# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:41:52 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)N2C=C(C)C(=O)NC2=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
 FDV  FDV  5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine  ligand  47  30  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FDV
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
 FDV  N1   N  NR6    0  -0.620   4.3024  -0.2959   0.7963
 FDV  C2   C  CR6    0   0.692   4.2008  -0.3842  -0.5721
 FDV  O2   O  O      0  -0.486   3.8508   0.5346  -1.2822
 FDV  N3   N  NR16   0  -0.628   4.5490  -1.6044  -1.0910
 FDV  C4   C  CR6    0   0.555   4.9653  -2.7347  -0.4120
 FDV  O4   O  O      0  -0.527   5.2369  -3.7566  -1.0161
 FDV  C5   C  CR6    0  -0.203   5.0330  -2.5738   1.0258
 FDV  C7   C  CH3    0  -0.698   5.4592  -3.7335   1.8647
 FDV  C6   C  CR16   0   0.131   4.6940  -1.3790   1.5400
 FDV  PA   P  P      0   1.329  -1.5264   2.0534  -0.2633
 FDV  PB   P  P      0   1.214  -3.8170   0.3575   0.4330
 FDV  PG   P  P      0   1.136  -4.4784  -2.5295  -0.4263
 FDV  C1'  C  CR15   0   0.256   3.8920   0.9281   1.4876
 FDV  O1A  O  OP    -1  -0.889  -1.3551   1.3368  -1.5696
 FDV  O2B  O  O      0  -0.771  -4.5056   1.1492  -0.6477
 FDV  O1G  O  OP    -1  -0.976  -5.6052  -1.8507  -1.2153
 FDV  C2'  C  CH2    0  -0.546   4.5732   2.2240   1.0417
 FDV  O2A  O  O      0  -0.856  -1.9485   3.4948  -0.2676
 FDV  O1B  O  OP    -1  -0.808  -4.4813   0.2077   1.7766
 FDV  C4B  C  CH3    0  -0.668  -2.0442  -1.7700   0.7061
 FDV  O2G  O  OP    -1  -0.958  -3.7553  -3.6286  -1.2249
 FDV  C3'  C  CR15   0   0.008   3.4685   3.0400   0.3699
 FDV  O3'  O  OH1    0  -0.721   3.4934   4.4150   0.6651
 FDV  O3A  O  O2     0  -0.716  -2.3977   1.2087   0.8067
 FDV  C3B  C  CH1    0  -0.757  -3.1579  -1.2187  -0.1787
 FDV  O3G  O  O      0  -0.884  -4.8961  -2.9912   0.9743
 FDV  C4'  C  CR15   0   0.041   2.1932   2.4313   0.9569
 FDV  O4'  O  O      0  -0.549   2.5143   1.1017   1.3339
 FDV  C5'  C  CH2    0  -0.166   1.0460   2.4302  -0.0242
 FDV  O5'  O  O2     0  -0.587  -0.1133   1.9329   0.5981
 FDV  H1   H  HNR6   0   0.457   4.4789  -1.6760  -2.0987
 FDV  H2   H  HCH3   0   0.248   4.7769  -4.5771   1.7511
 FDV  H3   H  HCH3   0   0.257   6.4544  -4.0825   1.5860
 FDV  H4   H  HCH3   0   0.242   5.4824  -3.4627   2.9191
 FDV  H5   H  HCR6   0   0.309   4.7191  -1.2103   2.6081
 FDV  H6   H  HCR5   0   0.291   4.1329   0.7302   2.5350
 FDV  H9   H  HCH2   0   0.248   4.9115   2.7566   1.9324
 FDV  H10  H  HCH2   0   0.295   5.4435   2.0574   0.4093
 FDV  H12  H  HCH3   0   0.211  -1.1869  -1.0986   0.7792
 FDV  H13  H  HCH3   0   0.172  -2.4151  -1.9569   1.7140
 FDV  H14  H  HCH3   0   0.249  -1.6916  -2.7238   0.3089
 FDV  H16  H  HCR5   0   0.237   3.4932   2.8800  -0.7114
 FDV  H17  H  HOH1   0   0.446   4.1717   4.8266   0.1222
 FDV  H18  H  HCH1   0   0.251  -2.7414  -0.9872  -1.1656
 FDV  H19  H  HCR5   0   0.270   1.9106   3.0069   1.8506
 FDV  H20  H  HCH2   0   0.227   0.9072   3.4643  -0.3676
 FDV  H21  H  HCH2   0   0.244   1.3219   1.8284  -0.8979

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
 FDV  O2   C2   double  1.213  0.020  1.213
