data_G1M
#
_chem_comp.id G1M
_chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H20 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 519.235
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G1M
_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 3JPP
_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
G1M N1 N1 N 0 1 N N N 9.696 8.878 8.100 -8.088 1.923 0.180 N1 G1M 1
G1M C2 C2 C 0 1 N N N 8.434 8.963 7.564 -7.524 1.447 1.326 C2 G1M 2
G1M N2 N2 N 0 1 N N N 8.341 9.509 6.340 -8.187 1.616 2.515 N2 G1M 3
G1M N3 N3 N 0 1 N N N 7.341 8.553 8.184 -6.364 0.830 1.324 N3 G1M 4
G1M C4 C4 C 0 1 Y N N 7.611 8.068 9.412 -5.682 0.642 0.188 C4 G1M 5
G1M C5 C5 C 0 1 Y N N 8.830 7.956 10.046 -6.208 1.109 -1.022 C5 G1M 6
G1M C6 C6 C 0 1 N N N 9.997 8.373 9.360 -7.458 1.771 -1.006 C6 G1M 7
G1M O6 O6 O 0 1 N N N 11.171 8.325 9.741 -7.954 2.193 -2.036 O6 G1M 8
G1M N7 N7 N 0 1 Y N N 8.678 7.416 11.316 -5.322 0.788 -1.996 N7 G1M 9
G1M C8 C8 C 0 1 Y N N 7.395 7.201 11.423 -4.308 0.167 -1.469 C8 G1M 10
G1M N9 N9 N 0 1 Y N N 6.693 7.559 10.296 -4.485 0.054 -0.120 N9 G1M 11
G1M PA PA P 0 1 N N N 4.972 5.038 14.688 2.027 -1.386 -0.794 PA G1M 12
G1M PB PB P 0 1 N N N 3.934 2.712 13.754 4.639 -0.049 -0.376 PB G1M 13
G1M PG PG P 0 1 N N N 3.835 1.215 16.575 6.930 1.470 0.767 PG G1M 14
G1M "C1'" "C1'" C 0 1 N N R 5.263 7.402 10.052 -3.563 -0.582 0.825 "C1'" G1M 15
G1M O1A O1A O 0 1 N N N 3.658 4.970 15.796 1.762 -1.132 -2.362 O1A G1M 16
G1M O1B O1B O 0 1 N N N 4.021 2.032 12.177 5.022 0.127 -1.929 O1B G1M 17
G1M O1G O1G O 0 1 N N N 3.385 2.813 17.026 7.356 2.793 1.578 O1G G1M 18
G1M "C2'" "C2'" C 0 1 N N N 4.895 5.977 9.624 -3.984 -2.045 1.063 "C2'" G1M 19
G1M O2A O2A O 0 1 N N N 6.355 5.162 15.213 2.608 -2.734 -0.604 O2A G1M 20
G1M O2B O2B O 0 1 N N N 2.614 3.124 14.298 5.355 -1.220 0.179 O2B G1M 21
G1M O2G O2G O 0 1 N N N 4.921 0.324 17.567 7.383 0.164 1.593 O2G G1M 22
G1M "C3'" "C3'" C 0 1 N N S 4.411 5.363 10.922 -2.743 -2.870 0.640 "C3'" G1M 23
G1M "O3'" "O3'" O 0 1 N N N 3.491 4.293 10.678 -2.515 -3.949 1.548 "O3'" G1M 24
G1M O3A O3A O 0 1 N N N 4.914 3.845 13.775 3.051 -0.276 -0.237 O3A G1M 25
G1M C3B C3B C 0 1 N N R 4.663 1.413 14.902 5.121 1.450 0.543 C3B G1M 26
G1M C3B2 2C3B C 0 0 N N N 4.536 0.072 14.198 4.690 2.690 -0.242 2C3B G1M 27
G1M O3G O3G O 0 1 N N N 2.600 0.416 16.388 7.591 1.469 -0.558 O3G G1M 28
G1M "C4'" "C4'" C 0 1 N N R 3.707 6.550 11.566 -1.608 -1.819 0.733 "C4'" G1M 29
G1M "O4'" "O4'" O 0 1 N N N 4.570 7.666 11.270 -2.236 -0.603 0.273 "O4'" G1M 30
G1M "C5'" "C5'" C 0 1 N N N 3.467 6.444 13.053 -0.443 -2.203 -0.182 "C5'" G1M 31
G1M "O5'" "O5'" O 0 1 N N N 4.703 6.305 13.757 0.635 -1.284 0.009 "O5'" G1M 32
G1M HN1 HN1 H 0 1 N N N 10.458 9.205 7.540 -8.948 2.371 0.215 HN1 G1M 33
G1M HN2 HN2 H 0 1 N N N 7.447 9.604 5.901 -9.045 2.069 2.532 HN2 G1M 34
G1M HN2A HN2A H 0 0 N N N 9.165 9.820 5.867 -7.799 1.282 3.339 HN2A G1M 35
G1M H8 H8 H 0 1 N N N 6.932 6.785 12.306 -3.453 -0.202 -2.016 H8 G1M 36
G1M "H1'" "H1'" H 0 1 N N N 4.987 8.095 9.244 -3.566 -0.037 1.769 "H1'" G1M 37
G1M "H2'" "H2'" H 0 1 N N N 4.113 5.970 8.850 -4.211 -2.210 2.116 "H2'" G1M 38
G1M "H2'A" "H2'A" H 0 0 N N N 5.759 5.436 9.211 -4.842 -2.302 0.442 "H2'A" G1M 39
G1M "H3'" "H3'" H 0 1 N N N 5.209 4.919 11.536 -2.851 -3.238 -0.380 "H3'" G1M 40
G1M "HO3'" "HO3'" H 0 0 N N N 3.204 3.927 11.506 -3.241 -4.587 1.592 "HO3'" G1M 41
