# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 23:02:15 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine
#   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)N[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
 C6T  C6T  2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine  ligand  49  29  .  2021-08-07  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_C6T
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
 C6T  O4   O  O     0  -0.458  10.6848   8.1655  10.9439
 C6T  C4   C  CR6   0   0.559   9.4833   7.9957  10.8354
 C6T  C5   C  CR6   0  -0.184   8.5973   7.5877  11.9050
 C6T  C7   C  CH3   0  -0.721   9.1679   7.3356  13.2626
 C6T  C6   C  CR16  0   0.043   7.2849   7.4644  11.6308
 C6T  N3   N  NR16  0  -0.731   8.8540   8.1913   9.6185
 C6T  C2   C  CR6   0   0.731   7.5252   8.0392   9.3269
 C6T  O2   O  O     0  -0.490   7.0824   8.1975   8.2052
 C6T  N1   N  NR6   0  -0.563   6.7394   7.6923  10.3979
 C6T  C1'  C  CH1   0   0.197   5.2995   7.5041  10.1260
 C6T  C2'  C  CH2   0  -0.535   4.9673   6.0988   9.6289
 C6T  C3'  C  CH1   0   0.008   4.4688   5.3904  10.8836
 C6T  O3'  O  OH1   0  -0.698   3.5904   4.3444  10.5960
 C6T  O4'  O  O2    0  -0.497   4.5837   7.6958  11.3131
 C6T  C4'  C  CH1   0   0.015   3.7838   6.5567  11.6043
 C6T  C5'  C  CH2   0  -0.230   3.5771   6.4325  13.0928
 C6T  O5'  O  O2    0  -0.583   4.8309   6.3273  13.7685
 C6T  PA   P  P     0   1.467   5.2637   5.2356  14.8427
 C6T  O1A  O  OH1   0  -0.746   4.0506   5.2632  15.8646
 C6T  O2A  O  O     0  -0.675   6.6172   5.5427  15.3425
 C6T  N3A  N  NH1   0  -0.977   5.2388   3.7141  14.1268
 C6T  PB   P  P     0   1.377   4.0759   2.5790  13.7192
 C6T  O1B  O  O     0  -0.681   4.1172   2.1934  12.2803
 C6T  O2B  O  OH1   0  -0.734   2.7540   3.3157  14.2237
 C6T  C3B  C  CH2   0  -1.023   4.3417   1.1561  14.8034
 C6T  PG   P  P     0   1.397   3.7069   1.2928  16.4903
 C6T  O2G  O  O     0  -0.692   2.2305   1.3099  16.5841
 C6T  O1G  O  OH1   0  -0.732   4.4378   0.1300  17.3126
 C6T  O3G  O  OH1   0  -0.761   4.4785   2.6056  17.0209
 C6T  H1   H  HCH3  0   0.251   8.4028   6.9625  13.9415
 C6T  H2   H  HCH3  0   0.244   9.9684   6.5958  13.2235
 C6T  H3   H  HCH3  0   0.244   9.5898   8.2443  13.6951
 C6T  H4   H  HCR6  0   0.316   6.5876   7.1898  12.4071
 C6T  H5   H  HNR6  0   0.425   9.4414   8.4565   8.8371
 C6T  H6   H  HCH1  0   0.276   5.0272   8.2691   9.3992
 C6T  H7   H  HCH2  0   0.266   4.1541   6.1581   8.9020
 C6T  H8   H  HCH2  0   0.279   5.8121   5.6058   9.1505
 C6T  H9   H  HCH1  0   0.223   5.3273   5.0411  11.4718
 C6T  H10  H  HOH1  0   0.460   3.7934   3.5758  11.1575
 C6T  H11  H  HCH1  0   0.248   2.7816   6.6829  11.1698
 C6T  H12  H  HCH2  0   0.274   3.0645   7.3137  13.4818
 C6T  H13  H  HCH2  0   0.253   2.9282   5.5746  13.2750
 C6T  H14  H  HOH1  0   0.497   4.0198   4.4951  16.4601
 C6T  H15  H  HNH1  0   0.449   6.1655   3.4275  13.8238
 C6T  H16  H  HOH1  0   0.508   1.9388   2.8010  14.1347
 C6T  H17  H  HCH2  0   0.344   3.8424   0.2944  14.3521
 C6T  H18  H  HCH2  0   0.346   5.4111   0.9336  14.8124
 C6T  H19  H  HOH1  0   0.502   3.8738  -0.6354  17.4878
 C6T  H20  H  HOH1  0   0.510   4.4011   2.7521  17.9764

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
 C6T  O2   C2   double  1.216  0.020  1.216
 C6T  C2   N3   single  1.369  0.020  1.369
