# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:57:26 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [[[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2
#
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
 3TT  3TT  '[[[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid'  ligand  38  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3TT
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
 3TT  O3G  O  OP    -1  -0.900  -2.5768   3.9286  -0.9241
 3TT  PG   P  P      0   1.246  -2.2833   3.2570   0.4136
 3TT  O1G  O  OP    -1  -0.862  -1.0693   3.8787   1.1520
 3TT  O2G  O  O      0  -0.892  -3.4846   3.1126   1.3415
 3TT  N3B  N  NH1    0  -0.965  -1.8002   1.6381  -0.0769
 3TT  PB   P  P      0   1.344  -1.8958   0.2980   0.9293
 3TT  O2B  O  OP    -1  -0.827  -1.4382   0.6784   2.3091
 3TT  O1B  O  O      0  -0.828  -3.1771  -0.4797   0.7658
 3TT  O3A  O  O2     0  -0.741  -0.6987  -0.6314   0.2096
 3TT  PA   P  P      0   1.350  -0.6161  -2.2501   0.2662
 3TT  O1A  O  OP    -1  -0.803  -1.2968  -2.8404  -0.9314
 3TT  O2A  O  O      0  -0.816  -0.9008  -2.7801   1.6393
 3TT  O5'  O  O2     0  -0.615   1.0182  -2.3639  -0.0203
 3TT  C5'  C  CH2    0  -0.135   1.8462  -3.1117   0.8251
 3TT  C4'  C  CH1    0  -0.128   3.3023  -2.8687   0.4857
 3TT  O4'  O  O2     0  -0.485   3.7101  -1.5534   0.7883
 3TT  S3'  S  S2     0  -0.021   3.7087  -3.1517  -1.2710
 3TT  C2'  C  CH2    0  -0.607   3.4704  -1.3944  -1.5926
 3TT  C1'  C  CH1    0   0.240   3.9554  -0.7168  -0.3091
 3TT  N1   N  NR6    0  -0.563   3.2887   0.5642  -0.0948
 3TT  C2   C  CR6    0   0.574   3.7598   1.6736  -0.8114
 3TT  O2   O  O      0  -0.547   4.7681   1.5388  -1.5051
 3TT  N3   N  N      0  -0.554   3.0828   2.8312  -0.7277
 3TT  C4   C  CR6    0   0.469   1.9663   2.9183  -0.0088
 3TT  N4   N  NH2    0  -0.858   1.2720   4.0457   0.0111
 3TT  C5   C  CR16   0  -0.471   1.4811   1.8119   0.7561
 3TT  C6   C  CR16   0   0.091   2.1622   0.6596   0.6618
 3TT  H3   H  HNH1   0   0.342  -2.0792   1.4496  -1.0308
 3TT  H6   H  HCH2   0   0.220   1.6985  -2.8574   1.8812
 3TT  H7   H  HCH2   0   0.214   1.6666  -4.1899   0.7304
 3TT  H8   H  HCH1   0   0.285   3.9044  -3.5621   1.0790
 3TT  H9   H  HCH2   0   0.296   4.0714  -1.0856  -2.4451
 3TT  H10  H  HCH2   0   0.292   2.4229  -1.1712  -1.7865
 3TT  H11  H  HCH1   0   0.261   5.0262  -0.5194  -0.3764
 3TT  H12  H  HNH2   0   0.363   1.5764   4.7986  -0.5844
 3TT  H13  H  HNH2   0   0.442   0.2948   4.0411   0.4445
 3TT  H14  H  HCR6   0   0.286   0.5682   1.8769   1.3259
 3TT  H15  H  HCR6   0   0.299   1.8374  -0.2252   1.1799

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
 3TT  O2G  PG   deloc   1.525  0.020  1.525
