# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:03:23 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[(R)-fluoro(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@H](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
 FDY  FDY  5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine  ligand  44  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_FDY
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
 FDY  C2   C  CR6    0   0.716  -4.8112  -0.3619   0.7379
 FDY  C4   C  CR6    0   0.531  -5.8355  -2.6091   0.5457
 FDY  C5   C  CR6    0  -0.179  -5.7026  -2.5050  -0.8931
 FDY  C6   C  CR16   0   0.003  -5.1613  -1.3810  -1.3933
 FDY  O4   O  O      0  -0.265  -6.3151  -3.5595   1.1371
 FDY  C7   C  CH3    0  -0.738  -6.1650  -3.6398  -1.7465
 FDY  N3   N  NR16   0  -0.749  -5.3648  -1.5110   1.2418
 FDY  O2   O  O      0  -0.523  -4.4293   0.5350   1.4595
 FDY  N1   N  NR6    0  -0.570  -4.7368  -0.3206  -0.6351
 FDY  C1'  C  CH1    0   0.243  -4.1339   0.8329  -1.3003
 FDY  C2'  C  CH2    0  -0.566  -4.7501   2.1981  -0.9760
 FDY  C3'  C  CH1    0   0.053  -3.6465   2.9588  -0.2404
 FDY  O3'  O  OH1    0  -0.701  -3.5336   4.3162  -0.5872
 FDY  O4'  O  O2     0  -0.463  -2.7768   0.8933  -0.9685
 FDY  C4'  C  CH1    0  -0.004  -2.3823   2.2256  -0.6878
 FDY  C5'  C  CH2    0  -0.132  -1.2946   2.2265   0.3581
 FDY  O5'  O  O2     0  -0.657  -0.1635   1.5522  -0.1394
 FDY  PA   P  P      0   1.314   1.3028   1.9009   0.5511
 FDY  O1A  O  OP    -1  -0.708   1.1546   1.8131   2.0409
 FDY  O2A  O  O      0  -0.802   1.8393   3.1568  -0.0677
 FDY  O3A  O  O2     0  -0.688   2.0226   0.5820  -0.0600
 FDY  PB   P  P      0   1.225   3.6823   0.3775  -0.2532
 FDY  O2B  O  O      0  -0.819   4.3615   1.1784   0.8199
 FDY  O1B  O  OP    -1  -0.905   3.9820   0.6262  -1.7045
 FDY  C3B  C  CH1    0  -0.344   3.7523  -1.4177   0.0811
 FDY  F2B  F  F      0  -0.413   3.5224  -1.5815   1.4692
 FDY  PG   P  P      0   1.122   5.3416  -2.2812  -0.4210
 FDY  O3G  O  O      0  -0.808   5.1538  -2.5274  -1.9191
 FDY  O2G  O  OP    -1  -0.991   6.4732  -1.3125  -0.0717
 FDY  O1G  O  OP    -1  -0.892   5.3419  -3.5614   0.4206
 FDY  H1   H  HCR6   0   0.317  -5.0364  -1.2534  -2.4600
 FDY  H2   H  HCH3   0   0.283  -7.2368  -3.8104  -1.6349
 FDY  H3   H  HCH3   0   0.243  -5.9651  -3.4425  -2.7985
 FDY  H4   H  HCH3   0   0.237  -5.6611  -4.5691  -1.4779
 FDY  H5   H  HNR6   0   0.399  -5.4315  -1.5491   2.2516
 FDY  H6   H  HCH1   0   0.237  -4.2532   0.6209  -2.3664
 FDY  H7   H  HCH2   0   0.245  -4.9730   2.7101  -1.9140
 FDY  H8   H  HCH2   0   0.282  -5.6801   2.1263  -0.4143
 FDY  H9   H  HCH1   0   0.214  -3.7759   2.8465   0.8401
 FDY  H10  H  HOH1   0   0.449  -4.2371   4.7991  -0.1441
 FDY  H11  H  HCH1   0   0.268  -2.0095   2.7043  -1.6059
 FDY  H12  H  HCH2   0   0.170  -1.0789   3.2741   0.6046
 FDY  H13  H  HCH2   0   0.176  -1.6697   1.7473   1.2698
 FDY  H16  H  HCH1   0   0.189   2.9146  -1.9073  -0.4302

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
