![\"dsgdb9nsd_129336\"](\"https://storage.googleapis.com/kaggle-forum-message-attachments/551081/13489/dsgdb9nsd_129336.jpg\")
I have tried to create a model for 3JHH. Current CV score is -0.186. According to the model, the molecule below has the largest error.
\n\ndsgdb9nsd_129336
\n\nIf I see only dihedral angle, y_pred looks not so bad. So, is the low y_true from 5 members ring which has negative charge, right?
\n\n
Sorry my bad. Here is the correct pic.\n![\"dsgdb9nsd_129336\"](\"https://storage.googleapis.com/kaggle-forum-message-attachments/551097/13490/201906123023.jpg\")
Please let me correct if I'm wrong. As the some double bonds are conjugated, this representation is also valid.
\n\n![\"conjugated\"](\"https://storage.googleapis.com/kaggle-forum-message-attachments/551216/13493/201906120409.jpg\")
As a result, the target proton is much more affected by the electron than it looks on my first picture. It would be a challenge to take this kind of complicated interaction into account.
", "rawMarkdown": "Please let me correct if I'm wrong. As the some double bonds are conjugated, this representation is also valid.\n\n\n\nAs a result, the target proton is much more affected by the electron than it looks on my first picture. It would be a challenge to take this kind of complicated interaction into account.", "votes": 2, "replies": [ { "id": 551408, "postDate": "2019-06-12T17:21:38.287Z", "content": "I think you should have used a red pen! ;)
", "rawMarkdown": "I think you should have used a red pen! ;)", "votes": 1 }, { "id": 552950, "postDate": "2019-06-14T21:15:19.170Z", "content": "I would have done this:
\n\nThe ring ain't charged though, but some atoms have partial charges
", "rawMarkdown": "I would have done this:\n\nThe ring ain't charged though, but some atoms have partial charges" }, { "id": 561409, "postDate": "2019-06-26T12:29:16.323Z", "content": "@akirasosa A (likely very unstable) zwitter ion makes sense to me!
", "rawMarkdown": "@akirasosa A (likely very unstable) zwitter ion makes sense to me!" } ] }, { "id": 551081, "postDate": "2019-06-12T10:10:23.887Z", "content": "I have tried to create a model for 3JHH. Current CV score is -0.186. According to the model, the molecule below has the largest error.
\n\ndsgdb9nsd_129336
\n\nIf I see only dihedral angle, y_pred looks not so bad. So, is the low y_true from 5 members ring which has negative charge, right?
\n\n
The neutral structure is inconsistent or faulty. Yes there are a number of tautomers (charge places are different) but the compound below has (C-N-H)[-] on nitrogen #1 an (C=NH2)[+] on nitrogen #8 so the structure is just wrong. The isomers are theoretical isomers from GDB-9, GDB-11, GDB-13, GDB-19 and they were optimized by DFT. Some of them are simply wrong. Its fine to exclude them.
", "rawMarkdown": "The neutral structure is inconsistent or faulty. Yes there are a number of tautomers (charge places are different) but the compound below has (C-N-H)[-] on nitrogen #1 an (C=NH2)[+] on nitrogen #8 so the structure is just wrong. The isomers are theoretical isomers from GDB-9, GDB-11, GDB-13, GDB-19 and they were optimized by DFT. Some of them are simply wrong. Its fine to exclude them. " }, { "id": 551407, "postDate": "2019-06-12T17:20:07.337Z", "content": "May I ask what package you are using to plot the molecule structure? Can you rotate the perspective a little bit?
", "rawMarkdown": "May I ask what package you are using to plot the molecule structure? Can you rotate the perspective a little bit? ", "replies": [ { "id": 551657, "postDate": "2019-06-13T01:47:50.803Z", "content": "I use Jmol. http://jmol.sourceforge.net/\nYou need to convert xyz to mol or mol2 in advance.
", "rawMarkdown": "I use Jmol. http://jmol.sourceforge.net/\nYou need to convert xyz to mol or mol2 in advance.", "votes": 1 }, { "id": 551691, "postDate": "2019-06-13T02:47:32.917Z", "content": "Thanks a lot.
