# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jul  5 21:30:40 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[dichloro(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(Cl)(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
 VT8  VT8  5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine  ligand  44  31  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VT8
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
 VT8  N1   N   NR6    0  -0.567   5.0571  -0.3054   0.5890
 VT8  C2   C   CR6    0   0.741   5.1814  -0.1870  -0.7758
 VT8  O2   O   O      0  -0.471   4.8375   0.7945  -1.3997
 VT8  N3   N   NR16   0  -0.734   5.7410  -1.2772  -1.3912
 VT8  C4   C   CR6    0   0.558   6.1739  -2.4564  -0.8128
 VT8  O4   O   O      0  -0.456   6.6587  -3.3404  -1.4956
 VT8  C5   C   CR6    0  -0.184   5.9906  -2.5186   0.6229
 VT8  C7   C   CH3    0  -0.707   6.4104  -3.7516   1.3534
 VT8  C6   C   CR16   0   0.059   5.4440  -1.4526   1.2324
 VT8  PA   P   P      0   1.339  -0.7771   1.8763  -0.8706
 VT8  PB   P   P      0   1.329  -3.3502   0.7341  -0.1010
 VT8  PG   P   P      0   1.211  -5.1238  -1.9409  -0.0193
 VT8  C1'  C   CH1    0   0.221   4.4483   0.7750   1.3638
 VT8  O1A  O   OP    -1  -0.802  -0.4376   1.1971  -2.1601
 VT8  O2B  O   O      0  -0.792  -3.7390   1.1202  -1.4945
 VT8  O1G  O   OP    -1  -0.876  -5.6020  -1.5675  -1.4161
 VT8  C2'  C   CH2    0  -0.561   5.0991   2.1545   1.2215
 VT8  O2A  O   O      0  -0.815  -1.2615   3.2956  -0.8785
 VT8  O1B  O   OP    -1  -0.785  -4.0152   1.3688   1.0820
 VT8  CL1  CL  CL     0  -0.170  -2.3383  -1.8232  -1.1669
 VT8  O2G  O   OP    -1  -0.884  -4.8181  -3.4204   0.1795
 VT8  C3'  C   CH1    0   0.024   4.0391   3.0202   0.5395
 VT8  O3'  O   OH1    0  -0.669   3.9323   4.3267   1.0479
 VT8  O3A  O   O2     0  -0.740  -1.7153   0.9514   0.0860
 VT8  C3B  C   CT     0  -0.555  -3.4087  -1.1077   0.0889
 VT8  O3G  O   O      0  -0.877  -5.8963  -1.2893   1.1196
 VT8  C4'  C   CH1    0   0.013   2.7450   2.2641   0.8409
 VT8  O4'  O   O2     0  -0.490   3.1048   0.9018   0.9983
 VT8  C5'  C   CH2    0  -0.151   1.7138   2.3968  -0.2522
 VT8  O5'  O   O2     0  -0.624   0.5231   1.7620   0.1496
 VT8  CL2  CL  CL     0  -0.184  -2.6761  -1.5104   1.6884
 VT8  H1   H   HNR6   0   0.424   5.8447  -1.1975  -2.3956
 VT8  H2   H   HCH3   0   0.247   5.8899  -4.6334   0.9777
 VT8  H3   H   HCH3   0   0.246   7.4797  -3.9355   1.2405
 VT8  H4   H   HCH3   0   0.247   6.1967  -3.6650   2.4174
 VT8  H5   H   HCR6   0   0.316   5.2818  -1.4487   2.3022
 VT8  H6   H   HCH1   0   0.252   4.5258   0.4358   2.3997
 VT8  H9   H   HCH2   0   0.266   5.2941   2.5509   2.2195
 VT8  H10  H   HCH2   0   0.274   6.0482   2.1255   0.6889
 VT8  H13  H   HCH1   0   0.232   4.2135   3.0413  -0.5399
 VT8  H14  H   HOH1   0   0.456   4.6395   4.8556   0.6680
 VT8  H15  H   HCH1   0   0.225   2.3310   2.6485   1.7851
 VT8  H16  H   HCH2   0   0.206   1.5550   3.4667  -0.4382
 VT8  H17  H   HCH2   0   0.207   2.1128   1.9575  -1.1746

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
