# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 04:40:37 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: [hydroxy-[[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2,5-dihydrofuran-2-yl]methoxy]phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)C=C2)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
 D4T  D4T  '[hydroxy-[[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2,5-dihydrofuran-2-yl]methoxy]phosphoryl] phosphono hydrogen phosphate'  ligand  43  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D4T
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
 D4T  PC    P  P     0   1.472  19.7924  42.8028  37.7736
 D4T  O1C   O  OH1   0  -0.719  20.0144  41.2507  37.5621
 D4T  O2C   O  OH1   0  -0.713  20.6830  43.0082  39.0624
 D4T  O3C   O  O     0  -0.677  18.4218  43.3324  37.7567
 D4T  O7'   O  O2    0  -0.699  20.7410  43.5137  36.6363
 D4T  PB    P  P     0   1.490  20.4204  43.5267  35.0611
 D4T  O1B   O  O     0  -0.671  19.4737  42.4925  34.6226
 D4T  O2B   O  OH1   0  -0.699  20.0689  45.0424  34.8066
 D4T  O6'   O  O2    0  -0.678  21.9074  43.4376  34.4576
 D4T  PA    P  P     0   1.496  22.9964  42.2596  34.7392
 D4T  O1A   O  O     0  -0.678  22.4122  41.0613  35.3608
 D4T  O2A   O  OH1   0  -0.701  23.5791  42.1884  33.2741
 D4T  O5'   O  O2    0  -0.573  24.1230  42.9997  35.5718
 D4T  C5'   C  CH2   0  -0.187  24.3498  42.7807  36.9686
 D4T  C4'   C  CR15  0  -0.025  24.6908  44.1046  37.6220
 D4T  O4'   O  O     0  -0.491  25.8118  44.7099  36.9967
 D4T  C1'   C  CR15  0   0.195  25.4697  45.9542  36.4466
 D4T  N1    N  NR6   0  -0.576  25.6138  45.9418  34.9870
 D4T  C6    C  CR16  0   0.090  24.5406  45.7776  34.1510
 D4T  C2    C  CR6   0   0.742  26.8951  46.0101  34.4864
 D4T  O2    O  OC    0  -0.485  27.8772  46.1348  35.1894
 D4T  N3    N  NR16  0  -0.737  26.9791  45.9279  33.1223
 D4T  C4    C  CR6   0   0.555  25.9468  45.7674  32.2139
 D4T  O4    O  OC    0  -0.455  26.1790  45.7001  31.0206
 D4T  C5    C  CR6   0  -0.178  24.6302  45.6960  32.8130
 D4T  C5A   C  CH3   0  -0.705  23.4398  45.5314  31.9268
 D4T  C2'   C  CR15  0  -0.322  24.0601  46.2004  36.8864
 D4T  C3'   C  CR15  0  -0.223  23.6181  45.1433  37.5460
 D4T  H1CO  H  HOH1  0   0.503  19.6425  40.8815  36.7481
 D4T  H2CO  H  HOH1  0   0.516  20.3841  43.7181  39.6474
 D4T  H2BO  H  HOH1  0   0.519  19.4669  45.2019  34.0654
 D4T  H2AO  H  HOH1  0   0.514  24.3252  41.5829  33.1578
 D4T  H5'1  H  HCH2  0   0.248  23.4790  42.3467  37.4639
 D4T  H5'2  H  HCH2  0   0.274  25.1800  42.0814  37.0737
 D4T  H4'C  H  HCR5  0   0.277  24.9393  43.8786  38.6666
 D4T  H1'C  H  HCR5  0   0.275  26.1550  46.7175  36.8194
 D4T  H66   H  HCR6  0   0.303  23.5783  45.7364  34.6396
 D4T  HN3   H  HNR6  0   0.425  27.9171  45.9791  32.7435
 D4T  HCA1  H  HCH3  0   0.244  23.3760  46.3351  31.1929
 D4T  HCA2  H  HCH3  0   0.246  23.4810  44.5902  31.3776
 D4T  HCA3  H  HCH3  0   0.240  22.5195  45.5352  32.5082
 D4T  H2'C  H  HCR5  0   0.293  23.5322  47.1216  36.6855
 D4T  H3'C  H  HCR5  0   0.277  22.6478  45.0223  38.0044

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
 D4T  PC   O1C   single    1.582  0.020  1.582
 D4T  PC   O2C   single    1.580  0.020  1.580