G1M H3B H3B H 0 1 N N N 5.691 1.748 15.107 4.634 1.450 1.519 H3B G1M 42
G1M HC3B HC3B H 0 0 N N N 4.953 -0.720 14.838 3.609 2.678 -0.376 HC3B G1M 43
G1M HC3A HC3A H 0 0 N N N 3.475 -0.138 13.999 4.979 3.586 0.307 HC3A G1M 44
G1M HC3C HC3C H 0 0 N N N 5.089 0.103 13.247 5.177 2.689 -1.218 HC3C G1M 45
G1M "H4'" "H4'" H 0 1 N N N 2.687 6.635 11.163 -1.269 -1.710 1.763 "H4'" G1M 46
G1M "H5'" "H5'" H 0 1 N N N 2.957 7.355 13.400 -0.108 -3.211 0.060 "H5'" G1M 47
G1M "H5'A" "H5'A" H 0 0 N N N 2.839 5.563 13.253 -0.770 -2.168 -1.221 "H5'A" G1M 48
G1M H17 H17 H 0 1 N N N 3.031 4.319 15.504 1.380 -0.266 -2.561 H17 G1M 49
G1M H18 H18 H 0 1 N N N 3.150 1.992 11.800 4.588 0.877 -2.359 H18 G1M 50
G1M H19 H19 H 0 1 N N N 2.438 2.876 17.068 8.307 2.870 1.734 H19 G1M 51
G1M H20 H20 H 0 1 N N N 4.525 -0.506 17.805 6.988 0.099 2.473 H20 G1M 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
G1M N1 C2 SING N N 1
G1M N1 C6 SING N N 2
G1M N1 HN1 SING N N 3
G1M C2 N2 SING N N 4
G1M C2 N3 DOUB N N 5
G1M N2 HN2 SING N N 6
G1M N2 HN2A SING N N 7
G1M N3 C4 SING N N 8
G1M C4 C5 DOUB Y N 9
G1M C4 N9 SING Y N 10
G1M C5 C6 SING N N 11
G1M C5 N7 SING Y N 12
G1M C6 O6 DOUB N N 13
G1M N7 C8 DOUB Y N 14
G1M C8 N9 SING Y N 15
G1M C8 H8 SING N N 16
G1M N9 "C1'" SING N N 17
G1M PA O1A SING N N 18
G1M PA O2A DOUB N N 19
G1M PA O3A SING N N 20
G1M PA "O5'" SING N N 21
G1M PB O1B SING N N 22
G1M PB O2B DOUB N N 23
G1M PB O3A SING N N 24
G1M PB C3B SING N N 25
G1M PG O1G SING N N 26
G1M PG O2G SING N N 27
G1M PG C3B SING N N 28
G1M PG O3G DOUB N N 29
G1M "C1'" "C2'" SING N N 30
G1M "C1'" "O4'" SING N N 31
G1M "C1'" "H1'" SING N N 32
G1M "C2'" "C3'" SING N N 33
G1M "C2'" "H2'" SING N N 34
G1M "C2'" "H2'A" SING N N 35
G1M "C3'" "O3'" SING N N 36
G1M "C3'" "C4'" SING N N 37
G1M "C3'" "H3'" SING N N 38
G1M "O3'" "HO3'" SING N N 39
G1M C3B C3B2 SING N N 40
G1M C3B H3B SING N N 41
G1M C3B2 HC3B SING N N 42
G1M C3B2 HC3A SING N N 43
G1M C3B2 HC3C SING N N 44
G1M "C4'" "O4'" SING N N 45
G1M "C4'" "C5'" SING N N 46
G1M "C4'" "H4'" SING N N 47
G1M "C5'" "O5'" SING N N 48
G1M "C5'" "H5'" SING N N 49
G1M "C5'" "H5'A" SING N N 50
G1M O1A H17 SING N N 51
G1M O1B H18 SING N N 52
G1M O1G H19 SING N N 53
G1M O2G H20 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
G1M SMILES ACDLabs 11.02 "O=P(O)(O)C(C)P(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O"
G1M SMILES_CANONICAL CACTVS 3.352 "C[C@H]([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"
G1M SMILES CACTVS 3.352 "C[CH]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH](C[CH]1O)n2cnc3C(=O)NC(=Nc23)N"
G1M SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@@H]([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"
G1M SMILES "OpenEye OEToolkits" 1.7.0 "CC(P(=O)(O)O)P(=O)(O)OP(=O)(O)OCC1C(CC(O1)n2cnc3c2N=C(NC3=O)N)O"
G1M InChI InChI 1.03 "InChI=1S/C12H20N5O12P3/c1-5(30(20,21)22)31(23,24)29-32(25,26)27-3-7-6(18)2-8(28-7)17-4-14-9-10(17)15-12(13)16-11(9)19/h4-8,18H,2-3H2,1H3,(H,23,24)(H,25,26)(H2,20,21,22)(H3,13,15,16,19)/t5-,6+,7-,8-/m1/s1"
G1M InChIKey InChI 1.03 KAYWITWNVLLSPS-ULAWRXDQSA-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
G1M "SYSTEMATIC NAME" ACDLabs 11.02 "2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine"
G1M "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]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
G1M "Create component" 2009-09-14 RCSB
G1M "Modify descriptor" 2011-06-04 RCSB
#