FMO DATABASE

FMODB ID: QVJJY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-877129.907712
FMO2-HF: Nuclear repulsion	832317.150874
FMO2-HF: Total energy	-44812.756837
FMO2-MP2: Total energy	-44939.789718

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.
-19.604	-10.964	3.924	-5.027	-7.535	-0.007

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 : 0.007 / q_NPA : -0.014

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	-0.933	-0.965	2.391	-6.776	-1.620	1.861	-3.087	-3.929	-0.021
4	A	13	LEU	0	0.007	-0.016	2.482	-7.174	-4.825	2.058	-1.582	-2.824	0.013
5	A	14	ASP	-1	-0.802	-0.908	4.062	-3.383	-2.702	0.004	-0.270	-0.415	0.001
6	A	15	TRP	0	-0.020	-0.004	6.100	-0.118	-0.118	0.000	0.000	0.000	0.000
7	A	16	LEU	0	-0.039	-0.023	7.294	-0.272	-0.272	0.000	0.000	0.000	0.000
8	A	17	MET	0	-0.050	-0.004	7.579	-0.306	-0.306	0.000	0.000	0.000	0.000
9	A	18	SER	0	0.005	-0.014	10.203	-0.138	-0.138	0.000	0.000	0.000	0.000
10	A	19	GLY	0	-0.006	-0.003	11.860	-0.057	-0.057	0.000	0.000	0.000	0.000
11	A	20	LEU	0	-0.053	-0.025	13.155	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	21	VAL	0	0.020	0.005	14.631	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	22	GLN	0	-0.087	-0.043	15.059	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	23	ARG	1	0.821	0.890	14.402	-0.401	-0.401	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.027	0.001	19.373	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	25	PRO	0	0.016	0.012	21.250	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	26	HIS	0	0.028	0.010	23.664	0.003	0.003	0.000	0.000	0.000	0.000
18	A	27	THR	0	-0.014	-0.006	18.684	0.000	0.000	0.000	0.000	0.000	0.000
19	A	28	THR	0	-0.039	-0.030	19.171	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	29	SER	0	-0.007	-0.004	14.725	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	30	ALA	0	0.000	0.005	12.435	0.018	0.018	0.000	0.000	0.000	0.000
22	A	31	VAL	0	0.026	0.013	10.349	0.004	0.004	0.000	0.000	0.000	0.000
23	A	32	LEU	0	-0.005	-0.003	6.837	0.022	0.022	0.000	0.000	0.000	0.000
24	A	33	LEU	0	-0.013	-0.007	8.935	-0.072	-0.072	0.000	0.000	0.000	0.000
25	A	34	SER	0	0.003	-0.029	11.138	0.066	0.066	0.000	0.000	0.000	0.000
26	A	35	CYS	0	-0.044	-0.031	12.526	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	36	ASP	-1	-0.930	-0.946	14.184	0.031	0.031	0.000	0.000	0.000	0.000
28	A	37	GLY	0	0.021	0.009	15.433	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	38	LEU	0	-0.014	0.006	10.674	-0.035	-0.035	0.000	0.000	0.000	0.000
30	A	39	VAL	0	0.048	0.020	7.513	0.097	0.097	0.000	0.000	0.000	0.000
31	A	40	LYS	1	0.817	0.908	5.928	-0.565	-0.565	0.000	0.000	0.000	0.000
32	A	41	SER	0	0.024	0.005	3.849	-0.312	0.036	0.002	-0.083	-0.267	0.000
33	A	42	VAL	0	-0.057	-0.029	5.475	0.163	0.163	0.000	0.000	0.000	0.000
34	A	43	HIS	0	0.038	0.044	8.564	-0.113	-0.113	0.000	0.000	0.000	0.000
35	A	44	GLY	0	0.024	-0.004	11.083	0.033	0.033	0.000	0.000	0.000	0.000
36	A	45	LEU	0	-0.033	-0.010	13.183	0.006	0.006	0.000	0.000	0.000	0.000
37	A	46	ASP	-1	-0.844	-0.887	12.649	-0.115	-0.115	0.000	0.000	0.000	0.000
38	A	47	PRO	0	0.045	-0.011	10.763	0.015	0.015	0.000	0.000	0.000	0.000
