import re
from pprint import pprint

content = ("ALA\n"
            "  CCTOOLS-0424210918\n\n"
            " 13 12  0  0  1  0  0  0  0  0999 V2000\n"
            "    2.2810   26.2130   12.8040 N   0  0  0  0  0\n"
            "    1.1690   26.9420   13.4110 C   0  0  0  0  0\n"
            "    1.5390   28.3440   13.8740 C   0  0  0  0  0\n"
            "    2.7090   28.6470   14.1140 O   0  0  0  0  0\n"
            "    0.6010   26.1430   14.5740 C   0  0  0  0  0\n"
            "    0.5230   29.1940   13.9970 O   0  0  0  0  0\n"
            "    2.0330   25.2730   12.4930 H   0  0  0  0  0\n"
            "    3.0800   26.1840   13.4360 H   0  0  0  0  0\n"
            "    0.3990   27.0670   12.6130 H   0  0  0  0  0\n"
            "   -0.2470   26.6990   15.0370 H   0  0  0  0  0\n"
            "    0.3080   25.1100   14.2700 H   0  0  0  0  0\n"
            "    1.3840   25.8760   15.3210 H   0  0  0  0  0\n"
            "    0.7530   30.0690   14.2860 H   0  0  0  0  0\n"
            "  1  2  1  0  0  0\n"
            "  1  7  1  0  0  0\n"
            "  1  8  1  0  0  0\n"
            "  2  3  1  0  0  0\n"
            "  2  5  1  0  0  0\n"
            "  2  9  1  0  0  0\n"
            "  3  4  2  0  0  0\n"
            "  3  6  1  0  0  0\n"
            "  5 10  1  0  0  0\n"
            "  5 11  1  0  0  0\n"
            "  5 12  1  0  0  0\n"
            "  6 13  1  0  0  0\n"
            "M  END\n"
            "$$$$")
match = re.search(r"^ {3,}-?\d.*(?:\r?\n {3,}-?\d.*)*", content, re.M)
datasplit = []

if match:
    for line in match.group().splitlines():
        datasplit.append([part for part in line.split()][:4])

pprint(datasplit)