# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 11:37:50 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](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)(Cl)[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
 VT6  VT6  5'-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](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_VT6
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
 VT6  O4   O   O     0  -0.458  10.7153   7.7217  11.0186
 VT6  C4   C   CR6   0   0.560   9.5094   7.6418  10.8654
 VT6  C5   C   CR6   0  -0.184   8.5538   7.3341  11.9079
 VT6  C7   C   CH3   0  -0.715   9.0489   7.0842  13.2951
 VT6  C6   C   CR16  0   0.042   7.2484   7.2948  11.5817
 VT6  N3   N   NR16  0  -0.732   8.9441   7.8514   9.6194
 VT6  C2   C   CR6   0   0.732   7.6205   7.7848   9.2763
 VT6  O2   O   O     0  -0.489   7.2343   7.9454   8.1342
 VT6  N1   N   NR6   0  -0.563   6.7703   7.5194  10.3212
 VT6  C1'  C   CH1   0   0.197   5.3335   7.4115   9.9897
 VT6  C2'  C   CH2   0  -0.535   4.9497   6.0265   9.4748
 VT6  C3'  C   CH1   0   0.001   4.3950   5.3387  10.7166
 VT6  O3'  O   OH1   0  -0.689   3.4835   4.3219  10.4214
 VT6  O4'  O   O2    0  -0.496   4.5789   7.6379  11.1472
 VT6  C4'  C   CH1   0   0.011   3.7321   6.5284  11.4166
 VT6  C5'  C   CH2   0  -0.231   3.4820   6.4030  12.8970
 VT6  O5'  O   O2    0  -0.579   4.7234   6.2237  13.5912
 VT6  PA   P   P     0   1.527   4.9748   5.2606  14.8237
 VT6  O1A  O   OH1   0  -0.727   3.6576   5.2203  15.6972
 VT6  O2A  O   O     0  -0.648   6.2632   5.5311  15.4677
 VT6  O3A  O   O2    0  -0.699   4.9378   3.7758  14.1655
 VT6  PB   P   P     0   1.421   3.9933   2.6045  13.6478
 VT6  O2B  O   O     0  -0.651   4.1831   2.2637  12.2230
 VT6  O1B  O   OH1   0  -0.710   2.5536   3.0607  14.1104
 VT6  C3B  C   CT    0  -0.150   4.4903   1.2115  14.7558
 VT6  F3B  F   F     0  -0.321   3.7359   0.1382  14.3591
 VT6  CL1  CL  CL    0  -0.049   6.1903   0.8618  14.4397
 VT6  PG   P   P     0   1.390   4.1692   1.3949  16.5778
 VT6  O3G  O   O     0  -0.664   2.7377   1.5798  16.8742
 VT6  O2G  O   OH1   0  -0.721   4.8672   0.1043  17.1950
 VT6  O1G  O   OH1   0  -0.723   5.1901   2.5678  16.8807
 VT6  H1   H   HCH3  0   0.246   8.2272   6.8241  13.9609
 VT6  H2   H   HCH3  0   0.245   9.7675   6.2638  13.3183
 VT6  H3   H   HCH3  0   0.245   9.5491   7.9624  13.7061
 VT6  H4   H   HCR6  0   0.318   6.5029   7.0951  12.3343
 VT6  H5   H   HNR6  0   0.425   9.5797   8.0520   8.8568
 VT6  H6   H   HCH1  0   0.279   5.1314   8.1929   9.2577
 VT6  H7   H   HCH2  0   0.268   4.1550   6.1267   8.7318
 VT6  H8   H   HCH2  0   0.282   5.7805   5.4969   9.0116
 VT6  H9   H   HCH1  0   0.232   5.2258   4.9619  11.3268
 VT6  H10  H   HOH1  0   0.461   3.7013   3.5393  10.9487
 VT6  H11  H   HCH1  0   0.256   2.7464   6.6904  10.9578
 VT6  H12  H   HCH2  0   0.286   3.0027   7.3012  13.2880
 VT6  H13  H   HCH2  0   0.250   2.7934   5.5698  13.0554
 VT6  H14  H   HOH1  0   0.515   3.5791   5.9268  16.3548
 VT6  H15  H   HOH1  0   0.522   1.8054   2.6458  13.6553
 VT6  H16  H   HOH1  0   0.510   4.2541  -0.5979  17.4549
 VT6  H17  H   HOH1  0   0.514   5.1424   2.9507  17.7695

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
 VT6  O2   C2   double  1.216  0.020  1.216
