- [x] I believe this to be a bug with Meeko resulting from OpenBabel issue #2433. I report it here because Meeko has the same error.
Environment Information
Operating system and version: Centos 7.4
Expected Behavior
Example 1. C1(NC2=NC(C3=CN=CC=C3)=CC=N2)=CC=CC=C1
As for example 1 molecule, obabel give a PDBQT file with 2 rotatable bond instead of 3. The correct one looks like as following:
REMARK Name = EX1
REMARK 3 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: _1 and _2
REMARK 2 A between atoms: _2 and _3
REMARK 3 A between atoms: _5 and _6
ROOT
ATOM 1 C1 UNL 1 3.354 0.587 0.763 0.00 0.00 0.041 A
ATOM 15 C11 UNL 1 4.730 0.740 0.977 0.00 0.00 -0.039 A
ATOM 16 C12 UNL 1 5.237 1.885 1.596 0.00 0.00 -0.060 A
ATOM 17 C13 UNL 1 4.371 2.898 1.998 0.00 0.00 -0.062 A
ATOM 18 C14 UNL 1 3.003 2.773 1.764 0.00 0.00 -0.060 A
ATOM 19 C15 UNL 1 2.501 1.632 1.133 0.00 0.00 -0.039 A
ENDROOT
BRANCH 1 2
ATOM 2 N1 UNL 1 2.812 -0.545 0.129 0.00 0.00 -0.324 N
ATOM 20 H1 UNL 1 2.532 -0.383 -0.830 0.00 0.00 0.170 HD
BRANCH 2 3
ATOM 3 C2 UNL 1 3.296 -1.851 0.224 0.00 0.00 0.227 A
ATOM 4 N2 UNL 1 3.942 -2.233 1.334 0.00 0.00 -0.213 NA
ATOM 5 C3 UNL 1 4.393 -3.501 1.427 0.00 0.00 0.077 A
ATOM 12 C9 UNL 1 4.180 -4.407 0.410 0.00 0.00 -0.017 A
ATOM 13 C10 UNL 1 3.504 -3.933 -0.691 0.00 0.00 0.033 A
ATOM 14 N4 UNL 1 3.060 -2.669 -0.809 0.00 0.00 -0.221 NA
BRANCH 5 6
ATOM 6 C4 UNL 1 5.110 -3.815 2.675 0.00 0.00 0.019 A
ATOM 7 C5 UNL 1 6.100 -4.795 2.757 0.00 0.00 0.036 A
ATOM 8 N3 UNL 1 6.792 -5.119 3.879 0.00 0.00 -0.264 NA
ATOM 9 C6 UNL 1 6.496 -4.421 4.994 0.00 0.00 0.027 A
ATOM 10 C7 UNL 1 5.546 -3.417 5.038 0.00 0.00 -0.043 A
ATOM 11 C8 UNL 1 4.853 -3.116 3.866 0.00 0.00 -0.050 A
ENDBRANCH 5 6
ENDBRANCH 2 3
ENDBRANCH 1 2
TORSDOF 3
Actual Behavior
The torsions in PDBQT file did not include bond C_2-N_3. This will result in docking failure. Let me show you an redocking failure: openbabel_2433
Steps to Reproduce
(base) [[email protected] demo]$ cat ex1.smi C1(NC2=NC(C3=CN=CC=C3)=CC=N2)=CC=CC=C1 EX01 (base) [[email protected] demo]$ obabel -ismi ex1.smi -opdbqt --gen3d --best REMARK Name = EX01 REMARK 2 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: C_1 and N_2 REMARK 2 A between atoms: C_5 and C_6 REMARK x y z vdW Elec q Type REMARK _______ _______ _______ _____ _____ ______ ____ ROOT ATOM 1 N UNL 1 2.812 -0.545 0.128 0.00 0.00 +0.000 N ATOM 2 C UNL 1 3.296 -1.851 0.224 0.00 0.00 +0.000 A ATOM 3 N UNL 1 3.942 -2.233 1.334 0.00 0.00 +0.000 NA ATOM 4 C UNL 1 4.393 -3.501 1.427 0.00 0.00 +0.000 A ATOM 5 C UNL 1 4.180 -4.407 0.410 0.00 0.00 +0.000 A ATOM 6 C UNL 1 3.504 -3.932 -0.691 0.00 0.00 +0.000 A ATOM 7 N UNL 1 3.060 -2.669 -0.809 0.00 0.00 +0.000 NA ATOM 8 H UNL 1 2.532 -0.383 -0.830 0.00 0.00 +0.000 HD ENDROOT BRANCH 1 9 ATOM 9 C UNL 1 3.354 0.587 0.763 0.00 0.00 +0.000 A ATOM 10 C UNL 1 4.730 0.740 0.977 0.00 0.00 +0.000 A ATOM 11 C UNL 1 5.237 1.885 1.596 0.00 0.00 +0.000 A ATOM 12 C UNL 1 4.371 2.898 1.998 0.00 0.00 +0.000 A ATOM 13 C UNL 1 3.003 2.773 1.765 0.00 0.00 +0.000 A ATOM 14 C UNL 1 2.501 1.632 1.133 0.00 0.00 +0.000 A ENDBRANCH 1 9 BRANCH 4 15 ATOM 15 C UNL 1 5.110 -3.815 2.675 0.00 0.00 +0.000 A ATOM 16 C UNL 1 6.100 -4.795 2.757 0.00 0.00 +0.000 A ATOM 17 N UNL 1 6.791 -5.119 3.879 0.00 0.00 +0.000 NA ATOM 18 C UNL 1 6.496 -4.421 4.994 0.00 0.00 +0.000 A ATOM 19 C UNL 1 5.546 -3.417 5.038 0.00 0.00 +0.000 A ATOM 20 C UNL 1 4.853 -3.116 3.867 0.00 0.00 +0.000 A ENDBRANCH 4 15 TORSDOF 2
Read more here: Source link