39	A	48	ASP	-1	-0.872	-0.926	12.244	-0.130	-0.130	0.000	0.000	0.000	0.000
40	A	49	SER	0	-0.050	-0.058	15.468	0.023	0.023	0.000	0.000	0.000	0.000
41	A	50	ALA	0	-0.041	-0.019	11.548	0.031	0.031	0.000	0.000	0.000	0.000
42	A	51	ASP	-1	-0.859	-0.929	11.889	-0.136	-0.136	0.000	0.000	0.000	0.000
43	A	52	HIS	0	-0.046	-0.022	14.062	0.030	0.030	0.000	0.000	0.000	0.000
44	A	53	MET	0	-0.016	0.004	14.955	0.023	0.023	0.000	0.000	0.000	0.000
45	A	54	ALA	0	0.010	0.005	12.763	0.030	0.030	0.000	0.000	0.000	0.000
46	A	55	ALA	0	0.046	0.040	14.818	0.016	0.016	0.000	0.000	0.000	0.000
47	A	56	LEU	0	-0.009	-0.012	18.156	0.011	0.011	0.000	0.000	0.000	0.000
48	A	57	ALA	0	0.004	-0.004	16.528	0.007	0.007	0.000	0.000	0.000	0.000
49	A	58	SER	0	-0.010	-0.016	16.911	0.008	0.008	0.000	0.000	0.000	0.000
50	A	59	GLY	0	0.001	0.009	18.620	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	60	LEU	0	-0.016	-0.019	21.453	0.000	0.000	0.000	0.000	0.000	0.000
52	A	61	TYR	0	-0.023	-0.035	19.583	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	62	SER	0	0.036	0.016	21.595	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	63	LEU	0	-0.058	-0.026	23.460	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	64	GLY	0	0.046	0.013	25.313	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	65	ARG	1	0.902	0.938	23.095	-0.098	-0.098	0.000	0.000	0.000	0.000
57	A	66	SER	0	-0.051	-0.027	25.845	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	67	ALA	0	-0.015	-0.006	29.023	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	68	GLY	0	0.016	0.012	28.764	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	69	ILE	0	-0.029	-0.009	27.670	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	70	ARG	1	0.885	0.951	31.208	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	71	PHE	0	-0.044	-0.037	33.456	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	72	GLY	0	-0.005	0.007	31.783	0.001	0.001	0.000	0.000	0.000	0.000
64	A	73	ASP	-1	-0.936	-0.968	32.739	0.069	0.069	0.000	0.000	0.000	0.000
65	A	74	GLY	0	0.001	0.002	30.956	0.001	0.001	0.000	0.000	0.000	0.000
66	A	75	GLY	0	-0.078	-0.034	27.214	0.005	0.005	0.000	0.000	0.000	0.000
67	A	76	ASP	-1	-0.808	-0.873	22.155	0.127	0.127	0.000	0.000	0.000	0.000
68	A	77	VAL	0	0.006	0.008	22.736	0.002	0.002	0.000	0.000	0.000	0.000
69	A	78	ARG	1	0.937	0.972	23.095	-0.128	-0.128	0.000	0.000	0.000	0.000
70	A	79	GLN	0	0.002	-0.024	20.964	0.007	0.007	0.000	0.000	0.000	0.000
71	A	80	VAL	0	-0.031	0.002	22.323	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	81	VAL	0	0.019	0.010	22.899	0.011	0.011	0.000	0.000	0.000	0.000
73	A	82	VAL	0	-0.026	-0.011	24.423	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	83	GLU	-1	-0.836	-0.907	26.041	0.069	0.069	0.000	0.000	0.000	0.000
75	A	84	LEU	0	-0.039	-0.013	25.790	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	85	ASP	-1	-0.887	-0.951	29.578	0.035	0.035	0.000	0.000	0.000	0.000
77	A	86	SER	0	-0.022	-0.019	29.895	0.002	0.002	0.000	0.000	0.000	0.000
78	A	87	THR	0	0.008	-0.001	24.801	0.002	0.002	0.000	0.000	0.000	0.000
