FMO DATABASE

FMODB ID: N1Q1Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-390680.70524
FMO2-HF: Nuclear repulsion	363073.009747
FMO2-HF: Total energy	-27607.695492
FMO2-MP2: Total energy	-27685.120481

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.
-3.505	0.941	2.426	-2.735	-4.135	-0.019

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 : 0.021 / q_NPA : 0.004

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	2	LEU	0	-0.039	-0.004	3.893	1.944	3.274	-0.009	-0.548	-0.773	0.001
4	A	3	TYR	0	-0.029	-0.039	6.491	-0.621	-0.621	0.000	0.000	0.000	0.000
5	A	4	HIS	1	0.838	0.909	9.225	0.163	0.163	0.000	0.000	0.000	0.000
6	A	5	TYR	0	0.021	0.012	13.270	-0.069	-0.069	0.000	0.000	0.000	0.000
7	A	6	GLN	0	0.014	0.005	16.973	0.006	0.006	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.785	-0.880	20.243	0.032	0.032	0.000	0.000	0.000	0.000
9	A	8	CYS	0	-0.068	0.017	23.908	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.045	0.030	26.300	0.003	0.003	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.925	0.926	27.844	0.036	0.036	0.000	0.000	0.000	0.000
12	A	11	GLY	0	-0.025	-0.004	29.637	0.005	0.005	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.036	-0.027	29.521	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.010	-0.001	27.151	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.018	-0.006	22.638	0.013	0.013	0.000	0.000	0.000	0.000
16	A	15	ILE	0	0.004	-0.005	23.408	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.035	-0.014	17.763	0.023	0.023	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.857	0.915	16.614	0.176	0.176	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.898	-0.964	14.931	-0.411	-0.411	0.000	0.000	0.000	0.000
20	A	19	PRO	0	-0.045	-0.014	9.856	0.054	0.054	0.000	0.000	0.000	0.000
21	A	20	CYS	0	-0.030	-0.009	6.850	0.609	0.609	0.000	0.000	0.000	0.000
22	A	21	PRO	0	0.012	0.012	11.746	0.019	0.019	0.000	0.000	0.000	0.000
23	A	22	SER	0	-0.030	-0.023	14.138	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.042	0.028	12.091	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.022	-0.023	11.553	0.101	0.101	0.000	0.000	0.000	0.000
26	A	25	TYR	0	-0.042	-0.034	12.311	-0.138	-0.138	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.850	-0.904	12.071	-0.863	-0.863	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.032	-0.009	15.309	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	28	ASN	0	-0.052	-0.018	17.673	0.004	0.004	0.000	0.000	0.000	0.000
30	A	29	SER	0	-0.001	0.013	21.005	0.035	0.035	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.002	0.008	21.775	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	31	PHE	0	0.012	0.012	17.899	0.008	0.008	0.000	0.000	0.000	0.000
33	A	32	HIS	0	0.008	0.004	22.133	0.015	0.015	0.000	0.000	0.000	0.000
34	A	33	PRO	0	0.021	0.014	21.602	0.007	0.007	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.014	-0.022	22.715	0.028	0.028	0.000	0.000	0.000	0.000
36	A	35	ALA	0	0.025	0.013	23.260	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	36	ASP	-1	-0.832	-0.920	23.393	-0.125	-0.125	0.000	0.000	0.000	0.000
38	A	37	ASN	0	-0.006	0.022	18.108	0.033	0.033	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.873	0.942	18.881	0.126	0.126	0.000	0.000	0.000	0.000
40	A	39	PHE	0	0.022	0.016	16.307	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	40	ALA	0	0.000	0.006	21.290	0.025	0.025	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.033	0.013	19.878	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	42	THR	0	0.011	0.011	24.300	0.016	0.016	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.028	-0.012	24.819	0.007	0.007	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.024	-0.018	23.858	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.017	0.024	20.522	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	47	HIS	0	0.034	0.009	15.181	0.064	0.064	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.004	0.000	15.034	0.023	0.023	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.012	-0.005	10.326	0.021	0.021	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.020	0.013	10.484	0.165	0.165	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.019	0.017	7.437	-0.398	-0.398	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.035	0.016	7.306	-0.343	-0.343	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.878	-0.925	5.496	-2.044	-2.044	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.008	0.005	4.336	-0.050	0.122	-0.001	-0.031	-0.140	0.000
55	A	56	THR	0	-0.093	-0.057	2.389	-7.015	-4.428	2.414	-2.271	-2.729	-0.020
56	A	57	ARG	1	0.836	0.906	3.307	4.022	4.379	0.022	0.115	-0.493	0.000
57	A	58	HIS	0	0.015	0.012	5.298	0.780	0.780	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.024	0.013	7.944	0.023	0.023	0.000	0.000	0.000	0.000
59	A	60	TYR	0	-0.004	-0.021	10.505	0.252	0.252	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.046	-0.024	13.994	0.008	0.008	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.006	0.008	17.293	0.033	0.033	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.913	0.948	20.717	-0.048	-0.048	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.033	0.012	23.609	0.008	0.008	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.842	0.914	26.674	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.050	0.031	29.798	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.006	0.000	32.809	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)