 C6T  C2   N1   single  1.373  0.020  1.373
 C6T  N3   C4   single  1.384  0.020  1.384
 C6T  C2'  C1'  single  1.527  0.020  1.527
 C6T  C2'  C3'  single  1.525  0.020  1.525
 C6T  C1'  N1   single  1.477  0.020  1.477
 C6T  C1'  O4'  single  1.399  0.020  1.399
 C6T  N1   C6   single  1.367  0.020  1.367
 C6T  O3'  C3'  single  1.396  0.020  1.396
 C6T  C4   O4   double  1.218  0.020  1.218
 C6T  C4   C5   single  1.448  0.020  1.448
 C6T  C3'  C4'  single  1.533  0.020  1.533
 C6T  O4'  C4'  single  1.422  0.020  1.422
 C6T  C6   C5   double  1.346  0.020  1.346
 C6T  C4'  C5'  single  1.508  0.020  1.508
 C6T  C5   C7   single  1.494  0.020  1.494
 C6T  O1B  PB   double  1.490  0.020  1.490
 C6T  C5'  O5'  single  1.428  0.020  1.428
 C6T  O5'  PA   single  1.592  0.020  1.592
 C6T  PB   N3A  single  1.675  0.020  1.675
 C6T  PB   O2B  single  1.595  0.020  1.595
 C6T  PB   C3B  single  1.809  0.020  1.809
 C6T  N3A  PA   single  1.682  0.020  1.682
 C6T  C3B  PG   single  1.807  0.020  1.807
 C6T  PA   O2A  double  1.475  0.020  1.475
 C6T  PA   O1A  single  1.586  0.020  1.586
 C6T  PG   O2G  double  1.479  0.020  1.479
 C6T  PG   O3G  single  1.613  0.020  1.613
 C6T  PG   O1G  single  1.601  0.020  1.601
 C6T  C7   H1   single  0.970  0.020  1.090
 C6T  C7   H2   single  0.970  0.020  1.090
 C6T  C7   H3   single  0.970  0.020  1.090
 C6T  C6   H4   single  0.930  0.020  1.080
 C6T  N3   H5   single  0.860  0.020  1.020
 C6T  C1'  H6   single  0.970  0.020  1.090
 C6T  C2'  H7   single  0.970  0.020  1.090
 C6T  C2'  H8   single  0.970  0.020  1.090
 C6T  C3'  H9   single  0.970  0.020  1.090
 C6T  O3'  H10  single  0.850  0.020  0.980
 C6T  C4'  H11  single  0.970  0.020  1.090
 C6T  C5'  H12  single  0.970  0.020  1.090
 C6T  C5'  H13  single  0.970  0.020  1.090
 C6T  O1A  H14  single  0.850  0.020  0.980
 C6T  N3A  H15  single  0.860  0.020  1.020
 C6T  O2B  H16  single  0.850  0.020  0.980
 C6T  C3B  H17  single  0.970  0.020  1.090
 C6T  C3B  H18  single  0.970  0.020  1.090
 C6T  O1G  H19  single  0.850  0.020  0.980
 C6T  O3G  H20  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
 C6T  N3   C4   C5   114.28  3.000
 C6T  C5   C4   O4   125.25  3.000
 C6T  N3   C4   O4   120.47  3.000
 C6T  C6   C5   C7   122.81  3.000
 C6T  C7   C5   C4   119.02  3.000
 C6T  C6   C5   C4   118.16  3.000
 C6T  H3   C7   H2   107.17  3.000
 C6T  H3   C7   H1   108.06  3.000
 C6T  H2   C7   H1   107.80  3.000
 C6T  H3   C7   C5   111.55  3.000
 C6T  H2   C7   C5   111.23  3.000
 C6T  H1   C7   C5   110.86  3.000
 C6T  H4   C6   N1   115.68  3.000
 C6T  H4   C6   C5   120.45  3.000
 C6T  N1   C6   C5   123.86  3.000
 C6T  H5   N3   C2   115.33  3.000
 C6T  H5   N3   C4   116.84  3.000
 C6T  C2   N3   C4   127.81  3.000
 C6T  N1   C2   O2   122.95  3.000
 C6T  N1   C2   N3   114.68  3.000
 C6T  O2   C2   N3   122.37  3.000
 C6T  C1'  N1   C2   116.52  3.000
 C6T  C1'  N1   C6   122.24  3.000
 C6T  C2   N1   C6   121.15  3.000
 C6T  H6   C1'  O4'  109.98  3.000
 C6T  H6   C1'  C2'  112.00  3.000
 C6T  O4'  C1'  C2'  106.92  3.000
 C6T  H6   C1'  N1   106.07  3.000
 C6T  O4'  C1'  N1   108.96  3.000
 C6T  C2'  C1'  N1   112.90  3.000
 C6T  H8   C2'  H7   108.04  3.000
 C6T  H8   C2'  C3'  113.88  3.000
 C6T  H7   C2'  C3'  109.24  3.000
 C6T  H8   C2'  C1'  113.01  3.000
 C6T  H7   C2'  C1'  109.18  3.000
