# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 11:36:12 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)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)N[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
 TTW  TTW  5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]thymidine  ligand  47  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_TTW
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
 TTW  O4   O  O     0  -0.458  -32.5945  -2.4145  -15.5518
 TTW  C4   C  CR6   0   0.559  -31.5958  -2.6208  -14.8853
 TTW  N3   N  NR16  0  -0.731  -30.3540  -2.7097  -15.4896
 TTW  C2   C  CR6   0   0.732  -29.1413  -2.9189  -14.8899
 TTW  O2   O  O     0  -0.489  -28.0992  -2.9344  -15.5165
 TTW  C5   C  CR6   0  -0.184  -31.5713  -2.7915  -13.4481
 TTW  C5M  C  CH3   0  -0.718  -32.8527  -2.7069  -12.6852
 TTW  C6   C  CR16  0   0.045  -30.3857  -3.0268  -12.8562
 TTW  N1   N  NR6   0  -0.563  -29.1986  -3.1061  -13.5308
 TTW  C1'  C  CR15  0   0.193  -27.9118  -3.3193  -12.8358
 TTW  O4'  O  O     0  -0.495  -28.1515  -4.0084  -11.6409
 TTW  C2'  C  CH2   0  -0.535  -27.2163  -2.0106  -12.4626
 TTW  C3'  C  CR15  0   0.013  -27.6312  -1.8108  -11.0127
 TTW  O3'  O  OH1   0  -0.689  -26.7422  -1.0029  -10.3051
 TTW  C4'  C  CR15  0  -0.002  -27.6516  -3.2674  -10.5343
 TTW  C5'  C  CH2   0  -0.217  -28.4496  -3.5715   -9.2940
 TTW  O5'  O  O2    0  -0.593  -29.7909  -3.0951   -9.4729
 TTW  PA   P  P     0   1.516  -30.9060  -2.8924   -8.3748
 TTW  O1A  O  O     0  -0.654  -32.2742  -2.9125   -8.9049
 TTW  O2A  O  OH1   0  -0.728  -30.5007  -3.9384   -7.2581
 TTW  O3A  O  O2    0  -0.699  -30.6198  -1.4279   -7.7258
 TTW  PB   P  P     0   1.501  -29.3274  -0.6262   -7.2042
 TTW  O1B  O  O     0  -0.679  -28.3941  -0.1675   -8.2558
 TTW  O2B  O  OH1   0  -0.724  -28.7491  -1.6762   -6.1668
 TTW  N3B  N  NH1   0  -0.939  -29.9972   0.6566   -6.3963
 TTW  PG   P  P     0   1.428  -31.3552   0.6792   -5.4046
 TTW  O1G  O  OH1   0  -0.726  -30.8297   1.6625   -4.2625
 TTW  O2G  O  OH1   0  -0.738  -31.2805  -0.8008   -4.8167
 TTW  O3G  O  O     0  -0.690  -32.6466   1.0590   -6.0114
 TTW  H1   H  HNR6  0   0.425  -30.3238  -2.5843  -16.4939
 TTW  H2   H  HCH3  0   0.248  -32.6796  -2.8457  -11.6189
 TTW  H3   H  HCH3  0   0.245  -33.3326  -1.7368  -12.8218
 TTW  H4   H  HCH3  0   0.245  -33.5644  -3.4662  -13.0125
 TTW  H5   H  HCR6  0   0.317  -30.3303  -3.1787  -11.7899
 TTW  H6   H  HCR5  0   0.278  -27.3036  -3.9307  -13.5015
 TTW  H7   H  HCH2  0   0.267  -26.1336  -2.1458  -12.5215
 TTW  H8   H  HCH2  0   0.281  -27.4901  -1.1855  -13.1185
 TTW  H9   H  HCR5  0   0.226  -28.6477  -1.3968  -10.9806
 TTW  H10  H  HOH1  0   0.460  -27.2117  -0.6717   -9.5212
 TTW  H11  H  HCR5  0   0.256  -26.6196  -3.5737  -10.3129
 TTW  H12  H  HCH2  0   0.284  -28.4707  -4.6451   -9.1012
 TTW  H13  H  HCH2  0   0.250  -27.9616  -3.0884   -8.4456
 TTW  H14  H  HOH1  0   0.512  -31.1634  -4.1025   -6.5721
 TTW  H15  H  HOH1  0   0.509  -27.9006  -1.4244   -5.7747
 TTW  H16  H  HNH1  0   0.455  -29.6605   1.5623   -6.7064
 TTW  H17  H  HOH1  0   0.502  -31.5365   2.1525   -3.8203
 TTW  H18  H  HOH1  0   0.504  -32.1450  -1.2107   -4.6791

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