 FDV  C2   N3   single  1.371  0.020  1.371
 FDV  C2   N1   single  1.375  0.020  1.375
 FDV  N3   C4   single  1.383  0.020  1.383
 FDV  C2'  C1'  single  1.530  0.020  1.530
 FDV  C2'  C3'  single  1.529  0.020  1.529
 FDV  C1'  N1   single  1.464  0.020  1.464
 FDV  C1'  O4'  single  1.397  0.020  1.397
 FDV  N1   C6   single  1.371  0.020  1.371
 FDV  C4   O4   double  1.218  0.020  1.218
 FDV  C4   C5   single  1.448  0.020  1.448
 FDV  O3'  C3'  single  1.406  0.020  1.406
 FDV  C3'  C4'  single  1.530  0.020  1.530
 FDV  O4'  C4'  single  1.419  0.020  1.419
 FDV  C6   C5   double  1.344  0.020  1.344
 FDV  C4'  C5'  single  1.510  0.020  1.510
 FDV  C5   C7   single  1.493  0.020  1.493
 FDV  O2B  PB   deloc   1.506  0.020  1.506
 FDV  C5'  O5'  single  1.407  0.020  1.407
 FDV  O5'  PA   single  1.659  0.020  1.659
 FDV  O3A  PB   single  1.697  0.020  1.697
 FDV  O3A  PA   single  1.618  0.020  1.618
 FDV  PB   O1B  deloc   1.506  0.020  1.506
 FDV  PB   C3B  single  1.815  0.020  1.815
 FDV  PA   O2A  deloc   1.502  0.020  1.502
 FDV  PA   O1A  deloc   1.500  0.020  1.500
 FDV  C4B  C3B  single  1.525  0.020  1.525
 FDV  C3B  PG   single  1.877  0.020  1.877
 FDV  PG   O3G  deloc   1.533  0.020  1.533
 FDV  PG   O1G  deloc   1.534  0.020  1.534
 FDV  PG   O2G  deloc   1.539  0.020  1.539
 FDV  N3   H1   single  0.860  0.020  1.020
 FDV  C7   H2   single  0.970  0.020  1.090
 FDV  C7   H3   single  0.970  0.020  1.090
 FDV  C7   H4   single  0.970  0.020  1.090
 FDV  C6   H5   single  0.930  0.020  1.080
 FDV  C1'  H6   single  0.970  0.020  1.090
 FDV  C2'  H9   single  0.970  0.020  1.090
 FDV  C2'  H10  single  0.970  0.020  1.090
 FDV  C4B  H12  single  0.970  0.020  1.090
 FDV  C4B  H13  single  0.970  0.020  1.090
 FDV  C4B  H14  single  0.970  0.020  1.090
 FDV  C3'  H16  single  0.970  0.020  1.090
 FDV  O3'  H17  single  0.850  0.020  0.980
 FDV  C3B  H18  single  0.970  0.020  1.090
 FDV  C4'  H19  single  0.970  0.020  1.090
 FDV  C5'  H20  single  0.970  0.020  1.090
 FDV  C5'  H21  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
 FDV  C1'  N1   C6   118.96  3.000
 FDV  C6   N1   C2   120.68  3.000
 FDV  C1'  N1   C2   120.19  3.000
 FDV  N3   C2   O2   121.74  3.000
 FDV  N3   C2   N1   114.52  3.000
 FDV  O2   C2   N1   123.73  3.000
 FDV  H1   N3   C4   116.85  3.000
 FDV  H1   N3   C2   114.96  3.000
 FDV  C4   N3   C2   128.19  3.000
 FDV  C5   C4   O4   125.12  3.000
 FDV  C5   C4   N3   114.25  3.000
 FDV  O4   C4   N3   120.63  3.000
 FDV  C6   C5   C7   123.18  3.000
 FDV  C7   C5   C4   118.99  3.000
 FDV  C6   C5   C4   117.82  3.000
 FDV  H4   C7   H3   107.91  3.000
 FDV  H4   C7   H2   107.85  3.000
 FDV  H3   C7   H2   107.26  3.000
 FDV  H4   C7   C5   110.91  3.000
 FDV  H3   C7   C5   111.42  3.000
 FDV  H2   C7   C5   111.32  3.000
 FDV  H5   C6   C5   120.70  3.000
 FDV  H5   C6   N1   114.78  3.000
 FDV  C5   C6   N1   124.52  3.000
 FDV  O5'  PA   O3A   94.44  3.000
 FDV  O3A  PA   O2A  110.58  3.000
 FDV  O5'  PA   O2A  108.09  3.000
 FDV  O2A  PA   O1A  119.23  3.000
 FDV  O3A  PA   O1A  112.83  3.000
 FDV  O5'  PA   O1A  108.67  3.000
 FDV  C3B  PB   O3A  101.90  3.000
 FDV  C3B  PB   O1B  111.99  3.000
 FDV  O3A  PB   O1B  102.85  3.000