 3TT  O1G  PG   deloc   1.551  0.020  1.551
 3TT  PG   N3B  single  1.759  0.020  1.759
 3TT  PG   O3G  deloc   1.525  0.020  1.525
 3TT  N3B  PB   single  1.678  0.020  1.678
 3TT  O2A  PA   deloc   1.499  0.020  1.499
 3TT  PB   O1B  deloc   1.508  0.020  1.508
 3TT  PB   O2B  deloc   1.503  0.020  1.503
 3TT  PB   O3A  single  1.678  0.020  1.678
 3TT  O1A  PA   deloc   1.499  0.020  1.499
 3TT  PA   O3A  single  1.622  0.020  1.622
 3TT  PA   O5'  single  1.663  0.020  1.663
 3TT  O5'  C5'  single  1.400  0.020  1.400
 3TT  N4   C4   single  1.324  0.020  1.324
 3TT  C5   C4   single  1.430  0.020  1.430
 3TT  C5   C6   double  1.342  0.020  1.342
 3TT  C5'  C4'  single  1.515  0.020  1.515
 3TT  C4   N3   double  1.331  0.020  1.331
 3TT  C6   N1   single  1.360  0.020  1.360
 3TT  O4'  C4'  single  1.410  0.020  1.410
 3TT  O4'  C1'  single  1.402  0.020  1.402
 3TT  C4'  S3'  single  1.825  0.020  1.825
 3TT  N3   C2   single  1.344  0.020  1.344
 3TT  N1   C2   single  1.402  0.020  1.402
 3TT  N1   C1'  single  1.460  0.020  1.460
 3TT  C2   O2   double  1.231  0.020  1.231
 3TT  C1'  C2'  single  1.530  0.020  1.530
 3TT  S3'  C2'  single  1.802  0.020  1.802
 3TT  N3B  H3   single  0.890  0.020  1.040
 3TT  C5'  H6   single  0.970  0.020  1.090
 3TT  C5'  H7   single  0.970  0.020  1.090
 3TT  C4'  H8   single  0.970  0.020  1.090
 3TT  C2'  H9   single  0.970  0.020  1.090
 3TT  C2'  H10  single  0.970  0.020  1.090
 3TT  C1'  H11  single  0.970  0.020  1.090
 3TT  N4   H12  single  0.860  0.020  1.020
 3TT  N4   H13  single  0.860  0.020  1.020
 3TT  C5   H14  single  0.930  0.020  1.080
 3TT  C6   H15  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
 3TT  N3B  PG   O2G  107.39  3.000
 3TT  N3B  PG   O1G  106.66  3.000
 3TT  O2G  PG   O1G  111.40  3.000
 3TT  N3B  PG   O3G  102.33  3.000
 3TT  O1G  PG   O3G  113.06  3.000
 3TT  O2G  PG   O3G  115.08  3.000
 3TT  H3   N3B  PB   113.63  3.000
 3TT  H3   N3B  PG   111.02  3.000
 3TT  PB   N3B  PG   123.50  3.000
 3TT  O3A  PB   O1B  105.91  3.000
 3TT  O3A  PB   O2B  108.47  3.000
 3TT  O1B  PB   O2B  119.27  3.000
 3TT  O3A  PB   N3B   98.31  3.000
 3TT  O2B  PB   N3B  109.33  3.000
 3TT  O1B  PB   N3B  113.28  3.000
 3TT  PA   O3A  PB   125.05  3.000
 3TT  O5'  PA   O2A  108.68  3.000
 3TT  O5'  PA   O1A  106.36  3.000
 3TT  O2A  PA   O1A  120.43  3.000
 3TT  O5'  PA   O3A   96.45  3.000
 3TT  O1A  PA   O3A  110.00  3.000
 3TT  O2A  PA   O3A  112.04  3.000
 3TT  C5'  O5'  PA   120.91  3.000
 3TT  H7   C5'  H6   106.81  3.000
 3TT  H7   C5'  C4'  107.19  3.000
 3TT  H6   C5'  C4'  107.94  3.000
 3TT  H7   C5'  O5'  112.09  3.000
 3TT  H6   C5'  O5'  112.22  3.000
 3TT  C4'  C5'  O5'  110.34  3.000
 3TT  H8   C4'  S3'  107.53  3.000