79	A	88	LEU	0	-0.002	0.004	24.620	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	89	LEU	0	0.015	0.016	18.855	0.005	0.005	0.000	0.000	0.000	0.000
81	A	90	PHE	0	-0.009	-0.003	20.092	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	91	VAL	0	0.034	0.011	17.518	0.020	0.020	0.000	0.000	0.000	0.000
83	A	92	SER	0	-0.022	-0.012	17.431	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	93	THR	0	-0.012	-0.031	16.936	0.031	0.031	0.000	0.000	0.000	0.000
85	A	94	ALA	0	-0.011	-0.016	13.642	0.009	0.009	0.000	0.000	0.000	0.000
86	A	95	GLY	0	-0.015	0.005	15.163	0.018	0.018	0.000	0.000	0.000	0.000
87	A	96	SER	0	-0.034	-0.043	13.628	0.017	0.017	0.000	0.000	0.000	0.000
88	A	97	GLY	0	0.037	0.019	13.823	0.012	0.012	0.000	0.000	0.000	0.000
89	A	98	THR	0	0.013	0.027	10.675	0.016	0.016	0.000	0.000	0.000	0.000
90	A	99	CYS	0	-0.024	-0.008	13.128	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	100	LEU	0	-0.016	0.017	12.200	0.061	0.061	0.000	0.000	0.000	0.000
92	A	101	ALA	0	-0.002	0.006	13.673	-0.050	-0.050	0.000	0.000	0.000	0.000
93	A	102	VAL	0	0.023	0.001	14.759	0.023	0.023	0.000	0.000	0.000	0.000
94	A	103	LEU	0	0.005	0.018	17.111	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	104	ALA	0	0.014	-0.006	19.576	0.013	0.013	0.000	0.000	0.000	0.000
96	A	105	GLY	0	0.070	0.048	22.308	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	106	ARG	1	0.748	0.854	25.762	-0.047	-0.047	0.000	0.000	0.000	0.000
98	A	107	GLU	-1	-0.929	-0.959	28.336	0.060	0.060	0.000	0.000	0.000	0.000
99	A	108	ALA	0	-0.044	-0.017	24.533	0.003	0.003	0.000	0.000	0.000	0.000
100	A	109	ASP	-1	-0.856	-0.931	26.549	0.106	0.106	0.000	0.000	0.000	0.000
101	A	110	ALA	0	0.014	-0.008	26.185	0.013	0.013	0.000	0.000	0.000	0.000
102	A	111	ALA	0	-0.022	-0.002	26.403	0.010	0.010	0.000	0.000	0.000	0.000
103	A	112	VAL	0	0.014	0.009	22.948	0.014	0.014	0.000	0.000	0.000	0.000
104	A	113	LEU	0	0.020	0.025	20.900	0.024	0.024	0.000	0.000	0.000	0.000
105	A	114	GLY	0	0.030	0.013	21.189	0.025	0.025	0.000	0.000	0.000	0.000
106	A	115	TYR	0	-0.030	-0.024	21.813	0.016	0.016	0.000	0.000	0.000	0.000
107	A	116	GLU	-1	-0.795	-0.903	18.155	0.331	0.331	0.000	0.000	0.000	0.000
108	A	117	MET	0	-0.016	0.012	17.059	0.049	0.049	0.000	0.000	0.000	0.000
109	A	118	ALA	0	-0.032	-0.011	17.005	0.043	0.043	0.000	0.000	0.000	0.000
110	A	119	MET	0	-0.048	-0.025	17.714	0.027	0.027	0.000	0.000	0.000	0.000
111	A	120	LEU	0	0.029	0.017	10.715	0.047	0.047	0.000	0.000	0.000	0.000
112	A	121	VAL	0	-0.001	0.011	12.601	0.135	0.135	0.000	0.000	0.000	0.000
113	A	122	LYS	1	0.909	0.944	13.607	-0.236	-0.236	0.000	0.000	0.000	0.000
114	A	123	SER	0	-0.029	-0.011	11.784	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	124	VAL	0	0.020	0.008	8.259	0.074	0.074	0.000	0.000	0.000	0.000
116	A	125	ARG	1	0.946	0.980	8.716	-0.217	-0.217	0.000	0.000	0.000	0.000
117	A	126	PRO	0	-0.004	-0.014	10.373	-0.054	-0.054	0.000	0.000	0.000	0.000
118	A	127	TYR	0	0.004	0.008	4.638	-0.173	-0.067	-0.001	-0.005	-0.100	0.000
119	A	128	LEU	0	-0.048	-0.008	5.493	-0.030	-0.030	0.000	0.000	0.000	0.000
120	A	129	MET	0	-0.067	-0.023	7.902	-0.214	-0.214	0.000	0.000	0.000	0.000

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