Query - Is there a system behind the numbering of trains?
Or, what do the 5 digits in a train number mean?
Answer - On December 20, 2010, IR switched to a system of 5-digit numbers that are supposed to be used for all passenger trains across its system.
The first digit
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the 5-digit train numbering scheme, the first digit indicates the type of the passenger train, as follows:

0 is for special trains (e.g., summer specials, holiday specials, etc.)
1 is for all long-distance trains, including the Rajdhani, Shatabdi, Jan Sadharan, Sampark Kranti, Garib Rath, Duronto, and other classes.
2 is also for long-distance trains; it is to be used when train numbers starting with 1 are exhausted in any series.
3 is for Kolkata suburban trains.
4 is for suburban trains in Chennai, New Delhi, Secunderabad, and other metropolitan areas.
5 is for passenger trains with conventional coaches
6 is for MEMU trains
7 is for DMU (DEMU) and railcar services.
8 is currently reserved
9 is for Mumbai area suburban trains

Second and later digits
The significance of the second and later digits depends on what the first digit is. Below, the different number series are explained, based on the first digit.
0, 1, 2: In the case of special trains, and long-distance express trains, i.e., trains starting with digits '0', '1', or '2', the remaining 4 digits signify the railway zone and division exactly as in the pre-2011 4-digit scheme. In fact, most 5-digit numbers for long-distance trains as of this writing [4/11] are created simply by prefixing '1' to the former 4-digit codes.

0 is for Konkan Railway
1 is for CR, WCR and NCR(?)
2 is for superfasts, Shatabdi, Jan Shatabdi, and some other classes of trains regardless of zones. For these, the next digit is usually the zone code.
3 is shared by ER and ECR
4 is for NR, NCR and NWR
5 is shared by NER and NFR
6 is for SR and SWR
7 is shared by SCR and SWR
8 is for SER and ECoR
9 is for WR, NWR and WCR

For other classes of trains, the remaining digits are used in a few different ways.
3: For Kolkata suburban trains starting with digit '3', there are two sets of numbers, depending on the zone that operates the services.
30xxx through 37xxx : trains run by ER
38xxx through 39xxx : trains run by SER
4: For suburban trains other than in Mumbai and Kolkata, the following conventions apply.
40xxx through 44xxx : Chennai area suburban trains
45xxx through 46xxx : Delhi area suburban trains
47xxx : Secunderabad suburban trains
48xxx through 49xxx : reserved
5, 6, 7: For trains starting with '5', '6', and '7', i.e., passenger trains, the second digit determines the zone as for long-distance trains and the third digit determines the division

9: Mumbai suburban trains use the following system. Up and down directions are generally reflected in the use of odd and even numbers, respectively.
90xxx: WR locals originating from Virar
91xxx: WR locals originating from Vasai Road / Bhayander
92xxx: WR locals originating from Borivali
93xxx: WR locals originating from Malad / Goregaon
94xxx: WR locals originating from Andheri / Bandra / Mumbai Central
95xxx: CR fast locals
96xxx: CR locals going north of Kalyan
97xxx: CR locals on the Harbour line
98xxx: CR locals on the trans-Harbour line
99xxx: CR locals going south of Kalyan