# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 19:12:52 2020
#   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  43  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_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  -0.456  -5.3160  -3.6422   1.2649
 TTW  C4   C  CR6    0   0.559  -4.9786  -2.6643   0.6225
 TTW  N3   N  NR16   0  -0.733  -4.6305  -1.4885   1.2613
 TTW  C2   C  CR6    0   0.743  -4.2277  -0.3052   0.6978
 TTW  O2   O  O      0  -0.472  -3.9381   0.6594   1.3736
 TTW  C5   C  CR6    0  -0.185  -4.8951  -2.6050  -0.8225
 TTW  C5M  C  CH3    0  -0.706  -5.2345  -3.8233  -1.6166
 TTW  C6   C  CR16   0   0.059  -4.5060  -1.4462  -1.3813
 TTW  N1   N  NR6    0  -0.567  -4.1920  -0.3120  -0.6773
 TTW  C1'  C  CH1    0   0.219  -3.7270   0.8689  -1.4052
 TTW  O4'  O  O2     0  -0.488  -2.3730   1.0770  -1.1273
 TTW  C2'  C  CH2    0  -0.561  -4.4646   2.1793  -1.1165
 TTW  C3'  C  CH1    0   0.022  -3.4332   3.0649  -0.4162
 TTW  O3'  O  OH1    0  -0.669  -3.4522   4.4141  -0.8119
 TTW  C4'  C  CH1    0   0.012  -2.1062   2.4421  -0.8523
 TTW  C5'  C  CH2    0  -0.149  -1.0317   2.5500   0.2016
 TTW  O5'  O  O2     0  -0.624   0.1764   2.0354  -0.3071
 TTW  PA   P  P      0   1.334   1.4309   1.8593   0.7584
 TTW  O1A  O  O      0  -0.810   1.8355   3.2198   1.2443
 TTW  O2A  O  OP    -1  -0.812   1.0749   0.7969   1.7592
 TTW  O3A  O  O2     0  -0.752   2.4729   1.3162  -0.3554
 TTW  PB   P  P      0   1.299   3.6518   0.1348  -0.0870
 TTW  O1B  O  O      0  -0.835   4.3242   0.5189   1.2062
 TTW  O2B  O  OP    -1  -0.823   4.4505   0.1272  -1.3594
 TTW  N3B  N  NH1    0  -0.992   2.7029  -1.2392   0.0114
 TTW  PG   P  P      0   1.184   3.3849  -2.8614  -0.2129
 TTW  O1G  O  OP    -1  -0.917   2.4894  -3.7107   0.6931
 TTW  O2G  O  OP    -1  -0.911   3.2308  -3.1730  -1.7004
 TTW  O3G  O  O      0  -0.911   4.8411  -2.7758   0.2486
 TTW  H1   H  HNR6   0   0.424  -4.6662  -1.4924   2.2734
 TTW  H2   H  HCH3   0   0.247  -4.5950  -4.6641  -1.3443
 TTW  H3   H  HCH3   0   0.246  -6.2663  -4.1344  -1.4474
 TTW  H4   H  HCH3   0   0.247  -5.1105  -3.6400  -2.6826
 TTW  H5   H  HCR6   0   0.316  -4.4234  -1.3493  -2.4557
 TTW  H6   H  HCH1   0   0.252  -3.8576   0.5991  -2.4560
 TTW  H7   H  HCH2   0   0.266  -4.7352   2.6385  -2.0690
 TTW  H8   H  HCH2   0   0.274  -5.3822   2.0403  -0.5474
 TTW  H9   H  HCH1   0   0.232  -3.5446   2.9802   0.6685
 TTW  H10  H  HOH1   0   0.456  -4.1786   4.8511  -0.3583
 TTW  H11  H  HCH1   0   0.225  -1.7739   2.9458  -1.7722
 TTW  H12  H  HCH2   0   0.206  -0.9299   3.6069   0.4775
 TTW  H13  H  HCH2   0   0.207  -1.3586   2.0047   1.0953
 TTW  H16  H  HNH1   0   0.346   2.0556  -1.1926   0.7883

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  1.213  0.020  1.213
 TTW  N3   C2   single  1.371  0.020  1.371
 TTW  N3   C4   single  1.383  0.020  1.383
 TTW  O4   C4   double  1.218  0.020  1.218
 TTW  C2   N1   single  1.376  0.020  1.376
 TTW  C4   C5   single  1.449  0.020  1.449
 TTW  N1   C1'  single  1.463  0.020  1.463
 TTW  N1   C6   single  1.371  0.020  1.371
 TTW  C5   C6   double  1.344  0.020  1.344
 TTW  C5   C5M  single  1.493  0.020  1.493
 TTW  C1'  C2'  single  1.531  0.020  1.531
 TTW  C1'  O4'  single  1.398  0.020  1.398
 TTW  C2'  C3'  single  1.529  0.020  1.529
 TTW  O4'  C4'  single  1.418  0.020  1.418
 TTW  C3'  C4'  single  1.529  0.020  1.529
 TTW  C3'  O3'  single  1.406  0.020  1.406
 TTW  C4'  C5'  single  1.509  0.020  1.509
 TTW  O5'  C5'  single  1.408  0.020  1.408
 TTW  O5'  PA   single  1.655  0.020  1.655
 TTW  O1A  PA   deloc   1.500  0.020  1.500
 TTW  O1B  PB   deloc   1.507  0.020  1.507
 TTW  PA   O3A  single  1.619  0.020  1.619
 TTW  PA   O2A  deloc   1.502  0.020  1.502
 TTW  O3A  PB   single  1.690  0.020  1.690
 TTW  PB   N3B  single  1.673  0.020  1.673
 TTW  PB   O2B  deloc   1.502  0.020  1.502
 TTW  N3B  PG   single  1.774  0.020  1.774
 TTW  PG   O3G  deloc   1.530  0.020  1.530
 TTW  PG   O2G  deloc   1.528  0.020  1.528
 TTW  PG   O1G  deloc   1.531  0.020  1.531
 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  N3B  H16  single  0.890  0.020  1.040