", "rawMarkdown": "Thanks a lot." }, { "id": 553122, "postDate": "2019-06-15T06:15:05.090Z", "content": "@scaomath \n1) avogadro (https://avogadro.cc/docs/getting-started/introduction/)\n2) jmol (http://wiki.jmol.org/index.php/Main_Page)\n3) vmd (http://www.ks.uiuc.edu/Research/vmd/)
\n\nHere is a list of XYZ visualization programs, many of them are easy to use:\nhttp://atomsk.univ-lille1.fr/doc/en/format_xyz.html
", "rawMarkdown": "@scaomath \n1) avogadro (https://avogadro.cc/docs/getting-started/introduction/)\n2) jmol (http://wiki.jmol.org/index.php/Main_Page)\n3) vmd (http://www.ks.uiuc.edu/Research/vmd/)\n\n\nHere is a list of XYZ visualization programs, many of them are easy to use:\nhttp://atomsk.univ-lille1.fr/doc/en/format_xyz.html\n\n" } ] }, { "id": 551106, "postDate": "2019-06-12T10:54:34.677Z", "content": "You're right, it probably has something to do with the double bonds and all the electron doublets on nitrogen/oxygen atoms.
\n\nThe aromatic ring is not negatively charged though, the whole molecule being neutral. However, if you draw it on paper, you'll see that all these electrons can delocalize and it probably explains the low coupling (because the magnetic shielding is high?)
", "rawMarkdown": "You're right, it probably has something to do with the double bonds and all the electron doublets on nitrogen/oxygen atoms. \n\nThe aromatic ring is not negatively charged though, the whole molecule being neutral. However, if you draw it on paper, you'll see that all these electrons can delocalize and it probably explains the low coupling (because the magnetic shielding is high?)", "replies": [ { "id": 551658, "postDate": "2019-06-13T01:50:00.550Z", "content": "@borisdee Thanks, I think the ring is charged because of the NH- on the left edge. But I'm not sure, because it's 15 years ago when I studied chemistry last time. ha ha.
", "rawMarkdown": "@borisdee Thanks, I think the ring is charged because of the NH- on the left edge. But I'm not sure, because it's 15 years ago when I studied chemistry last time. ha ha." } ] }, { "id": 551209, "postDate": "2019-06-12T13:11:41.633Z", "rawMarkdown": "", "isDeleted": true } ], "comments": [ { "id": 551097, "author_name": "AkiraSosa", "author_url": "", "post_date": "2019-06-12T10:32:04.543000", "content": "Sorry my bad. Here is the correct pic.\n
Please let me correct if I'm wrong. As the some double bonds are conjugated, this representation is also valid.
\n\n
As a result, the target proton is much more affected by the electron than it looks on my first picture. It would be a challenge to take this kind of complicated interaction into account.
", "votes": 2, "replies": [ { "id": 551408, "author_name": "Scirpus", "author_url": "", "post_date": "2019-06-12T17:21:38.287000", "content": "I think you should have used a red pen! ;)
", "votes": 1, "replies": [] }, { "id": 552950, "author_name": "Boris D.", "author_url": "", "post_date": "2019-06-14T21:15:19.170000", "content": "I would have done this:
\n\nThe ring ain't charged though, but some atoms have partial charges
", "votes": 0, "replies": [] }, { "id": 561409, "author_name": "Lars Bratholm", "author_url": "", "post_date": "2019-06-26T12:29:16.323000", "content": "@akirasosa A (likely very unstable) zwitter ion makes sense to me!
", "votes": 0, "replies": [] } ] }, { "id": 553118, "author_name": "DDgg", "author_url": "", "post_date": "2019-06-15T06:10:03.050000", "content": "The neutral structure is inconsistent or faulty. Yes there are a number of tautomers (charge places are different) but the compound below has (C-N-H)[-] on nitrogen #1 an (C=NH2)[+] on nitrogen #8 so the structure is just wrong. The isomers are theoretical isomers from GDB-9, GDB-11, GDB-13, GDB-19 and they were optimized by DFT. Some of them are simply wrong. Its fine to exclude them.
