SELECT  ul1_.ОГРН  ogrn__
FROM  свюл  ul1_,
  (SELECT ul2_.ИНН inn_
   FROM   свюл ul2_
   WHERE (ul2_.ОГРН  = 1001601569991 or ul2_.ИНН = '1643005102' and ('164301001' = '' or ul2_.КПП = '164301001'))
   GROUP BY  ul2_.ИНН ) AS ls_
WHERE ul1_.ИНН IN (ls_.inn_)
  AND ul1_.ОГРН NOT IN 
    (SELECT vs1_.ОГРН
     FROM видзап vs1_
     WHERE vs1_.ОГРН IN 
       (SELECT ОГРН FROM свюл WHERE ИНН IN (ls_.inn_))
       AND  vs1_.КодСПВЗ IN (SELECT код FROM ЛиквидКоды))
GROUP BY ul1_.ОГРН;

id select_type table      type        possible_keys               key             key_len ref                rows filtered Extra
1  PRIMARY     <derived2> ALL         NULL                        NULL            NULL    NULL               2    100.00   Using where; Using temporary
1  PRIMARY     ul1_       ref         PRIMARY,Key_inn,key_inn_kpp key_inn_kpp     43      ls_.inn_           1    100.00   Using index
1  PRIMARY     свюл       eq_ref      PRIMARY,Key_inn,key_inn_kpp PRIMARY         8       egrul.ul1_.ОГРН    1    100.00   Using where; Not exists
1  PRIMARY     vs1_       ref         Index2                      Index2          8       egrul.свюл.ОГРН    7    100.00   Using where
1  PRIMARY     ЛиквидКоды ref         Индекс 1                    Индекс 1        4       egrul.vs1_.КодСПВЗ 1    100.00   Using where; Using index
2  DERIVED     ul2_       index_merge PRIMARY,Key_inn,key_inn_kpp PRIMARY,Key_inn 8,43    NULL               2    100.00   Using union(PRIMARY,Key_inn); Using where; Using temporary

SELECT ul_.ОГРН
FROM свюл ul_
WHERE ul_.`ОГРН` IN
 (SELECT  ul1_.ОГРН  ogrn__
  FROM  свюл  ul1_,
    (SELECT ul2_.ИНН inn_
     FROM   свюл ul2_
     WHERE (ul2_.ОГРН  = 1001601569991 or ul2_.ИНН = '1643005102' and ('164301001' = '' or ul2_.КПП = '164301001'))
     GROUP BY  ul2_.ИНН ) AS ls_
  WHERE ul1_.ИНН IN (ls_.inn_)
    AND ul1_.ОГРН NOT IN 
      (SELECT vs1_.ОГРН
       FROM видзап vs1_
       WHERE vs1_.ОГРН IN 
         (SELECT ОГРН FROM свюл WHERE ИНН IN (ls_.inn_))
         AND  vs1_.КодСПВЗ IN (SELECT код FROM ЛиквидКоды))
  GROUP BY ul1_.ОГРН);

id select_type table      type        possible_keys               key             key_len ref                rows     filtered Extra
1  PRIMARY     ul_        index       NULL                        Key_inn         43      NULL               10453894 100.00   Using where; Using index
2  SUBQUERY    <derived3> ALL         NULL                        NULL            NULL    NULL               2        100.00   Using where
2  SUBQUERY    ul1_       ref         PRIMARY,Key_inn,key_inn_kpp key_inn_kpp     43      ls_.inn_           1        100.00   Using index
2  SUBQUERY    свюл       eq_ref      PRIMARY,Key_inn,key_inn_kpp PRIMARY         8       egrul.ul1_.ОГРН    1        100.00   Using where; Not exists
2  SUBQUERY    vs1_       ref         Index2                      Index2          8       egrul.ul1_.ОГРН    7        100.00   NULL
2  SUBQUERY    ЛиквидКоды ref         Индекс 1                    Индекс 1        4       egrul.vs1_.КодСПВЗ 1        100.00   Using where; Using index
3  DERIVED     ul2_       index_merge PRIMARY,Key_inn,key_inn_kpp PRIMARY,Key_inn 8,43    NULL               2        100.00   Using union(PRIMARY,Key_inn); Using where; Using temporary