FMO DATABASE

FMODB ID: QYK7Y

Calculation Name: 4WP2-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-(dimethylarsenic)cysteine

ligand 3-letter code: CAS

PDB ID: 4WP2

Chain ID: A

ChEMBL ID:

UniProt ID: G0SET4

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-339528.045847
FMO2-HF: Nuclear repulsion	313344.131886
FMO2-HF: Total energy	-26183.913961
FMO2-MP2: Total energy	-26252.673839

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:597:SER)

Summations of interaction energy for fragment #1(A:597:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-10.498	-5.144	2.5	-3.417	-4.438	0.025

Interaction energy analysis for fragmet #1(A:597:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.082 / q_NPA : 0.041

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	599	ALA	0	0.006	0.013	2.283	-7.627	-3.872	2.409	-2.835	-3.330	0.023
4	A	600	ALA	0	0.022	0.014	3.086	-2.930	-1.547	0.092	-0.546	-0.929	0.002
5	A	601	THR	0	0.018	0.000	4.508	-0.046	0.170	-0.001	-0.036	-0.179	0.000
6	A	602	LYS	1	0.935	0.981	6.782	-0.548	-0.548	0.000	0.000	0.000	0.000
7	A	603	ALA	0	0.014	0.014	7.593	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	604	GLN	0	-0.014	-0.007	7.705	0.201	0.201	0.000	0.000	0.000	0.000
9	A	605	LEU	0	-0.003	0.006	10.768	0.083	0.083	0.000	0.000	0.000	0.000
10	A	606	ILE	0	0.004	-0.007	10.668	0.050	0.050	0.000	0.000	0.000	0.000
11	A	607	ALA	0	-0.009	0.001	13.134	0.025	0.025	0.000	0.000	0.000	0.000
12	A	608	GLU	-1	-0.757	-0.845	14.897	-0.176	-0.176	0.000	0.000	0.000	0.000
13	A	609	VAL	0	0.013	0.002	16.723	0.026	0.026	0.000	0.000	0.000	0.000
14	A	610	SER	0	-0.056	-0.011	17.708	0.010	0.010	0.000	0.000	0.000	0.000
15	A	611	ARG	1	0.842	0.894	18.932	0.192	0.192	0.000	0.000	0.000	0.000
16	A	612	ARG	1	0.783	0.870	20.828	0.147	0.147	0.000	0.000	0.000	0.000
17	A	613	THR	0	0.007	-0.032	21.813	0.015	0.015	0.000	0.000	0.000	0.000
18	A	614	GLY	0	0.038	0.032	23.329	0.010	0.010	0.000	0.000	0.000	0.000
19	A	615	MET	0	0.004	0.005	21.329	0.009	0.009	0.000	0.000	0.000	0.000
20	A	616	ASN	0	0.042	0.036	20.466	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	617	VAL	0	0.048	0.004	14.751	0.003	0.003	0.000	0.000	0.000	0.000
22	A	618	GLU	-1	-0.888	-0.936	15.955	0.079	0.079	0.000	0.000	0.000	0.000
23	A	619	TYR	0	0.073	0.001	17.778	0.021	0.021	0.000	0.000	0.000	0.000
24	A	620	SER	0	-0.015	-0.023	17.179	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	621	GLN	0	-0.013	-0.013	11.509	0.078	0.078	0.000	0.000	0.000	0.000
26	A	622	MET	0	-0.039	-0.005	15.547	0.016	0.016	0.000	0.000	0.000	0.000
27	A	623	CAS	0	-0.009	0.020	18.600	0.003	0.003	0.000	0.000	0.000	0.000
28	A	624	LEU	0	-0.001	0.011	13.772	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	625	THR	0	-0.080	-0.033	14.461	0.026	0.026	0.000	0.000	0.000	0.000
30	A	626	GLY	0	0.032	0.014	16.656	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	627	ALA	0	0.001	-0.016	19.188	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	628	ALA	0	0.040	0.040	19.198	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	629	ASN	0	-0.030	-0.029	15.295	0.011	0.011	0.000	0.000	0.000	0.000
34	A	630	TRP	0	-0.015	-0.030	11.524	0.037	0.037	0.000	0.000	0.000	0.000
35	A	631	ASN	0	0.000	0.011	14.978	-0.073	-0.073	0.000	0.000	0.000	0.000
36	A	632	LEU	0	0.054	0.022	16.862	0.019	0.019	0.000	0.000	0.000	0.000
37	A	633	GLU	-1	-0.776	-0.885	18.379	-0.108	-0.108	0.000	0.000	0.000	0.000
38	A	634	LEU	0	-0.019	0.004	21.148	0.012	0.012	0.000	0.000	0.000	0.000
39	A	635	ALA	0	0.018	0.022	18.783	0.013	0.013	0.000	0.000	0.000	0.000
40	A	636	LEU	0	-0.009	-0.004	20.893	0.009	0.009	0.000	0.000	0.000	0.000
41	A	637	GLN	0	-0.016	-0.006	23.345	0.012	0.012	0.000	0.000	0.000	0.000
42	A	638	SER	0	-0.028	-0.024	23.433	0.009	0.009	0.000	0.000	0.000	0.000
43	A	639	PHE	0	0.053	0.004	23.884	0.003	0.003	0.000	0.000	0.000	0.000
44	A	640	GLU	-1	-0.901	-0.946	25.754	-0.045	-0.045	0.000	0.000	0.000	0.000
45	A	641	GLN	0	-0.030	-0.007	28.882	0.005	0.005	0.000	0.000	0.000	0.000
46	A	642	GLN	0	-0.013	-0.001	26.329	0.008	0.008	0.000	0.000	0.000	0.000
47	A	643	LYS	1	0.843	0.906	28.461	0.037	0.037	0.000	0.000	0.000	0.000
48	A	644	ALA	0	-0.023	-0.010	29.437	0.000	0.000	0.000	0.000	0.000	0.000
49	A	645	ASN	0	-0.070	-0.035	29.584	0.003	0.003	0.000	0.000	0.000	0.000
50	A	646	VAL	0	-0.034	-0.003	25.701	0.006	0.006	0.000	0.000	0.000	0.000
51	A	647	PRO	0	0.015	0.026	26.878	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	648	PRO	0	0.020	-0.003	28.489	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	649	GLU	-1	-0.879	-0.958	28.067	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	650	ALA	0	-0.033	0.000	24.221	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	651	PHE	0	-0.088	-0.040	24.154	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	652	ILE	0	-0.029	-0.015	20.434	0.002	0.002	0.000	0.000	0.000	0.000
57	A	653	SER	0	-0.064	-0.026	23.154	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	654	GLN	0	-0.013	-0.011	25.638	0.008	0.008	0.000	0.000	0.000	0.000
59	A	655	PRO	0	0.005	0.008	26.539	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	656	GLN	0	-0.077	-0.033	24.513	0.000	0.000	0.000	0.000	0.000	0.000
61	A	657	VAL	0	-0.003	0.017	25.358	-0.010	-0.010	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:597:SER)