FMO DATABASE

FMODB ID: YVZK2

Calculation Name: 3KTO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KTO

Chain ID: A

ChEMBL ID:

UniProt ID: Q15U25

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:

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1015793.091372
FMO2-HF: Nuclear repulsion	968390.997591
FMO2-HF: Total energy	-47402.093782
FMO2-MP2: Total energy	-47539.49496

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:12:PRO)

Summations of interaction energy for fragment #1(A:12:PRO)

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.
-13.81	-5.133	4.648	-5.083	-8.236	-0.018

Interaction energy analysis for fragmet #1(A:12:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.015

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

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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	14	ILE	0	0.018	0.014	3.789	-2.537	-0.113	-0.037	-1.197	-1.189	0.006
4	A	15	TYR	0	-0.007	-0.001	6.913	0.097	0.097	0.000	0.000	0.000	0.000
5	A	16	LEU	0	0.007	0.002	10.099	-0.052	-0.052	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.019	-0.013	13.194	0.025	0.025	0.000	0.000	0.000	0.000
7	A	18	ASP	-1	-0.761	-0.903	16.560	0.052	0.052	0.000	0.000	0.000	0.000
8	A	19	HIS	0	0.095	0.070	19.465	0.021	0.021	0.000	0.000	0.000	0.000
9	A	20	GLN	0	-0.051	-0.031	22.075	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	21	LYS	1	0.943	0.954	21.167	-0.080	-0.080	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.865	-0.933	20.919	0.090	0.090	0.000	0.000	0.000	0.000
12	A	23	ALA	0	-0.008	0.014	19.620	0.003	0.003	0.000	0.000	0.000	0.000
13	A	24	ARG	1	0.908	0.957	16.553	-0.133	-0.133	0.000	0.000	0.000	0.000
14	A	25	ALA	0	-0.004	0.017	16.098	0.023	0.023	0.000	0.000	0.000	0.000
15	A	26	ALA	0	-0.057	-0.061	17.129	0.011	0.011	0.000	0.000	0.000	0.000
16	A	27	LEU	0	0.041	0.015	14.146	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	28	SER	0	0.007	-0.010	12.385	0.014	0.014	0.000	0.000	0.000	0.000
18	A	29	LYS	1	0.877	0.944	12.656	-0.100	-0.100	0.000	0.000	0.000	0.000
19	A	30	LEU	0	0.009	0.006	14.404	0.000	0.000	0.000	0.000	0.000	0.000
20	A	31	LEU	0	0.011	0.001	9.426	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	32	SER	0	-0.028	0.007	9.263	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	33	PRO	0	-0.074	-0.028	9.676	0.026	0.026	0.000	0.000	0.000	0.000
23	A	34	LEU	0	-0.025	-0.011	7.317	-0.068	-0.068	0.000	0.000	0.000	0.000
24	A	35	ASP	-1	-0.972	-0.980	3.823	-1.862	-1.360	0.003	-0.166	-0.339	-0.001
25	A	36	VAL	0	-0.004	-0.010	2.496	-2.888	-0.907	0.657	-0.867	-1.770	-0.003
26	A	37	THR	0	-0.011	0.010	3.574	-0.737	-0.009	0.004	-0.197	-0.534	0.001
27	A	38	ILE	0	0.010	-0.005	5.844	-0.305	-0.305	0.000	0.000	0.000	0.000
28	A	39	GLN	0	0.022	0.023	8.585	0.078	0.078	0.000	0.000	0.000	0.000
29	A	40	CYS	0	-0.042	-0.021	10.311	-0.112	-0.112	0.000	0.000	0.000	0.000
30	A	41	PHE	0	-0.002	-0.002	12.058	0.007	0.007	0.000	0.000	0.000	0.000
31	A	42	ALA	0	-0.043	-0.028	16.721	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	43	SER	0	0.096	0.043	19.812	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.098	0.044	19.619	0.009	0.009	0.000	0.000	0.000	0.000
34	A	45	GLU	-1	-0.933	-0.962	20.271	0.071	0.071	0.000	0.000	0.000	0.000
35	A	46	SER	0	-0.061	-0.035	19.396	0.009	0.009	0.000	0.000	0.000	0.000
