# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 29 14:06:04 2020
#   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  45  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.520  -7.9602   1.6903   0.1892
 C6T  C4   C  CR6    0   0.527  -6.9295   1.0626   0.3542
 C6T  C5   C  CR6    0  -0.293  -6.4271   0.6040   1.6333
 C6T  C7   C  CH3    0  -0.695  -7.2137   0.8974   2.8681
 C6T  C6   C  CR16   0   0.103  -5.2587  -0.0617   1.6485
 C6T  N3   N  NR16   0  -0.670  -6.1378   0.7127  -0.7239
 C6T  C2   C  CR6    0   0.705  -4.9565   0.0171  -0.7183
 C6T  O2   O  O      0  -0.403  -4.3677  -0.2492  -1.7452
 C6T  N1   N  NR6    0  -0.610  -4.5271  -0.3661   0.5311
 C6T  C1'  C  CH1    0   0.234  -3.2701  -1.1005   0.6784
 C6T  C2'  C  CH2    0  -0.507  -3.1829  -2.4167  -0.1020
 C6T  C3'  C  CH1    0   0.049  -2.0596  -2.1943  -1.1138
 C6T  O3'  O  OH1    0  -0.679  -1.1881  -3.2823  -1.2833
 C6T  O4'  O  O2     0  -0.478  -2.2092  -0.2878   0.2706
 C6T  C4'  C  CH1    0  -0.025  -1.2807  -1.0249  -0.5082
 C6T  C5'  C  CH2    0  -0.179  -0.6578  -0.1494  -1.5670
 C6T  O5'  O  O2     0  -0.583   0.1642   0.8375  -0.9900
 C6T  PA   P  P      0   1.268   1.5940   1.2039  -1.7739
 C6T  O1A  O  OP    -1  -0.896   2.2116   2.2409  -0.8829
 C6T  O2A  O  O      0  -0.806   1.2472   1.5157  -3.2052
 C6T  N3A  N  NH1    0  -0.975   2.4529  -0.2358  -1.7273
 C6T  PB   P  P      0   1.164   3.7572  -0.7686  -0.7018
 C6T  O1B  O  O      0  -0.729   4.9498   0.0989  -1.0325
 C6T  O2B  O  OP    -1  -0.924   3.8491  -2.2507  -0.9923
 C6T  C3B  C  CH2    0  -0.964   3.1660  -0.4389   0.9751
 C6T  PG   P  P      0   1.144   4.4716  -0.5637   2.3186
 C6T  O2G  O  O      0  -0.861   5.3596  -1.7556   1.9472
 C6T  O1G  O  OP    -1  -0.927   5.2108   0.7796   2.3442
 C6T  O3G  O  OP    -1  -1.011   3.6584  -0.8114   3.6032
 C6T  H1   H  HCH3   0   0.232  -8.2215   0.4847   2.8048
 C6T  H2   H  HCH3   0   0.267  -6.7314   0.4691   3.7448
 C6T  H3   H  HCH3   0   0.263  -7.3122   1.9712   3.0307
 C6T  H4   H  HCR6   0   0.311  -4.8427  -0.4242   2.5789
 C6T  H5   H  HNR6   0   0.432  -6.4690   0.9919  -1.6394
 C6T  H6   H  HCH1   0   0.303  -3.1996  -1.3036   1.7498
 C6T  H7   H  HCH2   0   0.237  -2.9025  -3.2142   0.5872
 C6T  H8   H  HCH2   0   0.311  -4.1322  -2.6981  -0.5532
 C6T  H9   H  HCH1   0   0.162  -2.4812  -1.8850  -2.0755
 C6T  H10  H  HOH1   0   0.463  -1.6406  -3.9457  -1.8124
 C6T  H11  H  HCH1   0   0.239  -0.4864  -1.4269   0.1384
 C6T  H12  H  HCH2   0   0.239  -0.1092  -0.8224  -2.2360
 C6T  H13  H  HCH2   0   0.276  -1.4591   0.3090  -2.1603
