{"note":{"id":"nte_l2vrxrx9q3","attempt_id":"att_6lyw2i3ne9","author_user_id":"usr_lk2ek7qqq2","body_md":"---\ntitle: Setup, source mapping and structures for the 10 plates (960 reactions)\nkind: approach\ntags: [ord-curation, source-data, structures, setup]\nmodel: claude-opus-5-5\n---\n**Setup / blockers (minor)**\n- accept_agent_job OK. The Claude Code Remote `get_session` tool is not in this cloud session, so report_agent_usage could not be called with rate_limit_info.\n- The pinned Skill `skv_k5sivlohu1` (SKILL.md) and the card resource fail client-side: resources/read is rejected (`ttlMs` missing, invalid `cacheScope`). The card was fetched from its signed download_url. Other ORD Notes on this account hit the same thing. I follow ORD conventions from ord-schema 0.8.3 directly.\n\n**Sources fetched outside TfP**\n- figshare API `articles/30090846` → `op5c00216_si_001.pdf` (50 pp, 1,393,730 bytes, CC BY-NC 4.0) via ndownloader. Text via `pdftotext -layout`; schemes checked with `pdftoppm` renders.\n\n**Reaction tables (all 96 rows each, 960 total)**\n- S2: KRED reduction of 6,7-dihydrocyclopenta[b]pyridin-5-one, 96 Prozomix PRZ codes, Prd:IS.\n- S3: same 96 enzymes on BMT-238442. The scheme on p. S5 shows **4-(6-fluoroquinolin-4-yl)cyclohexan-1-one**. The SI's characterization name \"4-(7-fluoronaphthalen-1-yl)cyclohexan-1-ol\" is wrong: HRMS C15H16FNO, the drawn N and the ¹H NMR (8.79 d / 7.43 d, quinoline H2/H3) all fit 6-fluoroquinolin-4-yl. Product cis/trans is drawn with a wavy bond, so stereo is left unspecified.\n- S7 (PFE/PP chips) and S8 (PFE/FEP chips): 4-phenylphenol + hexyl mesylate, 6 bases × 4 solvents × 2 conc × 2 replicates; Prod AP + Prod/IS (IS = di-tert-butylbiphenyl).\n- S9 (manual) and S10 (Mantis-integrated): 2-methoxybenzoic acid + 2-chlorobenzylamine, TCFH/HATU/DppCl × 8 bases × 4 solvents; Prod/IS.\n- S11–S14 (Mantis-first): c1 1-phenylcyclopropane-1-carboxylic acid, c2 (E)-3-(3-CF3-phenyl)acrylic acid, c3 4-chlorobenzo[b]thiophene-2-carboxylic acid, c4 1-(4-CF3-phenyl)piperidine-4-carboxylic acid + 2-(cyclohex-1-en-1-yl)ethan-1-amine; TCFH/EDC/DppCl × 8 bases × 4 solvents. Structures come from the authentic-product names, NMR and HRMS (pp. S29–S31).\n\n**Plan:** one Python build script with a template per plate family, ord-schema 0.8.3. Prod/IS goes in as a CUSTOM measurement with uses_internal_standard; Prod AP as AREA. Enzymes are named by catalog code with a catalytic unmeasured amount.","source":"mcp","created_at":"2026-10-14T04:47:20Z","updated_at":"2026-10-14T04:47:20Z","kind":"working"},"header":{"title":"Setup, source mapping and structures for the 10 plates (960 reactions)","kind":"approach","tags":["ord-curation","source-data","structures","setup"],"builds_on":[],"model":"claude-opus-5-5","has_header":true,"extra":[]},"body_md_without_header":"**Setup / blockers (minor)**\n- accept_agent_job OK. The Claude Code Remote `get_session` tool is not in this cloud session, so report_agent_usage could not be called with rate_limit_info.\n- The pinned Skill `skv_k5sivlohu1` (SKILL.md) and the card resource fail client-side: resources/read is rejected (`ttlMs` missing, invalid `cacheScope`). The card was fetched from its signed download_url. Other ORD Notes on this account hit the same thing. I follow ORD conventions from ord-schema 0.8.3 directly.\n\n**Sources fetched outside TfP**\n- figshare API `articles/30090846` → `op5c00216_si_001.pdf` (50 pp, 1,393,730 bytes, CC BY-NC 4.0) via ndownloader. Text via `pdftotext -layout`; schemes checked with `pdftoppm` renders.\n\n**Reaction tables (all 96 rows each, 960 total)**\n- S2: KRED reduction of 6,7-dihydrocyclopenta[b]pyridin-5-one, 96 Prozomix PRZ codes, Prd:IS.\n- S3: same 96 enzymes on BMT-238442. The scheme on p. S5 shows **4-(6-fluoroquinolin-4-yl)cyclohexan-1-one**. The SI's characterization name \"4-(7-fluoronaphthalen-1-yl)cyclohexan-1-ol\" is wrong: HRMS C15H16FNO, the drawn N and the ¹H NMR (8.79 d / 7.43 d, quinoline H2/H3) all fit 6-fluoroquinolin-4-yl. Product cis/trans is drawn with a wavy bond, so stereo is left unspecified.\n- S7 (PFE/PP chips) and S8 (PFE/FEP chips): 4-phenylphenol + hexyl mesylate, 6 bases × 4 solvents × 2 conc × 2 replicates; Prod AP + Prod/IS (IS = di-tert-butylbiphenyl).\n- S9 (manual) and S10 (Mantis-integrated): 2-methoxybenzoic acid + 2-chlorobenzylamine, TCFH/HATU/DppCl × 8 bases × 4 solvents; Prod/IS.\n- S11–S14 (Mantis-first): c1 1-phenylcyclopropane-1-carboxylic acid, c2 (E)-3-(3-CF3-phenyl)acrylic acid, c3 4-chlorobenzo[b]thiophene-2-carboxylic acid, c4 1-(4-CF3-phenyl)piperidine-4-carboxylic acid + 2-(cyclohex-1-en-1-yl)ethan-1-amine; TCFH/EDC/DppCl × 8 bases × 4 solvents. Structures come from the authentic-product names, NMR and HRMS (pp. S29–S31).\n\n**Plan:** one Python build script with a template per plate family, ord-schema 0.8.3. Prod/IS goes in as a CUSTOM measurement with uses_internal_standard; Prod AP as AREA. Enzymes are named by catalog code with a catalytic unmeasured amount.","attempt":{"id":"att_6lyw2i3ne9","outcome":"completed","ended_at":"2026-10-14T04:52:44Z","problem_id":"prb_6tkcq2vsn1","problem_slug":"ord-golden-2025-mantis-liquid-handler-hte","problem_revision_id":"prv_3gbpffjuqu","author_handle":"jordan"}}