FMO DATABASE

FMODB ID: 98Y32

Calculation Name: 4KIA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KIA

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y563

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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1679739.996345
FMO2-HF: Nuclear repulsion	1614998.734397
FMO2-HF: Total energy	-64741.261948
FMO2-MP2: Total energy	-64931.165386

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-110.31	-99.396	15.927	-12.449	-14.391	-0.12

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.948

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	4	VAL	0	0.026	0.011	2.226	-32.655	-27.196	1.753	-3.803	-3.409	-0.038
4	A	5	PHE	0	-0.029	-0.020	4.685	6.116	6.209	-0.001	-0.012	-0.079	0.000
5	A	6	ILE	0	-0.002	-0.001	7.797	-0.436	-0.436	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.033	0.015	10.858	1.823	1.823	0.000	0.000	0.000	0.000
7	A	8	THR	0	0.006	0.012	13.978	-0.094	-0.094	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.047	0.024	17.329	0.346	0.346	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.034	0.015	20.400	-0.147	-0.147	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.771	-0.867	20.576	-14.398	-14.398	0.000	0.000	0.000	0.000
11	A	12	HIS	0	0.024	0.008	20.842	-0.641	-0.641	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.020	-0.030	18.113	-0.045	-0.045	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.022	0.004	15.537	-0.529	-0.529	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.843	0.888	16.846	14.336	14.336	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.070	-0.034	18.672	-0.080	-0.080	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.006	0.012	14.182	-0.302	-0.302	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.019	-0.027	13.523	-0.652	-0.652	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.006	0.007	14.310	-0.895	-0.895	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.027	0.001	14.885	1.449	1.449	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.064	-0.037	10.327	-1.281	-1.281	0.000	0.000	0.000	0.000
21	A	22	THR	0	0.013	0.009	11.009	0.634	0.634	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.030	0.025	8.619	-0.895	-0.895	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.032	0.003	4.445	-0.507	-0.480	-0.001	-0.006	-0.020	0.000
24	A	25	ASN	0	-0.074	-0.043	4.658	4.478	4.537	-0.001	-0.001	-0.058	0.000
25	A	26	VAL	0	0.012	0.025	7.079	0.532	0.532	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.011	-0.014	8.965	2.977	2.977	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.023	-0.009	11.336	-0.422	-0.422	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.025	-0.014	12.790	0.540	0.540	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.008	-0.010	16.277	0.745	0.745	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.087	0.054	19.614	0.292	0.292	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.019	-0.007	22.245	0.150	0.150	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.053	-0.019	24.735	0.377	0.377	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.005	0.007	20.366	-0.505	-0.505	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.012	-0.007	18.548	-0.072	-0.072	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.008	-0.008	12.616	0.020	0.020	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.021	-0.007	11.312	-0.063	-0.063	0.000	0.000	0.000	0.000
37	A	38	TYR	0	-0.045	-0.047	4.781	-0.406	-0.367	-0.001	0.000	-0.038	0.000
38	A	39	GLN	0	0.044	0.027	6.775	1.656	1.656	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.857	-0.903	1.642	-93.991	-96.548	12.448	-5.246	-4.645	-0.051
40	A	41	SER	0	0.025	0.012	2.763	8.674	9.806	0.072	-0.242	-0.962	-0.005
41	A	42	THR	0	-0.025	-0.042	2.689	-20.329	-16.296	0.664	-2.217	-2.480	-0.022
42	A	43	GLY	0	0.025	0.031	4.436	2.701	2.785	-0.001	-0.013	-0.070	0.000
43	A	44	GLU	-1	-0.780	-0.926	7.339	-25.418	-25.418	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.789	0.905	9.951	18.395	18.395	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.029	0.021	8.449	1.138	1.138	0.000	0.000	0.000	0.000
