# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 08:29:49 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-deoxy-1-[7-(5,5-difluoro-5-phosphonopentyl)-2,6,8-trioxo-1,2,3,6,7,8-hexahydro-9H-purin-9-yl]-D-arabinitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)CN1C(=O)N(CCCCC(F)(F)[P](O)(O)=O)C2=C1NC(=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
 TSF  TSF  1-deoxy-1-[7-(5,5-difluoro-5-phosphonopentyl)-2,6,8-trioxo-1,2,3,6,7,8-hexahydro-9H-purin-9-yl]-D-arabinitol  ligand  53  32  .  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_TSF
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
 TSF  O2P   O  O      0  -0.892  -8.5156  -1.1855   0.0067
 TSF  P     P  P      0   1.111  -7.2842  -0.7680   0.8075
 TSF  O3P   O  OP    -1  -0.892  -6.8287  -1.7808   1.8573
 TSF  O1P   O  OP    -1  -0.891  -7.2884   0.6857   1.2789
 TSF  C19   C  CT     0   0.449  -5.8810  -0.8009  -0.4451
 TSF  F1    F  F      0  -0.395  -5.7997  -2.0593  -1.0299
 TSF  F2    F  F      0  -0.395  -6.1798   0.0375  -1.5121
 TSF  C18   C  CH2    0  -0.541  -4.5189  -0.4318   0.0889
 TSF  C17   C  CH2    0  -0.438  -3.3847  -0.4311  -0.9310
 TSF  C16   C  CH2    0  -0.429  -2.0516  -0.0931  -0.2765
 TSF  C15   C  CH2    0  -0.303  -0.9094  -0.0874  -1.2830
 TSF  N5    N  NR5    0  -0.587   0.3537   0.2943  -0.6826
 TSF  C9    C  CR56   0   0.093   0.7651   1.5892  -0.3750
 TSF  C4    C  CR6    0   0.550   0.2023   2.8620  -0.6604
 TSF  O2    O  OC     0  -0.462  -0.8254   3.1085  -1.2677
 TSF  N3    N  NR16   0  -0.735   0.9876   3.8965  -0.1401
 TSF  C6    C  CR5    0   0.703   1.2420  -0.5924  -0.1628
 TSF  O4    O  OC     0  -0.503   1.2159  -1.8090  -0.2064
 TSF  N7    N  NR5    0  -0.566   2.2355   0.1699   0.4605
 TSF  C8    C  CR56   0   0.640   1.9340   1.4798   0.3122
 TSF  N1    N  NR16   0  -0.741   2.6275   2.5471   0.7723
 TSF  C2    C  CR6    0   0.670   2.1636   3.8252   0.5637
 TSF  O1    O  OC     0  -0.472   2.7526   4.8046   0.9698
 TSF  C10   C  CH2    0  -0.366   3.4072  -0.4132   1.0763
 TSF  C11   C  CH1    0   0.033   4.5221  -0.6357   0.0557
 TSF  O19   O  OH1    0  -0.658   4.8710   0.5668  -0.5876
 TSF  C12   C  CH1    0  -0.049   5.7128  -1.3341   0.7173
 TSF  O21   O  OH1    0  -0.666   6.2443  -0.5373   1.7584
 TSF  C13   C  CH1    0  -0.030   6.7989  -1.7426  -0.2936
 TSF  O23   O  OH1    0  -0.655   6.2465  -2.4224  -1.3933
 TSF  C14   C  CH2    0  -0.157   7.8867  -2.5589   0.3892
 TSF  O26   O  OH1    0  -0.669   8.9179  -2.8007  -0.5370
 TSF  H181  H  HCH2   0   0.229  -4.2894  -1.1246   0.9024
 TSF  H182  H  HCH2   0   0.229  -4.6041   0.5540   0.5537
 TSF  H171  H  HCH2   0   0.223  -3.5893   0.2960  -1.7213
 TSF  H172  H  HCH2   0   0.222  -3.3129  -1.4091  -1.4150
 TSF  H161  H  HCH2   0   0.228  -1.8328  -0.8174   0.5137
 TSF  H162  H  HCH2   0   0.228  -2.1147   0.8885   0.2021
 TSF  H151  H  HCH2   0   0.262  -1.1206   0.6010  -2.0995
 TSF  H152  H  HCH2   0   0.260  -0.7781  -1.0764  -1.7214
 TSF  H3    H  HNR6   0   0.430   0.6409   4.8341  -0.3000
 TSF  H1    H  HNR6   0   0.437   3.4826   2.4443   1.2988
 TSF  H101  H  HCH2   0   0.290   3.1090  -1.3609   1.5246
 TSF  H102  H  HCH2   0   0.277   3.7319   0.2283   1.8982
