FMO DATABASE

FMODB ID: 3Q6YL

Calculation Name: 2W9J-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-(dimethylarsenic)cysteine

ligand 3-letter code: CAS

PDB ID: 2W9J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9P372

Base Structure: X-ray

Registration Date: 2023-06-20

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-481662.265387
FMO2-HF: Nuclear repulsion	447138.519158
FMO2-HF: Total energy	-34523.746229
FMO2-MP2: Total energy	-34611.138776

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:1:MET)

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

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.
-2.337	-0.253	-0.012	-0.918	-1.154	0.004

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.009

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

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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	3	LEU	0	0.034	0.030	3.795	-1.194	0.890	-0.012	-0.918	-1.154	0.004
4	A	4	SER	0	0.088	0.056	6.064	0.630	0.630	0.000	0.000	0.000	0.000
5	A	5	ASN	0	0.007	-0.029	9.575	0.054	0.054	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.903	-0.952	12.052	-0.683	-0.683	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.903	-0.950	8.098	-1.259	-1.259	0.000	0.000	0.000	0.000
8	A	8	PHE	0	-0.049	-0.032	7.665	0.021	0.021	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.025	0.005	9.341	0.173	0.173	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.941	0.994	11.784	0.708	0.708	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.972	0.969	7.405	0.900	0.900	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.006	-0.004	10.476	0.152	0.152	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.016	0.010	12.316	0.143	0.143	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.882	-0.955	12.796	-0.466	-0.466	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.078	-0.017	9.786	0.106	0.106	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.021	-0.015	13.609	0.083	0.083	0.000	0.000	0.000	0.000
17	A	17	GLN	0	-0.038	-0.010	16.993	0.052	0.052	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.083	-0.051	15.702	0.041	0.041	0.000	0.000	0.000	0.000
19	A	19	HIS	0	-0.030	0.002	17.795	0.062	0.062	0.000	0.000	0.000	0.000
20	A	27	VAL	0	0.015	0.005	21.162	0.008	0.008	0.000	0.000	0.000	0.000
21	A	28	TYR	0	-0.064	-0.043	18.940	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	29	LEU	0	0.063	0.032	13.949	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	30	SER	0	-0.094	-0.023	15.188	0.037	0.037	0.000	0.000	0.000	0.000
24	A	31	GLN	0	0.122	0.061	13.838	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	32	LYS	1	0.889	0.941	13.437	0.129	0.129	0.000	0.000	0.000	0.000
26	A	33	CAS	0	0.011	0.025	13.610	-0.129	-0.129	0.000	0.000	0.000	0.000
27	A	34	ASN	0	-0.057	-0.029	14.007	0.070	0.070	0.000	0.000	0.000	0.000
28	A	35	PRO	0	0.065	0.036	14.974	-0.074	-0.074	0.000	0.000	0.000	0.000
29	A	36	VAL	0	-0.033	-0.031	12.406	0.020	0.020	0.000	0.000	0.000	0.000
30	A	37	ASP	-1	-0.905	-0.957	15.627	-0.238	-0.238	0.000	0.000	0.000	0.000
31	A	38	GLU	-1	-0.930	-0.956	14.064	-0.439	-0.439	0.000	0.000	0.000	0.000
32	A	39	GLY	0	0.003	-0.032	16.691	-0.054	-0.054	0.000	0.000	0.000	0.000
33	A	40	GLU	-1	-0.995	-0.966	16.296	-0.337	-0.337	0.000	0.000	0.000	0.000
