Package name: 50-48-6

Package ID: 200
Force-field: OPLS-AA | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2016-09-03 23:03:52
Modified at 2016-09-03 23:03:52

Abstract

The topology was generated using MOL2FF, with user-defined charges. These charges were obtained using the protocol P3 from Beckstein et al. (J Comput Aided Mol Des, 2014, 28, 265-276): geometry optimization and CHelpG charges calculation using Gaussian03 (http://www.gaussian.com) at the HF/6-31G* level, then a two-stage RESP fitting using AmberTools (http://ambermd.org).

Chemical structure
General view

 Detailed view

References
Authors: Beckstein O, Fourrier A, Iorga BI
Title: Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field.
Journal: J Comput Aided Mol Des
Year: 2014 Mar
Volume: 28
Pages: 265-76
DOI: 10.1007/s10822-014-9727-1
Pubmed ID:   24557853
Comments:

Reference validation values

These are experimental values or high-level quantum mechanics values, which will be used for comparison with computed values (found in individual versions).

Files and history

All deposited versions are available and can be downloaded individually. Higher version numbers are more recent. Files that changed between versions can be identified by differing SHA1 hash checksums.

Version 1 created at 2016-09-03

Score 1/5 "These parameters are not validated yet"

Computed validation values

grompp
preprocessor output "grompp-compatible"
Created at 2016-09-03 23:03:52 | Modified at 2016-09-03 23:03:52 | [download zip]
Type Description Hash (SHA1)
Topology SAMPL4_024_3.itp 07a381999edf426c65707fa4920daff85093b967
Structure SAMPL4_024_3.pdb 72154e0c60b55811d7258480f003a6dea4e54283