 VT8  O2   C2   double  1.213  0.020  1.213
 VT8  C2   N3   single  1.371  0.020  1.371
 VT8  C2   N1   single  1.376  0.020  1.376
 VT8  N3   C4   single  1.383  0.020  1.383
 VT8  C2'  C1'  single  1.532  0.020  1.532
 VT8  C2'  C3'  single  1.529  0.020  1.529
 VT8  C1'  N1   single  1.462  0.020  1.462
 VT8  C1'  O4'  single  1.398  0.020  1.398
 VT8  N1   C6   single  1.371  0.020  1.371
 VT8  O3'  C3'  single  1.406  0.020  1.406
 VT8  C3'  C4'  single  1.529  0.020  1.529
 VT8  C4   O4   double  1.218  0.020  1.218
 VT8  C4   C5   single  1.449  0.020  1.449
 VT8  O4'  C4'  single  1.418  0.020  1.418
 VT8  C4'  C5'  single  1.509  0.020  1.509
 VT8  C6   C5   double  1.344  0.020  1.344
 VT8  C5   C7   single  1.493  0.020  1.493
 VT8  O2B  PB   deloc   1.497  0.020  1.497
 VT8  C5'  O5'  single  1.408  0.020  1.408
 VT8  O5'  PA   single  1.657  0.020  1.657
 VT8  O3A  PB   single  1.660  0.020  1.660
 VT8  O3A  PA   single  1.628  0.020  1.628
 VT8  PB   O1B  deloc   1.498  0.020  1.498
 VT8  PB   C3B  single  1.852  0.020  1.852
 VT8  CL1  C3B  single  1.799  0.020  1.799
 VT8  PA   O2A  deloc   1.500  0.020  1.500
 VT8  PA   O1A  deloc   1.496  0.020  1.496
 VT8  C3B  CL2  single  1.805  0.020  1.805
 VT8  C3B  PG   single  1.910  0.020  1.910
 VT8  O3G  PG   deloc   1.523  0.020  1.523
 VT8  PG   O1G  deloc   1.523  0.020  1.523
 VT8  PG   O2G  deloc   1.524  0.020  1.524
 VT8  N3   H1   single  0.860  0.020  1.020
 VT8  C7   H2   single  0.970  0.020  1.090
 VT8  C7   H3   single  0.970  0.020  1.090
 VT8  C7   H4   single  0.970  0.020  1.090
 VT8  C6   H5   single  0.930  0.020  1.080
 VT8  C1'  H6   single  0.970  0.020  1.090
 VT8  C2'  H9   single  0.970  0.020  1.090
 VT8  C2'  H10  single  0.970  0.020  1.090
 VT8  C3'  H13  single  0.970  0.020  1.090
 VT8  O3'  H14  single  0.850  0.020  0.980
 VT8  C4'  H15  single  0.970  0.020  1.090
 VT8  C5'  H16  single  0.970  0.020  1.090
 VT8  C5'  H17  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
 VT8  C1'  N1   C6   119.15  3.000
 VT8  C6   N1   C2   120.81  3.000
 VT8  C1'  N1   C2   119.98  3.000
 VT8  N3   C2   O2   121.89  3.000
 VT8  N3   C2   N1   114.44  3.000
 VT8  O2   C2   N1   123.68  3.000
 VT8  H1   N3   C4   116.74  3.000
 VT8  H1   N3   C2   115.10  3.000
 VT8  C4   N3   C2   128.16  3.000
 VT8  C5   C4   O4   125.09  3.000
 VT8  C5   C4   N3   114.30  3.000
 VT8  O4   C4   N3   120.61  3.000
 VT8  C6   C5   C7   123.18  3.000
 VT8  C7   C5   C4   118.99  3.000
 VT8  C6   C5   C4   117.83  3.000
 VT8  H4   C7   H3   107.88  3.000
 VT8  H4   C7   H2   107.89  3.000
 VT8  H3   C7   H2   107.20  3.000
 VT8  H4   C7   C5   110.93  3.000
 VT8  H3   C7   C5   111.35  3.000
 VT8  H2   C7   C5   111.40  3.000
 VT8  H5   C6   C5   120.81  3.000
 VT8  H5   C6   N1   114.75  3.000
 VT8  C5   C6   N1   124.44  3.000
 VT8  O5'  PA   O3A   92.93  3.000
 VT8  O3A  PA   O2A  110.77  3.000
 VT8  O5'  PA   O2A  108.79  3.000
 VT8  O2A  PA   O1A  119.89  3.000
 VT8  O3A  PA   O1A  112.28  3.000
 VT8  O5'  PA   O1A  108.74  3.000