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   114.30  3.000
 TTW  C5   C4   O4   125.11  3.000
 TTW  N3   C4   O4   120.59  3.000
 TTW  H1   N3   C2   115.11  3.000
 TTW  H1   N3   C4   116.72  3.000
 TTW  C2   N3   C4   128.17  3.000
 TTW  N1   C2   O2   123.69  3.000
 TTW  N1   C2   N3   114.47  3.000
 TTW  O2   C2   N3   121.84  3.000
 TTW  C6   C5   C5M  123.24  3.000
 TTW  C5M  C5   C4   118.94  3.000
 TTW  C6   C5   C4   117.82  3.000
 TTW  H4   C5M  H3   107.92  3.000
 TTW  H4   C5M  H2   107.90  3.000
 TTW  H3   C5M  H2   107.21  3.000
 TTW  H4   C5M  C5   110.94  3.000
 TTW  H3   C5M  C5   111.41  3.000
 TTW  H2   C5M  C5   111.28  3.000
 TTW  H5   C6   N1   114.73  3.000
 TTW  H5   C6   C5   120.81  3.000
 TTW  N1   C6   C5   124.46  3.000
 TTW  C1'  N1   C6   119.01  3.000
 TTW  C6   N1   C2   120.75  3.000
 TTW  C1'  N1   C2   120.11  3.000
 TTW  H6   C1'  C2'  109.58  3.000
 TTW  H6   C1'  O4'  110.10  3.000
 TTW  C2'  C1'  O4'  107.56  3.000
 TTW  H6   C1'  N1   103.96  3.000
 TTW  O4'  C1'  N1   109.22  3.000
 TTW  C2'  C1'  N1   116.35  3.000
 TTW  C4'  O4'  C1'  111.36  3.000
 TTW  H8   C2'  H7   107.51  3.000
 TTW  H8   C2'  C3'  113.76  3.000
 TTW  H7   C2'  C3'  108.86  3.000
 TTW  H8   C2'  C1'  113.29  3.000
 TTW  H7   C2'  C1'  108.36  3.000
 TTW  C3'  C2'  C1'  104.90  3.000
 TTW  H9   C3'  C4'  109.86  3.000
 TTW  H9   C3'  O3'  110.61  3.000
 TTW  C4'  C3'  O3'  108.80  3.000
 TTW  H9   C3'  C2'  109.92  3.000
 TTW  O3'  C3'  C2'  114.69  3.000
 TTW  C4'  C3'  C2'  102.64  3.000
 TTW  H10  O3'  C3'  108.27  3.000
 TTW  H11  C4'  C5'  109.64  3.000
 TTW  H11  C4'  C3'  108.31  3.000
 TTW  C5'  C4'  C3'  112.93  3.000
 TTW  H11  C4'  O4'  109.60  3.000
 TTW  C5'  C4'  O4'  109.77  3.000
 TTW  C3'  C4'  O4'  106.51  3.000
 TTW  H13  C5'  H12  107.56  3.000
 TTW  H13  C5'  O5'  111.61  3.000
 TTW  H12  C5'  O5'  111.31  3.000
 TTW  H13  C5'  C4'  108.74  3.000
 TTW  H12  C5'  C4'  108.10  3.000
 TTW  O5'  C5'  C4'  109.42  3.000
 TTW  PA   O5'  C5'  117.17  3.000
 TTW  O3A  PA   O2A  111.94  3.000
 TTW  O2A  PA   O1A  119.31  3.000
 TTW  O3A  PA   O1A  110.70  3.000
 TTW  O2A  PA   O5'  108.93  3.000
 TTW  O3A  PA   O5'   94.62  3.000
 TTW  O1A  PA   O5'  108.44  3.000
 TTW  PB   O3A  PA   125.03  3.000
 TTW  N3B  PB   O2B  110.32  3.000
 TTW  O2B  PB   O1B  119.39  3.000
 TTW  N3B  PB   O1B  114.33  3.000
 TTW  O2B  PB   O3A  103.88  3.000
 TTW  N3B  PB   O3A  100.82  3.000
 TTW  O1B  PB   O3A  105.62  3.000
 TTW  H16  N3B  PG   112.64  3.000
 TTW  H16  N3B  PB   111.72  3.000
 TTW  PG   N3B  PB   121.71  3.000
 TTW  O3G  PG   O2G  113.65  3.000
 TTW  O2G  PG   O1G  113.84  3.000
 TTW  O3G  PG   O1G  114.15  3.000
 TTW  O1G  PG   N3B  101.98  3.000
 TTW  O2G  PG   N3B  105.72  3.000
 TTW  O3G  PG   N3B  106.06  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   -58.80  30.0  3
 TTW  Var_02    O1A  PA   O5'  C5'  -64.64  30.0  3
 TTW  Var_03    O1B  PB   O3A  PA   -46.47  30.0  3
 TTW  Var_04    PG   N3B  PB   O3A  160.65  30.0  3
 TTW  Var_05    O3G  PG   N3B  PB    29.22  30.0  3
 TTW  Var_06    H12  C5'  O5'  PA    69.11  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

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

