FMO DATABASE

FMODB ID: 76J9K

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	OptAll
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	-1686002.980743
FMO2-HF: Nuclear repulsion	1621260.804118
FMO2-HF: Total energy	-64742.176624
FMO2-MP2: Total energy	-64931.999832

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.
-133.925	-129.534	26.97	-15.926	-15.434	-0.166

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 : 0.833 / q_NPA : 0.906

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	0.025	0.005	2.077	-37.590	-32.991	2.997	-3.937	-3.659	-0.042
4	A	5	PHE	0	-0.023	-0.003	4.608	5.592	5.670	-0.001	-0.016	-0.061	0.000
5	A	6	ILE	0	0.004	0.000	8.049	-1.241	-1.241	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.035	0.025	10.956	1.027	1.027	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.004	0.001	14.178	-0.213	-0.213	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.047	0.024	17.458	0.414	0.414	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.029	0.007	20.858	-0.132	-0.132	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.744	-0.852	20.758	-14.498	-14.498	0.000	0.000	0.000	0.000
11	A	12	HIS	0	0.011	0.006	20.972	-0.676	-0.676	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.017	-0.028	18.492	-0.123	-0.123	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.013	0.013	15.912	-0.510	-0.510	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.849	0.897	17.005	13.915	13.915	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.047	-0.025	19.112	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.020	0.005	14.258	-0.244	-0.244	0.000	0.000	0.000	0.000
17	A	18	MET	0	0.001	-0.010	14.021	-0.411	-0.411	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.008	0.005	14.722	-0.691	-0.691	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.086	-0.032	15.538	1.184	1.184	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.021	-0.014	10.981	-1.186	-1.186	0.000	0.000	0.000	0.000
21	A	22	THR	0	0.028	0.008	11.553	0.699	0.699	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.013	0.020	9.023	-1.374	-1.374	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.046	0.007	4.802	0.333	0.333	0.000	0.000	0.000	0.000
24	A	25	ASN	0	-0.090	-0.062	4.555	1.229	1.305	-0.001	-0.002	-0.073	0.000
25	A	26	VAL	0	0.002	0.021	7.282	0.540	0.540	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.019	-0.015	9.449	2.903	2.903	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.023	-0.009	11.499	-0.347	-0.347	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.016	-0.011	12.388	0.357	0.357	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.046	-0.042	16.243	0.690	0.690	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.074	0.036	19.568	0.248	0.248	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.029	0.004	22.431	0.154	0.154	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.037	-0.004	24.939	0.299	0.299	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.010	0.020	19.753	-0.642	-0.642	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.025	-0.001	19.012	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.004	-0.007	12.413	0.110	0.110	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.008	-0.003	11.636	0.092	0.092	0.000	0.000	0.000	0.000
37	A	38	TYR	0	-0.007	-0.023	4.666	-0.394	-0.350	-0.001	-0.001	-0.042	0.000
38	A	39	GLN	0	0.018	0.000	7.240	2.072	2.072	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.788	-0.837	1.670	-116.418	-122.675	20.407	-8.579	-5.572	-0.096
40	A	41	SER	0	0.031	0.013	3.182	8.221	9.087	0.018	-0.240	-0.643	-0.002
41	A	42	THR	0	-0.049	-0.052	2.701	-12.899	-9.230	0.698	-1.952	-2.415	-0.020
42	A	43	GLY	0	0.038	0.034	4.522	1.900	1.972	-0.001	-0.019	-0.052	0.000
43	A	44	GLU	-1	-0.780	-0.915	7.930	-24.227	-24.227	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.793	0.893	9.925	17.865	17.865	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.036	0.029	9.004	1.086	1.086	0.000	0.000	0.000	0.000
46	A	47	PHE	0	-0.005	0.008	11.480	0.422	0.422	0.000	0.000	0.000	0.000
47	A	48	GLN	0	-0.015	-0.004	12.450	0.611	0.611	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.818	-0.886	16.120	-16.355	-16.355	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.005	0.014	14.513	0.586	0.586	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.043	-0.030	13.117	0.626	0.626	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.788	-0.903	8.601	-28.747	-28.747	0.000	0.000	0.000	0.000
52	A	53	TYR	0	0.005	-0.014	7.718	4.150	4.150	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.962	0.984	4.229	20.065	20.190	-0.001	-0.026	-0.097	0.000
54	A	55	VAL	0	-0.019	-0.012	1.941	0.179	1.014	2.857	-1.107	-2.585	-0.006
55	A	56	LEU	0	-0.052	-0.024	4.510	2.288	2.437	-0.001	-0.027	-0.121	0.000
56	A	57	GLN	0	0.031	-0.002	7.033	1.610	1.610	0.000	0.000	0.000	0.000
57	A	58	SER	0	0.020	0.009	4.826	-5.029	-5.029	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.035	-0.015	6.970	3.455	3.455	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.059	0.043	9.357	-1.492	-1.492	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.056	-0.035	9.358	-2.408	-2.408	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.005	-0.002	7.358	1.471	1.471	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.872	0.914	11.127	18.229	18.229	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.000	0.009	14.125	0.920	0.920	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.005	0.001	15.432	0.912	0.912	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.024	0.025	17.395	-0.660	-0.660	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.041	-0.030	18.068	0.339	0.339	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.015	-0.008	11.985	-0.955	-0.955	0.000	0.000	0.000	0.000