 VT8  C3B  PB   O3A   98.61  3.000
 VT8  C3B  PB   O1B  109.04  3.000
 VT8  O3A  PB   O1B  107.03  3.000
 VT8  C3B  PB   O2B  110.09  3.000
 VT8  O1B  PB   O2B  120.69  3.000
 VT8  O3A  PB   O2B  109.08  3.000
 VT8  O3G  PG   C3B  103.09  3.000
 VT8  O3G  PG   O2G  114.81  3.000
 VT8  C3B  PG   O2G  103.65  3.000
 VT8  O2G  PG   O1G  114.88  3.000
 VT8  O3G  PG   O1G  114.95  3.000
 VT8  C3B  PG   O1G  103.12  3.000
 VT8  H6   C1'  O4'  110.13  3.000
 VT8  H6   C1'  C2'  109.72  3.000
 VT8  O4'  C1'  C2'  107.60  3.000
 VT8  H6   C1'  N1   104.08  3.000
 VT8  O4'  C1'  N1   109.18  3.000
 VT8  C2'  C1'  N1   116.06  3.000
 VT8  H10  C2'  H9   107.53  3.000
 VT8  H10  C2'  C3'  113.65  3.000
 VT8  H9   C2'  C3'  109.03  3.000
 VT8  H10  C2'  C1'  113.07  3.000
 VT8  H9   C2'  C1'  108.55  3.000
 VT8  C3'  C2'  C1'  104.88  3.000
 VT8  H13  C3'  C4'  109.82  3.000
 VT8  H13  C3'  O3'  110.56  3.000
 VT8  C4'  C3'  O3'  108.90  3.000
 VT8  H13  C3'  C2'  109.91  3.000
 VT8  C4'  C3'  C2'  102.64  3.000
 VT8  O3'  C3'  C2'  114.68  3.000
 VT8  H14  O3'  C3'  108.21  3.000
 VT8  PB   O3A  PA   125.15  3.000
 VT8  CL2  C3B  CL1  106.77  3.000
 VT8  CL2  C3B  PG   108.51  3.000
 VT8  CL1  C3B  PG   108.74  3.000
 VT8  PG   C3B  PB   117.15  3.000
 VT8  CL2  C3B  PB   107.45  3.000
 VT8  CL1  C3B  PB   107.77  3.000
 VT8  H15  C4'  C5'  109.50  3.000
 VT8  H15  C4'  O4'  109.62  3.000
 VT8  C5'  C4'  O4'  109.78  3.000
 VT8  H15  C4'  C3'  108.36  3.000
 VT8  C5'  C4'  C3'  113.10  3.000
 VT8  O4'  C4'  C3'  106.40  3.000
 VT8  C4'  O4'  C1'  111.10  3.000
 VT8  H17  C5'  H16  107.49  3.000
 VT8  H17  C5'  O5'  111.53  3.000
 VT8  H16  C5'  O5'  111.44  3.000
 VT8  H17  C5'  C4'  109.00  3.000
 VT8  H16  C5'  C4'  107.90  3.000
 VT8  O5'  C5'  C4'  109.37  3.000
 VT8  C5'  O5'  PA   117.18  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
 VT8  CONST_01  C4   N3   C2   N1    0.00   0.0  0
 VT8  CONST_02  C5   C4   N3   C2    0.00   0.0  0
 VT8  CONST_03  C1'  N1   C2   N3  180.00   0.0  0
 VT8  CONST_04  C6   N1   C2   N3    0.00   0.0  0
 VT8  CONST_05  O4   C4   N3   C2  180.00   0.0  0
 VT8  CONST_06  C4   N3   C2   O2  180.00   0.0  0
 VT8  CONST_07  C1'  N1   C2   O2    0.00   0.0  0
 VT8  CONST_08  C6   N1   C2   O2  180.00   0.0  0
 VT8  CONST_09  H1   N3   C2   N1  180.00   0.0  0
 VT8  Var_01    H2   C7   C5   C4  -58.69  30.0  3
 VT8  Var_02    C4'  C5'  O5'  PA  176.11  30.0  2
 VT8  Var_03    O2B  PB   O3A  PA   18.72  30.0  3
 VT8  Var_04    O5'  PA   O3A  PB  169.90  30.0  3
 VT8  Var_05    O3G  PG   C3B  PB  -59.79  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
 VT8  chir_03  C1'  C2'  N1   O4'  positiv
 VT8  chir_04  C3'  O3'  C4'  C2'  positiv
 VT8  chir_05  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
 VT8  plan-1  N1   0.020
 VT8  plan-1  C2   0.020
 VT8  plan-1  O2   0.020
 VT8  plan-1  N3   0.020
 VT8  plan-1  C4   0.020
 VT8  plan-1  O4   0.020
 VT8  plan-1  C5   0.020
 VT8  plan-1  C7   0.020
 VT8  plan-1  C6   0.020
 VT8  plan-1  C1'  0.020
 VT8  plan-1  H1   0.020
 VT8  plan-1  H5   0.020

