data_GFM
#
_chem_comp.id GFM
_chem_comp.name "2'-deoxy-5'-O-[(S)-{[(S)-[(1R)-1-fluoro-1-phosphonoethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H19 F N5 O12 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-09-14
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 537.225
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code GFM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3JPS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
GFM N1 N1 N 0 1 N N N 9.797 8.752 8.126 -7.897 2.246 0.152 N1 GFM 1
GFM C2 C2 C 0 1 N N N 8.538 8.904 7.582 -7.481 1.553 1.250 C2 GFM 2
GFM N2 N2 N 0 1 N N N 8.472 9.434 6.340 -8.231 1.612 2.397 N2 GFM 3
GFM N3 N3 N 0 1 N N N 7.423 8.567 8.206 -6.384 0.831 1.241 N3 GFM 4
GFM C4 C4 C 0 1 Y N N 7.666 8.073 9.437 -5.621 0.744 0.145 C4 GFM 5
GFM C5 C5 C 0 1 Y N N 8.879 7.893 10.071 -5.994 1.432 -1.015 C5 GFM 6
GFM C6 C6 C 0 1 N N N 10.066 8.234 9.388 -7.178 2.206 -0.992 C6 GFM 7
GFM O6 O6 O 0 1 N N N 11.239 8.112 9.775 -7.541 2.822 -1.980 O6 GFM 8
GFM N7 N7 N 0 1 Y N N 8.697 7.366 11.340 -5.056 1.171 -1.957 N7 GFM 9
GFM C8 C8 C 0 1 Y N N 7.405 7.220 11.443 -4.151 0.382 -1.457 C8 GFM 10
GFM N9 N9 N 0 1 Y N N 6.726 7.609 10.313 -4.458 0.091 -0.159 N9 GFM 11
GFM PA PA P 0 1 N N N 5.069 5.038 14.750 1.938 -1.876 -0.552 PA GFM 12
GFM PB PB P 0 1 N N N 3.921 2.713 13.789 4.310 -0.104 -0.420 PB GFM 13
GFM PG PG P 0 1 N N N 3.764 1.100 16.432 6.519 1.740 0.345 PG GFM 14
GFM "C1'" "C1'" C 0 1 N N R 5.292 7.504 10.064 -3.683 -0.765 0.744 "C1'" GFM 15
GFM O1A O1A O 0 1 N N N 3.949 5.052 15.718 1.801 -1.645 -2.007 O1A GFM 16
GFM O1B O1B O 0 1 N N N 3.956 2.168 12.158 4.062 0.662 -1.814 O1B GFM 17
GFM O1G O1G O 0 1 N N N 3.664 2.752 16.901 6.372 2.590 -1.014 O1G GFM 18
GFM "C2'" "C2'" C 0 1 N N N 4.900 6.106 9.585 -4.249 -2.198 0.721 "C2'" GFM 19
GFM O2A O2A O 0 1 N N N 6.678 5.206 15.334 2.536 -3.349 -0.297 O2A GFM 20
GFM O2B O2B O 0 1 N N N 2.642 3.174 14.377 5.334 -1.156 -0.609 O2B GFM 21
GFM O2G O2G O 0 1 N N N 4.673 -0.004 17.388 7.088 2.690 1.513 O2G GFM 22
GFM "C3'" "C3'" C 0 1 N N S 4.506 5.431 10.883 -3.052 -3.071 0.272 "C3'" GFM 23
GFM "O3'" "O3'" O 0 1 N N N 3.620 4.325 10.660 -3.001 -4.289 1.018 "O3'" GFM 24
GFM O3A O3A O 0 1 N N N 4.999 3.762 13.934 2.934 -0.777 0.075 O3A GFM 25
GFM C3B C3B C 0 1 N N R 4.489 1.167 14.707 4.888 1.088 0.833 C3B GFM 26