 TSF  H11   H  HCH1   0   0.256   4.1304  -1.2926  -0.7235
 TSF  H19   H  HOH1   0   0.438   5.3796   1.1199   0.0157
 TSF  H12   H  HCH1   0   0.241   5.3284  -2.2456   1.1935
 TSF  H21   H  HOH1   0   0.454   6.9292   0.0415   1.4073
 TSF  H13   H  HCH1   0   0.234   7.2510  -0.8310  -0.7033
 TSF  H23   H  HOH1   0   0.448   5.9305  -3.2840  -1.0985
 TSF  H141  H  HCH2   0   0.196   7.4422  -3.4959   0.7586
 TSF  H142  H  HCH2   0   0.205   8.2506  -2.0151   1.2676
 TSF  H26   H  HOH1   0   0.456   9.6023  -3.3097  -0.0940

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
 TSF  O2P  P     deloc     1.527  0.020  1.527
 TSF  P    O3P   deloc     1.528  0.020  1.528
 TSF  P    O1P   deloc     1.528  0.020  1.528
 TSF  P    C19   single    1.881  0.020  1.881
 TSF  C19  F1    single    1.390  0.020  1.390
 TSF  C19  F2    single    1.390  0.020  1.390
 TSF  C19  C18   single    1.509  0.020  1.509
 TSF  C18  C17   single    1.525  0.020  1.525
 TSF  C18  H181  single    0.970  0.020  1.090
 TSF  C18  H182  single    0.970  0.020  1.090
 TSF  C17  C16   single    1.523  0.020  1.523
 TSF  C17  H171  single    0.970  0.020  1.090
 TSF  C17  H172  single    0.970  0.020  1.090
 TSF  C16  C15   single    1.522  0.020  1.522
 TSF  C16  H161  single    0.970  0.020  1.090
 TSF  C16  H162  single    0.970  0.020  1.090
 TSF  C15  N5    single    1.450  0.020  1.450
 TSF  C15  H151  single    0.970  0.020  1.090
 TSF  C15  H152  single    0.970  0.020  1.090
 TSF  N5   C9    aromatic  1.393  0.020  1.393
 TSF  N5   C6    aromatic  1.359  0.020  1.359
 TSF  C9   C4    aromatic  1.421  0.020  1.421
 TSF  C9   C8    aromatic  1.360  0.020  1.360
 TSF  C4   O2    double    1.219  0.020  1.219
 TSF  C4   N3    aromatic  1.399  0.020  1.399
 TSF  N3   C2    aromatic  1.372  0.020  1.372
 TSF  N3   H3    single    0.860  0.020  1.020
 TSF  C6   O4    double    1.218  0.020  1.218
 TSF  C6   N7    aromatic  1.399  0.020  1.399
 TSF  N7   C8    aromatic  1.352  0.020  1.352
 TSF  N7   C10   single    1.446  0.020  1.446
 TSF  C8   N1    aromatic  1.353  0.020  1.353
 TSF  N1   C2    aromatic  1.376  0.020  1.376
 TSF  N1   H1    single    0.860  0.020  1.020
 TSF  C2   O1    double    1.213  0.020  1.213
 TSF  C10  C11   single    1.528  0.020  1.528
 TSF  C10  H101  single    0.970  0.020  1.090
 TSF  C10  H102  single    0.970  0.020  1.090
 TSF  C11  O19   single    1.408  0.020  1.408
 TSF  C11  C12   single    1.531  0.020  1.531
 TSF  C11  H11   single    0.970  0.020  1.090
 TSF  O19  H19   single    0.850  0.020  0.980
 TSF  C12  O21   single    1.415  0.020  1.415
 TSF  C12  C13   single    1.539  0.020  1.539
 TSF  C12  H12   single    0.970  0.020  1.090
 TSF  O21  H21   single    0.850  0.020  0.980
 TSF  C13  O23   single    1.406  0.020  1.406
 TSF  C13  C14   single    1.522  0.020  1.522
 TSF  C13  H13   single    0.970  0.020  1.090
 TSF  O23  H23   single    0.850  0.020  0.980
 TSF  C14  O26   single    1.407  0.020  1.407
 TSF  C14  H141  single    0.970  0.020  1.090
 TSF  C14  H142  single    0.970  0.020  1.090
 TSF  O26  H26   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
 TSF  C19   P    O1P   102.95  3.000