 VT6  C2   N3   single  1.369  0.020  1.369
 VT6  C2   N1   single  1.373  0.020  1.373
 VT6  N3   C4   single  1.384  0.020  1.384
 VT6  C2'  C1'  single  1.527  0.020  1.527
 VT6  C2'  C3'  single  1.524  0.020  1.524
 VT6  C1'  N1   single  1.479  0.020  1.479
 VT6  C1'  O4'  single  1.400  0.020  1.400
 VT6  N1   C6   single  1.367  0.020  1.367
 VT6  O3'  C3'  single  1.397  0.020  1.397
 VT6  C4   O4   double  1.218  0.020  1.218
 VT6  C4   C5   single  1.447  0.020  1.447
 VT6  C3'  C4'  single  1.531  0.020  1.531
 VT6  O4'  C4'  single  1.422  0.020  1.422
 VT6  C6   C5   double  1.346  0.020  1.346
 VT6  C4'  C5'  single  1.507  0.020  1.507
 VT6  C5   C7   single  1.494  0.020  1.494
 VT6  O2B  PB   double  1.477  0.020  1.477
 VT6  C5'  O5'  single  1.434  0.020  1.434
 VT6  O5'  PA   single  1.584  0.020  1.584
 VT6  O3A  PB   single  1.591  0.020  1.591
 VT6  O3A  PA   single  1.625  0.020  1.625
 VT6  PB   O1B  single  1.579  0.020  1.579
 VT6  PB   C3B  single  1.848  0.020  1.848
 VT6  F3B  C3B  single  1.371  0.020  1.371
 VT6  PA   O2A  double  1.466  0.020  1.466
 VT6  PA   O1A  single  1.581  0.020  1.581
 VT6  C3B  CL1  single  1.764  0.020  1.764
 VT6  C3B  PG   single  1.859  0.020  1.859
 VT6  O3G  PG   double  1.474  0.020  1.474
 VT6  PG   O1G  single  1.584  0.020  1.584
 VT6  PG   O2G  single  1.592  0.020  1.592
 VT6  C7   H1   single  0.970  0.020  1.090
 VT6  C7   H2   single  0.970  0.020  1.090
 VT6  C7   H3   single  0.970  0.020  1.090
 VT6  C6   H4   single  0.930  0.020  1.080
 VT6  N3   H5   single  0.860  0.020  1.020
 VT6  C1'  H6   single  0.970  0.020  1.090
 VT6  C2'  H7   single  0.970  0.020  1.090
 VT6  C2'  H8   single  0.970  0.020  1.090
 VT6  C3'  H9   single  0.970  0.020  1.090
 VT6  O3'  H10  single  0.850  0.020  0.980
 VT6  C4'  H11  single  0.970  0.020  1.090
 VT6  C5'  H12  single  0.970  0.020  1.090
 VT6  C5'  H13  single  0.970  0.020  1.090
 VT6  O1A  H14  single  0.850  0.020  0.980
 VT6  O1B  H15  single  0.850  0.020  0.980
 VT6  O2G  H16  single  0.850  0.020  0.980
 VT6  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
 VT6  N3   C4   C5   114.26  3.000
 VT6  C5   C4   O4   125.23  3.000
 VT6  N3   C4   O4   120.50  3.000
 VT6  C6   C5   C7   122.79  3.000
 VT6  C7   C5   C4   119.05  3.000
 VT6  C6   C5   C4   118.16  3.000
 VT6  H3   C7   H2   107.17  3.000
 VT6  H3   C7   H1   107.93  3.000
 VT6  H2   C7   H1   107.72  3.000
 VT6  H3   C7   C5   111.54  3.000
 VT6  H2   C7   C5   111.34  3.000
 VT6  H1   C7   C5   110.95  3.000
 VT6  H4   C6   N1   115.62  3.000
 VT6  H4   C6   C5   120.46  3.000
 VT6  N1   C6   C5   123.92  3.000
 VT6  H5   N3   C2   115.32  3.000
 VT6  H5   N3   C4   116.84  3.000
 VT6  C2   N3   C4   127.82  3.000
 VT6  N1   C2   O2   122.92  3.000
 VT6  N1   C2   N3   114.67  3.000
 VT6  O2   C2   N3   122.41  3.000
 VT6  C1'  N1   C2   116.44  3.000
 VT6  C1'  N1   C6   122.33  3.000
 VT6  C2   N1   C6   121.13  3.000
 VT6  H6   C1'  O4'  109.84  3.000
 VT6  H6   C1'  C2'  112.17  3.000
 VT6  O4'  C1'  C2'  106.86  3.000
 VT6  H6   C1'  N1   106.17  3.000
 VT6  O4'  C1'  N1   109.06  3.000
 VT6  C2'  C1'  N1   112.71  3.000
 VT6  H8   C2'  H7   108.08  3.000
 VT6  H8   C2'  C3'  113.88  3.000