GFM F3B2 2F3B F 0 0 N N N 4.233 -0.015 14.086 3.974 2.142 0.931 2F3B GFM 27
GFM C3B3 3C3B C 0 0 N N N 6.017 1.306 14.875 5.004 0.387 2.188 3C3B GFM 28
GFM O3G O3G O 0 1 N N N 2.395 0.564 16.279 7.455 0.614 0.125 O3G GFM 29
GFM "C4'" "C4'" C 0 1 N N R 3.785 6.572 11.583 -1.842 -2.164 0.611 "C4'" GFM 30
GFM "O4'" "O4'" O 0 1 N N N 4.610 7.723 11.299 -2.319 -0.837 0.298 "O4'" GFM 31
GFM "C5'" "C5'" C 0 1 N N N 3.567 6.400 13.068 -0.638 -2.523 -0.261 "C5'" GFM 32
GFM "O5'" "O5'" O 0 1 N N N 4.815 6.261 13.756 0.494 -1.754 0.149 "O5'" GFM 33
GFM HN1 HN1 H 0 1 N N N 10.577 9.037 7.569 -8.714 2.766 0.190 HN1 GFM 34
GFM HN2 HN2 H 0 1 N N N 7.584 9.568 5.900 -9.044 2.141 2.419 HN2 GFM 35
GFM HN2A HN2A H 0 0 N N N 9.311 9.692 5.861 -7.949 1.124 3.187 HN2A GFM 36
GFM H8 H8 H 0 1 N N N 6.918 6.833 12.326 -3.286 0.013 -1.988 H8 GFM 37
GFM "H1'" "H1'" H 0 1 N N N 5.026 8.241 9.292 -3.724 -0.366 1.757 "H1'" GFM 38
GFM "H2'" "H2'" H 0 1 N N N 4.069 6.133 8.864 -4.583 -2.492 1.716 "H2'" GFM 39
GFM "H2'A" "H2'A" H 0 0 N N N 5.734 5.590 9.087 -5.067 -2.274 0.005 "H2'A" GFM 40
GFM "H3'" "H3'" H 0 1 N N N 5.349 5.000 11.442 -3.099 -3.274 -0.798 "H3'" GFM 41
GFM "HO3'" "HO3'" H 0 0 N N N 3.394 3.927 11.492 -3.781 -4.851 0.908 "HO3'" GFM 42
GFM HC3B HC3B H 0 0 N N N 6.409 0.427 15.408 5.716 -0.435 2.112 HC3B GFM 43
GFM HC3A HC3A H 0 0 N N N 6.490 1.375 13.884 5.350 1.099 2.938 HC3A GFM 44
GFM HC3C HC3C H 0 0 N N N 6.241 2.215 15.453 4.029 -0.004 2.480 HC3C GFM 45
GFM "H4'" "H4'" H 0 1 N N N 2.753 6.649 11.210 -1.589 -2.241 1.668 "H4'" GFM 46
GFM "H5'" "H5'" H 0 1 N N N 3.040 7.284 13.457 -0.415 -3.585 -0.153 "H5'" GFM 47
GFM "H5'A" "H5'A" H 0 0 N N N 2.962 5.497 13.239 -0.866 -2.305 -1.304 "H5'A" GFM 48
GFM H16 H16 H 0 1 N N N 3.084 2.227 11.785 3.402 1.367 -1.764 H16 GFM 49
GFM H17 H17 H 0 1 N N N 3.840 3.306 16.150 5.772 3.345 -0.943 H17 GFM 50
GFM H18 H18 H 0 1 N N N 6.664 5.295 16.280 2.653 -3.570 0.637 H18 GFM 51
GFM H19 H19 H 0 1 N N N 4.124 -0.740 17.631 7.955 3.073 1.321 H19 GFM 52
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
GFM N1 C2 SING N N 1
GFM N1 C6 SING N N 2
GFM N1 HN1 SING N N 3
GFM C2 N2 SING N N 4
GFM C2 N3 DOUB N N 5
GFM N2 HN2 SING N N 6
GFM N2 HN2A SING N N 7
GFM N3 C4 SING N N 8
GFM C4 C5 DOUB Y N 9
GFM C4 N9 SING Y N 10
GFM C5 C6 SING N N 11
GFM C5 N7 SING Y N 12
GFM C6 O6 DOUB N N 13
GFM N7 C8 DOUB Y N 14
GFM C8 N9 SING Y N 15
GFM C8 H8 SING N N 16
