FMO DATABASE

FMODB ID: 82M2Y

Calculation Name: 1XAK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XAK

Chain ID: A

ChEMBL ID:

UniProt ID: P59635

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	OptHSide
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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-391449.63337
FMO2-HF: Nuclear repulsion	363842.07606
FMO2-HF: Total energy	-27607.55731
FMO2-MP2: Total energy	-27684.967085

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:CYS)

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

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.
-4.649	0.382	1.687	-2.68	-4.039	-0.018

Interaction energy analysis for fragmet #1(A:-1:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.006

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	2	LEU	0	-0.029	-0.004	3.814	1.940	3.441	-0.013	-0.592	-0.896	0.001
4	A	3	TYR	0	-0.030	-0.037	6.437	-0.564	-0.564	0.000	0.000	0.000	0.000
5	A	4	HIS	1	0.833	0.903	9.349	0.249	0.249	0.000	0.000	0.000	0.000
6	A	5	TYR	0	0.002	-0.005	13.284	-0.058	-0.058	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.003	-0.002	16.853	0.012	0.012	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.804	-0.897	20.151	0.025	0.025	0.000	0.000	0.000	0.000
9	A	8	CYS	0	-0.068	-0.004	23.727	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.027	0.020	26.048	0.004	0.004	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.976	0.964	27.756	0.036	0.036	0.000	0.000	0.000	0.000
12	A	11	GLY	0	-0.020	0.001	29.968	0.006	0.006	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.039	-0.022	29.469	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.007	0.000	27.450	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.018	-0.009	22.558	0.013	0.013	0.000	0.000	0.000	0.000
16	A	15	ILE	0	0.004	-0.003	23.370	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.034	-0.009	17.811	0.023	0.023	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.820	0.895	16.846	0.182	0.182	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.892	-0.968	15.079	-0.402	-0.402	0.000	0.000	0.000	0.000
20	A	19	PRO	0	-0.051	-0.019	9.982	0.059	0.059	0.000	0.000	0.000	0.000
21	A	20	CYS	0	-0.056	-0.029	7.059	0.560	0.560	0.000	0.000	0.000	0.000
22	A	21	PRO	0	0.004	0.004	12.084	0.028	0.028	0.000	0.000	0.000	0.000
23	A	22	SER	0	-0.005	-0.009	13.980	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.049	0.043	12.581	-0.062	-0.062	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.020	-0.015	12.000	0.103	0.103	0.000	0.000	0.000	0.000
26	A	25	TYR	0	-0.033	-0.035	12.483	-0.134	-0.134	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.897	-0.934	12.874	-0.709	-0.709	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.042	-0.005	15.423	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	28	ASN	0	-0.046	-0.020	17.941	0.008	0.008	0.000	0.000	0.000	0.000
30	A	29	SER	0	-0.001	0.011	21.249	0.031	0.031	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.006	0.007	21.894	-0.031	-0.031	0.000	0.000	0.000	0.000
32	A	31	PHE	0	0.008	0.009	18.176	0.008	0.008	0.000	0.000	0.000	0.000
33	A	32	HIS	0	0.018	0.008	22.152	0.019	0.019	0.000	0.000	0.000	0.000
34	A	33	PRO	0	0.003	0.009	22.123	0.005	0.005	0.000	0.000	0.000	0.000
35	A	34	LEU	0	0.001	-0.008	23.045	0.027	0.027	0.000	0.000	0.000	0.000
36	A	35	ALA	0	0.016	0.012	23.734	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	36	ASP	-1	-0.889	-0.954	23.586	-0.128	-0.128	0.000	0.000	0.000	0.000
38	A	37	ASN	0	0.006	0.012	18.275	0.033	0.033	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.955	1.001	18.777	0.108	0.108	0.000	0.000	0.000	0.000
40	A	39	PHE	0	0.019	0.014	16.499	-0.020	-0.020	0.000	0.000	0.000	0.000
41	A	40	ALA	0	-0.004	0.002	21.547	0.021	0.021	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.033	0.012	19.960	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	42	THR	0	0.020	0.018	24.401	0.014	0.014	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.003	-0.026	24.813	0.008	0.008	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.025	-0.027	23.254	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.022	0.030	20.159	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	47	HIS	0	0.067	0.024	14.508	0.064	0.064	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.015	-0.002	15.236	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.003	-0.004	10.321	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.024	0.010	10.576	0.142	0.142	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.002	0.006	7.724	-0.409	-0.409	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.049	0.019	7.537	-0.336	-0.336	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.898	-0.930	5.601	-1.971	-1.971	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.001	0.004	4.444	-0.218	-0.040	-0.001	-0.028	-0.149	0.000
55	A	56	THR	0	-0.060	-0.049	2.518	-7.521	-4.896	1.690	-1.809	-2.506	-0.020
56	A	57	ARG	1	0.878	0.942	3.501	3.326	4.053	0.011	-0.251	-0.488	0.001
57	A	58	HIS	0	0.021	0.020	5.645	0.736	0.736	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.036	0.019	8.227	0.048	0.048	0.000	0.000	0.000	0.000
59	A	60	TYR	0	-0.017	-0.027	10.619	0.234	0.234	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.022	0.000	14.193	0.007	0.007	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.003	0.004	16.921	0.039	0.039	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.908	0.953	20.502	-0.044	-0.044	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.013	-0.002	23.223	0.005	0.005	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.897	0.948	26.549	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.023	0.019	29.566	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.016	0.004	33.007	0.002	0.002	0.000	0.000	0.000	0.000

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