 TSF  C19   P    O3P   102.91  3.000
 TSF  O1P   P    O3P   114.79  3.000
 TSF  C19   P    O2P   104.33  3.000
 TSF  O1P   P    O2P   114.81  3.000
 TSF  O3P   P    O2P   114.79  3.000
 TSF  C18   C19  F2    108.56  3.000
 TSF  C18   C19  F1    108.52  3.000
 TSF  F2    C19  F1    103.63  3.000
 TSF  C18   C19  P     115.68  3.000
 TSF  F2    C19  P     109.90  3.000
 TSF  F1    C19  P     109.85  3.000
 TSF  H182  C18  H181  105.75  3.000
 TSF  H182  C18  C17   109.99  3.000
 TSF  H181  C18  C17   109.99  3.000
 TSF  H182  C18  C19   107.50  3.000
 TSF  H181  C18  C19   107.33  3.000
 TSF  C17   C18  C19   115.77  3.000
 TSF  H172  C17  H171  106.69  3.000
 TSF  H172  C17  C16   109.34  3.000
 TSF  H171  C17  C16   109.08  3.000
 TSF  H172  C17  C18   110.14  3.000
 TSF  H171  C17  C18   110.15  3.000
 TSF  C16   C17  C18   111.32  3.000
 TSF  H162  C16  H161  106.83  3.000
 TSF  H162  C16  C15   109.22  3.000
 TSF  H161  C16  C15   109.27  3.000
 TSF  H162  C16  C17   109.67  3.000
 TSF  H161  C16  C17   109.79  3.000
 TSF  C15   C16  C17   111.92  3.000
 TSF  H152  C15  H151  107.19  3.000
 TSF  H152  C15  N5    107.49  3.000
 TSF  H151  C15  N5    108.25  3.000
 TSF  H152  C15  C16   110.67  3.000
 TSF  H151  C15  C16   110.66  3.000
 TSF  N5    C15  C16   112.39  3.000
 TSF  C6    N5   C9    109.21  3.000
 TSF  C6    N5   C15   123.80  3.000
 TSF  C9    N5   C15   126.41  3.000
 TSF  C8    C9   C4    120.92  3.000
 TSF  C8    C9   N5    106.89  3.000
 TSF  C4    C9   N5    132.18  3.000
 TSF  N3    C4   O2    120.60  3.000
 TSF  N3    C4   C9    111.44  3.000
 TSF  O2    C4   C9    127.97  3.000
 TSF  H3    N3   C2    115.00  3.000
 TSF  H3    N3   C4    115.71  3.000
 TSF  C2    N3   C4    129.29  3.000
 TSF  N7    C6   O4    125.15  3.000
 TSF  N7    C6   N5    106.21  3.000
 TSF  O4    C6   N5    128.64  3.000
 TSF  C10   N7   C8    128.16  3.000
 TSF  C10   N7   C6    123.05  3.000
 TSF  C8    N7   C6    108.70  3.000
 TSF  N1    C8   N7    127.76  3.000
 TSF  N1    C8   C9    123.27  3.000
 TSF  N7    C8   C9    108.96  3.000
 TSF  H1    N1   C2    117.35  3.000
 TSF  H1    N1   C8    122.08  3.000
 TSF  C2    N1   C8    120.55  3.000
 TSF  O1    C2   N1    122.39  3.000
 TSF  O1    C2   N3    123.08  3.000
 TSF  N1    C2   N3    114.52  3.000
 TSF  H102  C10  H101  106.42  3.000
 TSF  H102  C10  C11   111.80  3.000
 TSF  H101  C10  C11   110.35  3.000
 TSF  H102  C10  N7    108.93  3.000
 TSF  H101  C10  N7    107.70  3.000
 TSF  C11   C10  N7    111.44  3.000
 TSF  H11   C11  C12   108.24  3.000
 TSF  H11   C11  O19   106.06  3.000
 TSF  C12   C11  O19   113.23  3.000
 TSF  H11   C11  C10   107.61  3.000
 TSF  C12   C11  C10   110.21  3.000
 TSF  O19   C11  C10   111.21  3.000
 TSF  H19   O19  C11   109.58  3.000
 TSF  H12   C12  C13   108.16  3.000
 TSF  H12   C12  O21   106.25  3.000
 TSF  C13   C12  O21   111.58  3.000
 TSF  H12   C12  C11   107.09  3.000
 TSF  C13   C12  C11   112.72  3.000
 TSF  O21   C12  C11   110.69  3.000
 TSF  H21   O21  C12   109.72  3.000
 TSF  H13   C13  C14   108.58  3.000
 TSF  H13   C13  O23   105.76  3.000
 TSF  C14   C13  O23   111.87  3.000
 TSF  H13   C13  C12   108.39  3.000