46	A	47	PHE	0	-0.002	-0.004	11.464	0.532	0.532	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.001	0.019	12.265	0.562	0.562	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.839	-0.898	15.834	-16.543	-16.543	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.012	0.016	13.941	0.543	0.543	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.047	-0.027	12.737	0.682	0.682	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.773	-0.888	8.228	-30.017	-30.017	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.015	-0.015	7.754	4.182	4.182	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.964	0.985	3.987	21.146	21.296	-0.001	-0.035	-0.114	0.000
54	A	55	VAL	0	-0.027	-0.021	2.373	0.425	2.395	0.996	-0.762	-2.204	-0.004
55	A	56	LEU	0	-0.053	-0.031	3.946	0.521	0.858	0.001	-0.108	-0.230	0.000
56	A	57	GLN	0	0.017	-0.002	6.648	2.694	2.694	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.005	0.003	5.455	-3.829	-3.829	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.008	0.006	7.521	2.210	2.210	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.050	0.031	10.463	-1.029	-1.029	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.052	-0.040	9.791	-2.419	-2.419	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.002	0.004	7.735	1.556	1.556	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.978	0.981	11.486	18.207	18.207	0.000	0.000	0.000	0.000
63	A	64	GLY	0	-0.014	0.002	14.220	0.827	0.827	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.005	0.003	15.461	0.925	0.925	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.025	0.024	17.556	-0.626	-0.626	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.039	-0.023	18.515	0.279	0.279	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.031	-0.014	12.340	-0.861	-0.861	0.000	0.000	0.000	0.000
68	A	69	VAL	0	0.006	0.020	15.302	0.777	0.777	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.024	-0.017	11.118	-2.046	-2.046	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.863	-0.943	15.045	-15.913	-15.913	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.055	-0.034	14.192	-1.627	-1.627	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.033	-0.010	16.386	1.265	1.265	0.000	0.000	0.000	0.000
73	A	74	HIS	0	-0.029	-0.007	17.811	-1.057	-1.057	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.026	-0.007	16.877	0.403	0.403	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.834	0.882	20.462	11.434	11.434	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.840	-0.926	20.376	-13.678	-13.678	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.937	-0.983	20.776	-11.910	-11.910	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.829	-0.903	21.750	-12.610	-12.610	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.022	0.005	15.663	-0.541	-0.541	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.011	0.000	17.571	-0.697	-0.697	0.000	0.000	0.000	0.000
81	A	82	ILE	0	0.017	0.006	18.933	-0.323	-0.323	0.000	0.000	0.000	0.000
82	A	83	PHE	0	0.041	0.022	14.816	-0.208	-0.208	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.004	-0.007	12.732	-0.751	-0.751	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.015	0.002	16.030	-0.142	-0.142	0.000	0.000	0.000	0.000
85	A	86	MET	0	-0.044	-0.003	18.508	0.131	0.131	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.030	-0.001	12.433	-0.686	-0.686	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.019	-0.014	14.870	-0.666	-0.666	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.935	0.965	16.362	13.027	13.027	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.009	0.005	18.780	0.259	0.259	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.028	-0.024	14.215	-0.169	-0.169	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.047	-0.020	16.256	-0.476	-0.476	0.000	0.000	0.000	0.000
92	A	93	HIS	0	0.014	0.009	18.260	0.342	0.342	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.006	0.000	13.646	0.234	0.234	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.024	-0.019	17.738	-0.099	-0.099	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.912	-0.941	18.768	-13.224	-13.224	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.102	-0.036	19.585	0.700	0.700	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.023	-0.003	20.802	-0.524	-0.524	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.044	0.023	21.123	-0.074	-0.074	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.041	-0.006	14.982	-0.651	-0.651	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.086	-0.038	14.190	-1.412	-1.412	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.053	-0.049	9.631	-2.336	-2.336	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.039	0.043	10.928	0.515	0.515	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.912	0.963	4.712	42.542	42.630	-0.001	-0.004	-0.082	0.000