 C6T  H15  H  HNH1   0   0.359   2.2925  -0.8545  -2.5083
 C6T  H17  H  HCH2   0   0.242   2.7290   0.5609   0.9956
 C6T  H18  H  HCH2   0   0.206   2.3509  -1.1474   1.1581

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  1.213  0.020  1.213
 C6T  C2   N3   single  1.371  0.020  1.371
 C6T  C2   N1   single  1.376  0.020  1.376
 C6T  N3   C4   single  1.383  0.020  1.383
 C6T  C2'  C1'  single  1.533  0.020  1.533
 C6T  C2'  C3'  single  1.528  0.020  1.528
 C6T  C1'  N1   single  1.463  0.020  1.463
 C6T  C1'  O4'  single  1.397  0.020  1.397
 C6T  N1   C6   single  1.370  0.020  1.370
 C6T  O3'  C3'  single  1.404  0.020  1.404
 C6T  C4   O4   double  1.218  0.020  1.218
 C6T  C4   C5   single  1.449  0.020  1.449
 C6T  C3'  C4'  single  1.530  0.020  1.530
 C6T  O4'  C4'  single  1.418  0.020  1.418
 C6T  C6   C5   double  1.345  0.020  1.345
 C6T  C4'  C5'  single  1.508  0.020  1.508
 C6T  C5   C7   single  1.493  0.020  1.493
 C6T  O1B  PB   deloc   1.511  0.020  1.511
 C6T  C5'  O5'  single  1.408  0.020  1.408
 C6T  O5'  PA   single  1.671  0.020  1.671
 C6T  PB   N3A  single  1.743  0.020  1.743
 C6T  PB   O2B  deloc   1.513  0.020  1.513
 C6T  PB   C3B  single  1.808  0.020  1.808
 C6T  N3A  PA   single  1.677  0.020  1.677
 C6T  C3B  PG   single  1.878  0.020  1.878
 C6T  PA   O2A  deloc   1.505  0.020  1.505
 C6T  PA   O1A  deloc   1.500  0.020  1.500
 C6T  PG   O2G  deloc   1.532  0.020  1.532
 C6T  PG   O3G  deloc   1.540  0.020  1.540
 C6T  PG   O1G  deloc   1.533  0.020  1.533
 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  N3A  H15  single  0.860  0.020  1.020
 C6T  C3B  H17  single  0.970  0.020  1.090
 C6T  C3B  H18  single  0.970  0.020  1.090

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   114.19  3.000
 C6T  C5   C4   O4   125.19  3.000
 C6T  N3   C4   O4   120.62  3.000
 C6T  C6   C5   C7   123.06  3.000
 C6T  C7   C5   C4   119.03  3.000
 C6T  C6   C5   C4   117.91  3.000
 C6T  H3   C7   H2   107.90  3.000
 C6T  H3   C7   H1   107.32  3.000
 C6T  H2   C7   H1   107.89  3.000
 C6T  H3   C7   C5   111.37  3.000
 C6T  H2   C7   C5   110.82  3.000
 C6T  H1   C7   C5   111.37  3.000
 C6T  H4   C6   N1   114.94  3.000
 C6T  H4   C6   C5   120.65  3.000
 C6T  N1   C6   C5   124.38  3.000
 C6T  H5   N3   C2   115.17  3.000
 C6T  H5   N3   C4   116.61  3.000
 C6T  C2   N3   C4   128.22  3.000
 C6T  N1   C2   O2   123.78  3.000
 C6T  N1   C2   N3   114.46  3.000
 C6T  O2   C2   N3   121.74  3.000
 C6T  C1'  N1   C2   119.96  3.000
 C6T  C1'  N1   C6   119.22  3.000
 C6T  C2   N1   C6   120.81  3.000