 FDV  C3B  PB   O2B  112.38  3.000
 FDV  O1B  PB   O2B  119.39  3.000
 FDV  O3A  PB   O2B  106.06  3.000
 FDV  O3G  PG   C3B  106.36  3.000
 FDV  O3G  PG   O2G  112.77  3.000
 FDV  C3B  PG   O2G  103.69  3.000
 FDV  O2G  PG   O1G  113.22  3.000
 FDV  O3G  PG   O1G  113.77  3.000
 FDV  C3B  PG   O1G  106.00  3.000
 FDV  H6   C1'  O4'  110.20  3.000
 FDV  H6   C1'  C2'  109.54  3.000
 FDV  O4'  C1'  C2'  107.55  3.000
 FDV  H6   C1'  N1   103.85  3.000
 FDV  O4'  C1'  N1   109.17  3.000
 FDV  C2'  C1'  N1   116.45  3.000
 FDV  H10  C2'  H9   107.51  3.000
 FDV  H10  C2'  C3'  113.83  3.000
 FDV  H9   C2'  C3'  108.78  3.000
 FDV  H10  C2'  C1'  113.30  3.000
 FDV  H9   C2'  C1'  108.26  3.000
 FDV  C3'  C2'  C1'  104.97  3.000
 FDV  H14  C4B  H13  107.24  3.000
 FDV  H14  C4B  H12  107.94  3.000
 FDV  H13  C4B  H12  108.10  3.000
 FDV  H14  C4B  C3B  109.91  3.000
 FDV  H13  C4B  C3B  110.48  3.000
 FDV  H12  C4B  C3B  112.96  3.000
 FDV  H16  C3'  C4'  109.88  3.000
 FDV  H16  C3'  O3'  110.50  3.000
 FDV  C4'  C3'  O3'  108.85  3.000
 FDV  H16  C3'  C2'  109.89  3.000
 FDV  C4'  C3'  C2'  102.79  3.000
 FDV  O3'  C3'  C2'  114.63  3.000
 FDV  H17  O3'  C3'  108.21  3.000
 FDV  PB   O3A  PA   124.53  3.000
 FDV  H18  C3B  C4B  108.73  3.000
 FDV  H18  C3B  PG   107.23  3.000
 FDV  C4B  C3B  PG   109.74  3.000
 FDV  H18  C3B  PB   104.96  3.000
 FDV  PG   C3B  PB   113.30  3.000
 FDV  C4B  C3B  PB   112.55  3.000
 FDV  H19  C4'  C5'  109.47  3.000
 FDV  H19  C4'  O4'  109.43  3.000
 FDV  C5'  C4'  O4'  110.12  3.000
 FDV  H19  C4'  C3'  108.52  3.000
 FDV  C5'  C4'  C3'  112.60  3.000
 FDV  O4'  C4'  C3'  106.62  3.000
 FDV  C4'  O4'  C1'  111.65  3.000
 FDV  H21  C5'  H20  107.42  3.000
 FDV  H21  C5'  O5'  111.47  3.000
 FDV  H20  C5'  O5'  111.53  3.000
 FDV  H21  C5'  C4'  109.10  3.000
 FDV  H20  C5'  C4'  107.37  3.000
 FDV  O5'  C5'  C4'  109.82  3.000
 FDV  C5'  O5'  PA   116.52  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
 FDV  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 FDV  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 FDV  CONST_03  C1'  N1   C2   N3   180.00   0.0  0
 FDV  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 FDV  CONST_05  O4   C4   N3   C2   180.00   0.0  0
 FDV  CONST_06  C4   N3   C2   O2   180.00   0.0  0
 FDV  CONST_07  C1'  N1   C2   O2     0.00   0.0  0
 FDV  CONST_08  C6   N1   C2   O2   180.00   0.0  0
 FDV  CONST_09  H1   N3   C2   N1   180.00   0.0  0
 FDV  Var_01    H2   C7   C5   C4   -61.03  30.0  3
 FDV  Var_02    C4'  C5'  O5'  PA   171.80  30.0  1
 FDV  Var_03    O2B  PB   O3A  PA   -33.58  30.0  3
 FDV  Var_04    O5'  PA   O3A  PB  -155.33  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
 FDV  chir_03  C1'  C2'  N1   O4'  positiv
 FDV  chir_04  C3'  O3'  C4'  C2'  positiv
 FDV  chir_05  C3B  PB   C4B  PG   negativ
 FDV  chir_06  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
 FDV  plan-1  N1   0.020
 FDV  plan-1  C2   0.020
 FDV  plan-1  O2   0.020
 FDV  plan-1  N3   0.020
 FDV  plan-1  C4   0.020
 FDV  plan-1  O4   0.020
 FDV  plan-1  C5   0.020
 FDV  plan-1  C7   0.020
 FDV  plan-1  C6   0.020
 FDV  plan-1  C1'  0.020
 FDV  plan-1  H1   0.020
 FDV  plan-1  H5   0.020