 FDY  O2   C2   double  1.213  0.020  1.213
 FDY  C2   N3   single  1.371  0.020  1.371
 FDY  C2   N1   single  1.376  0.020  1.376
 FDY  N3   C4   single  1.383  0.020  1.383
 FDY  C2'  C1'  single  1.532  0.020  1.532
 FDY  C2'  C3'  single  1.529  0.020  1.529
 FDY  C1'  N1   single  1.462  0.020  1.462
 FDY  C1'  O4'  single  1.398  0.020  1.398
 FDY  N1   C6   single  1.371  0.020  1.371
 FDY  O3'  C3'  single  1.406  0.020  1.406
 FDY  C4   O4   double  1.218  0.020  1.218
 FDY  C4   C5   single  1.449  0.020  1.449
 FDY  C3'  C4'  single  1.528  0.020  1.528
 FDY  O4'  C4'  single  1.418  0.020  1.418
 FDY  C6   C5   double  1.344  0.020  1.344
 FDY  C4'  C5'  single  1.509  0.020  1.509
 FDY  C5   C7   single  1.493  0.020  1.493
 FDY  O2B  PB   deloc   1.501  0.020  1.501
 FDY  C5'  O5'  single  1.408  0.020  1.408
 FDY  O5'  PA   single  1.658  0.020  1.658
 FDY  PB   O3A  single  1.683  0.020  1.683
 FDY  PB   O1B  deloc   1.503  0.020  1.503
 FDY  PB   C3B  single  1.828  0.020  1.828
 FDY  F2B  C3B  single  1.417  0.020  1.417
 FDY  O3A  PA   single  1.622  0.020  1.622
 FDY  C3B  PG   single  1.877  0.020  1.877
 FDY  PA   O2A  deloc   1.499  0.020  1.499
 FDY  PA   O1A  deloc   1.500  0.020  1.500
 FDY  O3G  PG   deloc   1.530  0.020  1.530
 FDY  PG   O1G  deloc   1.532  0.020  1.532
 FDY  PG   O2G  deloc   1.530  0.020  1.530
 FDY  C6   H1   single  0.930  0.020  1.080
 FDY  C7   H2   single  0.970  0.020  1.090
 FDY  C7   H3   single  0.970  0.020  1.090
 FDY  C7   H4   single  0.970  0.020  1.090
 FDY  N3   H5   single  0.860  0.020  1.020
 FDY  C1'  H6   single  0.970  0.020  1.090
 FDY  C2'  H7   single  0.970  0.020  1.090
 FDY  C2'  H8   single  0.970  0.020  1.090
 FDY  C3'  H9   single  0.970  0.020  1.090
 FDY  O3'  H10  single  0.850  0.020  0.980
 FDY  C4'  H11  single  0.970  0.020  1.090
 FDY  C5'  H12  single  0.970  0.020  1.090
 FDY  C5'  H13  single  0.970  0.020  1.090
 FDY  C3B  H16  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
 FDY  N1   C2   O2   123.69  3.000
 FDY  N1   C2   N3   114.44  3.000
 FDY  O2   C2   N3   121.88  3.000
 FDY  N3   C4   O4   120.62  3.000
 FDY  O4   C4   C5   125.07  3.000
 FDY  N3   C4   C5   114.31  3.000
 FDY  C7   C5   C6   123.19  3.000
 FDY  C7   C5   C4   118.98  3.000
 FDY  C6   C5   C4   117.82  3.000
 FDY  H1   C6   N1   114.73  3.000
 FDY  H1   C6   C5   120.81  3.000
 FDY  N1   C6   C5   124.45  3.000
 FDY  H4   C7   H3   107.91  3.000
 FDY  H4   C7   H2   107.18  3.000
 FDY  H3   C7   H2   107.91  3.000
 FDY  H4   C7   C5   111.32  3.000
 FDY  H3   C7   C5   110.95  3.000
 FDY  H2   C7   C5   111.38  3.000
 FDY  H5   N3   C4   116.72  3.000
 FDY  H5   N3   C2   115.12  3.000
 FDY  C4   N3   C2   128.16  3.000
 FDY  C1'  N1   C6   119.11  3.000
 FDY  C6   N1   C2   120.80  3.000
 FDY  C1'  N1   C2   120.01  3.000
 FDY  H6   C1'  O4'  110.22  3.000
 FDY  H6   C1'  C2'  109.58  3.000
 FDY  O4'  C1'  C2'  107.55  3.000
 FDY  H6   C1'  N1   104.22  3.000
 FDY  O4'  C1'  N1   109.05  3.000
 FDY  C2'  C1'  N1   116.16  3.000
