# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 00:05:16 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine
#   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)O[P](O)(=O)C(F)(F)[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
 VT7  VT7  5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine  ligand  48  31  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VT7
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
 VT7  O4   O  O     0  -0.458  10.8471   7.7432  10.9434
 VT7  C4   C  CR6   0   0.559   9.6420   7.6742  10.7787
 VT7  C5   C  CR6   0  -0.183   8.6740   7.3721  11.8113
 VT7  C5M  C  CH3   0  -0.716   9.1542   7.1171  13.2028
 VT7  C6   C  CR16  0   0.042   7.3715   7.3416  11.4724
 VT7  N3   N  NR16  0  -0.732   9.0904   7.8936   9.5283
 VT7  C2   C  CR6   0   0.732   7.7692   7.8433   9.1737
 VT7  O2   O  O     0  -0.490   7.3935   8.0227   8.0308
 VT7  N1   N  NR6   0  -0.563   6.9077   7.5724  10.2074
 VT7  C1'  C  CH1   0   0.198   5.4713   7.4930   9.8611
 VT7  C2'  C  CH2   0  -0.535   5.0793   6.1339   9.2850
 VT7  C3'  C  CH1   0   0.009   4.5430   5.3963  10.5018
 VT7  O3'  O  OH1   0  -0.684   3.6682   4.3656  10.1573
 VT7  O4'  O  O2    0  -0.496   4.7119   7.6759  11.0221
 VT7  C4'  C  CH1   0  -0.000   3.8662   6.5536  11.2439
 VT7  C5'  C  CH2   0  -0.226   3.6075   6.3685  12.7155
 VT7  O5'  O  O2    0  -0.589   4.8399   6.0480  13.3761
 VT7  PA   P  P     0   1.525   4.9925   5.4907  14.8507
 VT7  O1A  O  OH1   0  -0.727   3.6738   5.8561  15.6465
 VT7  O2A  O  O     0  -0.646   6.2992   5.7974  15.4405
 VT7  O3A  O  O2    0  -0.691   4.7914   3.8821  14.7153
 VT7  PB   P  P     0   1.361   3.8058   2.8775  13.9631
 VT7  O2B  O  O     0  -0.657   3.8891   2.8465  12.4898
 VT7  O1B  O  OH1   0  -0.714   2.4101   3.2244  14.6215
 VT7  C3B  C  CT    0   0.279   4.3592   1.2752  14.7180
 VT7  PG   P  P     0   1.331   3.8812   0.9162  16.4796
 VT7  O3G  O  O     0  -0.670   2.4281   0.7260  16.6389
 VT7  O2G  O  OH1   0  -0.726   4.8160  -0.3173  16.8566
 VT7  O1G  O  OH1   0  -0.728   4.5888   2.1548  17.1690
 VT7  F2B  F  F     0  -0.321   5.7030   1.1970  14.5711
 VT7  F3B  F  F     0  -0.332   3.8026   0.2898  13.9650
 VT7  H1   H  HCH3  0   0.247   8.3231   6.8744  13.8634
 VT7  H2   H  HCH3  0   0.245   9.8583   6.2845  13.2340
 VT7  H3   H  HCH3  0   0.244   9.6670   7.9875  13.6150
 VT7  H4   H  HCR6  0   0.318   6.6179   7.1403  12.2168
 VT7  H5   H  HNR6  0   0.425   9.7344   8.0972   8.7735
 VT7  H6   H  HCH1  0   0.279   5.2807   8.3069   9.1618
 VT7  H7   H  HCH2  0   0.267   4.2785   6.2693   8.5540
 VT7  H8   H  HCH2  0   0.282   5.9054   5.6253   8.7913
 VT7  H9   H  HCH1  0   0.229   5.3844   5.0175  11.0964
 VT7  H10  H  HOH1  0   0.460   3.6165   3.7625  10.9147
 VT7  H11  H  HCH1  0   0.257   2.8833   6.7316  10.7857
 VT7  H12  H  HCH2  0   0.286   3.1883   7.2767  13.1513
 VT7  H13  H  HCH2  0   0.248   2.8685   5.5722  12.8306
 VT7  H14  H  HOH1  0   0.516   3.6701   6.7332  16.0576
 VT7  H15  H  HOH1  0   0.521   1.6248   2.9247  14.1391
 VT7  H16  H  HOH1  0   0.509   4.3749  -1.1784  16.8442
 VT7  H17  H  HOH1  0   0.513   4.3858   2.2925  18.1063

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
 VT7  O2   C2   double  1.216  0.020  1.216
 VT7  C2   N3   single  1.369  0.020  1.369
