data_GOM
#
_chem_comp.id GOM
_chem_comp.name GLUTAMOL-AMP
_chem_comp.type "RNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C15 H22 N6 O9 P"
_chem_comp.mon_nstd_parent_comp_id G
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge -1
_chem_comp.pdbx_initial_date 2002-11-26
_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 461.344
_chem_comp.one_letter_code G
_chem_comp.three_letter_code GOM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_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
GOM N N N 1 1 N N N 40.645 82.262 52.670 -5.945 -0.091 -1.974 N GOM 1
GOM C C C 0 1 N N N 38.660 80.829 52.998 -4.593 -0.242 0.062 C GOM 2
GOM CA CA C 0 1 N N S 39.187 82.229 52.651 -5.619 0.587 -0.713 CA GOM 3
GOM CB CB C 0 1 N N N 38.685 82.645 51.267 -6.889 0.741 0.127 CB GOM 4
GOM CG CG C 0 1 N N N 37.176 82.614 51.111 -7.866 1.673 -0.593 CG GOM 5
GOM CD CD C 0 1 N N N 36.725 83.107 49.755 -9.117 1.824 0.234 CD GOM 6
GOM OE1 OE1 O 0 1 N N N 36.693 84.339 49.530 -9.217 1.241 1.300 OE1 GOM 7
GOM OE2 OE2 O -1 1 N N N 36.412 82.249 48.911 -10.028 2.531 -0.163 OE2 GOM 8
GOM P P P 0 1 N N N 39.243 78.703 54.436 -2.339 -1.172 0.198 P GOM 9
GOM OP1 O1P O 0 1 N N N 40.422 77.871 54.077 -2.225 -0.581 1.620 OP1 GOM 10
GOM OP2 O2P O -1 1 N N N 38.806 78.778 55.863 -2.855 -2.626 0.284 OP2 GOM 11
GOM OP3 O3P O 0 1 N Y N 39.539 80.182 53.914 -3.367 -0.289 -0.671 OP3 GOM 12
GOM "O5'" O5* O 0 1 N N N 37.976 78.228 53.594 -0.891 -1.158 -0.506 "O5'" GOM 13
GOM "C5'" C5* C 0 1 N N N 38.116 77.541 52.355 0.000 -1.856 0.366 "C5'" GOM 14
GOM "C4'" C4* C 0 1 N N R 36.762 77.392 51.671 1.401 -1.879 -0.247 "C4'" GOM 15
GOM "O4'" O4* O 0 1 N N N 35.940 76.453 52.425 1.949 -0.543 -0.300 "O4'" GOM 16
GOM "C1'" C1* C 0 1 N N R 34.838 77.126 53.004 3.378 -0.722 -0.409 "C1'" GOM 17
GOM N9 N9 N 0 1 Y N N 34.546 76.608 54.343 4.078 0.493 0.013 N9 GOM 18
GOM C4 C4 C 0 1 Y N N 33.456 75.821 54.625 5.354 0.858 -0.335 C4 GOM 19
GOM N3 N3 N 0 1 Y N N 32.537 75.364 53.752 6.311 0.322 -1.085 N3 GOM 20
GOM C2 C2 C 0 1 Y N N 31.604 74.655 54.382 7.468 0.932 -1.233 C2 GOM 21
GOM N1 N1 N 0 1 Y N N 31.493 74.374 55.687 7.739 2.088 -0.655 N1 GOM 22
GOM C6 C6 C 0 1 Y N N 32.436 74.848 56.535 6.843 2.700 0.114 C6 GOM 23
GOM N6 N6 N 0 1 N N N 32.316 74.574 57.832 7.136 3.911 0.715 N6 GOM 24
GOM C5 C5 C 0 1 Y N N 33.484 75.610 55.991 5.595 2.085 0.307 C5 GOM 25
GOM N7 N7 N 0 1 Y N N 34.589 76.227 56.561 4.471 2.404 0.993 N7 GOM 26
