SELECT 
  category_id, 
  parent_id 
FROM 
  cscart_categories 
WHERE 
  parent_id IN(
    1531, 1533, 1535, 1537, 1541, 1538, 1542, 
    1543, 1544, 1545, 1548, 1551, 1565, 
    1566, 1567, 1569, 1576, 1577, 1605, 
    1613, 1614, 1615, 1619, 1627, 1628, 
    1675, 1673, 1839, 1840, 1841, 1842, 
    1843, 1845, 1857, 1871, 1891, 1885, 
    1894, 1895, 1897, 1898, 1902, 1903, 
    1922, 1924, 1925, 1927, 1928, 1929, 
    1933, 1935, 1936, 1938, 1939, 1940, 
    1941, 1946, 1948, 1954, 1956, 1957, 
    1962, 1963
  ) 
  AND category_id != 414

Query time 0.00082

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "57.61"
    },
    "table": {
      "table_name": "cscart_categories",
      "access_type": "range",
      "possible_keys": [
        "PRIMARY",
        "parent",
        "p_category_id"
      ],
      "key": "parent",
      "used_key_parts": [
        "parent_id"
      ],
      "key_length": "3",
      "rows_examined_per_scan": 93,
      "rows_produced_per_join": 93,
      "filtered": "100.00",
      "index_condition": "(`s2cart`.`cscart_categories`.`parent_id` in (1531,1533,1535,1537,1541,1538,1542,1543,1544,1545,1548,1551,1565,1566,1567,1569,1576,1577,1605,1613,1614,1615,1619,1627,1628,1675,1673,1839,1840,1841,1842,1843,1845,1857,1871,1891,1885,1894,1895,1897,1898,1902,1903,1922,1924,1925,1927,1928,1929,1933,1935,1936,1938,1939,1940,1941,1946,1948,1954,1956,1957,1962,1963))",
      "cost_info": {
        "read_cost": "48.31",
        "eval_cost": "9.30",
        "prefix_cost": "57.61",
        "data_read_per_join": "329K"
      },
      "used_columns": [
        "category_id",
        "parent_id"
      ],
      "attached_condition": "(`s2cart`.`cscart_categories`.`category_id` <> 414)"
    }
  }
}

Result

category_id parent_id
1539 1538
1540 1538
1568 1567
1616 1615
1617 1615
1629 1628
1630 1628
1631 1628
1632 1628
1674 1673
1676 1673
1844 1843
1886 1885
1887 1885
1888 1885
1889 1885
1890 1885
1892 1891
1893 1891
1899 1898
1900 1898
1901 1898
1904 1903
1905 1903
1906 1903
1907 1903
1908 1903
1909 1903
1910 1903
1911 1903
1912 1903
1913 1903
1914 1903
1915 1903
1916 1903
1917 1903
1918 1903
1930 1929
1931 1929
1932 1929
1942 1941
1943 1941
1944 1941