 VT6  H7   C2'  C3'  109.32  3.000
 VT6  H8   C2'  C1'  113.14  3.000
 VT6  H7   C2'  C1'  109.21  3.000
 VT6  C3'  C2'  C1'  103.07  3.000
 VT6  H9   C3'  C4'  109.90  3.000
 VT6  H9   C3'  O3'  111.19  3.000
 VT6  C4'  C3'  O3'  112.31  3.000
 VT6  H9   C3'  C2'  109.42  3.000
 VT6  C4'  C3'  C2'  100.33  3.000
 VT6  O3'  C3'  C2'  113.18  3.000
 VT6  H10  O3'  C3'  109.05  3.000
 VT6  C4'  O4'  C1'  110.58  3.000
 VT6  H11  C4'  C5'  105.87  3.000
 VT6  H11  C4'  O4'  109.88  3.000
 VT6  C5'  C4'  O4'  110.49  3.000
 VT6  H11  C4'  C3'  108.18  3.000
 VT6  C5'  C4'  C3'  117.15  3.000
 VT6  O4'  C4'  C3'  105.18  3.000
 VT6  H13  C5'  H12  107.41  3.000
 VT6  H13  C5'  O5'  112.34  3.000
 VT6  H12  C5'  O5'  108.06  3.000
 VT6  H13  C5'  C4'  108.09  3.000
 VT6  H12  C5'  C4'  110.90  3.000
 VT6  O5'  C5'  C4'  110.03  3.000
 VT6  PA   O5'  C5'  126.17  3.000
 VT6  O3A  PA   O2A  111.52  3.000
 VT6  O2A  PA   O1A  119.63  3.000
 VT6  O3A  PA   O1A  100.46  3.000
 VT6  O1A  PA   O5'  108.24  3.000
 VT6  O2A  PA   O5'  111.66  3.000
 VT6  O3A  PA   O5'  103.70  3.000
 VT6  H14  O1A  PA   115.10  3.000
 VT6  PB   O3A  PA   144.90  3.000
 VT6  C3B  PB   O1B  106.69  3.000
 VT6  C3B  PB   O2B  111.70  3.000
 VT6  O1B  PB   O2B  117.79  3.000
 VT6  C3B  PB   O3A  101.55  3.000
 VT6  O1B  PB   O3A  103.48  3.000
 VT6  O2B  PB   O3A  114.04  3.000
 VT6  H15  O1B  PB   116.26  3.000
 VT6  PG   C3B  CL1  111.20  3.000
 VT6  PG   C3B  F3B  105.42  3.000
 VT6  CL1  C3B  F3B  108.86  3.000
 VT6  PG   C3B  PB   117.82  3.000
 VT6  CL1  C3B  PB   107.53  3.000
 VT6  F3B  C3B  PB   105.59  3.000
 VT6  O1G  PG   O2G  104.10  3.000
 VT6  O2G  PG   O3G  116.73  3.000
 VT6  O1G  PG   O3G  119.65  3.000
 VT6  O2G  PG   C3B  102.96  3.000
 VT6  O1G  PG   C3B   98.58  3.000
 VT6  O3G  PG   C3B  112.16  3.000
 VT6  H16  O2G  PG   114.50  3.000
 VT6  H17  O1G  PG   115.87  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
 VT6  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 VT6  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 VT6  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 VT6  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 VT6  CONST_05  C2   N3   C4   O4    180.00   0.0  0
 VT6  CONST_06  O2   C2   N3   C4    180.00   0.0  0
 VT6  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 VT6  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 VT6  CONST_09  H5   N3   C4   C5    180.00   0.0  0
 VT6  Var_01    H1   C7   C5   C4   -177.55  30.0  3
 VT6  Var_02    O3A  PA   O5'  C5'    72.07  30.0  3
 VT6  Var_03    O2B  PB   O3A  PA    120.37  30.0  3
 VT6  Var_04    H12  C5'  O5'  PA     98.13  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
 VT6  chir_01  C1'  C2'  N1   O4'  positiv
 VT6  chir_02  C3'  O3'  C4'  C2'  positiv
 VT6  chir_03  C4'  O4'  C3'  C5'  negativ
 VT6  chir_06  C3B  F3B  CL1  PG   positiv
 VT6  chir_07  PA   O3A  O2A  O1A  both
 VT6  chir_08  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
 VT6  plan-1  O4   0.020
 VT6  plan-1  C4   0.020
 VT6  plan-1  C5   0.020
 VT6  plan-1  C7   0.020
 VT6  plan-1  C6   0.020
 VT6  plan-1  N3   0.020
 VT6  plan-1  C2   0.020
 VT6  plan-1  O2   0.020
 VT6  plan-1  N1   0.020
 VT6  plan-1  C1'  0.020
 VT6  plan-1  H4   0.020
 VT6  plan-1  H5   0.020

