Date: Fri, 24 Apr 2020 15:56:37 +0200
Hello,
below is a view of a structure after minimization (without NMR
restraints) (attached or see
https://drive.google.com/open?id=15hhtEI30I5T9Xp_p56Answ-nQWfX5Xh- ).
Clearly the N10 amide nitrogen
has an pyramidal character. And the omega dihedral angles are not good
The molecule was prepared as a mol2 file Nitrogen are N.am see below
I tried to create the non natural amino acid
Then
antechamber -i testsirius4.mol2 -fi mol2 -o ./prep/testsirius4.prepin
-fo prepi -c bcc -s 2 -nc 4 > ./prep/antechamber.out
Using the same way I tried with a structure of polymixin B solved with
CYANA and load as a mol2 file. Again some nitrogen atoms are pyramidal
Something is wrong but where?
Man thanks by advance for any suggestion
arnaud
92 N10 18.9273 -4.2156 -6.9272 N.am 1 UNK -0.3001
93 C28 19.2161 -4.9020 -5.6192 C.3 1 UNK 0.1305
94 C29 18.4539 -6.2190 -5.3899 C.2 1 UNK 0.2362
95 O7 17.3090 -6.3837 -5.7791 O.2 1 UNK -0.2737
96 C30 18.9294 -3.9948 -4.3811 C.3 1 UNK 0.1213
97 O8 17.5154 -3.7707 -4.2774 O.3 1 UNK -0.3842
98 C31 19.6691 -2.6414 -4.3199 C.3 1 UNK -0.0065
99 HN1 17.9521 -4.0328 -7.1379 H 1 UNK 0.1496
100 H28 20.2733 -5.1804 -5.6025 H 1 UNK 0.0623
101 H30 19.2454 -4.5518 -3.4937 H 1 UNK 0.0671
102 HO8 17.1331 -3.5231 -5.1721 H 1 UNK 0.2101
103 H311 20.7523 -2.7678 -4.2499 H 1 UNK 0.0839
104 H312 19.4179 -2.0212 -5.1828 H 1 UNK 0.0839
105 N11 19.1881 -1.9186 -3.0881 N.4 1 UNK 0.2204
106 HN11 19.4727 -2.3707 -2.1941 H 1 UNK 0.1995
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(image/png attachment: NamidePyr.png)