 TSF  C14   C13  C12   110.62  3.000
 TSF  O23   C13  C12   111.40  3.000
 TSF  H23   O23  C13   108.77  3.000
 TSF  H142  C14  H141  106.71  3.000
 TSF  H142  C14  O26   111.70  3.000
 TSF  H141  C14  O26   111.75  3.000
 TSF  H142  C14  C13   109.33  3.000
 TSF  H141  C14  C13   108.57  3.000
 TSF  O26   C14  C13   108.71  3.000
 TSF  H26   O26  C14   108.03  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
 TSF  CONST_01  N3   C4   C9   N5    180.00   0.0  0
 TSF  CONST_02  N7   C8   C9   N5      0.00   0.0  0
 TSF  CONST_03  N1   C8   C9   N5    180.00   0.0  0
 TSF  CONST_04  C8   N7   C6   N5      0.00   0.0  0
 TSF  CONST_05  N7   C6   N5   C9      0.00   0.0  0
 TSF  CONST_06  C2   N3   C4   C9      0.00   0.0  0
 TSF  CONST_07  C6   N7   C8   C9      0.00   0.0  0
 TSF  CONST_08  C2   N1   C8   C9      0.00   0.0  0
 TSF  CONST_09  C6   N5   C9   C4    180.00   0.0  0
 TSF  CONST_10  N7   C8   C9   C4    180.00   0.0  0
 TSF  CONST_11  N1   C8   C9   C4      0.00   0.0  0
 TSF  CONST_12  N1   C2   N3   C4      0.00   0.0  0
 TSF  CONST_13  C8   C9   C4   N3      0.00   0.0  0
 TSF  CONST_14  C8   N1   C2   N3      0.00   0.0  0
 TSF  CONST_15  C8   C9   N5   C6      0.00   0.0  0
 TSF  CONST_16  N1   C8   N7   C6    180.00   0.0  0
 TSF  CONST_17  C2   N1   C8   N7    180.00   0.0  0
 TSF  CONST_18  C4   C9   N5   C15     0.00   0.0  0
 TSF  CONST_19  C8   C9   N5   C15   180.00   0.0  0
 TSF  CONST_20  N7   C6   N5   C15   180.00   0.0  0
 TSF  CONST_21  O2   C4   C9   N5      0.00   0.0  0
 TSF  CONST_22  C10  N7   C6   N5    180.00   0.0  0
 TSF  CONST_23  O4   C6   N5   C9    180.00   0.0  0
 TSF  CONST_24  C10  N7   C8   C9    180.00   0.0  0
 TSF  CONST_25  O1   C2   N3   C4    180.00   0.0  0
 TSF  CONST_26  C8   C9   C4   O2    180.00   0.0  0
 TSF  CONST_27  C2   N3   C4   O2    180.00   0.0  0
 TSF  CONST_28  C8   N7   C6   O4    180.00   0.0  0
 TSF  CONST_29  O1   C2   N1   C8    180.00   0.0  0
 TSF  CONST_30  C10  N7   C8   N1      0.00   0.0  0
 TSF  CONST_31  H3   N3   C4   C9    180.00   0.0  0
 TSF  CONST_32  H1   N1   C8   C9    180.00   0.0  0
 TSF  CONST_33  O4   C6   N5   C15     0.00   0.0  0
 TSF  CONST_34  C10  N7   C6   O4      0.00   0.0  0
 TSF  Var_01    C9   N5   C15  C16   -78.61  30.0  2
 TSF  Var_02    C11  C10  N7   C6     85.74  30.0  2
 TSF  Var_03    N5   C15  C16  C17   177.30  30.0  3
 TSF  Var_04    F1   C19  P    O2P   -56.34  30.0  3
 TSF  Var_05    C17  C18  C19  P    -178.84  30.0  3
 TSF  Var_06    C16  C17  C18  C19  -178.02  30.0  3
 TSF  Var_07    C15  C16  C17  C18  -179.95  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
 TSF  chir_01  C11  C10  O19  C12  negativ
 TSF  chir_02  C12  O21  C11  C13  negativ
 TSF  chir_03  C13  O23  C12  C14  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
 TSF  plan-1  C15  0.020
 TSF  plan-1  N5   0.020
 TSF  plan-1  C9   0.020
 TSF  plan-1  C4   0.020
 TSF  plan-1  O2   0.020
 TSF  plan-1  N3   0.020
 TSF  plan-1  C6   0.020
 TSF  plan-1  O4   0.020
 TSF  plan-1  N7   0.020
 TSF  plan-1  C8   0.020
 TSF  plan-1  N1   0.020
 TSF  plan-1  C2   0.020
 TSF  plan-1  O1   0.020
 TSF  plan-1  C10  0.020
 TSF  plan-1  H3   0.020
 TSF  plan-1  H1   0.020

