# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 10 07:02:08 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}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)C[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
 N6T  N6T  2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine  ligand  45  29  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N6T
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
 N6T  O4   O  O      0  -0.456  -6.6552  -3.3968   0.9052
 N6T  C4   C  CR6    0   0.558  -6.1126  -2.4278   0.4053
 N6T  C5   C  CR6    0  -0.184  -6.0023  -2.1761  -1.0168
 N6T  C7   C  CH3    0  -0.706  -6.5894  -3.1592  -1.9752
 N6T  C6   C  CR16   0   0.059  -5.3701  -1.0565  -1.4083
 N6T  N3   N  NR16   0  -0.733  -5.5333  -1.4570   1.2021
 N6T  C2   C  CR6    0   0.740  -4.8910  -0.3109   0.8094
 N6T  O2   O  O      0  -0.472  -4.4243   0.4694   1.6122
 N6T  N1   N  NR6    0  -0.568  -4.8339  -0.1291  -0.5529
 N6T  C1'  C  CR15   0   0.221  -4.1464   1.0356  -1.1084
 N6T  C2'  C  CH2    0  -0.561  -4.6479   2.4045  -0.6367
 N6T  C3'  C  CR15   0   0.026  -3.4792   2.9991   0.1487
 N6T  O3'  O  OH1    0  -0.669  -3.2644   4.3720  -0.0659
 N6T  O4'  O  O      0  -0.490  -2.7850   0.9558  -0.8001
 N6T  C4'  C  CR15   0   0.014  -2.2824   2.2190  -0.3949
 N6T  C5'  C  CH2    0  -0.146  -1.1829   2.0328   0.6217
 N6T  O5'  O  O2     0  -0.639  -0.0962   1.3662   0.0288
 N6T  PA   P  P      0   1.267   1.3567   1.3818   0.8694
 N6T  O1A  O  OP    -1  -0.822   1.0612   0.9234   2.2748
 N6T  O2A  O  O      0  -0.815   1.9818   2.7374   0.6630
 N6T  C3A  C  CH2    0  -0.990   2.2077   0.1039  -0.1007
 N6T  PB   P  P      0   1.231   4.0458   0.1109   0.1177
 N6T  O1B  O  O      0  -0.842   4.2992   0.2166   1.6099
 N6T  O2B  O  OP    -1  -0.839   4.6462   1.1538  -0.7957
 N6T  N3B  N  NH1    0  -0.975   4.4271  -1.4256  -0.4895
 N6T  PG   P  P      0   1.184   6.0171  -1.8536  -1.1378
 N6T  O2G  O  O      0  -0.918   7.0682  -1.1526  -0.2732
 N6T  O1G  O  OP    -1  -0.926   6.0139  -3.3795  -0.9796
 N6T  O3G  O  OP    -1  -0.917   6.0143  -1.3861  -2.5925
 N6T  H1   H  HCH3   0   0.247  -7.6704  -3.2383  -1.8506
 N6T  H2   H  HCH3   0   0.247  -6.3926  -2.8633  -3.0044
 N6T  H3   H  HCH3   0   0.247  -6.1738  -4.1568  -1.8277
 N6T  H4   H  HCR6   0   0.316  -5.2570  -0.8235  -2.4586
 N6T  H5   H  HNR6   0   0.424  -5.5825  -1.6014   2.2033
 N6T  H6   H  HCR5   0   0.252  -4.2952   0.9424  -2.1870
 N6T  H7   H  HCH2   0   0.265  -4.8385   3.0248  -1.5144
 N6T  H8   H  HCH2   0   0.274  -5.5752   2.3507  -0.0686
 N6T  H9   H  HCR5   0   0.229  -3.6044   2.7909   1.2152
 N6T  H10  H  HOH1   0   0.456  -3.9283   4.8612   0.4286
 N6T  H11  H  HCR5   0   0.221  -1.8875   2.7580  -1.2694
 N6T  H12  H  HCH2   0   0.197  -0.9021   3.0304   0.9852
 N6T  H13  H  HCH2   0   0.200  -1.5771   1.4738   1.4792
 N6T  H15  H  HCH2   0   0.233   1.8087  -0.8712   0.1929
 N6T  H16  H  HCH2   0   0.234   1.9811   0.2279  -1.1630
 N6T  H18  H  HNH1   0   0.328   4.0810  -2.1627   0.1127

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
 N6T  O2   C2   double  1.213  0.020  1.213
 N6T  C2   N3   single  1.371  0.020  1.371