 C6T  H6   C1'  O4'  110.20  3.000
 C6T  H6   C1'  C2'  109.63  3.000
 C6T  O4'  C1'  C2'  107.92  3.000
 C6T  H6   C1'  N1   104.32  3.000
 C6T  O4'  C1'  N1   109.33  3.000
 C6T  C2'  C1'  N1   115.38  3.000
 C6T  H8   C2'  H7   107.28  3.000
 C6T  H8   C2'  C3'  113.85  3.000
 C6T  H7   C2'  C3'  109.63  3.000
 C6T  H8   C2'  C1'  112.56  3.000
 C6T  H7   C2'  C1'  108.72  3.000
 C6T  C3'  C2'  C1'  104.72  3.000
 C6T  H9   C3'  C4'  109.14  3.000
 C6T  H9   C3'  O3'  110.60  3.000
 C6T  C4'  C3'  O3'  108.90  3.000
 C6T  H9   C3'  C2'  109.87  3.000
 C6T  C4'  C3'  C2'  102.91  3.000
 C6T  O3'  C3'  C2'  115.05  3.000
 C6T  H10  O3'  C3'  107.99  3.000
 C6T  C4'  O4'  C1'  110.79  3.000
 C6T  H11  C4'  C5'  109.05  3.000
 C6T  H11  C4'  O4'  109.87  3.000
 C6T  C5'  C4'  O4'  110.74  3.000
 C6T  H11  C4'  C3'  108.72  3.000
 C6T  C5'  C4'  C3'  112.08  3.000
 C6T  O4'  C4'  C3'  106.33  3.000
 C6T  H13  C5'  H12  106.98  3.000
 C6T  H13  C5'  O5'  110.79  3.000
 C6T  H12  C5'  O5'  112.84  3.000
 C6T  H13  C5'  C4'  108.69  3.000
 C6T  H12  C5'  C4'  106.19  3.000
 C6T  O5'  C5'  C4'  111.11  3.000
 C6T  PA   O5'  C5'  117.45  3.000
 C6T  N3A  PA   O2A  108.80  3.000
 C6T  O2A  PA   O1A  121.08  3.000
 C6T  N3A  PA   O1A  111.47  3.000
 C6T  O1A  PA   O5'  103.02  3.000
 C6T  O2A  PA   O5'  107.12  3.000
 C6T  N3A  PA   O5'  103.71  3.000
 C6T  H15  N3A  PB   112.76  3.000
 C6T  H15  N3A  PA   115.05  3.000
 C6T  PB   N3A  PA   131.46  3.000
 C6T  C3B  PB   O2B  112.11  3.000
 C6T  C3B  PB   O1B  110.87  3.000
 C6T  O2B  PB   O1B  118.18  3.000
 C6T  C3B  PB   N3A  104.20  3.000
 C6T  O2B  PB   N3A  103.41  3.000
 C6T  O1B  PB   N3A  106.64  3.000
 C6T  H18  C3B  H17  106.94  3.000
 C6T  H18  C3B  PG   110.79  3.000
 C6T  H17  C3B  PG   109.02  3.000
 C6T  H18  C3B  PB   106.28  3.000
 C6T  H17  C3B  PB   108.38  3.000
 C6T  PG   C3B  PB   115.09  3.000
 C6T  O3G  PG   O1G  112.42  3.000
 C6T  O1G  PG   O2G  113.97  3.000
 C6T  O3G  PG   O2G  112.53  3.000
 C6T  O1G  PG   C3B  106.79  3.000
 C6T  O3G  PG   C3B  103.90  3.000
 C6T  O2G  PG   C3B  106.34  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     58.24  30.0  3
 C6T  Var_02    N3A  PA   O5'  C5'   -62.31  30.0  3
 C6T  Var_03    PB   N3A  PA   O5'  -101.12  30.0  1
 C6T  Var_04    O1B  PB   N3A  PA    -66.68  30.0  2
 C6T  Var_05    PG   C3B  PB   N3A  -167.72  30.0  3
 C6T  Var_06    O2G  PG   C3B  PB    -39.00  30.0  3
 C6T  Var_07    H12  C5'  O5'  PA     21.89  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

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

