FMO DATABASE

FMODB ID: Z67RN

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	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-337425.065206
FMO2-HF: Nuclear repulsion	311241.383402
FMO2-HF: Total energy	-26183.681804
FMO2-MP2: Total energy	-26252.431475

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.
-13.666	-7.834	2.066	-3.326	-4.571	0.027

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 : 0.053 / q_NPA : 0.012

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	0.009	0.013	2.409	-6.219	-2.896	1.837	-2.282	-2.878	0.017
4	A	600	ALA	0	0.033	0.019	2.791	-5.600	-3.367	0.230	-0.996	-1.466	0.010
5	A	601	THR	0	0.027	0.016	4.148	-0.525	-0.249	-0.001	-0.048	-0.227	0.000
6	A	602	LYS	1	0.943	0.969	6.173	-1.183	-1.183	0.000	0.000	0.000	0.000
7	A	603	ALA	0	0.031	0.018	7.233	-0.227	-0.227	0.000	0.000	0.000	0.000
8	A	604	GLN	0	-0.018	-0.003	8.363	-0.391	-0.391	0.000	0.000	0.000	0.000
9	A	605	LEU	0	0.015	0.007	10.616	-0.041	-0.041	0.000	0.000	0.000	0.000
10	A	606	ILE	0	0.001	-0.003	10.727	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	607	ALA	0	-0.020	-0.010	12.946	-0.051	-0.051	0.000	0.000	0.000	0.000
12	A	608	GLU	-1	-0.787	-0.863	14.735	-0.046	-0.046	0.000	0.000	0.000	0.000
13	A	609	VAL	0	0.013	0.000	16.693	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	610	SER	0	-0.048	-0.009	17.623	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	611	ARG	1	0.819	0.885	18.909	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	612	ARG	1	0.920	0.957	20.819	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	613	THR	0	0.003	-0.017	21.673	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	614	GLY	0	0.039	0.032	23.104	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	615	MET	0	-0.010	0.001	21.246	0.012	0.012	0.000	0.000	0.000	0.000
20	A	616	ASN	0	0.067	0.046	20.272	0.033	0.033	0.000	0.000	0.000	0.000
21	A	617	VAL	0	0.051	-0.006	14.655	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	618	GLU	-1	-0.954	-0.964	16.086	0.510	0.510	0.000	0.000	0.000	0.000
23	A	619	TYR	0	0.078	0.001	17.708	0.000	0.000	0.000	0.000	0.000	0.000
24	A	620	SER	0	-0.013	-0.015	16.963	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	621	GLN	0	-0.011	-0.016	11.805	0.183	0.183	0.000	0.000	0.000	0.000
26	A	622	MET	0	-0.041	-0.005	15.644	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	623	CAS	0	-0.010	0.027	18.805	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	624	LEU	0	-0.032	-0.011	13.907	-0.042	-0.042	0.000	0.000	0.000	0.000
29	A	625	THR	0	-0.074	-0.026	14.092	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	626	GLY	0	0.043	0.020	16.563	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	627	ALA	0	0.003	-0.013	18.838	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	628	ALA	0	0.042	0.034	19.179	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	629	ASN	0	-0.035	-0.025	15.399	0.007	0.007	0.000	0.000	0.000	0.000
34	A	630	TRP	0	-0.018	-0.025	11.125	0.028	0.028	0.000	0.000	0.000	0.000
35	A	631	ASN	0	0.004	0.016	15.016	-0.061	-0.061	0.000	0.000	0.000	0.000
36	A	632	LEU	0	0.046	0.007	16.574	0.037	0.037	0.000	0.000	0.000	0.000
37	A	633	GLU	-1	-0.903	-0.957	18.104	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	634	LEU	0	-0.010	-0.003	21.245	0.017	0.017	0.000	0.000	0.000	0.000
39	A	635	ALA	0	0.016	0.017	18.877	0.020	0.020	0.000	0.000	0.000	0.000
40	A	636	LEU	0	-0.018	-0.016	20.992	0.018	0.018	0.000	0.000	0.000	0.000
41	A	637	GLN	0	0.034	0.023	23.305	0.009	0.009	0.000	0.000	0.000	0.000
42	A	638	SER	0	-0.026	-0.019	23.582	0.004	0.004	0.000	0.000	0.000	0.000
43	A	639	PHE	0	0.030	0.002	23.802	0.002	0.002	0.000	0.000	0.000	0.000
44	A	640	GLU	-1	-0.978	-0.996	25.660	0.041	0.041	0.000	0.000	0.000	0.000
45	A	641	GLN	0	-0.042	-0.029	28.852	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	642	GLN	0	-0.004	-0.003	26.357	0.011	0.011	0.000	0.000	0.000	0.000
47	A	643	LYS	1	0.929	0.980	28.493	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	644	ALA	0	-0.029	-0.019	29.506	0.007	0.007	0.000	0.000	0.000	0.000
49	A	645	ASN	0	-0.051	-0.023	29.806	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	646	VAL	0	-0.041	-0.004	25.693	0.015	0.015	0.000	0.000	0.000	0.000
51	A	647	PRO	0	0.021	0.029	26.668	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	648	PRO	0	0.042	0.004	28.258	0.008	0.008	0.000	0.000	0.000	0.000
53	A	649	GLU	-1	-0.892	-0.960	27.757	0.195	0.195	0.000	0.000	0.000	0.000
54	A	650	ALA	0	-0.052	-0.015	24.070	0.017	0.017	0.000	0.000	0.000	0.000
55	A	651	PHE	0	-0.072	-0.032	23.968	0.019	0.019	0.000	0.000	0.000	0.000
56	A	652	ILE	0	-0.010	-0.001	20.370	0.001	0.001	0.000	0.000	0.000	0.000
57	A	653	SER	0	-0.061	-0.029	23.250	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	654	GLN	0	0.012	0.004	25.805	0.003	0.003	0.000	0.000	0.000	0.000
59	A	655	PRO	0	0.006	0.009	26.757	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	656	GLN	0	-0.092	-0.039	24.248	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	657	VAL	0	-0.014	0.004	25.684	-0.014	-0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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