FMO DATABASE

FMODB ID: KGR83

Calculation Name: 3KT9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KT9

Chain ID: A

ChEMBL ID:

UniProt ID: Q7Z2E3

Base Structure: X-ray

Registration Date: 2023-09-20

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-823211.544691
FMO2-HF: Nuclear repulsion	781336.056799
FMO2-HF: Total energy	-41875.487892
FMO2-MP2: Total energy	-41995.238166

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.
-2.885	-1.618	-0.011	-0.636	-0.62	0.002

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 : 0.021 / q_NPA : -0.012

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	ARG	1	0.938	0.977	3.753	-1.175	0.092	-0.011	-0.636	-0.620	0.002
4	A	4	VAL	0	-0.003	-0.012	6.313	0.727	0.727	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.034	-0.001	8.117	-0.012	-0.012	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.017	-0.001	11.022	0.125	0.125	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.020	0.006	14.522	0.007	0.007	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.024	-0.010	17.801	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.846	0.924	20.201	0.074	0.074	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.019	-0.005	23.944	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.835	-0.914	25.070	-0.081	-0.081	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.061	-0.037	26.213	0.001	0.001	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.930	0.941	18.935	0.242	0.242	0.000	0.000	0.000	0.000
14	A	14	HIS	0	0.022	0.009	21.146	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.036	-0.004	21.446	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.944	0.975	13.762	0.385	0.385	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.017	0.009	17.708	0.007	0.007	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.967	0.988	8.181	0.299	0.299	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.024	-0.016	13.487	0.048	0.048	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.033	0.010	11.362	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	21	HIS	0	0.074	0.026	9.558	-0.132	-0.132	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.082	-0.046	11.611	0.051	0.051	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.943	-0.948	14.080	0.494	0.494	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.088	-0.056	16.649	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.032	0.022	17.286	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.029	-0.018	20.358	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.026	0.023	22.169	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.067	0.016	25.150	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.797	0.935	28.392	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.001	-0.014	29.671	0.008	0.008	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.006	0.000	27.450	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.885	-0.943	22.596	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.011	-0.024	24.922	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.940	0.967	26.625	0.063	0.063	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.002	0.024	28.705	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.005	-0.017	31.764	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.786	-0.857	35.140	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.957	0.954	35.920	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.930	0.980	37.929	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	CYS	0	0.029	0.057	31.618	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.022	0.011	32.639	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.980	0.976	31.409	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.004	0.011	28.582	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.035	-0.023	28.860	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.062	0.033	24.408	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.012	-0.011	22.926	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.002	-0.001	19.523	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.960	0.984	17.801	-0.204	-0.204	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.054	0.034	13.463	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.848	-0.925	12.625	0.574	0.574	0.000	0.000	0.000	0.000
51	A	51	CYS	0	0.019	-0.002	8.563	-0.064	-0.064	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.013	-0.003	7.268	-0.294	-0.294	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.899	0.939	9.692	-0.477	-0.477	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.019	0.014	12.954	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.000	-0.007	14.143	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.020	0.006	16.129	0.031	0.031	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.872	0.955	18.343	-0.254	-0.254	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.056	0.026	21.198	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.959	0.990	23.839	-0.144	-0.144	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.032	0.032	26.682	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.004	-0.008	27.962	0.006	0.006	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.012	-0.005	30.734	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.014	-0.018	33.331	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.063	-0.047	36.409	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	PRO	0	0.032	0.026	34.595	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	THR	0	0.012	-0.008	28.314	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.010	-0.001	30.721	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.008	-0.005	25.526	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.812	-0.905	28.398	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.031	-0.013	30.695	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.004	0.011	32.127	0.004	0.004	0.000	0.000	0.000	0.000
72	A	72	VAL	0	-0.034	-0.032	32.028	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.044	-0.007	27.577	0.003	0.003	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.044	0.017	31.858	0.004	0.004	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.915	0.947	32.625	-0.052	-0.052	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.927	-0.973	31.274	0.083	0.083	0.000	0.000	0.000	0.000
77	A	77	GLN	0	-0.068	-0.005	31.185	0.012	0.012	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.919	-1.000	24.084	0.165	0.165	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.013	0.014	26.285	0.003	0.003	0.000	0.000	0.000	0.000
80	A	80	LYS	1	0.881	0.945	20.730	-0.145	-0.145	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.038	0.031	20.673	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.022	-0.029	19.893	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	PRO	0	0.032	0.003	17.378	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	84	GLY	0	-0.017	-0.001	20.054	0.013	0.013	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.024	0.031	23.148	0.012	0.012	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.009	-0.006	23.957	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.032	-0.011	23.574	0.014	0.014	0.000	0.000	0.000	0.000
88	A	88	HIS	0	0.024	0.021	26.393	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.024	-0.010	25.091	0.014	0.014	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.023	-0.028	29.473	0.010	0.010	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.029	-0.014	33.246	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.893	-0.946	33.642	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.014	0.014	33.555	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.086	-0.109	29.742	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.065	0.052	27.829	0.006	0.006	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.032	-0.035	22.490	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.034	0.030	20.516	0.009	0.009	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.023	-0.017	16.711	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.835	-0.901	15.315	-0.291	-0.291	0.000	0.000	0.000	0.000
100	A	100	PHE	0	-0.042	-0.033	10.894	0.032	0.032	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.927	-0.958	10.170	-0.696	-0.696	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.936	-0.957	5.774	-2.069	-2.069	0.000	0.000	0.000	0.000

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