From 6c86e6ed3a47064fe257f17c08972f31214584a6 Mon Sep 17 00:00:00 2001 From: Keitaro Yamashita Date: Tue, 15 Jul 2025 17:40:02 +0100 Subject: [PATCH 1/4] ener_lib: fix for nitrogen hb_types and missing explanations --- ener_lib.cif | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/ener_lib.cif b/ener_lib.cif index 0b157c373..1fc44eb93 100644 --- a/ener_lib.cif +++ b/ener_lib.cif @@ -64,7 +64,10 @@ data_energy #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 #HEADER N Nitrogen SP3 # N with four bonds #ATOMTYPE N = without hydrogen @@ -183,12 +186,12 @@ _lib_atom.sp N33 14.00670 B 1.550 1.600 1.32 N 3 3 NPA 14.00670 A 1.550 1.600 1.32 N 3 2 NPB 14.00670 A 1.550 1.600 1.32 N 3 2 - NR5 14.00670 A 1.550 1.600 1.32 N 3 2 + NR5 14.00670 N 1.550 1.600 1.32 N 3 2 NR15 14.00670 D 1.550 1.600 1.32 N 3 2 NRD5 14.00670 A 1.550 1.600 1.32 N 3 2 - NR56 14.00670 A 1.550 1.600 1.32 N 3 2 - NR55 14.00670 A 1.550 1.600 1.32 N 3 2 - NR6 14.00670 A 1.550 1.600 1.32 N 3 2 + NR56 14.00670 N 1.550 1.600 1.32 N 3 2 + NR55 14.00670 N 1.550 1.600 1.32 N 3 2 + NR6 14.00670 N 1.550 1.600 1.32 N 3 2 NR66 14.00670 N 1.550 1.600 1.32 N 3 2 NR16 14.00670 D 1.550 1.600 1.32 N 3 2 NRD6 14.00670 A 1.550 1.600 1.32 N 3 2 From 93c37d78e7a8af7d866960ff018f1e81aeb47e4d Mon Sep 17 00:00:00 2001 From: Keitaro Yamashita Date: Thu, 24 Jul 2025 11:03:59 +0100 Subject: [PATCH 2/4] new types --- ener_lib.cif | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/ener_lib.cif b/ener_lib.cif index 1fc44eb93..8734e584e 100644 --- a/ener_lib.cif +++ b/ener_lib.cif @@ -52,11 +52,16 @@ data_energy #ATOMTYPE NS = without hydrogen ( triple bond ) = NSP #ATOMTYPE NS1 = connected to 1 hydrogen = NSP1 #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 ) +## 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 +## OBSOLETE +#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 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 @@ -168,13 +173,15 @@ _lib_atom.sp NSP 14.00670 A 1.550 1.600 1.32 N 3 1 NS1 14.00670 D 1.550 1.600 1.32 N 3 1 NSP1 14.00670 D 1.550 1.600 1.32 N 3 1 - N 14.00670 B 1.550 1.600 1.32 N 3 2 + N 14.00670 N 1.550 1.600 1.32 N 3 2 NC1 14.00670 D 1.550 1.600 1.32 N 3 2 NH0 14.00670 N 1.550 1.600 1.32 N 3 2 NH1 14.00670 D 1.550 1.600 1.32 N 3 2 NC2 14.00670 D 1.550 1.600 1.32 N 3 2 NH2 14.00670 D 1.550 1.600 1.32 N 3 2 NC3 14.00670 D 1.550 1.600 1.32 N 3 2 + N20 14.00670 A 1.550 1.600 1.32 N 3 2 + N21 14.00670 D 1.550 1.600 1.32 N 3 2 NT 14.00670 N 1.550 1.600 1.32 N 3 3 NT1 14.00670 D 1.550 1.600 1.32 N 3 3 NT2 14.00670 D 1.550 1.600 1.32 N 3 3 @@ -186,12 +193,12 @@ _lib_atom.sp N33 14.00670 B 1.550 1.600 1.32 N 3 3 NPA 14.00670 A 1.550 1.600 1.32 N 3 2 NPB 14.00670 A 1.550 1.600 1.32 N 3 2 - NR5 14.00670 N 1.550 1.600 1.32 N 3 2 + NR5 14.00670 A 1.550 1.600 1.32 N 3 2 NR15 14.00670 D 1.550 1.600 1.32 N 3 2 NRD5 14.00670 A 1.550 1.600 1.32 N 3 2 NR56 14.00670 N 1.550 1.600 1.32 N 3 2 NR55 14.00670 N 1.550 1.600 1.32 N 3 2 - NR6 14.00670 N 1.550 1.600 1.32 N 3 2 + NR6 14.00670 A 1.550 1.600 1.32 N 3 2 NR66 14.00670 N 1.550 1.600 1.32 N 3 2 NR16 14.00670 D 1.550 1.600 1.32 N 3 2 NRD6 14.00670 A 1.550 1.600 1.32 N 3 2 From 0cec187e4452848c71c5627f31ff493200afcd1d Mon Sep 17 00:00:00 2001 From: keitaroyam Date: Tue, 5 Aug 2025 22:04:23 +0900 Subject: [PATCH 3/4] HB type of N21 (sp2 N with two bonds attached to one hydrogen atoms) should be B --- ener_lib.cif | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ener_lib.cif b/ener_lib.cif index 8734e584e..6a93b3c02 100644 --- a/ener_lib.cif +++ b/ener_lib.cif @@ -181,7 +181,7 @@ _lib_atom.sp NH2 14.00670 D 1.550 1.600 1.32 N 3 2 NC3 14.00670 D 1.550 1.600 1.32 N 3 2 N20 14.00670 A 1.550 1.600 1.32 N 3 2 - N21 14.00670 D 1.550 1.600 1.32 N 3 2 + N21 14.00670 B 1.550 1.600 1.32 N 3 2 NT 14.00670 N 1.550 1.600 1.32 N 3 3 NT1 14.00670 D 1.550 1.600 1.32 N 3 3 NT2 14.00670 D 1.550 1.600 1.32 N 3 3 @@ -2856,3 +2856,4 @@ _lib_hbond.dist HOH2 HNH1 0.000 0.000 HOH2 HOH1 0.000 0.000 # ----------------------------------------------------------------------- + From c5d0d1d2f87831c8e0c6ec0dbf80f8c6f1a75adf Mon Sep 17 00:00:00 2001 From: keitaroyam Date: Wed, 6 Aug 2025 08:24:16 +0900 Subject: [PATCH 4/4] newline accidentally inserted --- ener_lib.cif | 1 - 1 file changed, 1 deletion(-) diff --git a/ener_lib.cif b/ener_lib.cif index 6a93b3c02..dea7c7f28 100644 --- a/ener_lib.cif +++ b/ener_lib.cif @@ -2856,4 +2856,3 @@ _lib_hbond.dist HOH2 HNH1 0.000 0.000 HOH2 HOH1 0.000 0.000 # ----------------------------------------------------------------------- -