 D4T  PC   O3C   double    1.469  0.020  1.469
 D4T  PC   O7'   single    1.643  0.020  1.643
 D4T  O1C  H1CO  single    0.850  0.020  0.980
 D4T  O2C  H2CO  single    0.850  0.020  0.980
 D4T  O7'  PB    single    1.608  0.020  1.608
 D4T  PB   O1B   double    1.469  0.020  1.469
 D4T  PB   O2B   single    1.577  0.020  1.577
 D4T  PB   O6'   single    1.607  0.020  1.607
 D4T  O2B  H2BO  single    0.850  0.020  0.980
 D4T  O6'  PA    single    1.629  0.020  1.629
 D4T  PA   O1A   double    1.471  0.020  1.471
 D4T  PA   O2A   single    1.578  0.020  1.578
 D4T  PA   O5'   single    1.584  0.020  1.584
 D4T  O2A  H2AO  single    0.850  0.020  0.980
 D4T  O5'  C5'   single    1.432  0.020  1.432
 D4T  C5'  C4'   single    1.515  0.020  1.515
 D4T  C5'  H5'1  single    0.970  0.020  1.090
 D4T  C5'  H5'2  single    0.970  0.020  1.090
 D4T  C4'  O4'   single    1.419  0.020  1.419
 D4T  C4'  C3'   single    1.495  0.020  1.495
 D4T  C4'  H4'C  single    0.970  0.020  1.090
 D4T  O4'  C1'   single    1.403  0.020  1.403
 D4T  C1'  N1    single    1.467  0.020  1.467
 D4T  C1'  C2'   single    1.497  0.020  1.497
 D4T  C1'  H1'C  single    0.970  0.020  1.090
 D4T  N1   C6    aromatic  1.370  0.020  1.370
 D4T  N1   C2    aromatic  1.377  0.020  1.377
 D4T  C6   C5    aromatic  1.343  0.020  1.343
 D4T  C6   H66   single    0.930  0.020  1.080
 D4T  C2   O2    double    1.214  0.020  1.214
 D4T  C2   N3    aromatic  1.369  0.020  1.369
 D4T  N3   C4    aromatic  1.384  0.020  1.384
 D4T  N3   HN3   single    0.860  0.020  1.020
 D4T  C4   O4    double    1.218  0.020  1.218
 D4T  C4   C5    aromatic  1.448  0.020  1.448
 D4T  C5   C5A   single    1.493  0.020  1.493
 D4T  C5A  HCA1  single    0.970  0.020  1.090
 D4T  C5A  HCA2  single    0.970  0.020  1.090
 D4T  C5A  HCA3  single    0.970  0.020  1.090
 D4T  C2'  C3'   double    1.322  0.020  1.322
 D4T  C2'  H2'C  single    0.930  0.020  1.080
 D4T  C3'  H3'C  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
 D4T  O7'   PC   O3C   112.00  3.000
 D4T  O7'   PC   O2C   100.54  3.000
 D4T  O3C   PC   O2C   119.23  3.000
 D4T  O7'   PC   O1C   104.54  3.000
 D4T  O3C   PC   O1C   118.87  3.000
 D4T  O2C   PC   O1C    99.06  3.000
 D4T  H1CO  O1C  PC    115.64  3.000
 D4T  H2CO  O2C  PC    114.50  3.000
 D4T  PB    O7'  PC    124.52  3.000
 D4T  O6'   PB   O2B   101.48  3.000
 D4T  O6'   PB   O1B   116.43  3.000
 D4T  O2B   PB   O1B   119.01  3.000
 D4T  O6'   PB   O7'   100.54  3.000
 D4T  O2B   PB   O7'   102.15  3.000
 D4T  O1B   PB   O7'   114.54  3.000
 D4T  H2BO  O2B  PB    114.87  3.000
 D4T  PA    O6'  PB    126.42  3.000
 D4T  O5'   PA   O2A   104.26  3.000
 D4T  O5'   PA   O1A   116.16  3.000
 D4T  O2A   PA   O1A   120.15  3.000
 D4T  O5'   PA   O6'   103.20  3.000
 D4T  O2A   PA   O6'    96.83  3.000
 D4T  O1A   PA   O6'   113.37  3.000
 D4T  H2AO  O2A  PA    115.11  3.000
 D4T  C5'   O5'  PA    123.62  3.000
 D4T  H5'2  C5'  H5'1  107.97  3.000
 D4T  H5'2  C5'  C4'   110.33  3.000
 D4T  H5'1  C5'  C4'   109.34  3.000
 D4T  H5'2  C5'  O5'   108.22  3.000
 D4T  H5'1  C5'  O5'   112.15  3.000
 D4T  C4'   C5'  O5'   108.83  3.000
 D4T  H4'C  C4'  C3'   110.73  3.000
 D4T  H4'C  C4'  O4'   109.17  3.000
 D4T  C3'   C4'  O4'   104.36  3.000
 D4T  H4'C  C4'  C5'   106.36  3.000