 VT7  C2   N1   single  1.373  0.020  1.373
 VT7  N3   C4   single  1.384  0.020  1.384
 VT7  C2'  C1'  single  1.527  0.020  1.527
 VT7  C2'  C3'  single  1.521  0.020  1.521
 VT7  C1'  N1   single  1.480  0.020  1.480
 VT7  C1'  O4'  single  1.399  0.020  1.399
 VT7  N1   C6   single  1.367  0.020  1.367
 VT7  O3'  C3'  single  1.395  0.020  1.395
 VT7  C4   O4   double  1.218  0.020  1.218
 VT7  C4   C5   single  1.447  0.020  1.447
 VT7  C3'  C4'  single  1.532  0.020  1.532
 VT7  O4'  C4'  single  1.423  0.020  1.423
 VT7  C6   C5   double  1.346  0.020  1.346
 VT7  C4'  C5'  single  1.506  0.020  1.506
 VT7  C5   C5M  single  1.494  0.020  1.494
 VT7  O2B  PB   double  1.476  0.020  1.476
 VT7  C5'  O5'  single  1.435  0.020  1.435
 VT7  O5'  PA   single  1.584  0.020  1.584
 VT7  PB   O3A  single  1.596  0.020  1.596
 VT7  PB   O1B  single  1.582  0.020  1.582
 VT7  PB   C3B  single  1.856  0.020  1.856
 VT7  O3A  PA   single  1.627  0.020  1.627
 VT7  F3B  C3B  single  1.359  0.020  1.359
 VT7  PA   O2A  double  1.466  0.020  1.466
 VT7  PA   O1A  single  1.583  0.020  1.583
 VT7  C3B  F2B  single  1.354  0.020  1.354
 VT7  C3B  PG   single  1.860  0.020  1.860
 VT7  O3G  PG   double  1.474  0.020  1.474
 VT7  PG   O1G  single  1.584  0.020  1.584
 VT7  PG   O2G  single  1.593  0.020  1.593
 VT7  C5M  H1   single  0.970  0.020  1.090
 VT7  C5M  H2   single  0.970  0.020  1.090
 VT7  C5M  H3   single  0.970  0.020  1.090
 VT7  C6   H4   single  0.930  0.020  1.080
 VT7  N3   H5   single  0.860  0.020  1.020
 VT7  C1'  H6   single  0.970  0.020  1.090
 VT7  C2'  H7   single  0.970  0.020  1.090
 VT7  C2'  H8   single  0.970  0.020  1.090
 VT7  C3'  H9   single  0.970  0.020  1.090
 VT7  O3'  H10  single  0.850  0.020  0.980
 VT7  C4'  H11  single  0.970  0.020  1.090
 VT7  C5'  H12  single  0.970  0.020  1.090
 VT7  C5'  H13  single  0.970  0.020  1.090
 VT7  O1A  H14  single  0.850  0.020  0.980
 VT7  O1B  H15  single  0.850  0.020  0.980
 VT7  O2G  H16  single  0.850  0.020  0.980
 VT7  O1G  H17  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
 VT7  N3   C4   C5   114.27  3.000
 VT7  C5   C4   O4   125.23  3.000
 VT7  N3   C4   O4   120.49  3.000
 VT7  C6   C5   C5M  122.79  3.000
 VT7  C5M  C5   C4   119.03  3.000
 VT7  C6   C5   C4   118.18  3.000
 VT7  H3   C5M  H2   107.14  3.000
 VT7  H3   C5M  H1   107.90  3.000
 VT7  H2   C5M  H1   107.77  3.000
 VT7  H3   C5M  C5   111.51  3.000
 VT7  H2   C5M  C5   111.37  3.000
 VT7  H1   C5M  C5   110.96  3.000
 VT7  H4   C6   N1   115.67  3.000
 VT7  H4   C6   C5   120.45  3.000
 VT7  N1   C6   C5   123.87  3.000
 VT7  H5   N3   C2   115.35  3.000
 VT7  H5   N3   C4   116.85  3.000
 VT7  C2   N3   C4   127.79  3.000
 VT7  N1   C2   O2   122.87  3.000
 VT7  N1   C2   N3   114.71  3.000
 VT7  O2   C2   N3   122.42  3.000
 VT7  C1'  N1   C2   116.34  3.000
 VT7  C1'  N1   C6   122.47  3.000
 VT7  C2   N1   C6   121.15  3.000
 VT7  H6   C1'  O4'  109.87  3.000
 VT7  H6   C1'  C2'  112.19  3.000
 VT7  O4'  C1'  C2'  106.86  3.000
 VT7  H6   C1'  N1   106.25  3.000
 VT7  O4'  C1'  N1   109.00  3.000
 VT7  C2'  C1'  N1   112.66  3.000
 VT7  H8   C2'  H7   108.10  3.000
 VT7  H8   C2'  C3'  113.83  3.000
 VT7  H7   C2'  C3'  109.69  3.000
 VT7  H8   C2'  C1'  113.08  3.000
