FMO DATABASE

FMODB ID: R8VV8

Calculation Name: 3KYE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KYE

Chain ID: A

ChEMBL ID:

UniProt ID: Q82MM8

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	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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-876409.856715
FMO2-HF: Nuclear repulsion	831597.412642
FMO2-HF: Total energy	-44812.444073
FMO2-MP2: Total energy	-44939.48149

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:10:VAL)

Summations of interaction energy for fragment #1(A:10:VAL)

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.
-13.692	-8.144	3.437	-2.991	-5.992	0.014

Interaction energy analysis for fragmet #1(A:10:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.003

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	12	ASP	-1	-0.937	-0.963	2.215	-0.512	1.838	1.588	-1.276	-2.661	0.003
4	A	13	LEU	0	-0.004	-0.022	2.486	-7.012	-4.974	1.845	-1.358	-2.524	0.010
5	A	14	ASP	-1	-0.824	-0.919	4.059	-3.324	-2.609	0.004	-0.272	-0.448	0.001
6	A	15	TRP	0	-0.019	-0.002	6.113	-0.176	-0.176	0.000	0.000	0.000	0.000
7	A	16	LEU	0	-0.039	-0.026	7.298	-0.350	-0.350	0.000	0.000	0.000	0.000
8	A	17	MET	0	-0.043	-0.004	7.774	-0.312	-0.312	0.000	0.000	0.000	0.000
9	A	18	SER	0	0.028	-0.001	10.264	-0.136	-0.136	0.000	0.000	0.000	0.000
10	A	19	GLY	0	-0.013	-0.008	11.856	-0.067	-0.067	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.041	-0.021	13.156	-0.062	-0.062	0.000	0.000	0.000	0.000
12	A	21	VAL	0	0.007	0.003	14.348	-0.051	-0.051	0.000	0.000	0.000	0.000
13	A	22	GLN	0	-0.099	-0.049	15.616	-0.026	-0.026	0.000	0.000	0.000	0.000
14	A	23	ARG	1	0.872	0.936	14.129	-0.435	-0.435	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.031	-0.001	19.247	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	25	PRO	0	0.025	0.009	21.301	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	26	HIS	0	0.049	0.019	23.706	0.000	0.000	0.000	0.000	0.000	0.000
18	A	27	THR	0	-0.024	-0.002	18.812	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	28	THR	0	-0.036	-0.029	19.203	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	29	SER	0	-0.012	-0.003	14.772	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	30	ALA	0	0.018	0.010	12.371	0.020	0.020	0.000	0.000	0.000	0.000
22	A	31	VAL	0	0.030	0.013	10.219	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	32	LEU	0	-0.001	0.004	6.994	0.043	0.043	0.000	0.000	0.000	0.000
24	A	33	LEU	0	-0.019	-0.013	8.962	-0.109	-0.109	0.000	0.000	0.000	0.000
25	A	34	SER	0	0.003	0.001	11.164	0.072	0.072	0.000	0.000	0.000	0.000
26	A	35	CYS	0	-0.030	-0.024	12.544	0.000	0.000	0.000	0.000	0.000	0.000
27	A	36	ASP	-1	-0.966	-0.980	14.664	-0.074	-0.074	0.000	0.000	0.000	0.000
28	A	37	GLY	0	0.027	0.015	15.442	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	38	LEU	0	-0.014	0.004	10.898	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	39	VAL	0	0.044	0.019	7.547	0.087	0.087	0.000	0.000	0.000	0.000
31	A	40	LYS	1	0.846	0.924	5.870	-0.327	-0.327	0.000	0.000	0.000	0.000
32	A	41	SER	0	-0.011	-0.012	3.903	-0.648	-0.295	0.001	-0.082	-0.271	0.000
33	A	42	VAL	0	-0.011	0.005	5.498	0.209	0.209	0.000	0.000	0.000	0.000
34	A	43	HIS	0	0.023	0.029	8.580	-0.079	-0.079	0.000	0.000	0.000	0.000
