하고 있었다, 있었다, 없었다
Now, I’m pretty good at Korean and I understand a lot, but when natives say “하고 있었다”, “있었다”, or “없었다” it really throws me off.
I can understand the meaning of 있었다 and 없었다:
펜이 있었다 — There was a pen / 펜이 없었다 - There wasn’t a pen (but we now have a pen)
But, it just throws me off.
Could you guys give me examples with 있었다 and 없었다?
And then, 하고 있었다
Is it like “I was doing ....”?
Ex. 그림을 그리고 있었어 - I was drawing a picture
Please explain the usage of putting 하고 있다 in past tense.

Question

하고 있었다, 있었다, 없었다
Now, I’m pretty good at Korean and I understand a lot, but when natives say “하고 있었다”, “있었다”, or “없었다” it really throws me off. 
I can understand the meaning of 있었다 and 없었다:
펜이 있었다 —> There was a pen / 펜이 없었다 -> There wasn’t a pen (but we now have a pen)
But, it just throws me off.
Could you guys give me examples with 있었다 and 없었다?
And then, 하고 있었다 
Is it like “I was doing ....”?
Ex. 그림을 그리고 있었어 -> I was drawing a picture 
Please explain the usage of putting 하고 있다 in past tense.

Answer

Hmm, it's  just past tense. 있었다 = I had/there existed (something), that I/there may or may not still have/exist. Same with 없었다.
하고 있었다 = was doing something, with emphasis on the time span it occupied more than the action itself (I think). For example 전화가  왔을 때 티비를 보고 있었다. "When I got (lit. there came) a phone call, I was watching TV."

Answer

It’s a hard feeling to explain. I understand it in already written text, but when I’m having a conversation in Korean, the fact that it’s in past tense throws me off.

Answer

있다 has a few different common meanings.

1) there is/exists.  펜이 있다. 펜이 없다. 나 오늘 중요한 일이 있어.  
2) to stay at a place.  나는 여기 있을게 = I will stay here. 가만히 있어 봐 = Be still for a second.  
3) to pass/wait (an amount of) time.  일주일 더 있으면 방학이다 = One more week and it's school break.

And 없다 has the meaning of #1 negated.

So -하고 있다 means "is doing something" and -하고 있었다 "was doing something" as you said.

e.g.
- 그림을 그리고 있었어 = I was/have been painting.
- 나는 티브이를 보고 있었어 = I was watching TV.
- 지금 뭐하고 있어? = What are you doing now?

- 시간이 없다 = There is no time.
- 어떻게도 할 수가 없었어 = I couldn't do anything / There was nothing I could do.
- 외딴 역의 대합실엔 아무도 없었다 = There was no one in the waiting room of a remote station.

Answer

You understand the meaning, but it throws you off? The sounds a little strange to me.

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