", "votes": 0, "replies": [] }, { "id": 551407, "author_name": "Shuhao Cao", "author_url": "", "post_date": "2019-06-12T17:20:07.337000", "content": "May I ask what package you are using to plot the molecule structure? Can you rotate the perspective a little bit?
", "votes": 0, "replies": [ { "id": 551657, "author_name": "AkiraSosa", "author_url": "", "post_date": "2019-06-13T01:47:50.803000", "content": "I use Jmol. http://jmol.sourceforge.net/\nYou need to convert xyz to mol or mol2 in advance.
", "votes": 1, "replies": [] }, { "id": 551691, "author_name": "Shuhao Cao", "author_url": "", "post_date": "2019-06-13T02:47:32.917000", "content": "Thanks a lot.
", "votes": 0, "replies": [] }, { "id": 553122, "author_name": "DDgg", "author_url": "", "post_date": "2019-06-15T06:15:05.090000", "content": "@scaomath \n1) avogadro (https://avogadro.cc/docs/getting-started/introduction/)\n2) jmol (http://wiki.jmol.org/index.php/Main_Page)\n3) vmd (http://www.ks.uiuc.edu/Research/vmd/)
\n\nHere is a list of XYZ visualization programs, many of them are easy to use:\nhttp://atomsk.univ-lille1.fr/doc/en/format_xyz.html
", "votes": 0, "replies": [] } ] }, { "id": 551106, "author_name": "Boris D.", "author_url": "", "post_date": "2019-06-12T10:54:34.677000", "content": "You're right, it probably has something to do with the double bonds and all the electron doublets on nitrogen/oxygen atoms.
\n\nThe aromatic ring is not negatively charged though, the whole molecule being neutral. However, if you draw it on paper, you'll see that all these electrons can delocalize and it probably explains the low coupling (because the magnetic shielding is high?)
", "votes": 0, "replies": [ { "id": 551658, "author_name": "AkiraSosa", "author_url": "", "post_date": "2019-06-13T01:50:00.550000", "content": "@borisdee Thanks, I think the ring is charged because of the NH- on the left edge. But I'm not sure, because it's 15 years ago when I studied chemistry last time. ha ha.
", "votes": 0, "replies": [] } ] }, { "id": 551209, "author_name": "", "author_url": "", "post_date": "2019-06-12T13:11:41.633000", "content": "", "votes": 0, "replies": [] } ], "raw_markdown_by_id": { "551097": "Sorry my bad. Here is the correct pic.\n", "551216": "Please let me correct if I'm wrong. As the some double bonds are conjugated, this representation is also valid.\n\n\n\nAs a result, the target proton is much more affected by the electron than it looks on my first picture. It would be a challenge to take this kind of complicated interaction into account.", "551081": "I have tried to create a model for 3JHH. Current CV score is -0.186. According to the model, the molecule below has the largest error.\n\ndsgdb9nsd_129336\n\n* y_true : 5.325060\n* y_pred : 12.583338\n\nIf I see only dihedral angle, y_pred looks not so bad. So, is the low y_true from 5 members ring which has negative charge, right?\n\n", "553118": "The neutral structure is inconsistent or faulty. Yes there are a number of tautomers (charge places are different) but the compound below has (C-N-H)[-] on nitrogen #1 an (C=NH2)[+] on nitrogen #8 so the structure is just wrong. The isomers are theoretical isomers from GDB-9, GDB-11, GDB-13, GDB-19 and they were optimized by DFT. Some of them are simply wrong. Its fine to exclude them. ", "551407": "May I ask what package you are using to plot the molecule structure? Can you rotate the perspective a little bit? ", "551106": "You're right, it probably has something to do with the double bonds and all the electron doublets on nitrogen/oxygen atoms. \n\nThe aromatic ring is not negatively charged though, the whole molecule being neutral. However, if you draw it on paper, you'll see that all these electrons can delocalize and it probably explains the low coupling (because the magnetic shielding is high?)", "551209": "" } }