104	A	105	LEU	0	0.011	0.031	8.308	2.876	2.876	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.026	-0.034	6.475	-3.755	-3.755	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.923	0.963	8.602	24.154	24.154	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.005	0.014	9.497	-2.236	-2.236	0.000	0.000	0.000	0.000
108	A	109	MET	0	-0.044	-0.018	8.025	-0.063	-0.063	0.000	0.000	0.000	0.000
109	A	110	ASN	0	0.024	0.007	11.194	0.020	0.020	0.000	0.000	0.000	0.000
110	A	111	MET	0	0.017	0.017	14.655	0.967	0.967	0.000	0.000	0.000	0.000
111	A	112	ASN	0	0.004	0.009	14.819	-2.121	-2.121	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.943	0.981	15.361	19.291	19.291	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.008	-0.013	12.543	-1.724	-1.724	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.015	0.002	10.542	1.431	1.431	0.000	0.000	0.000	0.000
115	A	116	ILE	0	0.006	0.010	10.972	-2.894	-2.894	0.000	0.000	0.000	0.000
116	A	117	ILE	0	-0.009	0.014	8.077	0.976	0.976	0.000	0.000	0.000	0.000
117	A	118	SER	0	0.025	0.010	11.353	-0.942	-0.942	0.000	0.000	0.000	0.000
118	A	119	PHE	0	0.000	0.000	8.972	0.622	0.622	0.000	0.000	0.000	0.000
119	A	120	TRP	0	0.054	0.008	13.990	0.448	0.448	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.840	-0.929	17.689	-15.734	-15.734	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.039	-0.032	20.203	0.506	0.506	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.817	-0.911	22.097	-13.174	-13.174	0.000	0.000	0.000	0.000
123	A	124	VAL	0	0.007	0.007	23.488	0.084	0.084	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.028	0.018	22.194	0.156	0.156	0.000	0.000	0.000	0.000
125	A	126	PHE	0	0.004	0.025	20.064	-0.074	-0.074	0.000	0.000	0.000	0.000
126	A	127	HIS	0	-0.008	-0.042	22.065	0.141	0.141	0.000	0.000	0.000	0.000
127	A	128	ASP	-1	-0.953	-0.982	25.562	-11.029	-11.029	0.000	0.000	0.000	0.000
128	A	129	TRP	0	0.025	0.010	19.025	0.321	0.321	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.883	0.952	22.747	13.289	13.289	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.839	0.938	25.121	11.205	11.205	0.000	0.000	0.000	0.000
131	A	132	SER	0	-0.050	-0.035	23.456	0.275	0.275	0.000	0.000	0.000	0.000
132	A	133	PRO	0	0.024	-0.013	25.719	-0.060	-0.060	0.000	0.000	0.000	0.000
133	A	134	LEU	0	0.044	0.036	17.825	0.030	0.030	0.000	0.000	0.000	0.000
134	A	135	SER	0	0.023	0.043	21.879	0.033	0.033	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.936	0.952	22.816	10.774	10.774	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.927	-0.958	23.148	-12.671	-12.671	0.000	0.000	0.000	0.000
137	A	138	ILE	0	0.045	0.015	18.075	0.162	0.162	0.000	0.000	0.000	0.000
138	A	139	THR	0	0.013	0.008	21.942	0.132	0.132	0.000	0.000	0.000	0.000
139	A	140	ASN	0	-0.012	0.006	24.630	0.700	0.700	0.000	0.000	0.000	0.000
140	A	141	ILE	0	-0.006	-0.008	21.579	0.387	0.387	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.027	-0.001	19.538	0.287	0.287	0.000	0.000	0.000	0.000
142	A	143	ARG	1	0.847	0.913	24.192	10.560	10.560	0.000	0.000	0.000	0.000
143	A	144	LYS	1	0.916	0.951	27.585	10.885	10.885	0.000	0.000	0.000	0.000
144	A	145	ASN	0	0.035	0.022	24.476	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	146	ASN	0	0.021	0.015	26.513	0.547	0.547	0.000	0.000	0.000	0.000
146	A	147	THR	0	0.011	0.017	26.549	-0.357	-0.357	0.000	0.000	0.000	0.000
147	A	148	GLN	0	0.006	0.008	27.950	-0.227	-0.227	0.000	0.000	0.000	0.000
148	A	149	SER	0	-0.047	-0.032	22.632	-0.197	-0.197	0.000	0.000	0.000	0.000
149	A	150	GLY	0	0.015	0.020	22.947	-0.594	-0.594	0.000	0.000	0.000	0.000
150	A	151	PHE	0	-0.005	-0.015	24.086	0.147	0.147	0.000	0.000	0.000	0.000
151	A	152	SER	0	0.000	0.004	21.290	-0.894	-0.894	0.000	0.000	0.000	0.000
152	A	153	HIS	1	0.789	0.883	19.136	16.510	16.510	0.000	0.000	0.000	0.000
153	A	154	GLU	-1	-0.799	-0.901	19.513	-15.418	-15.418	0.000	0.000	0.000	0.000
154	A	155	ASP	-1	-0.847	-0.898	18.000	-15.307	-15.307	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.025	0.002	18.136	-1.022	-1.022	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.069	-0.036	16.449	0.404	0.404	0.000	0.000	0.000	0.000
157	A	158	HIS	0	0.034	0.014	18.450	-0.007	-0.007	0.000	0.000	0.000	0.000
158	A	159	TYR	0	0.041	0.009	14.275	-1.271	-1.271	0.000	0.000	0.000	0.000
159	A	160	PRO	0	-0.026	0.005	17.891	0.751	0.751	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)