Merge pull request NMRLipids#163 from comcon1/add-pvpa-pvpg

Add PVPA and PVPG (E.coli intermediates of major CL species)

Author: batukav

Molecules/membrane/PVPA/mappingPVPAcharmm.yaml

@@ -0,0 +1,348 @@
+M_G1_M:
+  ATOMNAME: C3
+  FRAGMENT: glycerol backbone
+M_G1H1_M:
+  ATOMNAME: HY
+  FRAGMENT: glycerol backbone
+M_G1H2_M:
+  ATOMNAME: HX
+  FRAGMENT: glycerol backbone
+M_G1O1_M:
+  ATOMNAME: O31
+  FRAGMENT: glycerol backbone
+M_G1C2_M:
+  ATOMNAME: C31
+  FRAGMENT: sn-1
+M_G1C2O1_M:
+  ATOMNAME: O32
+  FRAGMENT: sn-1
+M_G1C3_M:
+  ATOMNAME: C32
+  FRAGMENT: sn-1
+M_G1C3H1_M:
+  ATOMNAME: H2X
+  FRAGMENT: sn-1
+M_G1C3H2_M:
+  ATOMNAME: H2Y
+  FRAGMENT: sn-1
+M_G1C4_M:
+  ATOMNAME: C33
+  FRAGMENT: sn-1
+M_G1C4H1_M:
+  ATOMNAME: H3X
+  FRAGMENT: sn-1
+M_G1C4H2_M:
+  ATOMNAME: H3Y
+  FRAGMENT: sn-1
+M_G1C5_M:
+  ATOMNAME: C34
+  FRAGMENT: sn-1
+M_G1C5H1_M:
+  ATOMNAME: H4X
+  FRAGMENT: sn-1
+M_G1C5H2_M:
+  ATOMNAME: H4Y
+  FRAGMENT: sn-1
+M_G1C6_M:
+  ATOMNAME: C35
+  FRAGMENT: sn-1
+M_G1C6H1_M:
+  ATOMNAME: H5X
+  FRAGMENT: sn-1
+M_G1C6H2_M:
+  ATOMNAME: H5Y
+  FRAGMENT: sn-1
+M_G1C7_M:
+  ATOMNAME: C36
+  FRAGMENT: sn-1
+M_G1C7H1_M:
+  ATOMNAME: H6X
+  FRAGMENT: sn-1
+M_G1C7H2_M:
+  ATOMNAME: H6Y
+  FRAGMENT: sn-1
+M_G1C8_M:
+  ATOMNAME: C37
+  FRAGMENT: sn-1
+M_G1C8H1_M:
+  ATOMNAME: H7X
+  FRAGMENT: sn-1
+M_G1C8H2_M:
+  ATOMNAME: H7Y
+  FRAGMENT: sn-1
+M_G1C9_M:
+  ATOMNAME: C38
+  FRAGMENT: sn-1
+M_G1C9H1_M:
+  ATOMNAME: H8X
+  FRAGMENT: sn-1
+M_G1C9H2_M:
+  ATOMNAME: H8Y
+  FRAGMENT: sn-1
+M_G1C10_M:
+  ATOMNAME: C39
+  FRAGMENT: sn-1
+M_G1C10H1_M:
+  ATOMNAME: H9X
+  FRAGMENT: sn-1
+M_G1C10H2_M:
+  ATOMNAME: H9Y
+  FRAGMENT: sn-1
+M_G1C11_M:
+  ATOMNAME: C310
+  FRAGMENT: sn-1
+M_G1C11H1_M:
+  ATOMNAME: H10X
+  FRAGMENT: sn-1
+M_G1C11H2_M:
+  ATOMNAME: H10Y
+  FRAGMENT: sn-1
+M_G1C12_M:
+  ATOMNAME: C311
+  FRAGMENT: sn-1
+M_G1C12H1_M:
+  ATOMNAME: H11X
+  FRAGMENT: sn-1
+M_G1C12H2_M:
+  ATOMNAME: H11Y
+  FRAGMENT: sn-1
+M_G1C13_M:
+  ATOMNAME: C312
+  FRAGMENT: sn-1
+M_G1C13H1_M:
+  ATOMNAME: H12X
+  FRAGMENT: sn-1
+M_G1C13H2_M:
+  ATOMNAME: H12Y
+  FRAGMENT: sn-1
+M_G1C14_M:
+  ATOMNAME: C313
+  FRAGMENT: sn-1
+M_G1C14H1_M:
+  ATOMNAME: H13X
+  FRAGMENT: sn-1
+M_G1C14H2_M:
+  ATOMNAME: H13Y
+  FRAGMENT: sn-1