 VT7  H7   C2'  C1'  109.28  3.000
 VT7  C3'  C2'  C1'  102.73  3.000
 VT7  H9   C3'  C4'  109.68  3.000
 VT7  H9   C3'  O3'  111.06  3.000
 VT7  C4'  C3'  O3'  113.62  3.000
 VT7  H9   C3'  C2'  109.30  3.000
 VT7  C4'  C3'  C2'  100.19  3.000
 VT7  O3'  C3'  C2'  112.45  3.000
 VT7  H10  O3'  C3'  107.47  3.000
 VT7  C4'  O4'  C1'  110.42  3.000
 VT7  H11  C4'  C5'  105.89  3.000
 VT7  H11  C4'  O4'  109.81  3.000
 VT7  C5'  C4'  O4'  110.58  3.000
 VT7  H11  C4'  C3'  108.39  3.000
 VT7  C5'  C4'  C3'  117.16  3.000
 VT7  O4'  C4'  C3'  104.93  3.000
 VT7  H13  C5'  H12  107.75  3.000
 VT7  H13  C5'  O5'  111.70  3.000
 VT7  H12  C5'  O5'  109.39  3.000
 VT7  H13  C5'  C4'  107.99  3.000
 VT7  H12  C5'  C4'  110.74  3.000
 VT7  O5'  C5'  C4'  109.26  3.000
 VT7  PA   O5'  C5'  126.17  3.000
 VT7  O3A  PA   O2A  110.52  3.000
 VT7  O2A  PA   O1A  119.47  3.000
 VT7  O3A  PA   O1A   99.62  3.000
 VT7  O1A  PA   O5'  107.85  3.000
 VT7  O2A  PA   O5'  112.76  3.000
 VT7  O3A  PA   O5'  104.98  3.000
 VT7  H14  O1A  PA   115.18  3.000
 VT7  PB   O3A  PA   137.57  3.000
 VT7  C3B  PB   O1B  106.45  3.000
 VT7  C3B  PB   O2B  111.78  3.000
 VT7  O1B  PB   O2B  118.03  3.000
 VT7  C3B  PB   O3A   99.65  3.000
 VT7  O1B  PB   O3A  102.16  3.000
 VT7  O2B  PB   O3A  116.67  3.000
 VT7  H15  O1B  PB   116.11  3.000
 VT7  F3B  C3B  F2B  107.72  3.000
 VT7  F2B  C3B  PG   110.28  3.000
 VT7  F3B  C3B  PG   106.23  3.000
 VT7  PG   C3B  PB   118.37  3.000
 VT7  F2B  C3B  PB   107.56  3.000
 VT7  F3B  C3B  PB   106.17  3.000
 VT7  O1G  PG   O2G  103.90  3.000
 VT7  O2G  PG   O3G  116.93  3.000
 VT7  O1G  PG   O3G  119.61  3.000
 VT7  O2G  PG   C3B  102.87  3.000
 VT7  O1G  PG   C3B   98.42  3.000
 VT7  O3G  PG   C3B  112.37  3.000
 VT7  H16  O2G  PG   114.75  3.000
 VT7  H17  O1G  PG   116.00  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
 VT7  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 VT7  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 VT7  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 VT7  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 VT7  CONST_05  C2   N3   C4   O4    180.00   0.0  0
 VT7  CONST_06  O2   C2   N3   C4    180.00   0.0  0
 VT7  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 VT7  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 VT7  CONST_09  H5   N3   C4   C5    180.00   0.0  0
 VT7  Var_01    H1   C5M  C5   C4   -178.28  30.0  3
 VT7  Var_02    O3A  PA   O5'  C5'    84.39  30.0  3
 VT7  Var_03    O2B  PB   O3A  PA     67.11  30.0  1
 VT7  Var_04    F3B  C3B  PB   O3A  -167.30  30.0  3
 VT7  Var_05    O3G  PG   C3B  PB     66.88  30.0  3
 VT7  Var_06    H12  C5'  O5'  PA     71.79  30.0  2

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
 VT7  chir_01  C1'  C2'  N1   O4'  positiv
 VT7  chir_02  C3'  O3'  C4'  C2'  positiv
 VT7  chir_03  C4'  O4'  C3'  C5'  negativ
 VT7  chir_04  PA   O3A  O2A  O1A  both
 VT7  chir_05  PB   O3A  O1B  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
 VT7  plan-1  O4   0.020
 VT7  plan-1  C4   0.020
 VT7  plan-1  C5   0.020
 VT7  plan-1  C5M  0.020
 VT7  plan-1  C6   0.020
 VT7  plan-1  N3   0.020
 VT7  plan-1  C2   0.020
 VT7  plan-1  O2   0.020
 VT7  plan-1  N1   0.020
 VT7  plan-1  C1'  0.020
 VT7  plan-1  H4   0.020
 VT7  plan-1  H5   0.020