35	A	44	GLY	0	0.021	-0.007	11.108	0.029	0.029	0.000	0.000	0.000	0.000
36	A	45	LEU	0	-0.035	-0.009	13.194	0.008	0.008	0.000	0.000	0.000	0.000
37	A	46	ASP	-1	-0.847	-0.893	12.671	-0.167	-0.167	0.000	0.000	0.000	0.000
38	A	47	PRO	0	0.032	-0.014	10.699	0.009	0.009	0.000	0.000	0.000	0.000
39	A	48	ASP	-1	-0.859	-0.918	12.119	-0.194	-0.194	0.000	0.000	0.000	0.000
40	A	49	SER	0	-0.049	-0.060	15.416	0.022	0.022	0.000	0.000	0.000	0.000
41	A	50	ALA	0	-0.029	-0.012	11.539	0.032	0.032	0.000	0.000	0.000	0.000
42	A	51	ASP	-1	-0.867	-0.932	11.962	-0.266	-0.266	0.000	0.000	0.000	0.000
43	A	52	HIS	0	-0.043	-0.022	14.153	0.034	0.034	0.000	0.000	0.000	0.000
44	A	53	MET	0	-0.019	0.006	15.001	0.028	0.028	0.000	0.000	0.000	0.000
45	A	54	ALA	0	0.009	0.004	12.745	0.031	0.031	0.000	0.000	0.000	0.000
46	A	55	ALA	0	0.049	0.029	14.826	0.020	0.020	0.000	0.000	0.000	0.000
47	A	56	LEU	0	-0.016	-0.020	18.185	0.016	0.016	0.000	0.000	0.000	0.000
48	A	57	ALA	0	0.007	0.004	16.507	0.012	0.012	0.000	0.000	0.000	0.000
49	A	58	SER	0	-0.006	-0.008	16.860	0.014	0.014	0.000	0.000	0.000	0.000
50	A	59	GLY	0	0.000	0.009	18.639	0.002	0.002	0.000	0.000	0.000	0.000
51	A	60	LEU	0	-0.010	-0.015	21.544	0.004	0.004	0.000	0.000	0.000	0.000
52	A	61	TYR	0	-0.022	-0.026	19.595	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	62	SER	0	-0.007	-0.002	21.627	0.003	0.003	0.000	0.000	0.000	0.000
54	A	63	LEU	0	-0.008	-0.012	23.484	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	64	GLY	0	0.041	0.013	25.340	0.000	0.000	0.000	0.000	0.000	0.000
56	A	65	ARG	1	0.923	0.964	22.893	-0.057	-0.057	0.000	0.000	0.000	0.000
57	A	66	SER	0	-0.043	-0.017	25.879	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	67	ALA	0	-0.020	-0.008	29.052	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	68	GLY	0	0.017	0.012	28.806	0.000	0.000	0.000	0.000	0.000	0.000
60	A	69	ILE	0	-0.027	-0.006	27.942	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	70	ARG	1	0.888	0.948	31.242	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	71	PHE	0	-0.049	-0.036	33.499	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	72	GLY	0	-0.002	0.009	31.712	0.002	0.002	0.000	0.000	0.000	0.000
64	A	73	ASP	-1	-0.940	-0.973	32.638	0.054	0.054	0.000	0.000	0.000	0.000
65	A	74	GLY	0	-0.003	0.002	30.869	0.001	0.001	0.000	0.000	0.000	0.000
66	A	75	GLY	0	-0.081	-0.036	27.124	0.003	0.003	0.000	0.000	0.000	0.000
67	A	76	ASP	-1	-0.811	-0.887	22.056	0.090	0.090	0.000	0.000	0.000	0.000
68	A	77	VAL	0	0.007	-0.002	22.783	0.004	0.004	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.915	0.968	23.087	-0.111	-0.111	0.000	0.000	0.000	0.000
70	A	79	GLN	0	0.009	-0.020	21.138	0.007	0.007	0.000	0.000	0.000	0.000
71	A	80	VAL	0	-0.028	0.004	22.373	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	81	VAL	0	0.016	0.007	22.943	0.009	0.009	0.000	0.000	0.000	0.000
73	A	82	VAL	0	-0.031	-0.010	24.425	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	83	GLU	-1	-0.905	-0.961	26.078	0.053	0.053	0.000	0.000	0.000	0.000
75	A	84	LEU	0	-0.037	-0.012	25.625	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.865	-0.938	29.609	0.022	0.022	0.000	0.000	0.000	0.000
77	A	86	SER	0	-0.026	-0.027	30.231	0.002	0.002	0.000	0.000	0.000	0.000