+M_G1C15_M:
+  ATOMNAME: C314
+  FRAGMENT: sn-1
+M_G1C15H1_M:
+  ATOMNAME: H14X
+  FRAGMENT: sn-1
+M_G1C15H2_M:
+  ATOMNAME: H14Y
+  FRAGMENT: sn-1
+M_G1C16_M:
+  ATOMNAME: C315
+  FRAGMENT: sn-1
+M_G1C16H1_M:
+  ATOMNAME: H15X
+  FRAGMENT: sn-1
+M_G1C16H2_M:
+  ATOMNAME: H15Y
+  FRAGMENT: sn-1
+M_G1C17_M:
+  ATOMNAME: C316
+  FRAGMENT: sn-1
+M_G1C17H1_M:
+  ATOMNAME: H16X
+  FRAGMENT: sn-1
+M_G1C17H2_M:
+  ATOMNAME: H16Y
+  FRAGMENT: sn-1
+M_G1C17H3_M:
+  ATOMNAME: H16Z
+  FRAGMENT: sn-1
+M_G2_M:
+  ATOMNAME: C2
+  FRAGMENT: glycerol backbone
+M_G2H1_M:
+  ATOMNAME: HS
+  FRAGMENT: glycerol backbone
+M_G2O1_M:
+  ATOMNAME: O21
+  FRAGMENT: glycerol backbone
+M_G2C2_M:
+  ATOMNAME: C21
+  FRAGMENT: sn-2
+M_G2C2O1_M:
+  ATOMNAME: O22
+  FRAGMENT: sn-2
+M_G2C3_M:
+  ATOMNAME: C22
+  FRAGMENT: sn-2
+M_G2C3H1_M:
+  ATOMNAME: H2R
+  FRAGMENT: sn-2
+M_G2C3H2_M:
+  ATOMNAME: H2S
+  FRAGMENT: sn-2
+M_G2C4_M:
+  ATOMNAME: C23
+  FRAGMENT: sn-2
+M_G2C4H1_M:
+  ATOMNAME: H3R
+  FRAGMENT: sn-2
+M_G2C4H2_M:
+  ATOMNAME: H3S
+  FRAGMENT: sn-2
+M_G2C5_M:
+  ATOMNAME: C24
+  FRAGMENT: sn-2
+M_G2C5H1_M:
+  ATOMNAME: H4R
+  FRAGMENT: sn-2
+M_G2C5H2_M:
+  ATOMNAME: H4S
+  FRAGMENT: sn-2
+M_G2C6_M:
+  ATOMNAME: C25
+  FRAGMENT: sn-2
+M_G2C6H1_M:
+  ATOMNAME: H5R
+  FRAGMENT: sn-2
+M_G2C6H2_M:
+  ATOMNAME: H5S
+  FRAGMENT: sn-2
+M_G2C7_M:
+  ATOMNAME: C26
+  FRAGMENT: sn-2
+M_G2C7H1_M:
+  ATOMNAME: H6R
+  FRAGMENT: sn-2
+M_G2C7H2_M:
+  ATOMNAME: H6S
+  FRAGMENT: sn-2
+M_G2C8_M:
+  ATOMNAME: C27
+  FRAGMENT: sn-2
+M_G2C8H1_M:
+  ATOMNAME: H7R
+  FRAGMENT: sn-2
+M_G2C8H2_M:
+  ATOMNAME: H7S
+  FRAGMENT: sn-2
+M_G2C9_M:
+  ATOMNAME: C28
+  FRAGMENT: sn-2
+M_G2C9H1_M:
+  ATOMNAME: H8R
+  FRAGMENT: sn-2
+M_G2C9H2_M:
+  ATOMNAME: H8S
+  FRAGMENT: sn-2
+M_G2C10_M:
+  ATOMNAME: C29
+  FRAGMENT: sn-2
+M_G2C10H1_M:
+  ATOMNAME: H9R
+  FRAGMENT: sn-2
+M_G2C10H2_M:
+  ATOMNAME: H9S
+  FRAGMENT: sn-2
+M_G2C11_M:
+  ATOMNAME: C210
+  FRAGMENT: sn-2
+M_G2C11H1_M:
+  ATOMNAME: H10R
+  FRAGMENT: sn-2
+M_G2C11H2_M:
+  ATOMNAME: H10S
+  FRAGMENT: sn-2
+M_G2C12_M:
+  ATOMNAME: C211
+  FRAGMENT: sn-2
+M_G2C12H1_M:
+  ATOMNAME: H111
+  FRAGMENT: sn-2
+M_G2C13_M:
+  ATOMNAME: C212
+  FRAGMENT: sn-2
+M_G2C13H1_M:
+  ATOMNAME: H121
+  FRAGMENT: sn-2
+M_G2C14_M:
+  ATOMNAME: C213