GOM C8 C8 C 0 1 Y N N 35.192 76.796 55.542 3.581 1.469 0.825 C8 GOM 27
GOM "C2'" C2* C 0 1 N N R 34.985 78.637 52.818 3.706 -1.892 0.546 "C2'" GOM 28
GOM "O2'" O2* O 0 1 N N N 33.728 79.164 52.448 4.728 -2.725 -0.006 "O2'" GOM 29
GOM "C3'" C3* C 0 1 N N S 35.980 78.710 51.662 2.373 -2.669 0.656 "C3'" GOM 30
GOM "O3'" O3* O 0 1 N N N 35.519 79.196 50.400 2.531 -4.005 0.174 "O3'" GOM 31
GOM HN2 HN2 H 0 1 N N N 41.045 81.549 52.060 -5.108 -0.192 -2.528 HN2 GOM 32
GOM HN3 HN3 H 0 1 N N N 40.995 83.192 52.440 -6.330 -1.002 -1.776 HN3 GOM 33
GOM H H H 0 1 N N N 41.016 81.931 53.561 -6.622 0.456 -2.485 H GOM 34
GOM HC1 1HC H 0 1 N N N 38.484 80.213 52.085 -4.973 -1.255 0.198 HC1 GOM 35
GOM HC2 2HC H 0 1 N N N 37.613 80.862 53.380 -4.417 0.214 1.036 HC2 GOM 36
GOM HA HA H 0 1 N N N 38.808 82.942 53.420 -5.203 1.572 -0.926 HA GOM 37
GOM HB1 1HB H 0 1 N N N 39.170 82.027 50.476 -7.353 -0.235 0.266 HB1 GOM 38
GOM HB2 2HB H 0 1 N N N 39.083 83.650 50.995 -6.633 1.163 1.099 HB2 GOM 39
GOM HG1 1HG H 0 1 N N N 36.676 83.181 51.931 -7.402 2.649 -0.732 HG1 GOM 40
GOM HG2 2HG H 0 1 N N N 36.771 81.597 51.324 -8.122 1.251 -1.565 HG2 GOM 41
GOM "H5'" 1H5* H 0 1 N N N 38.627 76.558 52.482 -0.353 -2.878 0.505 "H5'" GOM 42
GOM "H5''" 2H5* H 0 0 N N N 38.864 78.033 51.691 0.034 -1.349 1.331 "H5''" GOM 43
GOM "H4'" H4* H 0 1 N N N 36.964 77.051 50.629 1.370 -2.316 -1.245 "H4'" GOM 44
GOM "H1'" H1* H 0 1 N N N 33.888 76.903 52.465 3.651 -0.980 -1.433 "H1'" GOM 45
GOM H2 H2 H 0 1 N N N 30.813 74.243 53.733 8.225 0.470 -1.850 H2 GOM 46
GOM HN61 1HN6 H 0 0 N N N 32.239 73.564 57.952 8.003 4.324 0.578 HN61 GOM 47
GOM HN62 2HN6 H 0 0 N N N 33.026 74.931 58.471 6.473 4.350 1.271 HN62 GOM 48
GOM H8 H8 H 0 1 N N N 36.128 77.363 55.677 2.594 1.468 1.263 H8 GOM 49
GOM "H2'" H2* H 0 1 N N N 35.320 79.205 53.717 4.009 -1.512 1.522 "H2'" GOM 50
GOM "HO2'" *HO2 H 0 0 N N N 33.819 80.103 52.333 4.843 -3.466 0.605 "HO2'" GOM 51
GOM "H3'" H3* H 0 1 N N N 36.676 79.562 51.843 2.018 -2.675 1.687 "H3'" GOM 52
GOM "HO3'" *HO3 H 0 0 N Y N 35.034 80.013 50.394 3.145 -4.448 0.775 "HO3'" GOM 53
#
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
GOM N CA SING N N 1
GOM N HN2 SING N N 2
GOM N HN3 SING N N 3
GOM N H SING N N 4
GOM C CA SING N N 5
GOM C OP3 SING N N 6
GOM C HC1 SING N N 7
GOM C HC2 SING N N 8
GOM CA CB SING N N 9
GOM CA HA SING N N 10
GOM CB CG SING N N 11
GOM CB HB1 SING N N 12
