FMO DATABASE

FMODB ID: MNYKZ

Calculation Name: 4J11-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J11

Chain ID: A

ChEMBL ID:

UniProt ID: A0A2B6

Base Structure: X-ray

Registration Date: 2023-09-23

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-494884.456686
FMO2-HF: Nuclear repulsion	460906.176711
FMO2-HF: Total energy	-33978.279975
FMO2-MP2: Total energy	-34077.80167

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:ASN)

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

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.
-2.235	0.566	0.01	-1.075	-1.736	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : -0.011

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].
3	A	1	MET	0	-0.016	-0.009	2.958	-2.309	0.040	0.002	-0.974	-1.377
4	A	2	ALA	0	-0.033	0.003	3.485	0.374	0.800	0.009	-0.098	-0.337
5	A	3	GLU	-1	-0.924	-0.960	5.106	0.104	0.130	-0.001	-0.003	-0.022
6	A	4	ILE	0	-0.025	-0.011	8.611	-0.037	-0.037	0.000	0.000	0.000
7	A	5	LYS	1	0.958	0.976	10.490	-0.200	-0.200	0.000	0.000	0.000
8	A	6	ILE	0	0.023	0.007	13.236	-0.053	-0.053	0.000	0.000	0.000
9	A	7	THR	0	0.007	-0.010	16.023	0.010	0.010	0.000	0.000	0.000
10	A	8	PRO	0	0.021	0.004	18.874	0.006	0.006	0.000	0.000	0.000
11	A	9	GLU	-1	-0.758	-0.859	18.667	-0.185	-0.185	0.000	0.000	0.000
12	A	10	GLU	-1	-0.825	-0.889	14.963	-0.319	-0.319	0.000	0.000	0.000
13	A	11	LEU	0	-0.051	-0.010	18.818	0.015	0.015	0.000	0.000	0.000
14	A	12	GLU	-1	-0.760	-0.864	22.006	-0.117	-0.117	0.000	0.000	0.000
15	A	13	ARG	1	0.842	0.913	16.327	0.264	0.264	0.000	0.000	0.000
16	A	14	ILE	0	-0.009	-0.010	18.229	0.012	0.012	0.000	0.000	0.000
17	A	15	ALA	0	0.020	0.008	22.418	0.014	0.014	0.000	0.000	0.000
18	A	16	GLY	0	0.033	0.024	25.236	0.011	0.011	0.000	0.000	0.000
19	A	17	ASN	0	-0.022	-0.012	20.921	-0.003	-0.003	0.000	0.000	0.000
20	A	18	PHE	0	-0.007	-0.001	24.316	0.010	0.010	0.000	0.000	0.000
21	A	19	LYS	1	0.849	0.914	28.071	0.060	0.060	0.000	0.000	0.000
22	A	20	ASN	0	0.016	-0.006	27.080	0.009	0.009	0.000	0.000	0.000
23	A	21	ALA	0	0.026	0.027	28.439	0.004	0.004	0.000	0.000	0.000
24	A	22	ALA	0	0.004	0.001	30.364	0.006	0.006	0.000	0.000	0.000
25	A	23	GLY	0	0.007	0.006	33.341	0.004	0.004	0.000	0.000	0.000
26	A	24	GLU	-1	-0.964	-0.988	29.920	-0.070	-0.070	0.000	0.000	0.000
27	A	25	ALA	0	-0.016	-0.012	34.151	0.004	0.004	0.000	0.000	0.000
28	A	26	GLN	0	0.007	-0.010	35.779	0.004	0.004	0.000	0.000	0.000
29	A	27	SER	0	-0.030	-0.017	37.263	0.002	0.002	0.000	0.000	0.000
30	A	28	GLN	0	-0.058	-0.035	35.309	0.004	0.004	0.000	0.000	0.000
31	A	29	ILE	0	0.029	0.023	38.991	0.002	0.002	0.000	0.000	0.000
32	A	30	ASN	0	0.034	0.011	41.700	0.004	0.004	0.000	0.000	0.000
33	A	31	ARG	1	0.928	0.971	36.891	0.041	0.041	0.000	0.000	0.000
34	A	32	LEU	0	0.028	0.021	40.530	0.002	0.002	0.000	0.000	0.000
35	A	33	GLU	-1	-0.816	-0.888	44.521	-0.015	-0.015	0.000	0.000	0.000
36	A	34	GLY	0	-0.030	-0.019	46.956	0.001	0.001	0.000	0.000	0.000
37	A	35	ASP	-1	-0.864	-0.927	45.486	-0.020	-0.020	0.000	0.000	0.000
38	A	36	ILE	0	-0.023	-0.005	48.182	0.002	0.002	0.000	0.000	0.000
39	A	37	ASN	0	0.000	-0.005	50.702	0.003	0.003	0.000	0.000	0.000
40	A	38	SER	0	-0.079	-0.035	51.637	0.000	0.000	0.000	0.000	0.000