+  FRAGMENT: sn-2
+M_G2C14H1_M:
+  ATOMNAME: H13R
+  FRAGMENT: sn-2
+M_G2C14H2_M:
+  ATOMNAME: H13S
+  FRAGMENT: sn-2
+M_G2C15_M:
+  ATOMNAME: C214
+  FRAGMENT: sn-2
+M_G2C15H1_M:
+  ATOMNAME: H14R
+  FRAGMENT: sn-2
+M_G2C15H2_M:
+  ATOMNAME: H14S
+  FRAGMENT: sn-2
+M_G2C16_M:
+  ATOMNAME: C215
+  FRAGMENT: sn-2
+M_G2C16H1_M:
+  ATOMNAME: H15R
+  FRAGMENT: sn-2
+M_G2C16H2_M:
+  ATOMNAME: H15S
+  FRAGMENT: sn-2
+M_G2C17_M:
+  ATOMNAME: C216
+  FRAGMENT: sn-2
+M_G2C17H1_M:
+  ATOMNAME: H16R
+  FRAGMENT: sn-2
+M_G2C17H2_M:
+  ATOMNAME: H16S
+  FRAGMENT: sn-2
+M_G2C18_M:
+  ATOMNAME: C217
+  FRAGMENT: sn-2
+M_G2C18H1_M:
+  ATOMNAME: H17R
+  FRAGMENT: sn-2
+M_G2C18H2_M:
+  ATOMNAME: H17S
+  FRAGMENT: sn-2
+M_G2C19_M:
+  ATOMNAME: C218
+  FRAGMENT: sn-2
+M_G2C19H1_M:
+  ATOMNAME: H18R
+  FRAGMENT: sn-2
+M_G2C19H2_M:
+  ATOMNAME: H18S
+  FRAGMENT: sn-2
+M_G2C19H3_M:
+  ATOMNAME: H18T
+  FRAGMENT: sn-2
+M_G3_M:
+  ATOMNAME: C1
+  FRAGMENT: glycerol backbone
+M_G3H1_M:
+  ATOMNAME: HA
+  FRAGMENT: glycerol backbone
+M_G3H2_M:
+  ATOMNAME: HB
+  FRAGMENT: glycerol backbone
+M_G3O1_M:
+  ATOMNAME: O11
+  FRAGMENT: glycerol backbone
+M_G3P2_M:
+  ATOMNAME: P
+  FRAGMENT: headgroup
+M_G3P2O1_M:
+  ATOMNAME: O14
+  FRAGMENT: headgroup
+M_G3P2O2_M:
+  ATOMNAME: O13
+  FRAGMENT: headgroup
+M_G3O3_M:
+  ATOMNAME: O12
+  FRAGMENT: headgroup
+M_G3O3H1_M:
+  ATOMNAME: H12
+  FRAGMENT: headgroup

Molecules/membrane/PVPA/metadata.yaml

@@ -0,0 +1,17 @@
+NMRlipids:
+  id: PVPA
+  name: "1-hexadecanoyl-2-(11Z-octadecenoyl)-sn-glycero-3-phosphate"
+  charge: -1
+sameAs:
+  ChEBI: CHEBI:89530
+  pubchem.compound: 9547158
+  lipidmaps: LMGP10010007
+  slm: SLM:000026217
+bioschema_properties:
+  iupacName: "[(2R)-1-hexadecanoyloxy-3-phosphonooxypropan-2-yl](Z)-octadec-11-enoate"
+  name: "palmitoyl-cis-vaccenoylphosphatidic acid"
+  smiles: CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCCCC/C=C\CCCCCC
+  inChI: InChI=1S/C37H71O8P/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-37(39)45-35(34-44-46(40,41)42)33-43-36(38)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h13,15,35H,3-12,14,16-34H2,1-2H3,(H2,40,41,42)/b15-13-/t35-/m1/s1
+  inChIKey: YDFKTEAAIYLUQP-JUOLSMOWSA-N
+  molecularFormula: C37H71O8P
+  molecularWeight: 674.9