FMO DATABASE

FMODB ID: ZVVMN

Calculation Name: 3KJK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KJK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JZJ4

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-919947.754962
FMO2-HF: Nuclear repulsion	874178.396927
FMO2-HF: Total energy	-45769.358035
FMO2-MP2: Total energy	-45900.44616

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.
-7.234	-4.775	6.681	-3.439	-5.701	0

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 : -0.033 / q_NPA : -0.034

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	3	ILE	0	-0.037	-0.026	3.870	1.580	2.683	-0.004	-0.435	-0.663	0.002
4	A	4	ARG	1	0.892	0.961	6.364	-0.613	-0.613	0.000	0.000	0.000	0.000
5	A	5	TYR	0	0.011	-0.011	9.530	-0.009	-0.009	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.016	0.009	11.296	0.061	0.061	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.079	0.033	15.847	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.017	-0.009	15.909	0.000	0.000	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.042	0.030	18.531	0.014	0.014	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.027	-0.037	20.099	-0.033	-0.033	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.886	0.950	21.185	0.132	0.132	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.068	-0.036	17.462	-0.042	-0.042	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.042	0.011	14.773	-0.035	-0.035	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.833	-0.866	16.709	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.032	0.012	14.424	0.043	0.043	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.008	-0.003	9.813	-0.098	-0.098	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.025	0.010	8.287	0.125	0.125	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.004	0.010	3.016	-1.029	-0.661	0.075	-0.117	-0.326	0.000
19	A	19	ASN	0	-0.013	-0.015	2.219	-4.824	-4.273	6.585	-2.677	-4.460	-0.003
20	A	20	GLY	0	0.011	0.020	3.881	-2.132	-1.695	0.025	-0.210	-0.252	0.001
21	A	21	LEU	0	0.002	0.010	5.828	-0.891	-0.891	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.005	-0.010	8.069	-0.046	-0.046	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.033	-0.020	6.661	-0.068	-0.068	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.018	0.018	12.024	-0.064	-0.064	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.011	-0.028	15.559	-0.044	-0.044	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.025	-0.012	17.533	0.039	0.039	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.044	0.003	19.511	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.040	0.002	23.005	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.020	0.014	26.545	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.873	-0.917	27.858	0.053	0.053	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.092	-0.054	31.337	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.023	0.010	33.807	0.005	0.005	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.994	-0.996	36.408	0.025	0.025	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.049	-0.050	38.158	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.041	0.020	34.146	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.004	0.002	33.602	0.009	0.009	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.813	-0.880	34.130	0.066	0.066	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.005	-0.010	31.972	0.006	0.006	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.012	-0.026	29.121	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.013	-0.010	29.266	0.013	0.013	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.777	-0.871	30.062	0.086	0.086	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.034	0.015	24.948	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.003	-0.016	24.954	0.016	0.016	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.012	0.015	25.676	0.024	0.024	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.074	-0.065	24.202	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.004	-0.004	20.483	0.021	0.021	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.816	-0.897	21.083	0.294	0.294	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.780	0.890	22.297	-0.079	-0.079	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.010	-0.030	18.271	0.020	0.020	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.002	0.005	16.387	0.052	0.052	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.000	0.007	17.180	0.076	0.076	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.920	-0.961	17.465	0.235	0.235	0.000	0.000	0.000	0.000
53	A	53	CYS	0	-0.082	-0.033	13.050	0.019	0.019	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.032	-0.011	13.268	0.171	0.171	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.035	-0.047	14.662	0.063	0.063	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.757	-0.860	16.659	0.447	0.447	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.884	0.934	19.365	-0.195	-0.195	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.016	0.008	21.648	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.090	-0.050	16.383	0.056	0.056	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.032	0.019	16.097	0.100	0.100	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.056	-0.027	12.157	0.016	0.016	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.878	-0.938	14.907	0.258	0.258	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.028	0.019	17.005	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.019	0.003	18.540	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.035	0.006	21.214	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.018	0.012	20.398	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.052	0.012	26.240	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.851	0.937	30.070	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.850	-0.922	32.546	0.030	0.030	0.000	0.000	0.000	0.000
70	A	70	MET	0	0.003	-0.002	30.465	0.009	0.009	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.015	-0.001	34.773	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.778	-0.869	34.186	0.056	0.056	0.000	0.000	0.000	0.000
73	A	73	TYR	0	-0.033	-0.014	29.760	0.012	0.012	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.012	-0.018	33.699	0.009	0.009	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.830	-0.914	36.135	0.072	0.072	0.000	0.000	0.000	0.000
76	A	76	MET	0	-0.015	0.009	29.481	0.011	0.011	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.047	0.016	31.069	0.019	0.019	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.018	0.017	32.511	0.010	0.010	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.038	-0.005	31.428	0.004	0.004	0.000	0.000	0.000	0.000
80	A	80	TRP	0	0.029	-0.003	22.770	0.014	0.014	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.901	-0.972	29.245	0.180	0.180	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.070	-0.022	31.241	0.007	0.007	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.040	-0.020	22.722	0.010	0.010	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.022	-0.015	25.247	0.022	0.022	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.003	0.008	24.573	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.044	0.017	26.519	0.009	0.009	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.042	-0.023	27.907	0.010	0.010	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.775	0.865	19.799	-0.521	-0.521	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.030	0.031	22.831	0.013	0.013	0.000	0.000	0.000	0.000
90	A	90	PRO	0	-0.015	0.005	19.472	0.017	0.017	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.004	0.000	18.578	-0.039	-0.039	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.842	0.906	20.396	-0.166	-0.166	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.019	-0.002	21.987	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	94	CYS	0	-0.079	-0.037	23.672	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.012	0.005	25.176	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.813	-0.879	27.763	0.028	0.028	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.016	-0.022	27.229	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.826	0.897	29.149	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.033	0.036	26.918	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.004	-0.011	27.577	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.836	0.914	29.645	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.039	-0.033	33.032	0.006	0.006	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.763	-0.870	35.537	0.001	0.001	0.000	0.000	0.000	0.000
104	A	104	TRP	0	-0.069	-0.015	28.189	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.821	0.847	32.514	-0.046	-0.046	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.018	0.000	28.086	0.002	0.002	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.876	-0.948	22.911	0.005	0.005	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.032	-0.015	21.642	0.008	0.008	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.901	0.977	13.329	-0.148	-0.148	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.022	0.001	16.418	0.025	0.025	0.000	0.000	0.000	0.000
111	A	111	THR	0	-0.043	-0.040	11.144	-0.058	-0.058	0.000	0.000	0.000	0.000
112	A	112	ALA	0	0.011	0.008	12.536	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.006	0.004	10.684	0.190	0.190	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.805	0.904	10.041	-1.915	-1.915	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.857	0.915	12.698	-0.475	-0.475	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.871	-0.919	12.372	1.551	1.551	0.000	0.000	0.000	0.000

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