From e2464e007099cf30f0c86304afc6463f930e159c Mon Sep 17 00:00:00 2001 From: Daniel <46388253+dbkchu@users.noreply.github.com> Date: Fri, 19 Jul 2024 13:52:17 -0400 Subject: [PATCH] replace PF3 with SMILES generated mol2 (#251) * replace PF3 with SMILES generated mol2 * [pre-commit.ci] auto fixes from pre-commit hooks --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- molSimplify/Ligands/ligands.dict | 2 +- molSimplify/Ligands/pf3.mol2 | 19 +++++++++++++++++++ molSimplify/Ligands/phosphorustrifluoride.mol | 12 ------------ 3 files changed, 20 insertions(+), 13 deletions(-) create mode 100644 molSimplify/Ligands/pf3.mol2 delete mode 100644 molSimplify/Ligands/phosphorustrifluoride.mol diff --git a/molSimplify/Ligands/ligands.dict b/molSimplify/Ligands/ligands.dict index 2c4b08ee9..8dbaff613 100644 --- a/molSimplify/Ligands/ligands.dict +++ b/molSimplify/Ligands/ligands.dict @@ -183,7 +183,7 @@ ox:oxalate.mol,oxate,1 4,build bidentate,A,-2 oxo:oxygen.mol,oxo,0,build small,N,-2 pcy3:PCy3.mol,pcy3,0,build bulky big,BA,0 pentacyanopentadienide:pentacyanocyclopentadienide.mol,pcyanopent,1,build bulky,A,-1 -pf3:phosphorustrifluoride.mol,pf3,1,build small,BA,0 +pf3:pf3.mol2,pf3,1,build small,BA,0 ph2-:ph2-.mol,ph2-,0,build functionalize small,N,-1 ph3:ph3.mol,ph3,0,build functionalize small,N,0 phen:phen.mol,phen,9 12,build bidentate,BA,0 diff --git a/molSimplify/Ligands/pf3.mol2 b/molSimplify/Ligands/pf3.mol2 new file mode 100644 index 000000000..24bae2040 --- /dev/null +++ b/molSimplify/Ligands/pf3.mol2 @@ -0,0 +1,19 @@ +@MOLECULE +pf3.mol2 +4 3 1 +SMALL +PartialCharges +**** +Generated from molSimplify + +@ATOM +1 F1 1.215917934819222 0.0666657847598425 -0.005857293024108329 F 1 RES1 0.0 +2 P1 2.7546239026034516 -0.2682925621616243 -0.034209056581309884 P.3 1 RES1 0.0 +3 F2 3.1090617015157433 0.8313972878801463 -1.1045721415058223 F 1 RES1 0.0 +4 F3 3.1090574085440688 0.635819556544132 1.2057809186362327 F 1 RES1 0.0 +@BOND +1 1 2 1 +1 2 3 1 +1 2 4 1 +@SUBSTRUCTURE +1 RES1 4 diff --git a/molSimplify/Ligands/phosphorustrifluoride.mol b/molSimplify/Ligands/phosphorustrifluoride.mol deleted file mode 100644 index 102a10587..000000000 --- a/molSimplify/Ligands/phosphorustrifluoride.mol +++ /dev/null @@ -1,12 +0,0 @@ -PF3 Phosphorus trifluoride 7783553 -##CCCBDB 5172217:13 -Geometry Optimized at CCSD(T)/6-31G* - 4 3 0 0 0 0 0 0 0 0999 V2000 - 0.0000 0.0000 0.4923 N 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0000 1.2439 -0.1276 F 0 0 0 0 0 0 0 0 0 0 0 0 - 1.0772 -0.6219 -0.1276 F 0 0 0 0 0 0 0 0 0 0 0 0 - -1.0772 -0.6219 -0.1276 F 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 - 1 3 1 0 0 0 - 1 4 1 0 0 0 -M END