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Representative pubchem structure

Error in enumerating valence parameter

Missing SMARTS and probable solution

https://pubchem.ncbi.nlm.nih.gov/compound/6433205#section=2D-Structure

Code Block

Proper torsion assignment failed for  [H:7][C:1]([H:8])([H:9])[N+:2](=[N:3][C:4]([H:10])([H:11])[O:5][H:12])[O-:6]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (2, 1, 0, 6): names and elements ( N), ( N), ( C), ( H), 
- Topology indices (2, 1, 0, 7): names and elements ( N), ( N), ( C), ( H), 
- Topology indices (2, 1, 0, 8): names and elements ( N), ( N), ( C), ( H),

Specific smarts: [#7X2:1]=[#7X3+1:2]-[#6X4:3]-[*:4].

One solution can be to make

t51: [*:1]-[#6X4:2]-[#7X3:3]-[*:4]" more general by

t51_edit: [*:1]~[#6X4:2]-[#7X3:3]~[*:4]"

(opls can parameterize)

https://pubchem.ncbi.nlm.nih.gov/compound/67166915

Code Block

Angle assignment failed for  [H:34][c:13]1[c:12]([c:11]([c:10]([c:15]([c:14]1[H:35])[H:36])[P:8](=[O:9])([N+:16](=[O:17])[O-:18])[O:7][C:6]([H:30])([H:31])[C:5]([H:28])([H:29])[N+:2]([C:1]([H:19])([H:20])[H:21])([C:3]([H:22])([H:23])[H:24])[C:4]([H:25])([H:26])[H:27])[H:32])[H:33]
AngleHandler was not able to find parameters for the following valence terms:

- Topology indices (7, 15, 16): names and elements ( P), ( N), ( O),

Specific smarts:[#8X1:1]=[#7X3+1:2]-[#15X4:3].

a18 is "[*:1]-[#7X4,#7X3,#7X2-1:2]-[*:3]" , can make it more general "[*:1]~[#7X4,#7X3,#7X2-1:2]~[*:3]"

(even opls doesn’t have)

https://pubchem.ncbi.nlm.nih.gov/compound/118984389#section=2D-Structure

Code Block

Proper torsion assignment failed for  [H:26][C:10](=[C:9](/[C:8](=[N:7]/[N+:4]([C:5]([H:20])([H:21])[H:22])([C:6]([H:23])([H:24])[H:25])[C:3]([H:18])([H:19])[C:2]([H:17])([C:1]([H:14])([H:15])[H:16])[O:13][H:31])/[O-:12])[C:11]([H:28])([H:29])[H:30])[H:27]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (4, 3, 6, 7): names and elements ( C), ( N), ( N), ( C), 
- Topology indices (5, 3, 6, 7): names and elements ( C), ( N), ( N), ( C), 
- Topology indices (2, 3, 6, 7): names and elements ( C), ( N), ( N), ( C),

Specific smarts pattern: [#6:1]~[#7X2:2]-[#7X4+1:3]~[#6:4].

Making t138: "[*:1]~[#7X2:2]-[#7X3:3]~[*:4]" to include #7X4 as well in the third position, "[*:1]~[#7X2:2]-[#7X3,#7X4:3]~[*:4]", can be a general solution, but that would be mixing multiplicities, so a new parameter can be t138a: "[*:1]~[#7X2:2]-[#7X4:3]~[*:4]"

(opls can parameterize)

https://pubchem.ncbi.nlm.nih.gov/compound/104806#section=2D-Structure

Code Block
Bond assignment failed for [N:1](=[O:2])[O:3][O-:4] BondHandler was not able to find parameters for the following valence terms: - Topology indices (2, 3): names and elements ( O), ( O),

Specific smarts pattern: "[#8X2:1]-[#8X1-1:2]".

The bond parameter b43: "[#8X2:1]-[#8X2:2]" can be made more general by making it "[#8X2:1]-[#8X2,#8X1-1:2]"

(even opls doesn’t have)

Only a simple molecule can be found on pubchem matching the [N]-[S-1] pattern, https://pubchem.ncbi.nlm.nih.gov/compound/19977646

Example from the torsion set is below and the corresponding error is in the right column

Code Block
UnassignedBondParameterException: BondHandler was not able to find parameters for the following valence terms: - Topology indices (3, 6): names and elements ( N), ( S),

Specific smarts pattern is [#16X1-1:1]-[#7X3:2].

Can be resolved by modifying b53: "[#16X2:1]-[#7:2]" to a more general "[#16X2,#16X1-1:1]-[#7:2]".

(even opls doesn’t have)

https://pubchem.ncbi.nlm.nih.gov/compound/135436526#section=IUPAC-Name

Code Block

Proper torsion assignment failed for  [H:11][C:1]([H:12])([H:13])[N:2]([C:3](=[N:4][H:14])[N:5]([H:15])[N+:6](=[O:7])[O-:8])[N:9]=[O:10]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (2, 4, 5, 6): names and elements ( C), ( N), ( N), ( O), 
- Topology indices (6, 5, 4, 14): names and elements ( O), ( N), ( N), ( H),

Specific smarts pattern is "[*:1]-[#7X3:2]-[#7X3+1:3]-[*:4]".