 3TT  H8   C4'  O4'  108.42  3.000
 3TT  S3'  C4'  O4'  106.67  3.000
 3TT  H8   C4'  C5'  107.82  3.000
 3TT  S3'  C4'  C5'  113.88  3.000
 3TT  O4'  C4'  C5'  112.31  3.000
 3TT  C1'  O4'  C4'  116.07  3.000
 3TT  C2'  S3'  C4'   89.49  3.000
 3TT  H10  C2'  H9   109.51  3.000
 3TT  H10  C2'  C1'  111.32  3.000
 3TT  H9   C2'  C1'  110.88  3.000
 3TT  H10  C2'  S3'  111.04  3.000
 3TT  H9   C2'  S3'  110.10  3.000
 3TT  C1'  C2'  S3'  103.90  3.000
 3TT  H11  C1'  N1   107.37  3.000
 3TT  H11  C1'  C2'  109.84  3.000
 3TT  N1   C1'  C2'  111.53  3.000
 3TT  H11  C1'  O4'  109.15  3.000
 3TT  C2'  C1'  O4'  109.69  3.000
 3TT  N1   C1'  O4'  109.20  3.000
 3TT  C6   N1   C2   120.46  3.000
 3TT  C2   N1   C1'  117.76  3.000
 3TT  C6   N1   C1'  121.42  3.000
 3TT  N3   C2   O2   122.82  3.000
 3TT  O2   C2   N1   118.45  3.000
 3TT  N3   C2   N1   118.72  3.000
 3TT  C4   N3   C2   120.85  3.000
 3TT  C5   C4   N4   118.21  3.000
 3TT  C5   C4   N3   121.54  3.000
 3TT  N4   C4   N3   120.25  3.000
 3TT  H13  N4   H12  121.28  3.000
 3TT  H13  N4   C4   118.80  3.000
 3TT  H12  N4   C4   117.98  3.000
 3TT  H14  C5   C6   121.24  3.000
 3TT  H14  C5   C4   121.57  3.000
 3TT  C6   C5   C4   117.04  3.000
 3TT  H15  C6   C5   121.29  3.000
 3TT  H15  C6   N1   117.40  3.000
 3TT  C5   C6   N1   121.31  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
 3TT  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 3TT  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 3TT  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 3TT  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 3TT  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 3TT  CONST_06  N4   C4   N3   C2    180.00   0.0  0
 3TT  CONST_07  C4   N3   C2   O2    180.00   0.0  0
 3TT  CONST_08  C6   N1   C2   O2    180.00   0.0  0
 3TT  CONST_09  H12  N4   C4   N3      0.00   0.0  0
 3TT  CONST_10  H13  N4   C4   N3    180.00   0.0  0
 3TT  Var_01    C1'  C2'  S3'  C4'    34.16  30.0  1
 3TT  Var_02    C4'  C5'  O5'  PA   -170.61  30.0  3
 3TT  Var_03    PB   N3B  PG   O3G  -156.74  30.0  3
 3TT  Var_04    O1B  PB   N3B  PG     94.00  30.0  3
 3TT  Var_05    O2A  PA   O3A  PB    -43.76  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
 3TT  chir_03  C4'  C5'  O4'  S3'  positiv
 3TT  chir_04  C1'  O4'  N1   C2'  positiv

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
 3TT  plan-1  C1'  0.020
 3TT  plan-1  N1   0.020
 3TT  plan-1  C2   0.020
 3TT  plan-1  O2   0.020
 3TT  plan-1  N3   0.020
 3TT  plan-1  C4   0.020
 3TT  plan-1  N4   0.020
 3TT  plan-1  C5   0.020
 3TT  plan-1  C6   0.020
 3TT  plan-1  H12  0.020
 3TT  plan-1  H13  0.020
 3TT  plan-1  H14  0.020
 3TT  plan-1  H15  0.020