41	A	39	LEU	0	0.017	0.005	51.071	0.000	0.000	0.000	0.000	0.000
42	A	40	GLU	-1	-0.846	-0.904	55.015	-0.007	-0.007	0.000	0.000	0.000
43	A	41	GLY	0	-0.026	-0.015	57.734	-0.001	-0.001	0.000	0.000	0.000
44	A	42	GLN	0	-0.027	0.000	56.831	0.001	0.001	0.000	0.000	0.000
45	A	43	TRP	0	-0.026	-0.029	52.649	0.001	0.001	0.000	0.000	0.000
46	A	44	ALA	0	-0.010	-0.004	60.280	0.000	0.000	0.000	0.000	0.000
47	A	45	GLY	0	0.067	0.025	60.220	0.000	0.000	0.000	0.000	0.000
48	A	46	ALA	0	-0.006	-0.006	60.173	0.000	0.000	0.000	0.000	0.000
49	A	47	THR	0	0.007	0.003	55.865	0.001	0.001	0.000	0.000	0.000
50	A	48	GLN	0	0.002	0.006	54.648	0.001	0.001	0.000	0.000	0.000
51	A	49	ALA	0	-0.007	-0.001	55.404	0.000	0.000	0.000	0.000	0.000
52	A	50	LYS	1	0.815	0.898	50.818	-0.005	-0.005	0.000	0.000	0.000
53	A	51	PHE	0	0.029	0.008	49.554	0.001	0.001	0.000	0.000	0.000
54	A	52	ARG	1	0.849	0.913	50.599	0.010	0.010	0.000	0.000	0.000
55	A	53	GLY	0	0.009	0.002	51.332	0.000	0.000	0.000	0.000	0.000
56	A	54	GLU	-1	-0.793	-0.883	47.894	0.006	0.006	0.000	0.000	0.000
57	A	55	PHE	0	-0.006	0.010	44.518	0.000	0.000	0.000	0.000	0.000
58	A	56	ILE	0	0.015	0.012	46.581	-0.001	-0.001	0.000	0.000	0.000
59	A	57	GLN	0	-0.001	0.002	46.661	0.000	0.000	0.000	0.000	0.000
60	A	58	SER	0	-0.050	-0.033	42.483	0.000	0.000	0.000	0.000	0.000
61	A	59	LYS	1	0.846	0.902	42.456	0.016	0.016	0.000	0.000	0.000
62	A	60	GLN	0	-0.017	-0.017	43.613	0.000	0.000	0.000	0.000	0.000
63	A	61	ALA	0	0.023	0.015	40.314	0.000	0.000	0.000	0.000	0.000
64	A	62	MET	0	0.008	0.011	37.153	0.000	0.000	0.000	0.000	0.000
65	A	63	GLN	0	-0.044	-0.035	39.349	-0.003	-0.003	0.000	0.000	0.000
66	A	64	GLN	0	-0.021	0.006	39.848	0.000	0.000	0.000	0.000	0.000
67	A	65	TYR	0	-0.017	-0.014	31.391	0.001	0.001	0.000	0.000	0.000
68	A	66	ILE	0	0.048	0.019	35.287	-0.002	-0.002	0.000	0.000	0.000
69	A	67	PRO	0	0.026	0.007	35.447	-0.003	-0.003	0.000	0.000	0.000
70	A	68	ILE	0	0.006	0.015	32.621	0.000	0.000	0.000	0.000	0.000
71	A	69	LEU	0	-0.018	-0.001	29.937	-0.001	-0.001	0.000	0.000	0.000
72	A	70	GLU	-1	-0.878	-0.932	31.097	-0.046	-0.046	0.000	0.000	0.000
73	A	71	GLY	0	0.019	0.017	32.923	-0.004	-0.004	0.000	0.000	0.000
74	A	72	ILE	0	0.030	0.019	27.153	0.000	0.000	0.000	0.000	0.000
75	A	73	SER	0	-0.058	-0.034	28.280	-0.005	-0.005	0.000	0.000	0.000
76	A	74	THR	0	-0.039	-0.031	29.207	-0.006	-0.006	0.000	0.000	0.000
77	A	75	ASP	-1	-0.853	-0.917	29.540	-0.010	-0.010	0.000	0.000	0.000
78	A	76	LEU	0	-0.035	-0.013	23.320	0.002	0.002	0.000	0.000	0.000
79	A	77	LYS	1	0.825	0.891	26.350	0.082	0.082	0.000	0.000	0.000
80	A	78	ARG	1	0.874	0.922	28.452	0.010	0.010	0.000	0.000	0.000
81	A	79	ILE	0	-0.025	-0.011	24.708	0.002	0.002	0.000	0.000	0.000
82	A	80	ALA	0	0.014	0.011	24.874	-0.001	-0.001	0.000	0.000	0.000
83	A	81	ASP	-1	-0.798	-0.899	25.828	-0.076	-0.076	0.000	0.000	0.000
84	A	82	LYS	1	0.900	0.959	28.078	0.009	0.009	0.000	0.000	0.000
85	A	83	PHE	0	-0.024	-0.017	21.657	0.005	0.005	0.000	0.000	0.000
86	A	84	ARG	1	0.760	0.855	23.024	0.140	0.140	0.000	0.000	0.000
87	A	85	ASN	0	-0.104	-0.037	27.135	0.004	0.004	0.000	0.000	0.000

Top

Graph

Manual

About

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