Can be resolved by making t130 : "[*:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[*:4]" more general by making the single bonds flexible, "[*:1]~[#7X4,#7X3:2]-[#7X4,#7X3:3]~[*:4]".

(opls can parameterize)

Image Added

Larger molecule with this substructure found in ChemBL30

Code Block

Proper torsion assignment failed for  c1ccccc1S(F)(F)(F)(F)(F)
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (4, 5, 6, 9): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (0, 5, 6, 11): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (0, 5, 6, 8): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (0, 5, 6, 7): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (4, 5, 6, 8): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (0, 5, 6, 10): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (4, 5, 6, 11): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (4, 5, 6, 7): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (0, 5, 6, 9): names and elements ( C), ( C), ( S), ( F), 
- Topology indices (4, 5, 6, 10): names and elements ( C), ( C), ( S), ( F),

No general torsion term for [#6X3]-[#16] central bond. It’s always either #16{X1-1, X2, X3, X3+1 X4] or [#6X3]=[#16]. Can be a new generic parameter before t107.

Image Added

Found on CheMBL30 (CHEMBL1982357)

Code Block

Proper torsion assignment failed for  [CH3:1][P:2](=[S:3])([CH3:4])[P:5](=[S:6])([CH3:7])[CH3:8]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (3, 1, 4, 5): names and elements ( C), ( P), ( P), ( S), 
- Topology indices (0, 1, 4, 5): names and elements ( C), ( P), ( P), ( S), 
- Topology indices (3, 1, 4, 7): names and elements ( C), ( P), ( P), ( C), 
- Topology indices (0, 1, 4, 7): names and elements ( C), ( P), ( P), ( C), 
- Topology indices (2, 1, 4, 7): names and elements ( S), ( P), ( P), ( C), 
- Topology indices (2, 1, 4, 6): names and elements ( S), ( P), ( P), ( C), 
- Topology indices (3, 1, 4, 6): names and elements ( C), ( P), ( P), ( C), 
- Topology indices (0, 1, 4, 6): names and elements ( C), ( P), ( P), ( C), 
- Topology indices (2, 1, 4, 5): names and elements ( S), ( P), ( P), ( S),

May need a P-P central bond generic torsion

Image Added

Found on CheMBL30 (CHEMBL331810)

Image Added

Code Block

Proper torsion assignment failed for  [H:12][c:1]1[c:2]([c:3]([c:4]2[c:5]([c:6]1[H:15])[C:7](=[O:8])[O:9][I:10]2[O:11][H:16])[H:14])[H:13]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (4, 11, 10, 8): names and elements ( C), ( I), ( O), ( C), 
- Topology indices (10, 11, 12, 13): names and elements ( O), ( I), ( O), ( H), 
- Topology indices (5, 4, 11, 10): names and elements ( C), ( C), ( I), ( O), 
- Topology indices (3, 4, 11, 12): names and elements ( C), ( C), ( I), ( O), 
- Topology indices (3, 4, 11, 10): names and elements ( C), ( C), ( I), ( O), 
- Topology indices (4, 11, 12, 13): names and elements ( C), ( I), ( O), ( H), 
- Topology indices (5, 4, 11, 12): names and elements ( C), ( C), ( I), ( O), 
- Topology indices (8, 10, 11, 12): names and elements ( C), ( O), ( I), ( O),

Code Block

Proper torsion assignment failed for  [H:14][c:3]1[c:4]([c:5]([c:6]([c:7]([c:2]1[C:1]([H:11])([H:12])[H:13])[H:17])[H:16])[I:8](=[O:9])=[O:10])[H:15]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (4, 3, 13, 14): names and elements ( C), ( C), ( I), ( O), 
- Topology indices (4, 3, 13, 15): names and elements ( C), ( C), ( I), ( O), 
- Topology indices (2, 3, 13, 14): names and elements ( C), ( C), ( I), ( O), 
- Topology indices (2, 3, 13, 15): names and elements ( C), ( C), ( I), ( O),

Image Added

In conjunction with a nitro salt at CHEMBL3391852

Code Block

Proper torsion assignment failed for  [H:21][c:4]1[c:5]([c:6]([c:7]([c:8]([c:3]1[O:2][C:1]([H:18])([H:19])[H:20])[H:24])[H:23])[I+:9][c:10]2[c:11]([c:12]([c:13]([c:14]([c:15]2[H:28])[H:27])[O:16][C:17]([H:29])([H:30])[H:31])[H:26])[H:25])[H:22]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (3, 14, 15, 16): names and elements ( C), ( I), ( C), ( C), 
- Topology indices (2, 3, 14, 15): names and elements ( C), ( C), ( I), ( C), 
- Topology indices (4, 3, 14, 15): names and elements ( C), ( C), ( I), ( C), 
- Topology indices (3, 14, 15, 20): names and elements ( C), ( I), ( C), ( C),