78	A	87	THR	0	-0.012	-0.010	24.800	0.002	0.002	0.000	0.000	0.000	0.000
79	A	88	LEU	0	0.006	0.009	24.502	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	89	LEU	0	0.015	0.020	18.922	0.004	0.004	0.000	0.000	0.000	0.000
81	A	90	PHE	0	-0.015	-0.003	20.136	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	91	VAL	0	0.038	0.011	17.581	0.015	0.015	0.000	0.000	0.000	0.000
83	A	92	SER	0	-0.023	-0.013	17.512	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	93	THR	0	-0.018	-0.040	16.987	0.021	0.021	0.000	0.000	0.000	0.000
85	A	94	ALA	0	-0.009	-0.013	13.616	0.014	0.014	0.000	0.000	0.000	0.000
86	A	95	GLY	0	-0.013	0.008	15.073	0.020	0.020	0.000	0.000	0.000	0.000
87	A	96	SER	0	-0.037	-0.044	13.494	0.010	0.010	0.000	0.000	0.000	0.000
88	A	97	GLY	0	0.035	0.011	13.747	0.000	0.000	0.000	0.000	0.000	0.000
89	A	98	THR	0	0.020	0.023	10.766	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	99	CYS	0	-0.036	-0.013	13.150	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	100	LEU	0	-0.007	0.016	12.034	0.044	0.044	0.000	0.000	0.000	0.000
92	A	101	ALA	0	-0.007	0.004	13.716	-0.038	-0.038	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.021	-0.004	14.800	0.020	0.020	0.000	0.000	0.000	0.000
94	A	103	LEU	0	-0.009	0.013	17.155	-0.020	-0.020	0.000	0.000	0.000	0.000
95	A	104	ALA	0	0.017	-0.003	19.615	0.015	0.015	0.000	0.000	0.000	0.000
96	A	105	GLY	0	0.076	0.051	22.348	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	106	ARG	1	0.804	0.892	25.800	-0.034	-0.034	0.000	0.000	0.000	0.000
98	A	107	GLU	-1	-0.936	-0.962	28.290	0.052	0.052	0.000	0.000	0.000	0.000
99	A	108	ALA	0	-0.039	-0.013	24.562	0.004	0.004	0.000	0.000	0.000	0.000
100	A	109	ASP	-1	-0.848	-0.920	26.599	0.102	0.102	0.000	0.000	0.000	0.000
101	A	110	ALA	0	0.021	-0.012	26.244	0.013	0.013	0.000	0.000	0.000	0.000
102	A	111	ALA	0	-0.026	-0.004	26.465	0.009	0.009	0.000	0.000	0.000	0.000
103	A	112	VAL	0	0.000	0.005	22.916	0.013	0.013	0.000	0.000	0.000	0.000
104	A	113	LEU	0	0.027	0.024	20.911	0.024	0.024	0.000	0.000	0.000	0.000
105	A	114	GLY	0	0.023	0.011	21.204	0.022	0.022	0.000	0.000	0.000	0.000
106	A	115	TYR	0	-0.036	-0.025	21.864	0.019	0.019	0.000	0.000	0.000	0.000
107	A	116	GLU	-1	-0.837	-0.945	18.486	0.311	0.311	0.000	0.000	0.000	0.000
108	A	117	MET	0	-0.031	0.004	17.022	0.050	0.050	0.000	0.000	0.000	0.000
109	A	118	ALA	0	-0.026	-0.008	17.009	0.036	0.036	0.000	0.000	0.000	0.000
110	A	119	MET	0	-0.053	-0.028	17.706	0.025	0.025	0.000	0.000	0.000	0.000
111	A	120	LEU	0	0.015	0.012	11.118	0.051	0.051	0.000	0.000	0.000	0.000
112	A	121	VAL	0	0.009	0.015	12.601	0.125	0.125	0.000	0.000	0.000	0.000
113	A	122	LYS	1	0.905	0.939	13.521	-0.230	-0.230	0.000	0.000	0.000	0.000
114	A	123	SER	0	-0.032	-0.013	12.367	0.038	0.038	0.000	0.000	0.000	0.000
115	A	124	VAL	0	0.047	0.022	8.195	0.091	0.091	0.000	0.000	0.000	0.000
116	A	125	ARG	1	0.942	0.981	8.649	-0.201	-0.201	0.000	0.000	0.000	0.000
117	A	126	PRO	0	-0.002	-0.015	10.214	-0.074	-0.074	0.000	0.000	0.000	0.000
118	A	127	TYR	0	0.011	0.010	4.684	-0.130	-0.038	-0.001	-0.003	-0.088	0.000
119	A	128	LEU	0	-0.059	-0.011	5.454	-0.136	-0.136	0.000	0.000	0.000	0.000
120	A	129	MET	0	-0.077	-0.028	7.850	-0.185	-0.185	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:VAL)