34	A	41	GLY	0	0.058	0.045	18.831	0.043	0.043	0.000	0.000	0.000	0.000
35	A	42	SER	0	-0.081	-0.047	20.315	-0.025	-0.025	0.000	0.000	0.000	0.000
36	A	43	SER	0	-0.070	-0.029	20.990	0.028	0.028	0.000	0.000	0.000	0.000
37	A	44	ALA	0	-0.010	0.007	19.674	0.009	0.009	0.000	0.000	0.000	0.000
38	A	45	SER	0	-0.004	0.001	15.802	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	46	VAL	0	-0.009	-0.004	15.128	0.042	0.042	0.000	0.000	0.000	0.000
40	A	47	LEU	0	-0.021	0.011	7.972	-0.105	-0.105	0.000	0.000	0.000	0.000
41	A	48	ILE	0	0.026	0.001	11.383	0.184	0.184	0.000	0.000	0.000	0.000
42	A	49	ARG	1	0.797	0.897	8.976	0.041	0.041	0.000	0.000	0.000	0.000
43	A	50	ALA	0	0.076	0.040	9.196	0.156	0.156	0.000	0.000	0.000	0.000
44	A	51	LYS	1	0.956	0.976	9.486	-0.224	-0.224	0.000	0.000	0.000	0.000
45	A	52	SER	0	0.051	0.029	11.764	0.015	0.015	0.000	0.000	0.000	0.000
46	A	53	GLY	0	0.038	0.012	14.159	0.027	0.027	0.000	0.000	0.000	0.000
47	A	54	ALA	0	-0.028	-0.027	14.895	0.030	0.030	0.000	0.000	0.000	0.000
48	A	55	ALA	0	-0.008	0.025	11.016	0.076	0.076	0.000	0.000	0.000	0.000
49	A	56	GLU	-1	-0.920	-0.958	6.520	0.494	0.494	0.000	0.000	0.000	0.000
50	A	57	LYS	1	0.873	0.927	5.419	-0.998	-0.998	0.000	0.000	0.000	0.000
51	A	58	ILE	0	0.029	0.027	4.848	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	59	SER	0	-0.048	-0.048	4.838	1.104	1.104	0.000	0.000	0.000	0.000
53	A	60	THR	0	0.015	0.001	6.065	-0.793	-0.793	0.000	0.000	0.000	0.000
54	A	61	VAL	0	0.046	0.013	8.643	0.255	0.255	0.000	0.000	0.000	0.000
55	A	62	VAL	0	-0.019	0.004	11.320	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	63	GLU	-1	-0.806	-0.918	14.786	-0.510	-0.510	0.000	0.000	0.000	0.000
57	A	64	LEU	0	0.017	0.003	17.419	0.013	0.013	0.000	0.000	0.000	0.000
58	A	65	ASP	-1	-0.852	-0.926	20.970	-0.320	-0.320	0.000	0.000	0.000	0.000
59	A	66	TYR	0	-0.009	-0.008	17.284	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	67	PHE	0	-0.030	-0.018	17.861	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	68	THR	0	-0.006	-0.007	20.779	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	69	ASP	-1	-0.875	-0.927	21.033	-0.372	-0.372	0.000	0.000	0.000	0.000
63	A	70	PHE	0	-0.002	0.002	13.115	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	71	PHE	0	-0.024	-0.042	17.643	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	72	GLN	0	-0.008	0.010	20.153	0.025	0.025	0.000	0.000	0.000	0.000
66	A	73	SER	0	0.030	0.004	18.163	0.015	0.015	0.000	0.000	0.000	0.000
67	A	74	TYR	0	-0.107	-0.082	14.363	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	75	ALA	0	0.001	-0.005	18.227	0.022	0.022	0.000	0.000	0.000	0.000
69	A	76	GLU	-1	-0.975	-0.978	20.891	-0.272	-0.272	0.000	0.000	0.000	0.000
70	A	77	VAL	0	0.013	0.011	15.870	0.028	0.028	0.000	0.000	0.000	0.000
71	A	78	CAS	0	-0.041	-0.020	19.198	0.015	0.015	0.000	0.000	0.000	0.000
72	A	79	LYS	1	0.947	0.958	20.452	0.268	0.268	0.000	0.000	0.000	0.000
73	A	80	GLY	0	-0.025	-0.006	22.596	0.024	0.024	0.000	0.000	0.000	0.000
74	A	81	GLN	0	-0.034	-0.025	18.614	0.035	0.035	0.000	0.000	0.000	0.000
75	A	82	ILE	0	-0.049	-0.003	22.115	0.023	0.023	0.000	0.000	0.000	0.000
76	A	83	VAL	0	-0.035	-0.003	24.997	0.019	0.019	0.000	0.000	0.000	0.000

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