 FDY  H8   C2'  H7   107.45  3.000
 FDY  H8   C2'  C3'  113.64  3.000
 FDY  H7   C2'  C3'  109.11  3.000
 FDY  H8   C2'  C1'  113.20  3.000
 FDY  H7   C2'  C1'  108.55  3.000
 FDY  C3'  C2'  C1'  104.76  3.000
 FDY  H9   C3'  C4'  109.74  3.000
 FDY  H9   C3'  O3'  110.63  3.000
 FDY  C4'  C3'  O3'  108.94  3.000
 FDY  H9   C3'  C2'  109.80  3.000
 FDY  C4'  C3'  C2'  102.56  3.000
 FDY  O3'  C3'  C2'  114.82  3.000
 FDY  H10  O3'  C3'  108.21  3.000
 FDY  C4'  O4'  C1'  110.96  3.000
 FDY  H11  C4'  C5'  109.50  3.000
 FDY  H11  C4'  O4'  109.75  3.000
 FDY  C5'  C4'  O4'  109.78  3.000
 FDY  H11  C4'  C3'  108.41  3.000
 FDY  C5'  C4'  C3'  113.14  3.000
 FDY  O4'  C4'  C3'  106.18  3.000
 FDY  H13  C5'  H12  107.32  3.000
 FDY  H13  C5'  O5'  111.07  3.000
 FDY  H12  C5'  O5'  112.25  3.000
 FDY  H13  C5'  C4'  109.24  3.000
 FDY  H12  C5'  C4'  107.33  3.000
 FDY  O5'  C5'  C4'  109.51  3.000
 FDY  PA   O5'  C5'  117.56  3.000
 FDY  O3A  PA   O2A  111.52  3.000
 FDY  O2A  PA   O1A  119.63  3.000
 FDY  O3A  PA   O1A  111.75  3.000
 FDY  O1A  PA   O5'  108.30  3.000
 FDY  O2A  PA   O5'  108.71  3.000
 FDY  O3A  PA   O5'   93.70  3.000
 FDY  PB   O3A  PA   125.42  3.000
 FDY  C3B  PB   O1B  109.37  3.000
 FDY  C3B  PB   O2B  112.08  3.000
 FDY  O1B  PB   O2B  120.79  3.000
 FDY  C3B  PB   O3A   97.82  3.000
 FDY  O1B  PB   O3A  106.70  3.000
 FDY  O2B  PB   O3A  107.41  3.000
 FDY  H16  C3B  PG   108.46  3.000
 FDY  H16  C3B  F2B  106.34  3.000
 FDY  PG   C3B  F2B  110.27  3.000
 FDY  H16  C3B  PB   108.90  3.000
 FDY  PG   C3B  PB   115.81  3.000
 FDY  F2B  C3B  PB   106.66  3.000
 FDY  O1G  PG   O2G  113.80  3.000
 FDY  O2G  PG   O3G  114.60  3.000
 FDY  O1G  PG   O3G  113.80  3.000
 FDY  O2G  PG   C3B  105.89  3.000
 FDY  O1G  PG   C3B  103.74  3.000
 FDY  O3G  PG   C3B  103.42  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
 FDY  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 FDY  CONST_02  N3   C2   N1   C6     0.00   0.0  0
 FDY  CONST_03  C1'  N1   C2   N3   180.00   0.0  0
 FDY  CONST_04  O2   C2   N3   C4   180.00   0.0  0
 FDY  CONST_05  O2   C2   N1   C6   180.00   0.0  0
 FDY  CONST_06  C1'  N1   C2   O2     0.00   0.0  0
 FDY  CONST_07  H5   N3   C2   N1   180.00   0.0  0
 FDY  Var_01    H2   C7   C5   C4    62.21  30.0  3
 FDY  Var_02    O3A  PA   O5'  C5'  163.76  30.0  3
 FDY  Var_03    O2B  PB   O3A  PA    29.68  30.0  1
 FDY  Var_04    H12  C5'  O5'  PA    38.36  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
 FDY  chir_01  C1'  C2'  N1   O4'  positiv
 FDY  chir_02  C3'  O3'  C4'  C2'  positiv
 FDY  chir_03  C4'  O4'  C3'  C5'  negativ
 FDY  chir_06  C3B  PB   F2B  PG   positiv

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
 FDY  plan-1  C2   0.020
 FDY  plan-1  C4   0.020
 FDY  plan-1  C5   0.020
 FDY  plan-1  C6   0.020
 FDY  plan-1  O4   0.020
 FDY  plan-1  C7   0.020
 FDY  plan-1  N3   0.020
 FDY  plan-1  O2   0.020
 FDY  plan-1  N1   0.020
 FDY  plan-1  C1'  0.020
 FDY  plan-1  H1   0.020
 FDY  plan-1  H5   0.020

