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ener_lib: fix for sp2 nitrogen#64

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keitaroyam merged 4 commits intomasterfrom
fix-enerlib-n
Aug 5, 2025
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ener_lib: fix for sp2 nitrogen#64
keitaroyam merged 4 commits intomasterfrom
fix-enerlib-n

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@keitaroyam keitaroyam commented Jul 16, 2025

Explanations were added for NR55/NR56/NR66. Now here is the list of sp2 nitrogen atom types:

#HEADER        N Nitrogen SP2
#ATOMTYPE NC1  = connected to 1 hyd. in a charged group ( NE of ARG )
#ATOMTYPE NC2  = connected to 2 hyd. in a charged group ( NH2 of ARG )
#ATOMTYPE NH0  = connected to 0 hydrogen
#ATOMTYPE NH1  = connected to 1 hydrogen ( N of main chain )
#ATOMTYPE NH2  = connected to 2 hydrogen ( NE2 of GLU )
#ATOMTYPE NPA  = without hydrogen ( NA and NC of HEME )
#ATOMTYPE NPB  = without hydrogen ( NB and ND of HEME )
#ATOMTYPE NRD5 = without hydrogen but with electronic doublet in 5 atoms ring
#ATOMTYPE NRD6 = without hydrogen but with electronic doublet in 6 atoms ring 
#ATOMTYPE NR15 = connected to 1 hyd. in 5 atoms ring ( ND1 of HIS )
#ATOMTYPE NR16 = connected to 1 hyd. in 6  atoms ring 
#ATOMTYPE NR5  = connected to 3 non-hydrogen atoms in 5 atoms ring
#ATOMTYPE NR55 = between two atoms in 5-5 rings
#ATOMTYPE NR56 = between two atoms in 5-6 rings
#ATOMTYPE NR6  = connected to 3 non-hydrogen atoms in 6 atoms ring
#ATOMTYPE NR66 = between two atoms in 6-6 rings

And the hb_type was changed to N (neither) for NR5/NR6/NR55/NR56. Examples are

  • NR5: N8 of ZPA
  • NR6: N5 of 4IG
  • NR55: N17 of UEF
  • NR56: NAR of OF8

The current monomer library has a problem of nitrogen atom types and they need to be updated.

@keitaroyam
ener_lib: fix for nitrogen
6c86e6e 
hb_types and missing explanations
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GaribMurshudov commented Jul 16, 2025 •
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N8 of ZPA should be NH0
N5 of 4IG should be NH0
N17 of UEF should be NR55 (it is correct, NR55 should be made N for HB)
NAR of OF8 should be NR56 (it is correct, NR56 should be made N for HB)

We should correct ener_lib and add some more.

@flong-mrc I think acedrg should be adjusted also

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keitaroyam commented Jul 24, 2025

I see these NR* types are for aromatic atoms, while it's not documented. We would need only five types for sp2 nitrogen (N20 and N21 are the new addition, and we can make all others obsolete). Please review the updated file. I believe Fei has already updated Acedrg (not committed yet) to support these types.

#HEADER        N Nitrogen SP2
## N with three bonds
#ATOMTYPE NH0  = connected to 0 hydrogen
#ATOMTYPE NH1  = connected to 1 hydrogen ( N of main chain )
#ATOMTYPE NH2  = connected to 2 hydrogen ( NE2 of GLU )
## N with two bonds
#ATOMTYPE N20  = connected to 0 hydrogen
#ATOMTYPE N21  = connected to 1 hydrogen

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GaribMurshudov commented Aug 5, 2025

Just for records: HB type of N21 (sp2 N with two bonds attached to one hydrogen atoms) should be B (both acceptor and donor)

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keitaroyam commented Aug 5, 2025

Corrected!

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GaribMurshudov reviewed Aug 5, 2025
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I think it looks fine now

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keitaroyam commented Aug 5, 2025

Could you approve this?

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GaribMurshudov commented Aug 5, 2025

Done ( I think)

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GaribMurshudov approved these changes Aug 5, 2025
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It looks fine to me now.

@keitaroyam keitaroyam merged commit 24f62e3 into master Aug 5, 2025
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@keitaroyam keitaroyam deleted the fix-enerlib-n branch August 5, 2025 23:29
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