 C6T  C3'  C2'  C1'  103.34  3.000
 C6T  H9   C3'  C4'  109.86  3.000
 C6T  H9   C3'  O3'  111.35  3.000
 C6T  C4'  C3'  O3'  112.70  3.000
 C6T  H9   C3'  C2'  109.46  3.000
 C6T  C4'  C3'  C2'  100.34  3.000
 C6T  O3'  C3'  C2'  112.61  3.000
 C6T  H10  O3'  C3'  109.98  3.000
 C6T  C4'  O4'  C1'  110.59  3.000
 C6T  H11  C4'  C5'  105.94  3.000
 C6T  H11  C4'  O4'  109.87  3.000
 C6T  C5'  C4'  O4'  110.19  3.000
 C6T  H11  C4'  C3'  107.99  3.000
 C6T  C5'  C4'  C3'  117.56  3.000
 C6T  O4'  C4'  C3'  105.18  3.000
 C6T  H13  C5'  H12  107.22  3.000
 C6T  H13  C5'  O5'  112.65  3.000
 C6T  H12  C5'  O5'  107.65  3.000
 C6T  H13  C5'  C4'  108.13  3.000
 C6T  H12  C5'  C4'  110.48  3.000
 C6T  O5'  C5'  C4'  110.66  3.000
 C6T  PA   O5'  C5'  127.49  3.000
 C6T  N3A  PA   O2A  110.25  3.000
 C6T  O2A  PA   O1A  118.67  3.000
 C6T  N3A  PA   O1A  106.18  3.000
 C6T  O1A  PA   O5'  102.41  3.000
 C6T  O2A  PA   O5'  109.60  3.000
 C6T  N3A  PA   O5'  109.22  3.000
 C6T  H14  O1A  PA   113.89  3.000
 C6T  H15  N3A  PB   111.67  3.000
 C6T  H15  N3A  PA   111.63  3.000
 C6T  PB   N3A  PA   136.62  3.000
 C6T  C3B  PB   O2B  107.19  3.000
 C6T  C3B  PB   O1B  111.79  3.000
 C6T  O2B  PB   O1B  116.60  3.000
 C6T  C3B  PB   N3A  106.57  3.000
 C6T  O2B  PB   N3A  100.68  3.000
 C6T  O1B  PB   N3A  113.02  3.000
 C6T  H16  O2B  PB   115.03  3.000
 C6T  H18  C3B  H17  106.85  3.000
 C6T  H18  C3B  PG   110.58  3.000
 C6T  H17  C3B  PG   106.53  3.000
 C6T  H18  C3B  PB   108.00  3.000
 C6T  H17  C3B  PB   107.79  3.000
 C6T  PG   C3B  PB   116.64  3.000
 C6T  O3G  PG   O1G  101.76  3.000
 C6T  O1G  PG   O2G  115.56  3.000
 C6T  O3G  PG   O2G  116.57  3.000
 C6T  O1G  PG   C3B  105.31  3.000
 C6T  O3G  PG   C3B  101.57  3.000
 C6T  O2G  PG   C3B  114.23  3.000
 C6T  H19  O1G  PG   113.69  3.000
 C6T  H20  O3G  PG   114.14  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
 C6T  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 C6T  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 C6T  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 C6T  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 C6T  CONST_05  C2   N3   C4   O4    180.00   0.0  0
 C6T  CONST_06  O2   C2   N3   C4    180.00   0.0  0
 C6T  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 C6T  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 C6T  CONST_09  H5   N3   C4   C5    180.00   0.0  0
 C6T  Var_01    H1   C7   C5   C4   -175.55  30.0  3
 C6T  Var_02    N3A  PA   O5'  C5'    62.31  30.0  3
 C6T  Var_03    PB   N3A  PA   O5'   -78.66  30.0  2
 C6T  Var_04    O1B  PB   N3A  PA    124.78  30.0  1
 C6T  Var_05    PG   C3B  PB   N3A    79.07  30.0  3
 C6T  Var_06    O2G  PG   C3B  PB     68.27  30.0  3
 C6T  Var_07    H12  C5'  O5'  PA    109.83  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
 C6T  chir_01  C1'  C2'  N1   O4'  positiv
 C6T  chir_02  C3'  O3'  C4'  C2'  positiv
 C6T  chir_03  C4'  O4'  C3'  C5'  negativ
 C6T  chir_04  PA   N3A  O2A  O1A  both
 C6T  chir_05  PB   O2B  N3A  C3B  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
 C6T  plan-1  O4   0.020
 C6T  plan-1  C4   0.020
 C6T  plan-1  C5   0.020
 C6T  plan-1  C7   0.020
 C6T  plan-1  C6   0.020
 C6T  plan-1  N3   0.020
 C6T  plan-1  C2   0.020
 C6T  plan-1  O2   0.020
 C6T  plan-1  N1   0.020
 C6T  plan-1  C1'  0.020
 C6T  plan-1  H4   0.020
 C6T  plan-1  H5   0.020