 TTW  O2   C2   double  1.216  0.020  1.216
 TTW  N3   C2   single  1.369  0.020  1.369
 TTW  N3   C4   single  1.384  0.020  1.384
 TTW  O4   C4   double  1.218  0.020  1.218
 TTW  C2   N1   single  1.373  0.020  1.373
 TTW  C4   C5   single  1.447  0.020  1.447
 TTW  N1   C1'  single  1.478  0.020  1.478
 TTW  N1   C6   single  1.368  0.020  1.368
 TTW  C5   C6   double  1.346  0.020  1.346
 TTW  C5   C5M  single  1.494  0.020  1.494
 TTW  C1'  C2'  single  1.528  0.020  1.528
 TTW  C1'  O4'  single  1.400  0.020  1.400
 TTW  C2'  C3'  single  1.521  0.020  1.521
 TTW  O4'  C4'  single  1.423  0.020  1.423
 TTW  C3'  C4'  single  1.533  0.020  1.533
 TTW  C3'  O3'  single  1.394  0.020  1.394
 TTW  C4'  C5'  single  1.506  0.020  1.506
 TTW  O5'  C5'  single  1.435  0.020  1.435
 TTW  O5'  PA   single  1.578  0.020  1.578
 TTW  O1A  PA   double  1.467  0.020  1.467
 TTW  O1B  PB   double  1.479  0.020  1.479
 TTW  PA   O3A  single  1.627  0.020  1.627
 TTW  PA   O2A  single  1.583  0.020  1.583
 TTW  O3A  PB   single  1.608  0.020  1.608
 TTW  PB   N3B  single  1.657  0.020  1.657
 TTW  PB   O2B  single  1.585  0.020  1.585
 TTW  N3B  PG   single  1.682  0.020  1.682
 TTW  PG   O3G  double  1.477  0.020  1.477
 TTW  PG   O2G  single  1.594  0.020  1.594
 TTW  PG   O1G  single  1.596  0.020  1.596
 TTW  N3   H1   single  0.860  0.020  1.020
 TTW  C5M  H2   single  0.970  0.020  1.090
 TTW  C5M  H3   single  0.970  0.020  1.090
 TTW  C5M  H4   single  0.970  0.020  1.090
 TTW  C6   H5   single  0.930  0.020  1.080
 TTW  C1'  H6   single  0.970  0.020  1.090
 TTW  C2'  H7   single  0.970  0.020  1.090
 TTW  C2'  H8   single  0.970  0.020  1.090
 TTW  C3'  H9   single  0.970  0.020  1.090
 TTW  O3'  H10  single  0.850  0.020  0.980
 TTW  C4'  H11  single  0.970  0.020  1.090
 TTW  C5'  H12  single  0.970  0.020  1.090
 TTW  C5'  H13  single  0.970  0.020  1.090
 TTW  O2A  H14  single  0.850  0.020  0.980
 TTW  O2B  H15  single  0.850  0.020  0.980
 TTW  N3B  H16  single  0.860  0.020  1.020
 TTW  O1G  H17  single  0.850  0.020  0.980
 TTW  O2G  H18  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
 TTW  C5   C4   N3   114.25  3.000
 TTW  C5   C4   O4   125.24  3.000
 TTW  N3   C4   O4   120.50  3.000
 TTW  H1   N3   C2   115.28  3.000
 TTW  H1   N3   C4   116.86  3.000
 TTW  C2   N3   C4   127.84  3.000
 TTW  N1   C2   O2   122.96  3.000
 TTW  N1   C2   N3   114.68  3.000
 TTW  O2   C2   N3   122.36  3.000
 TTW  C6   C5   C5M  122.75  3.000
 TTW  C5M  C5   C4   119.07  3.000
 TTW  C6   C5   C4   118.18  3.000
 TTW  H4   C5M  H3   107.12  3.000
 TTW  H4   C5M  H2   107.98  3.000
 TTW  H3   C5M  H2   107.81  3.000
 TTW  H4   C5M  C5   111.53  3.000
 TTW  H3   C5M  C5   111.33  3.000
 TTW  H2   C5M  C5   110.89  3.000
 TTW  H5   C6   N1   115.78  3.000
 TTW  H5   C6   C5   120.31  3.000
 TTW  N1   C6   C5   123.90  3.000
 TTW  C1'  N1   C6   122.15  3.000
 TTW  C6   N1   C2   121.10  3.000
 TTW  C1'  N1   C2   116.67  3.000
 TTW  H6   C1'  C2'  112.07  3.000
 TTW  H6   C1'  O4'  109.92  3.000
 TTW  C2'  C1'  O4'  106.92  3.000
 TTW  H6   C1'  N1   106.24  3.000
 TTW  O4'  C1'  N1   108.86  3.000
 TTW  C2'  C1'  N1   112.80  3.000
 TTW  C4'  O4'  C1'  110.33  3.000
 TTW  H8   C2'  H7   108.08  3.000
