Insight II



D       Fragment Definitions

Following are the contents of the Insight II help file named frags.def. Each entry in this file is comprised of five columns of data.

1. An up-to-4-letter descriptor that is used as the fragment's lookup key.

2. A 1-letter descriptor of the fragment type:

blank = amino acid (fragment)
H = hydrocarbon (fragment)
G = functional group (fragment)
A = atom (fragment)
U = user library fragment (fragment)
R = ring library fragment, etc. (fragment)
V = vinyls (repeat unit)
O = olefins (repeat unit)
I = rings (repeat unit)
D = dienes (repeat unit)
E = heteroatom (repeat unit)
0 = RNA-DNA base fragment
1 = A RNA single strand fragment
2 = A RNA double strand fragment
4 = A DNA single strand fragment
5 = A DNA double strand fragment
6 = A DNA triple strand fragment
7 = B DNA single strand fragment
8 = B DNA double strand fragment
9 = Z DNA double strand fragment
b = A RNA-DNA hybrid fragment
t = RNA, DNA terminal group fragment
S = repeat_unit user fragment (and carbohydrates)

Note that when you add to this file, you may use any of the defined descriptors to identify a new fragment. Note also that the relative ordering of the entries for each class of fragment determines where the fragment is displayed in the list of fragments.

3. A molecule descriptor (of up to 8 characters) that appears under the object on the display.

4. A descriptor to designate the forward hydrogen in the fragment to be used during chain-building operations. This is necessary for fragments able to form chains (using the Repeat command in the Residue pulldown) but is optional if the fragment will not be used in a chain (use an arbitrary hydrogen).

5. A descriptor to designate the backward hydrogen in the fragment to be used during chain-building operations. This is necessary for fragments able to form chains (using the Repeat command) but is optional if the fragment will not be used in a chain (use an arbitrary hydrogen). Note that when molecules are built using the Repeat command, the forward and backward hydrogens are used for fragment alignment, and are then deleted.

Key Type Description Forward Backward
Hydrogen Hydrogen

ALA Alanine HN2 HC
ARG Arginine HN2 HC
ASP AspAcid HN2 HC
ASN Aspagine HN2 HC
CYS Cysteine HN2 HC
GLU GlutAcid HN2 HC
GLN Glutamin HN2 HC
GLY Glycine HN1 HC
HIS Histidin HN2 HC
ILE Isoleuc HN1 HC
LEU Leucine HN1 HC
LYS Lysine HN2 HC
MET Methion HN2 HC
PHE Phenalan HN2 HC
PRO Proline HN HC
SER Serine HN2 HC
THR Threonin HN2 HC
TRP Tryptphn HN2 HC
TYR Tyrosine HN2 HC
VAL Valine HN2 HC
ASPM Aspartic- HN2 HC
ARGP Arginine+ HN2 HC
LYSP Lysine+ HN2 HC
HISD HistidineD HN2 HC
HISP Histidine+ HN2 HC
GLUM Glutamic- HN2 HC
DPRO Dproline HN HC
AIB AIB HN1 HC
PGLU pyroglu HN HC
ACE acetyl HA1 HC
NM nmethyl HN1 HA1

Key Type Description Forward Backward
Hydrogen Hydrogen

OH Hyrdoxyl H1 H2
NH2 NH2group HN1 HN2
CH3 CH3group HC1 HC2
CSP3 A C(SP3) HN1 HC
CSP2 A C(SP2) HN1 HC
CSP A C(SP) HN1 HC
CAR A C(Arom) HN1 HC
NSP3 A N(SP3) HN1 HC
AMDE A N(Amide) HN1 HC
NSP2 A N(SP2) HN1 HC
NAR A N(Arom) HN1 HC
NP3P A N+(SP3) HN1 HC
NP2P A N+(SP2) HN1 HC
NSPP A N+(SP) HN1 HC
NARP A N+(Arom) HN1 HC
OSP3 A O(SP3) H12 H11
PSP3 A P(SP3) HN1 HC
PSP2 A P(SP2) HN1 HC
P5V A P(5BOND) HN1 HC
SSP3 A S(SP3) HN1 HC
SP3P A S+(SP3) HN1 HC
ALHD G Aldehyde HN1 HC
BCBN G B-Carbyl HN1 HC
OHH G Hydroxy H12 H11
AMIN G Amine HN1 HC
AMID G Amide HN1 HC
AMN4 G QuatAmin HN1 HC
AZO G Azo HN1 HC
ACDN G AcAnhydr HN1 HC
CBXA G CarboxAc HN1 HC
CBXM G Crbxlate HN1 HC
DAZP G Diazo+ HN1 HC
GCRL G Glycerol HN1 HC
GYCO G Glycol HN1 HC
HDAZ G Hydrazon HN1 HC
MTXY G Methoxy HN1 HC
NTRL G Nitrile HN1 HC
NTRO G Nitro HN1 HC
NTSO G Nitroso HN1 HC
OXIM G Oxime HN1 HC
PROX G PerOxide HN1 HC
PHOS G Phosph HN1 HC
SLFA G SulfAcid HN1 HC
SLMD G SulfAmid HN1 HC