 N6T  C2   N1   single  1.376  0.020  1.376
 N6T  N3   C4   single  1.383  0.020  1.383
 N6T  C2'  C1'  single  1.532  0.020  1.532
 N6T  C2'  C3'  single  1.529  0.020  1.529
 N6T  C1'  N1   single  1.462  0.020  1.462
 N6T  C1'  O4'  single  1.398  0.020  1.398
 N6T  N1   C6   single  1.371  0.020  1.371
 N6T  O3'  C3'  single  1.406  0.020  1.406
 N6T  C4   O4   double  1.218  0.020  1.218
 N6T  C4   C5   single  1.448  0.020  1.448
 N6T  C3'  C4'  single  1.529  0.020  1.529
 N6T  O4'  C4'  single  1.419  0.020  1.419
 N6T  C4'  C5'  single  1.509  0.020  1.509
 N6T  C6   C5   double  1.344  0.020  1.344
 N6T  C5   C7   single  1.493  0.020  1.493
 N6T  O1B  PB   deloc   1.517  0.020  1.517
 N6T  C5'  O5'  single  1.406  0.020  1.406
 N6T  O5'  PA   single  1.679  0.020  1.679
 N6T  PB   O2B  deloc   1.511  0.020  1.511
 N6T  PB   C3A  single  1.851  0.020  1.851
 N6T  PB   N3B  single  1.696  0.020  1.696
 N6T  C3A  PA   single  1.816  0.020  1.816
 N6T  N3B  PG   single  1.770  0.020  1.770
 N6T  PA   O2A  deloc   1.507  0.020  1.507
 N6T  PA   O1A  deloc   1.508  0.020  1.508
 N6T  PG   O2G  deloc   1.531  0.020  1.531
 N6T  PG   O3G  deloc   1.528  0.020  1.528
 N6T  PG   O1G  deloc   1.534  0.020  1.534
 N6T  C7   H1   single  0.970  0.020  1.090
 N6T  C7   H2   single  0.970  0.020  1.090
 N6T  C7   H3   single  0.970  0.020  1.090
 N6T  C6   H4   single  0.930  0.020  1.080
 N6T  N3   H5   single  0.860  0.020  1.020
 N6T  C1'  H6   single  0.970  0.020  1.090
 N6T  C2'  H7   single  0.970  0.020  1.090
 N6T  C2'  H8   single  0.970  0.020  1.090
 N6T  C3'  H9   single  0.970  0.020  1.090
 N6T  O3'  H10  single  0.850  0.020  0.980
 N6T  C4'  H11  single  0.970  0.020  1.090
 N6T  C5'  H12  single  0.970  0.020  1.090
 N6T  C5'  H13  single  0.970  0.020  1.090
 N6T  C3A  H15  single  0.970  0.020  1.090
 N6T  C3A  H16  single  0.970  0.020  1.090
 N6T  N3B  H18  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
 N6T  N3   C4   C5   114.31  3.000
 N6T  C5   C4   O4   125.11  3.000
 N6T  N3   C4   O4   120.58  3.000
 N6T  C6   C5   C7   123.12  3.000
 N6T  C7   C5   C4   119.06  3.000
 N6T  C6   C5   C4   117.82  3.000
 N6T  H3   C7   H2   107.91  3.000
 N6T  H3   C7   H1   107.21  3.000
 N6T  H2   C7   H1   107.86  3.000
 N6T  H3   C7   C5   111.44  3.000
 N6T  H2   C7   C5   110.90  3.000
 N6T  H1   C7   C5   111.35  3.000
 N6T  H4   C6   N1   114.79  3.000
 N6T  H4   C6   C5   120.76  3.000
 N6T  N1   C6   C5   124.45  3.000
 N6T  H5   N3   C2   115.15  3.000
 N6T  H5   N3   C4   116.68  3.000
 N6T  C2   N3   C4   128.16  3.000
 N6T  N1   C2   O2   123.68  3.000
 N6T  N1   C2   N3   114.42  3.000
 N6T  O2   C2   N3   121.90  3.000
 N6T  C1'  N1   C2   120.07  3.000
 N6T  C1'  N1   C6   119.06  3.000
 N6T  C2   N1   C6   120.82  3.000
 N6T  H6   C1'  O4'  110.20  3.000
 N6T  H6   C1'  C2'  109.61  3.000
 N6T  O4'  C1'  C2'  107.57  3.000
 N6T  H6   C1'  N1   104.06  3.000
 N6T  O4'  C1'  N1   109.18  3.000
 N6T  C2'  C1'  N1   116.16  3.000
 N6T  H8   C2'  H7   107.39  3.000
 N6T  H8   C2'  C3'  113.73  3.000
 N6T  H7   C2'  C3'  109.00  3.000
 N6T  H8   C2'  C1'  113.28  3.000