 TTW  H8   C2'  C3'  113.95  3.000
 TTW  H7   C2'  C3'  109.74  3.000
 TTW  H8   C2'  C1'  112.79  3.000
 TTW  H7   C2'  C1'  109.38  3.000
 TTW  C3'  C2'  C1'  102.78  3.000
 TTW  H9   C3'  C4'  109.68  3.000
 TTW  H9   C3'  O3'  110.92  3.000
 TTW  C4'  C3'  O3'  113.62  3.000
 TTW  H9   C3'  C2'  109.26  3.000
 TTW  O3'  C3'  C2'  112.70  3.000
 TTW  C4'  C3'  C2'  100.15  3.000
 TTW  H10  O3'  C3'  107.38  3.000
 TTW  H11  C4'  C5'  105.99  3.000
 TTW  H11  C4'  C3'  108.37  3.000
 TTW  C5'  C4'  C3'  117.12  3.000
 TTW  H11  C4'  O4'  109.97  3.000
 TTW  C5'  C4'  O4'  110.44  3.000
 TTW  C3'  C4'  O4'  104.88  3.000
 TTW  H13  C5'  H12  107.86  3.000
 TTW  H13  C5'  O5'  111.59  3.000
 TTW  H12  C5'  O5'  109.32  3.000
 TTW  H13  C5'  C4'  108.30  3.000
 TTW  H12  C5'  C4'  110.76  3.000
 TTW  O5'  C5'  C4'  109.01  3.000
 TTW  PA   O5'  C5'  128.07  3.000
 TTW  O3A  PA   O2A  105.56  3.000
 TTW  O2A  PA   O1A  118.98  3.000
 TTW  O3A  PA   O1A  108.69  3.000
 TTW  O2A  PA   O5'  103.01  3.000
 TTW  O3A  PA   O5'  105.60  3.000
 TTW  O1A  PA   O5'  113.94  3.000
 TTW  H14  O2A  PA   115.90  3.000
 TTW  PB   O3A  PA   136.02  3.000
 TTW  N3B  PB   O2B  109.94  3.000
 TTW  O2B  PB   O1B  116.13  3.000
 TTW  N3B  PB   O1B  111.20  3.000
 TTW  O2B  PB   O3A  100.09  3.000
 TTW  N3B  PB   O3A  102.66  3.000
 TTW  O1B  PB   O3A  115.55  3.000
 TTW  H15  O2B  PB   114.36  3.000
 TTW  H16  N3B  PG   115.86  3.000
 TTW  H16  N3B  PB   114.06  3.000
 TTW  PG   N3B  PB   128.63  3.000
 TTW  O3G  PG   O2G  115.55  3.000
 TTW  O2G  PG   O1G  107.01  3.000
 TTW  O3G  PG   O1G  115.06  3.000
 TTW  O1G  PG   N3B   99.47  3.000
 TTW  O2G  PG   N3B   99.62  3.000
 TTW  O3G  PG   N3B  117.86  3.000
 TTW  H17  O1G  PG   113.50  3.000
 TTW  H18  O2G  PG   113.85  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
 TTW  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 TTW  CONST_02  C1'  N1   C2   N3    180.00   0.0  0
 TTW  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 TTW  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 TTW  CONST_05  C2   N3   C4   O4    180.00   0.0  0
 TTW  CONST_06  O2   C2   N3   C4    180.00   0.0  0
 TTW  CONST_07  C1'  N1   C2   O2      0.00   0.0  0
 TTW  CONST_08  C6   N1   C2   O2    180.00   0.0  0
 TTW  CONST_09  H1   N3   C4   C5    180.00   0.0  0
 TTW  Var_01    H2   C5M  C5   C4   -179.51  30.0  3
 TTW  Var_02    O1A  PA   O5'  C5'  -156.94  30.0  3
 TTW  Var_03    O1B  PB   O3A  PA     71.01  30.0  3
 TTW  Var_04    PG   N3B  PB   O3A    39.53  30.0  3
 TTW  Var_05    O3G  PG   N3B  PB    -95.02  30.0  3
 TTW  Var_06    H12  C5'  O5'  PA     73.25  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
 TTW  chir_01  C1'  N1   C2'  O4'  negativ
 TTW  chir_02  C3'  O3'  C4'  C2'  positiv
 TTW  chir_03  C4'  O4'  C3'  C5'  negativ
 TTW  chir_04  PA   O1A  O3A  O2A  both
 TTW  chir_05  PB   O3A  O1B  N3B  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
 TTW  plan-1  O4   0.020
 TTW  plan-1  C4   0.020
 TTW  plan-1  N3   0.020
 TTW  plan-1  C2   0.020
 TTW  plan-1  O2   0.020
 TTW  plan-1  C5   0.020
 TTW  plan-1  C5M  0.020
 TTW  plan-1  C6   0.020
 TTW  plan-1  N1   0.020
 TTW  plan-1  C1'  0.020
 TTW  plan-1  H1   0.020
 TTW  plan-1  H5   0.020