36	A	47	PHE	0	0.080	0.025	12.135	0.010	0.010	0.000	0.000	0.000	0.000
37	A	48	MET	0	-0.029	-0.013	16.366	0.000	0.000	0.000	0.000	0.000	0.000
38	A	49	ARG	1	0.836	0.927	18.683	-0.093	-0.093	0.000	0.000	0.000	0.000
39	A	50	GLN	0	-0.058	-0.020	12.110	0.023	0.023	0.000	0.000	0.000	0.000
40	A	51	GLN	0	-0.035	-0.015	13.714	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	52	ILE	0	-0.014	-0.010	9.998	0.049	0.049	0.000	0.000	0.000	0.000
42	A	53	SER	0	0.029	0.014	6.640	-0.112	-0.112	0.000	0.000	0.000	0.000
43	A	54	ASP	-1	-0.895	-0.948	7.771	-0.188	-0.188	0.000	0.000	0.000	0.000
44	A	55	ASP	-1	-0.939	-0.965	2.714	-1.686	-0.924	0.125	-0.213	-0.674	-0.001
45	A	56	ALA	0	-0.078	-0.027	2.408	-2.409	-1.135	2.357	-1.897	-1.734	-0.020
46	A	57	ILE	0	0.013	0.006	2.167	-1.049	-0.276	1.541	-0.527	-1.786	0.000
47	A	58	GLY	0	0.004	-0.011	5.315	0.023	0.058	-0.001	0.000	-0.033	0.000
48	A	59	MET	0	-0.075	-0.026	7.848	0.044	0.044	0.000	0.000	0.000	0.000
49	A	60	ILE	0	0.022	0.016	10.876	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.012	-0.008	13.438	0.026	0.026	0.000	0.000	0.000	0.000
51	A	62	GLU	-1	-0.847	-0.906	16.903	0.024	0.024	0.000	0.000	0.000	0.000
52	A	63	ALA	0	0.044	-0.008	20.296	0.000	0.000	0.000	0.000	0.000	0.000
53	A	64	HIS	0	-0.020	-0.003	22.771	0.000	0.000	0.000	0.000	0.000	0.000
54	A	65	LEU	0	-0.002	0.009	20.241	0.006	0.006	0.000	0.000	0.000	0.000
55	A	66	GLU	-1	-0.980	-1.015	24.320	0.058	0.058	0.000	0.000	0.000	0.000
56	A	67	ASP	-1	-0.916	-0.954	27.147	0.029	0.029	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.826	0.941	27.898	-0.041	-0.041	0.000	0.000	0.000	0.000
58	A	69	LYS	1	0.911	0.939	27.826	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	70	ASP	-1	-0.775	-0.907	26.085	0.003	0.003	0.000	0.000	0.000	0.000
60	A	71	SER	0	-0.001	-0.001	25.456	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	72	GLY	0	-0.008	-0.006	21.387	0.002	0.002	0.000	0.000	0.000	0.000
62	A	73	ILE	0	-0.033	-0.015	20.687	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	74	GLU	-1	-0.937	-0.953	22.356	0.010	0.010	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.039	-0.015	17.458	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	76	LEU	0	0.008	0.003	16.571	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	77	GLU	-1	-0.775	-0.893	19.130	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	78	THR	0	-0.075	-0.037	21.066	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	79	LEU	0	-0.035	-0.028	14.900	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	80	VAL	0	0.052	0.043	18.110	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.898	0.956	19.245	0.011	0.011	0.000	0.000	0.000	0.000
71	A	82	ARG	1	0.833	0.908	19.286	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	83	GLY	0	0.036	0.023	18.729	0.000	0.000	0.000	0.000	0.000	0.000
73	A	84	PHE	0	-0.008	0.006	13.162	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	85	HIS	0	-0.045	-0.029	14.010	0.016	0.016	0.000	0.000	0.000	0.000
75	A	86	LEU	0	0.032	0.025	8.221	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	87	PRO	0	0.018	0.017	9.103	0.035	0.035	0.000	0.000	0.000	0.000
77	A	88	THR	0	0.017	-0.002	10.790	0.009	0.009	0.000	0.000	0.000	0.000
78	A	89	ILE	0	-0.008	0.013	11.774	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	90	VAL	0	0.008	-0.001	14.817	0.016	0.016	0.000	0.000	0.000	0.000
80	A	91	MET	0	-0.023	-0.006	17.135	0.001	0.001	0.000	0.000	0.000	0.000