 D4T  C3'   C4'  C5'   115.06  3.000
 D4T  O4'   C4'  C5'   111.13  3.000
 D4T  C1'   O4'  C4'   111.01  3.000
 D4T  H1'C  C1'  C2'   112.08  3.000
 D4T  H1'C  C1'  N1    106.51  3.000
 D4T  C2'   C1'  N1    112.72  3.000
 D4T  H1'C  C1'  O4'   109.46  3.000
 D4T  C2'   C1'  O4'   105.09  3.000
 D4T  N1    C1'  O4'   111.02  3.000
 D4T  C2    N1   C6    120.85  3.000
 D4T  C2    N1   C1'   116.92  3.000
 D4T  C6    N1   C1'   122.09  3.000
 D4T  H66   C6   C5    120.52  3.000
 D4T  H66   C6   N1    115.23  3.000
 D4T  C5    C6   N1    124.24  3.000
 D4T  N3    C2   O2    122.23  3.000
 D4T  N3    C2   N1    114.60  3.000
 D4T  O2    C2   N1    123.17  3.000
 D4T  HN3   N3   C4    116.81  3.000
 D4T  HN3   N3   C2    115.24  3.000
 D4T  C4    N3   C2    127.95  3.000
 D4T  C5    C4   O4    125.18  3.000
 D4T  C5    C4   N3    114.34  3.000
 D4T  O4    C4   N3    120.48  3.000
 D4T  C5A   C5   C4    118.99  3.000
 D4T  C5A   C5   C6    122.99  3.000
 D4T  C4    C5   C6    118.01  3.000
 D4T  HCA3  C5A  HCA2  107.69  3.000
 D4T  HCA3  C5A  HCA1  107.91  3.000
 D4T  HCA2  C5A  HCA1  107.42  3.000
 D4T  HCA3  C5A  C5    110.90  3.000
 D4T  HCA2  C5A  C5    111.34  3.000
 D4T  HCA1  C5A  C5    111.40  3.000
 D4T  H2'C  C2'  C3'   127.67  3.000
 D4T  H2'C  C2'  C1'   123.07  3.000
 D4T  C3'   C2'  C1'   109.26  3.000
 D4T  H3'C  C3'  C2'   126.99  3.000
 D4T  H3'C  C3'  C4'   123.04  3.000
 D4T  C2'   C3'  C4'   109.94  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
 D4T  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 D4T  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 D4T  CONST_03  N3    C2   N1   C6      0.00   0.0  0
 D4T  CONST_04  N3    C4   C5   C6      0.00   0.0  0
 D4T  CONST_05  C5    C6   N1   C2      0.00   0.0  0
 D4T  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 D4T  CONST_07  C5    C6   N1   C1'   180.00   0.0  0
 D4T  CONST_08  N3    C2   N1   C1'   180.00   0.0  0
 D4T  CONST_09  O2    C2   N1   C1'     0.00   0.0  0
 D4T  CONST_10  C5A   C5   C6   N1    180.00   0.0  0
 D4T  CONST_11  O2    C2   N1   C6    180.00   0.0  0
 D4T  CONST_12  O4    C4   C5   C6    180.00   0.0  0
 D4T  CONST_13  O4    C4   N3   C2    180.00   0.0  0
 D4T  CONST_14  C4    N3   C2   O2    180.00   0.0  0
 D4T  CONST_15  C5A   C5   C4   N3    180.00   0.0  0
 D4T  CONST_16  H66   C6   N1   C1'     0.00   0.0  0
 D4T  CONST_17  HN3   N3   C2   N1    180.00   0.0  0
 D4T  Var_01    C1'   C2'  C3'  C4'     0.67  30.0  1
 D4T  Var_02    HCA1  C5A  C5   C6    122.81  30.0  2
 D4T  Var_03    C4'   C5'  O5'  PA   -141.42  30.0  3
 D4T  Var_04    O1B   PB   O7'  PC    -19.73  30.0  3
 D4T  Var_05    O1A   PA   O6'  PB     14.06  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
 D4T  chir_03  C4'  C5'  O4'  C3'  negativ
 D4T  chir_04  C1'  O4'  N1   C2'  negativ
 D4T  chir_05  PB   O1B  O2B  O6'  both
 D4T  chir_06  PA   O1A  O2A  O5'  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
 D4T  plan-1  C1'  0.020
 D4T  plan-1  N1   0.020
 D4T  plan-1  C6   0.020
 D4T  plan-1  C2   0.020
 D4T  plan-1  O2   0.020
 D4T  plan-1  N3   0.020
 D4T  plan-1  C4   0.020
 D4T  plan-1  O4   0.020
 D4T  plan-1  C5   0.020
 D4T  plan-1  C5A  0.020
 D4T  plan-1  H66  0.020
 D4T  plan-1  HN3  0.020