GFM N9 "C1'" SING N N 17
GFM PA O1A DOUB N N 18
GFM PA O2A SING N N 19
GFM PA O3A SING N N 20
GFM PA "O5'" SING N N 21
GFM PB O1B SING N N 22
GFM PB O2B DOUB N N 23
GFM PB O3A SING N N 24
GFM PB C3B SING N N 25
GFM PG O1G SING N N 26
GFM PG O2G SING N N 27
GFM PG C3B SING N N 28
GFM PG O3G DOUB N N 29
GFM "C1'" "C2'" SING N N 30
GFM "C1'" "O4'" SING N N 31
GFM "C1'" "H1'" SING N N 32
GFM "C2'" "C3'" SING N N 33
GFM "C2'" "H2'" SING N N 34
GFM "C2'" "H2'A" SING N N 35
GFM "C3'" "O3'" SING N N 36
GFM "C3'" "C4'" SING N N 37
GFM "C3'" "H3'" SING N N 38
GFM "O3'" "HO3'" SING N N 39
GFM C3B F3B2 SING N N 40
GFM C3B C3B3 SING N N 41
GFM C3B3 HC3B SING N N 42
GFM C3B3 HC3A SING N N 43
GFM C3B3 HC3C SING N N 44
GFM "C4'" "O4'" SING N N 45
GFM "C4'" "C5'" SING N N 46
GFM "C4'" "H4'" SING N N 47
GFM "C5'" "O5'" SING N N 48
GFM "C5'" "H5'" SING N N 49
GFM "C5'" "H5'A" SING N N 50
GFM O1B H16 SING N N 51
GFM O1G H17 SING N N 52
GFM O2A H18 SING N N 53
GFM O2G H19 SING N N 54
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
GFM SMILES ACDLabs 11.02 "O=P(O)(O)C(F)(C)P(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O"
GFM SMILES_CANONICAL CACTVS 3.352 "C[C@@](F)([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N"
GFM SMILES CACTVS 3.352 "C[C](F)([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH](C[CH]1O)n2cnc3C(=O)NC(=Nc23)N"
GFM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@](F)([P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](C[C@@H](O1)n2cnc3c2N=C(NC3=O)N)O)P(=O)(O)O"
GFM SMILES "OpenEye OEToolkits" 1.7.0 "CC(F)(P(=O)(O)O)P(=O)(O)OP(=O)(O)OCC1C(CC(O1)n2cnc3c2N=C(NC3=O)N)O"
GFM InChI InChI 1.03
"InChI=1S/C12H19FN5O12P3/c1-12(13,31(21,22)23)32(24,25)30-33(26,27)28-3-6-5(19)2-7(29-6)18-4-15-8-9(18)16-11(14)17-10(8)20/h4-7,19H,2-3H2,1H3,(H,24,25)(H,26,27)(H2,21,22,23)(H3,14,16,17,20)/t5-,6+,7+,12+/m0/s1"
GFM InChIKey InChI 1.03 MKPYQNARCBWQRN-WGVJZOHMSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
GFM "SYSTEMATIC NAME" ACDLabs 11.02 "2'-deoxy-5'-O-[(S)-{[(S)-[(1R)-1-fluoro-1-phosphonoethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine"
GFM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(1R)-1-[[[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]-1-fluoro-ethyl]phosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GFM "Create component" 2009-09-14 RCSB
GFM "Modify descriptor" 2011-06-04 RCSB
#