81	A	92	ALA	0	0.040	0.024	19.936	0.005	0.005	0.000	0.000	0.000	0.000
82	A	93	SER	0	-0.029	0.000	23.640	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	94	SER	0	-0.006	0.001	26.118	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	95	SER	0	0.058	-0.002	26.834	0.000	0.000	0.000	0.000	0.000	0.000
85	A	96	ASP	-1	-0.831	-0.877	29.005	0.000	0.000	0.000	0.000	0.000	0.000
86	A	97	ILE	0	0.048	0.001	29.767	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	98	PRO	0	-0.033	-0.030	29.862	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	99	THR	0	0.016	0.005	26.004	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	100	ALA	0	0.022	0.026	25.271	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	101	VAL	0	-0.027	-0.021	25.168	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	102	ARG	1	0.771	0.871	25.841	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	103	ALA	0	0.030	0.015	21.684	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	104	MET	0	-0.003	-0.001	20.304	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.897	0.944	22.736	0.018	0.018	0.000	0.000	0.000	0.000
95	A	106	ALA	0	-0.022	0.015	21.660	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	107	SER	0	-0.067	-0.048	18.287	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	108	ALA	0	-0.003	0.013	17.123	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	109	ALA	0	-0.032	-0.023	14.232	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	110	ASP	-1	-0.832	-0.896	16.198	-0.050	-0.050	0.000	0.000	0.000	0.000
100	A	111	PHE	0	-0.030	-0.017	18.059	0.007	0.007	0.000	0.000	0.000	0.000
101	A	112	ILE	0	-0.026	-0.012	16.610	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	113	GLU	-1	-0.937	-0.967	20.837	0.001	0.001	0.000	0.000	0.000	0.000
103	A	114	LYS	1	0.838	0.916	20.137	-0.044	-0.044	0.000	0.000	0.000	0.000
104	A	115	PRO	0	0.012	-0.013	23.889	0.001	0.001	0.000	0.000	0.000	0.000
105	A	116	PHE	0	0.037	0.024	17.585	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	117	ILE	0	-0.007	0.006	21.802	0.004	0.004	0.000	0.000	0.000	0.000
107	A	118	GLU	-1	-0.896	-0.963	17.974	0.008	0.008	0.000	0.000	0.000	0.000
108	A	119	HIS	0	0.050	0.012	16.965	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	120	VAL	0	0.011	0.017	17.100	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	121	LEU	0	0.026	0.015	13.658	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	122	VAL	0	0.007	-0.007	12.514	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	123	HIS	0	-0.018	-0.004	12.147	-0.028	-0.028	0.000	0.000	0.000	0.000
113	A	124	ASH	0	-0.046	-0.069	12.893	-0.029	-0.029	0.000	0.000	0.000	0.000
114	A	125	VAL	0	0.008	0.002	7.792	-0.021	-0.021	0.000	0.000	0.000	0.000
115	A	126	GLN	0	0.012	0.007	8.109	-0.114	-0.114	0.000	0.000	0.000	0.000
116	A	127	GLN	0	-0.011	0.000	8.997	-0.049	-0.049	0.000	0.000	0.000	0.000
117	A	128	ILE	0	-0.014	-0.005	6.030	-0.025	-0.025	0.000	0.000	0.000	0.000
118	A	129	ILE	0	0.019	0.012	4.379	-0.233	-0.035	-0.001	-0.019	-0.177	0.000
119	A	130	ASN	0	-0.058	-0.065	5.643	-0.151	-0.151	0.000	0.000	0.000	0.000
120	A	131	GLY	0	-0.048	-0.018	8.579	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	132	ALA	0	-0.032	0.006	4.835	0.020	0.020	0.000	0.000	0.000	0.000
122	A	133	LYS	1	0.916	0.979	5.493	0.678	0.678	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:PRO)