Key Type Description Forward Backward
Hydrogen Hydrogen

SFCL G SulfCl HN1 HC
SLFS G SulfEstr HN1 HC
ACCL G AcidCl HN1 HC
METH H Methyl HN1 HC
ETHL H Ethyl HN1 HC
ETEN H Ethylene HN1 HC
PROP H Propyl HN1 HC
PRPN H Propylen HN1 HC
BUTL H Butyl HN1 HC
TBTL H T-Butyl HN1 HC
C2BN H C2Butene HN1 HC
T2BN H T2Butene HN1 HC
IBTN H Isobuten HN1 HC
BTDN H Butadie HN1 HC
ALKN H Alkyne HN1 HC
ALLN H Allene HN1 HC
CYPD R Cyptdien HN1 HC
PYRO R Pyrrole HN1 HC
CYHX R Cyhexane HN1 HC
BENZ R Benzene HN1 HC
INDO R Indole HN1 HC
NAPH R Naphlene HN1 HC
ANTH R Anthcene HN1 HC
PHAN R Phenanth HN1 HC
PHDN R Phenanrd HN1 HC
NPCN R Naphcene HN1 HC
BZAN R Benzancn HN1 HC
CRYN R Chrysene HN1 HC
PYEN R Pyrene HN1 HC
TRPH R Triphyln HN1 HC
PORN R Porphin HN1 HC
TOLN R Toluene HN1 HC
NTMD R NictnAmd HN1 HC
CYTO R Cytosine HN1 HC
TYMN R Thymine HN1 HC
VICL V VinylCl H12 H21
DCLE V dClEth H12 H2
VIF V VinylF H12 H21
DFE V dFluoEth HC1 H1
TFE V tFluoEth HC H1
VALC V VinylAlc H12 H21
VAMD V VinylAm H4 H1
VACE V VinylAce H5 H7
VIET V VinEther H12 H21

Key Type Description Forward Backward
Hydrogen Hydrogen

ACAC V AcrylAc HC3 H12
MA V MethyAcr HC3 H12
MMA V MMethac HC3 H1
ACNI V AcrylNit HC2 H11
STYR V Styrene H72 H61
AMST V aMethSty H72 H6
ETHE O Ethylene H12 H22
PREN O Proplene H11 H21
IBEN O Isobutl H13 H2
BUTE O 1Butene H11 H21
PHE1 I pPhenyl H6 H3
PHE2 I mPhenyl H1 H3
PHEO I pPhenOx H6 HO
XYLY I pXylylen H73 H63
PYR I Pyrrole H3 H1
PHDA I PhenDiam H4 HN3
PHBN I pHydbenzo H9 H2
BIMD I Benzimid H6 H3
PBAM I pBenzAmid H12 H1
ETTE I EtTerep H3 H13
PHOX I Phenoxy H5 H15
CARB I Carbonat H5 H2
DI2 D TrButaDi H12 H43
DI1 D CisButaD HC1 H33
DI3 D 12ButaDi H33 H21
DIC2 D TrNeopr H12 H43
DIC1 D CisNeopr HC1 H33
DIM2 D TrIsopr HC2 H33
DIM1 D CisIsopr H33 H43
DMBD D DMethBut H52 H43
HDI1 D 14HexaDi HC1 H11
OMET E OxyMeth H13 HO
OET E OxyEth H13 HO
OPRO E OxyProp H3 HO5
DMS E DimethSi HSI H1
MPS E MePhensi HSI HO
UREA E Urea HN2 H11
ETUR E EtUreth HN1 H23
NYL6 E Nylon6 HC3 H12
ADE 0 Adenine HN9 HC
CYT 0 Cytosine HN1 HC
GUA 0 Guanine HN9 HC
THY 0 Thymine HN1 HC
URA 0 Uracil HN1 HC

Key Type Description Forward Backward
Hydrogen Hydrogen

ARA1 1 ARNA_A HO3' HP
ARC1 1 ARNA_C HO3' HP
ARG1 1 ARNA_G HO3' HP
ARU1 1 ARNA_U HO3' HP
ARAU 2 ARNA_AU HO3' HP
ARCG 2 ARNA_CG HO3' HP
ARGC 2 ARNA_GC HO3' HP
ARUA 2 ARNA_UA HO3' HP
ADA1 4 ADNA_A HO3' HP
ADC1 4 ADNA_C HO3' HP
ADG1 4 ADNA_G HO3' HP
ADT1 4 ADNA_T HO3' HP
ADAT 5 ADNA_AT HO3' HP
ADCG 5 ADNA_CG HO3' HP
ADGC 5 ADNA_GC HO3' HP
ADTA 5 ADNA_TA HO3' HP
D3AT 6 ADNA_ATT HO3' HP
BDA1 7 BDNA_A HO3 HP
BDC1 7 BDNA_C HO3' HP
BDG1 7 BDNA_G HO3' HP
BDT1 7 BDNA_T HO3' HP
BDAT 8 BDNA_AT HO3' HP
BDCG 8 BDNA_CG HO3' HP
BDGC 8 BDNA_GC HO3' HP
BDTA 8 BDNA_TA HO3' HP
ZDCG 9 ZDCG_CG HO3' HP
ZDGC 9 ZDGC_GC HO3' HP
DRAU b ADRNA_AU HO3' HP
DRCG b ADRNA_CG HO3' HP
DRGC b ADRNA_GC HO3' HP
DRTA b ADRNA_TA HO3' HP
RDAT b ARDNA_AT HO3' HP
RDCG b ARDNA_CG HO3' HP
RDGC b ARDNA_GC HO3' HP
RDUA b ARDNA_UA HO3' HP
HBNA t H5_TERM HB HB
HENA t H3_TERM HE HE
POM t PO2_TERM HB HB




Last updated December 17, 1998 at 04:29PM PST.
Copyright © 1998, Molecular Simulations Inc. All rights reserved.