 TTE  O3'   C3'  C2'   114.67  3.000
 TTE  HO'3  O3'  C3'   108.18  3.000
 TTE  H4'   C4'  C5'   109.55  3.000
 TTE  H4'   C4'  O4'   109.46  3.000
 TTE  C5'   C4'  O4'   109.80  3.000
 TTE  H4'   C4'  C3'   108.15  3.000
 TTE  C5'   C4'  C3'   113.17  3.000
 TTE  O4'   C4'  C3'   106.61  3.000
 TTE  C4'   O4'  C1'   111.47  3.000
 TTE  H5'2  C5'  H5'1  107.51  3.000
 TTE  H5'2  C5'  O5'   112.28  3.000
 TTE  H5'1  C5'  O5'   110.55  3.000
 TTE  H5'2  C5'  C4'   108.33  3.000
 TTE  H5'1  C5'  C4'   108.23  3.000
 TTE  O5'   C5'  C4'   109.80  3.000
 TTE  PA    O5'  C5'   117.28  3.000
 TTE  O3A   PA   O2A   111.91  3.000
 TTE  O3A   PA   O1A   111.54  3.000
 TTE  O2A   PA   O1A   119.29  3.000
 TTE  O3A   PA   O5'    93.62  3.000
 TTE  O2A   PA   O5'   108.70  3.000
 TTE  O1A   PA   O5'   108.62  3.000
 TTE  PB    O3A  PA    123.96  3.000
 TTE  CC    PB   O2B   111.57  3.000
 TTE  CC    PB   O1B   112.11  3.000
 TTE  O2B   PB   O1B   119.38  3.000
 TTE  CC    PB   O3A    98.25  3.000
 TTE  O2B   PB   O3A   106.40  3.000
 TTE  O1B   PB   O3A   106.61  3.000
 TTE  HCC2  CC   HCC1  106.04  3.000
 TTE  HCC2  CC   PG    108.71  3.000
 TTE  HCC1  CC   PG    109.33  3.000
 TTE  HCC2  CC   PB    109.36  3.000
 TTE  HCC1  CC   PB    107.59  3.000
 TTE  PG    CC   PB    115.41  3.000
 TTE  O3G   PG   O2G   113.06  3.000
 TTE  O3G   PG   O1G   114.06  3.000
 TTE  O2G   PG   O1G   113.42  3.000
 TTE  O3G   PG   CC    105.97  3.000
 TTE  O2G   PG   CC    103.90  3.000
 TTE  O1G   PG   CC    105.25  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    62.57  30.0  3
 TTE  Var_02    O1A   PA   O5'  C5'   66.74  30.0  3
 TTE  Var_03    O1B   PB   O3A  PA    32.74  30.0  3
 TTE  Var_04    PG    CC   PB   O3A  165.94  30.0  3
 TTE  Var_05    O1G   PG   CC   PB    44.78  30.0  3
 TTE  Var_06    H5'1  C5'  O5'  PA    94.08  30.0  2

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

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