Compound details
Ligand code TP0
Molecule identifier CD7A62A0E59FA073
Displayed name 50-48-6
Canonical IUPAC name 3-(5,6-dihydrodibenzo[2,1-b:2prime,1prime-f][7]annulen-11-ylidene)-N,N-dimethyl-propan-1-amine
Formula C20H23N
Molecular weight 277.41
Charge 0
Number of atoms 44
SMILES CN(C)CCC=C2C1=CC=CC=C1CCC3=CC=CC=C23
PubChem CID 2160
CAS RN 50-48-6
Other names 50-48-6 • 30227-34-0 • BAS 00269727 • Spectrum4_000146 • 1-Propanamine, 3-(10,11-dihydro-5H-dibenzo(a,d)cyclohepten-5-ylidene)-N,N-dimethyl- • 10,11-Dihydro-5-(gamma-dimethylaminopropylidene)-5H-dibenzo(a,d)cycloheptene • 10,11-Dihydro-N,N-dimethyl-5H-dibenzo(a,d)heptalene-delta(sup 5),gamma-propylamine • 3-(10,11-Dihydro-5H-dibenzo(a,d)cyclohepten-5-yliden)-N,N-dimethylpropylamin • 3-(10,11-Dihydro-5H-dibenzo(a,d)cyclohepten-5-ylidene)-N,N-dimethyl-1-propanamine • 5-(3prime-Dimethylaminopropylidene)-dibenzo-(a,d)(1,4)-cycloheptadiene • 5-(3-Dimethylaminopropylidene)-10,11-dihydro-5H-dibenzo(a,d)cycloheptene • 5-(gamma-Dimethylaminopropylidene)-10,11-dihydro-5H-dibenzo(a,d)cycloheptene • 5-(gamma-Dimethylaminopropylidine)-5H-dibenzo(a,d)(1,4)cycloheptadiene • 5H-Dibenzo(a,d)cycloheptene-delta(sup 5),gamma-propylamine, 10,11-dihydro-N,N-dimethyl- • 5H-Dibenzo(a,d)cycloheptene-delta5,gamma-propylamine, 10,11-dihydro-N,N-dimethyl- • Adepress • KBioGR_000592 • Amitriptilina [Italian] • Amitriptylin [German] • Amitriptylinum [INN-Latin] • Amytriptylin • BRN 2217885 • Damilen • Damitriptyline • EINECS 200-041-6 • Flavyl • Lantron • MK 230 • N 750 • Proheptadiene • Ro 4-1575 • Seroten • Triptanol • Triptilin • Triptisol • Prestwick2_000074 • 3-(10,11-Dihydro-5H-dibenzo-[a,d]cyclohepten-5-ylidene)-N,N-dimethyl-1-propanamine, hydrochloride • 549-18-8 (HCL) • AIDS-001620 • AIDS001620 • Antihistamine compound • Damilan • Laroxil • NSC169910 (HCL) • SPBio_002208 • BSPBio_001836 • Prestwick3_000074 • [3-(10,11-Dihydro-dibenzo[a,d]cyclohepten-5-ylidene)-propyl]-dimethyl-amine • DivK1c_000766 • BPBio1_000317 • Lopac-A-8404 • NCGC00015095-01 • CAS-549-18-8 • NCGC00015095-02 • KBioGR_002261 • KBio3_002741 • KBioSS_002262 • 1-propanamine, 3-(10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-ylidene)-N,N-dimethyl- • 10,11-dihydro-5-(gamma-dimethylaminopropylidene)-5H-dibenzo[a,d]cycloheptene • 10,11-dihydro-N,N-dimethl-5H-dibenzo[a,d]cycloheptene-(delta(5, gamma))-propylamine • 3-(10,11-Dihydro-5H-dibenzo[a,d]cyclohepten-5-ylidene)-N,N-dimethyl-1-propanamine • 5-(3prime-Dimethylaminopropylidene)-dibenzo-[a,d][1,4]-cycloheptadiene • BSPBio_000287 • 5-(3-dimethylaminopropylidene)dibenzo[a,d][1,4]-cycloheptadiene • 5-(gamma-Dimethylaminopropylidene)-5H-dibenzo(a,d)(1,4)cycloheptadiene • 5-(gamma-Dimethylaminopropylidene)-5H-dibenzo[a,d]10,11-dihydrocycloheptene • 5H-Dibenzo[a,d]cycloheptene-Delta5,gamma-propylamine, 10,11-dihydro-N,N-dimethyl- (6CI,8CI) 5-(gamma-Dimethylaminopropylidene)-10,11-dihydro-5H-dibenzo[a,d]cycloheptene • Amitriprolidine • Amitriptylin • Spectrum3_000298 • KBio2_002261 • KBio2_004829 • KBio2_007397 • NCGC00024433-05 • 5-(3-Dimethylaminopropylidene)-5H-dibenzo[a,d]-10,11-dihydrocycloheptene • Prestwick0_000074 • IDI1_000766 • Oprea1_479304 • Spectrum5_000806 • PDSP2_001548 • KBio1_000766 • KBio3_001336 • 3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N,N-dimethylpropan-1-amine • 3-(10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-ylidene)-N,N-dimethylpropan-1-amine • 5-(3-dimethylaminopropylidene)-10,11-dihydro-5H-dibenzo(a,d)cycloheptatriene • 5-(gamma-dimethylaminopropylidene)-5H-dibenzo[a,d][1,4]cycloheptadiene • CHEBI:2666 • ST5220564 • Prestwick1_000074 • cMAP_000001 • Spectrum_000044 • Amitriptyline • C06824 • KBioSS_000424 • Amitriptilina [INN-Spanish] • NINDS_000766 • 5H-Dibenzo[a,d]cycloheptene-.delta.5,.gamma.-propylamine, 10,11-dihydro-N,N-dimethyl- • KBio2_000424 • KBio2_002992 • KBio2_005560 • SPBio_000082 • 10,11-dihydro-N,N-dimethyl-5H-dibenzo(a,d)heptalene-Delta(5),gamma-propylamine • Spectrum2_000101 • Lopac0_000112 • PDSP1_001564

License
Type CC BY-SA – Creative Commons Attribution-Share Alike License
Name Bogdan I. Iorga
Email (hidden)
Source MOL2FF (http://mol2ff.icsn.cnrs-gif.fr)

Ligandbook is described in

Jan Domański, Oliver Beckstein, Bogdan I. Iorga; Ligandbook: an online repository for small and drug-like molecule force field parameters, Bioinformatics, Volume 33, Issue 11, 1 June 2017, Pages 1747–1749, https://doi.org/10.1093/bioinformatics/btx037

Actions
Documentation
Support

"I Smell Smoke From a Gun Named Extinction" (Pixies)