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I have the impression that the generation of molfile V3000 does not correctly set the SGroup count if there are some.
I have this file that is not compatible with some other packages because the number of Sgroup is expect to be 0 based on the counts line.
Actelion Java MolfileCreator 2.0
0 0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 15 15 0 0 0
M V30 BEGIN ATOM
M V30 1 C -3.8971 1.5 0 0
M V30 2 C -5.1961 2.25 0 0
M V30 3 C -3.8971 0 0 0
M V30 4 C -2.598 2.25 0 0
M V30 5 C -1.2991 1.5 0 0
M V30 6 C -1.2991 0 0 0
M V30 7 C 0 -0.75 0 0
M V30 8 C 1.2991 0 0 0
M V30 9 C 1.2991 1.5 0 0
M V30 10 C 0 2.25 0 0
M V30 11 C 2.598 -0.75 0 0
M V30 12 C 2.598 -2.25 0 0
M V30 13 C 3.8971 0 0 0
M V30 14 O 3.8971 1.5 0 0
M V30 15 O 5.1961 -0.75 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 1 3
M V30 3 1 1 4
M V30 4 1 4 5
M V30 5 1 5 6
M V30 6 2 6 7
M V30 7 1 7 8
M V30 8 2 8 9
M V30 9 1 9 10
M V30 10 2 5 10
M V30 11 1 8 11
M V30 12 1 11 12
M V30 13 1 11 13
M V30 14 2 13 14
M V30 15 1 13 15
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 1 ATOMS=(1 1) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" -3.8971 -1.5000 DA ALL 1 5" FIELDDATA="]10"
M V30 2 DAT 2 ATOMS=(1 2) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" -5.1961 -2.2500 DA ALL 1 5" FIELDDATA="]11"
M V30 3 DAT 3 ATOMS=(1 3) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" -3.8971 0.0000 DA ALL 1 5" FIELDDATA="]12"
M V30 4 DAT 4 ATOMS=(1 4) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" -2.5980 -2.2500 DA ALL 1 5" FIELDDATA="]9"
M V30 5 DAT 5 ATOMS=(1 5) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" -1.2991 -1.5000 DA ALL 1 5" FIELDDATA="]6"
M V30 6 DAT 6 ATOMS=(1 6) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" -1.2991 0.0000 DA ALL 1 5" FIELDDATA="]7"
M V30 7 DAT 7 ATOMS=(1 7) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" 0.0000 0.7500 DA ALL 1 5" FIELDDATA="]8"
M V30 8 DAT 8 ATOMS=(1 8) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" 1.2991 0.0000 DA ALL 1 5" FIELDDATA="]3"
M V30 9 DAT 9 ATOMS=(1 9) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" 1.2991 -1.5000 DA ALL 1 5" FIELDDATA="]4"
M V30 10 DAT 10 ATOMS=(1 10) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" 0.0000 -2.2500 DA ALL 1 5" FIELDDATA="]5"
M V30 11 DAT 11 ATOMS=(1 11) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" 2.5980 0.7500 DA ALL 1 5" FIELDDATA="]2"
M V30 12 DAT 12 ATOMS=(1 12) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" 2.5980 2.2500 DA ALL 1 5" FIELDDATA="]13"
M V30 13 DAT 13 ATOMS=(1 13) FIELDNAME="NOSEARCH_OCL_CUSTOM_LABEL" -
M V30 FIELDDISP=" 3.8971 0.0000 DA ALL 1 5" FIELDDATA="]1"
M V30 END SGROUP
M V30 END CTAB
M END
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