GOM CB HB2 SING N N 13
GOM CG CD SING N N 14
GOM CG HG1 SING N N 15
GOM CG HG2 SING N N 16
GOM CD OE1 DOUB N N 17
GOM CD OE2 SING N N 18
GOM P OP1 DOUB N N 19
GOM P OP2 SING N N 20
GOM P OP3 SING N N 21
GOM P "O5'" SING N N 22
GOM "O5'" "C5'" SING N N 23
GOM "C5'" "C4'" SING N N 24
GOM "C5'" "H5'" SING N N 25
GOM "C5'" "H5''" SING N N 26
GOM "C4'" "O4'" SING N N 27
GOM "C4'" "C3'" SING N N 28
GOM "C4'" "H4'" SING N N 29
GOM "O4'" "C1'" SING N N 30
GOM "C1'" N9 SING N N 31
GOM "C1'" "C2'" SING N N 32
GOM "C1'" "H1'" SING N N 33
GOM N9 C4 SING Y N 34
GOM N9 C8 SING Y N 35
GOM C4 N3 DOUB Y N 36
GOM C4 C5 SING Y N 37
GOM N3 C2 SING Y N 38
GOM C2 N1 DOUB Y N 39
GOM C2 H2 SING N N 40
GOM N1 C6 SING Y N 41
GOM C6 N6 SING N N 42
GOM C6 C5 DOUB Y N 43
GOM N6 HN61 SING N N 44
GOM N6 HN62 SING N N 45
GOM C5 N7 SING Y N 46
GOM N7 C8 DOUB Y N 47
GOM C8 H8 SING N N 48
GOM "C2'" "O2'" SING N N 49
GOM "C2'" "C3'" SING N N 50
GOM "C2'" "H2'" SING N N 51
GOM "O2'" "HO2'" SING N N 52
GOM "C3'" "O3'" SING N N 53
GOM "C3'" "H3'" SING N N 54
GOM "O3'" "HO3'" SING N N 55
#
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
GOM SMILES ACDLabs 10.04 "[O-]C(=O)CCC([NH3+])COP([O-])(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O"
GOM SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P]([O-])(=O)OC[C@@H]([NH3+])CCC([O-])=O)[C@@H](O)[C@H]3O"
GOM SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P]([O-])(=O)OC[CH]([NH3+])CCC([O-])=O)[CH](O)[CH]3O"
GOM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)([O-])OC[C@H](CCC(=O)[O-])[NH3+])O)O)N"
GOM SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)([O-])OCC(CCC(=O)[O-])[NH3+])O)O)N"
GOM InChI InChI 1.03
"InChI=1S/C15H23N6O9P/c16-7(1-2-9(22)23)3-28-31(26,27)29-4-8-11(24)12(25)15(30-8)21-6-20-10-13(17)18-5-19-14(10)21/h5-8,11-12,15,24-25H,1-4,16H2,(H,22,23)(H,26,27)(H2,17,18,19)/p-1/t7-,8+,11+,12+,15+/m0/s1"
GOM InChIKey InChI 1.03 JDELUWYDJMPPMI-SBZSCLMQSA-M
#
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
GOM "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-({[(2S)-2-ammonio-4-carboxylatobutyl]oxy}phosphinato)adenosine"
GOM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(4S)-5-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-oxido-phosphoryl]oxy-4-azaniumyl-pentanoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
GOM "Create component" 2002-11-26 RCSB
GOM "Modify descriptor" 2011-06-04 RCSB
#