 N6T  H7   C2'  C1'  108.50  3.000
 N6T  C3'  C2'  C1'  104.80  3.000
 N6T  H9   C3'  C4'  109.83  3.000
 N6T  H9   C3'  O3'  110.62  3.000
 N6T  C4'  C3'  O3'  108.93  3.000
 N6T  H9   C3'  C2'  109.84  3.000
 N6T  C4'  C3'  C2'  102.55  3.000
 N6T  O3'  C3'  C2'  114.73  3.000
 N6T  H10  O3'  C3'  108.23  3.000
 N6T  C4'  O4'  C1'  110.92  3.000
 N6T  H11  C4'  C5'  109.53  3.000
 N6T  H11  C4'  O4'  109.65  3.000
 N6T  C5'  C4'  O4'  109.92  3.000
 N6T  H11  C4'  C3'  108.27  3.000
 N6T  C5'  C4'  C3'  113.20  3.000
 N6T  O4'  C4'  C3'  106.18  3.000
 N6T  H13  C5'  H12  107.22  3.000
 N6T  H13  C5'  O5'  111.45  3.000
 N6T  H12  C5'  O5'  111.88  3.000
 N6T  H13  C5'  C4'  109.13  3.000
 N6T  H12  C5'  C4'  107.29  3.000
 N6T  O5'  C5'  C4'  109.73  3.000
 N6T  PA   O5'  C5'  116.96  3.000
 N6T  C3A  PA   O2A  111.43  3.000
 N6T  O2A  PA   O1A  118.85  3.000
 N6T  C3A  PA   O1A  112.08  3.000
 N6T  O1A  PA   O5'  107.12  3.000
 N6T  O2A  PA   O5'  107.39  3.000
 N6T  C3A  PA   O5'   97.56  3.000
 N6T  H16  C3A  H15  106.63  3.000
 N6T  H16  C3A  PB   108.67  3.000
 N6T  H15  C3A  PB   109.51  3.000
 N6T  H16  C3A  PA   110.01  3.000
 N6T  H15  C3A  PA   108.24  3.000
 N6T  PB   C3A  PA   113.56  3.000
 N6T  N3B  PB   O2B  108.64  3.000
 N6T  N3B  PB   O1B  112.20  3.000
 N6T  O2B  PB   O1B  118.69  3.000
 N6T  N3B  PB   C3A  100.23  3.000
 N6T  O2B  PB   C3A  109.02  3.000
 N6T  O1B  PB   C3A  106.39  3.000
 N6T  H18  N3B  PG   110.41  3.000
 N6T  H18  N3B  PB   111.70  3.000
 N6T  PG   N3B  PB   123.53  3.000
 N6T  O3G  PG   O1G  113.74  3.000
 N6T  O1G  PG   O2G  113.49  3.000
 N6T  O3G  PG   O2G  113.51  3.000
 N6T  O1G  PG   N3B  101.59  3.000
 N6T  O3G  PG   N3B  105.85  3.000
 N6T  O2G  PG   N3B  107.41  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
 N6T  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 N6T  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 N6T  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 N6T  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 N6T  CONST_05  C2   N3   C4   O4   180.00   0.0  0
 N6T  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 N6T  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 N6T  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 N6T  CONST_09  H5   N3   C4   C5   180.00   0.0  0
 N6T  Var_01    H1   C7   C5   C4    62.41  30.0  3
 N6T  Var_02    C3A  PA   O5'  C5'  167.14  30.0  3
 N6T  Var_03    PB   C3A  PA   O5'  162.37  30.0  2
 N6T  Var_04    O1B  PB   C3A  PA    46.18  30.0  1
 N6T  Var_05    PG   N3B  PB   C3A  156.10  30.0  3
 N6T  Var_06    O2G  PG   N3B  PB    37.84  30.0  3
 N6T  Var_07    H12  C5'  O5'  PA    46.96  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
 N6T  chir_01  C1'  C2'  N1   O4'  positiv
 N6T  chir_02  C3'  O3'  C4'  C2'  positiv
 N6T  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
 N6T  plan-1  O4   0.020
 N6T  plan-1  C4   0.020
 N6T  plan-1  C5   0.020
 N6T  plan-1  C7   0.020
 N6T  plan-1  C6   0.020
 N6T  plan-1  N3   0.020
 N6T  plan-1  C2   0.020
 N6T  plan-1  O2   0.020
 N6T  plan-1  N1   0.020
 N6T  plan-1  C1'  0.020
 N6T  plan-1  H4   0.020
 N6T  plan-1  H5   0.020