Image Added

Found on CheMBL30

Image Added

Code Block

Proper torsion assignment failed for  [H:19][C:7]1=[N:6][P:4](=[O:5])([O:3][C:2]([C:1]1([H:15])[H:16])([H:17])[H:18])[N:8]([C:9]([H:20])([H:21])[C:10]([H:22])([H:23])[Cl:11])[C:12]([H:24])([H:25])[C:13]([H:26])([H:27])[Cl:14]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (1, 2, 3, 4): names and elements ( C), ( N), ( P), ( O), 
- Topology indices (1, 2, 3, 5): names and elements ( C), ( N), ( P), ( O), 
- Topology indices (1, 2, 3, 12): names and elements ( C), ( N), ( P), ( N),

Code Block

Proper torsion assignment failed for  [N:1]1=[P:2]([N:3]=[P:4]([N:5]=[P:6]1([Cl:7])[Cl:8])([Cl:9])[Cl:10])([Cl:11])[Cl:12]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (1, 0, 5, 6): names and elements ( P), ( N), ( P), ( Cl), 
- Topology indices (5, 4, 3, 9): names and elements ( P), ( N), ( P), ( Cl), 
- Topology indices (0, 1, 2, 3): names and elements ( N), ( P), ( N), ( P), 
- Topology indices (1, 0, 5, 7): names and elements ( P), ( N), ( P), ( Cl), 
- Topology indices (1, 0, 5, 4): names and elements ( P), ( N), ( P), ( N), 
- Topology indices (2, 3, 4, 5): names and elements ( N), ( P), ( N), ( P), 
- Topology indices (5, 4, 3, 8): names and elements ( P), ( N), ( P), ( Cl), 
- Topology indices (3, 2, 1, 11): names and elements ( P), ( N), ( P), ( Cl), 
- Topology indices (3, 2, 1, 10): names and elements ( P), ( N), ( P), ( Cl),

Image Added

Representative substructure of a larger molecule (along with a salt) found on CheMBL30

Code Block

Proper torsion assignment failed for  [CH3:25][C@@H:16]1[C@H:18]([CH2:9][CH2:11][CH2:13][O:15]1)[O:20][SH+:21]([OH:22])([OH:23])[O-:24]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (23, 10, 12, 25): names and elements ( H), ( S), ( O), ( H), 
- Topology indices (3, 9, 10, 11): names and elements ( C), ( O), ( S), ( O), 
- Topology indices (11, 10, 12, 25): names and elements ( O), ( S), ( O), ( H), 
- Topology indices (9, 10, 12, 25): names and elements ( O), ( S), ( O), ( H), 
- Topology indices (3, 9, 10, 23): names and elements ( C), ( O), ( S), ( H), 
- Topology indices (13, 10, 11, 24): names and elements ( O), ( S), ( O), ( H), 
- Topology indices (3, 9, 10, 13): names and elements ( C), ( O), ( S), ( O), 
- Topology indices (23, 10, 11, 24): names and elements ( H), ( S), ( O), ( H), 
- Topology indices (9, 10, 11, 24): names and elements ( O), ( S), ( O), ( H), 
- Topology indices (13, 10, 12, 25): names and elements ( O), ( S), ( O), ( H), 
- Topology indices (3, 9, 10, 12): names and elements ( C), ( O), ( S), ( O), 
- Topology indices (12, 10, 11, 24): names and elements ( O), ( S), ( O), ( H),

There are some occurrences of [S+] in conjunction with salts.

Image Added

Representative substructure of a larger molecule found on CheMBL30

Code Block

Proper torsion assignment failed for  CC=[P](C)(C)(C)
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (4, 2, 1, 9): names and elements ( C), ( P), ( C), ( H), 
- Topology indices (3, 2, 1, 9): names and elements ( C), ( P), ( C), ( H), 
- Topology indices (0, 1, 2, 4): names and elements ( C), ( C), ( P), ( C), 
- Topology indices (0, 1, 2, 3): names and elements ( C), ( C), ( P), ( C), 
- Topology indices (5, 2, 1, 9): names and elements ( C), ( P), ( C), ( H), 
- Topology indices (0, 1, 2, 5): names and elements ( C), ( C), ( P), ( C),

This is weird since the double bond is perceived as rotatable bond, might be a backend issue.

Image Added

Code Block

Proper torsion assignment failed for  [CH:8](=[C:9]([O-:12])[O+:10]=[NH:11])[NH2:7]
ProperTorsionHandler was not able to find parameters for the following valence terms:

- Topology indices (1, 3, 4, 7): names and elements ( C), ( O), ( N), ( H),

Again double bond is perceived as rotatable bond.

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