68	A	69	VAL	0	-0.023	-0.001	14.363	1.054	1.054	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.011	-0.005	10.681	-2.351	-2.351	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.830	-0.934	14.650	-16.800	-16.800	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.037	-0.021	14.432	-1.667	-1.667	0.000	0.000	0.000	0.000
72	A	73	ILE	0	0.022	-0.012	16.298	1.379	1.379	0.000	0.000	0.000	0.000
73	A	74	HIS	0	-0.015	-0.005	17.545	-1.298	-1.298	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.051	-0.015	17.244	0.441	0.441	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.838	0.905	20.477	11.719	11.719	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.839	-0.933	19.612	-14.397	-14.397	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.858	-0.945	20.790	-12.214	-12.214	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.839	-0.920	22.239	-12.660	-12.660	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.020	0.010	15.831	-0.617	-0.617	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.009	-0.005	17.828	-0.745	-0.745	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.001	0.008	19.210	-0.269	-0.269	0.000	0.000	0.000	0.000
82	A	83	PHE	0	0.074	0.028	15.122	-0.281	-0.281	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.004	-0.002	12.851	-0.890	-0.890	0.000	0.000	0.000	0.000
84	A	85	GLN	0	0.017	0.012	16.179	-0.059	-0.059	0.000	0.000	0.000	0.000
85	A	86	MET	0	-0.031	0.010	18.026	0.082	0.082	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.029	0.000	10.945	0.154	0.154	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.028	-0.015	14.260	-0.989	-0.989	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.883	0.940	16.221	13.669	13.669	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.024	0.012	18.155	0.413	0.413	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.039	-0.039	13.875	-0.210	-0.210	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.057	-0.030	15.905	-0.471	-0.471	0.000	0.000	0.000	0.000
92	A	93	HIS	0	0.030	0.022	18.258	0.736	0.736	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.022	0.001	12.817	0.070	0.070	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.049	-0.053	16.991	-0.361	-0.361	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.854	-0.889	18.095	-14.205	-14.205	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.087	-0.039	18.577	0.714	0.714	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.015	-0.009	19.961	-0.508	-0.508	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.023	0.010	20.603	-0.226	-0.226	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.030	0.007	14.221	-0.591	-0.591	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.107	-0.063	13.424	-1.041	-1.041	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.009	-0.016	8.488	-2.629	-2.629	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.041	0.028	9.975	0.858	0.858	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.864	0.934	4.007	45.196	45.331	-0.001	-0.020	-0.114	0.000
104	A	105	LEU	0	0.017	0.045	7.696	2.990	2.990	0.000	0.000	0.000	0.000
105	A	106	THR	0	-0.031	-0.042	6.089	-4.261	-4.261	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.880	0.930	8.623	23.388	23.388	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.006	0.013	9.550	-2.103	-2.103	0.000	0.000	0.000	0.000
108	A	109	MET	0	-0.050	-0.026	8.352	0.084	0.084	0.000	0.000	0.000	0.000
109	A	110	ASN	0	0.000	0.004	11.092	0.076	0.076	0.000	0.000	0.000	0.000
110	A	111	MET	0	0.050	0.044	14.471	0.937	0.937	0.000	0.000	0.000	0.000
111	A	112	ASN	0	-0.011	0.002	14.838	-2.221	-2.221	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.924	0.975	15.253	19.643	19.643	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.022	-0.015	12.693	-1.648	-1.648	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.012	-0.004	10.445	1.416	1.416	0.000	0.000	0.000	0.000
115	A	116	ILE	0	-0.003	0.023	10.604	-3.056	-3.056	0.000	0.000	0.000	0.000
116	A	117	ILE	0	-0.011	0.006	7.533	1.001	1.001	0.000	0.000	0.000	0.000
117	A	118	SER	0	0.010	0.006	10.443	-1.021	-1.021	0.000	0.000	0.000	0.000
118	A	119	PHE	0	0.008	0.011	8.389	0.532	0.532	0.000	0.000	0.000	0.000
119	A	120	TRP	0	0.052	0.000	13.391	0.432	0.432	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.771	-0.869	17.045	-16.502	-16.502	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.027	-0.028	19.702	0.745	0.745	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.806	-0.903	21.478	-13.650	-13.650	0.000	0.000	0.000	0.000
123	A	124	VAL	0	-0.004	0.009	22.629	0.111	0.111	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.028	0.023	21.433	0.138	0.138	0.000	0.000	0.000	0.000
125	A	126	PHE	0	0.033	0.037	18.474	-0.144	-0.144	0.000	0.000	0.000	0.000
126	A	127	HIS	0	-0.008	-0.039	21.313	0.183	0.183	0.000	0.000	0.000	0.000
127	A	128	ASP	-1	-0.887	-0.933	24.786	-11.225	-11.225	0.000	0.000	0.000	0.000
128	A	129	TRP	0	0.023	0.012	18.058	0.304	0.304	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.834	0.911	21.821	14.098	14.098	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.801	0.895	24.311	11.497	11.497	0.000	0.000	0.000	0.000
131	A	132	SER	0	-0.029	-0.016	22.675	0.340	0.340	0.000	0.000	0.000	0.000
132	A	133	PRO	0	0.022	-0.013	24.791	-0.024	-0.024	0.000	0.000	0.000	0.000
133	A	134	LEU	0	0.036	0.028	17.031	0.076	0.076	0.000	0.000	0.000	0.000
134	A	135	SER	0	0.052	0.042	20.900	0.038	0.038	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.879	0.951	21.846	11.345	11.345	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.930	-0.965	22.659	-13.190	-13.190	0.000	0.000	0.000	0.000
137	A	138	ILE	0	0.033	0.010	17.492	0.182	0.182	0.000	0.000	0.000	0.000
138	A	139	THR	0	0.000	-0.010	21.269	0.174	0.174	0.000	0.000	0.000	0.000
139	A	140	ASN	0	-0.017	-0.012	24.114	0.738	0.738	0.000	0.000	0.000	0.000
140	A	141	ILE	0	-0.007	-0.004	21.230	0.411	0.411	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.050	-0.020	19.140	0.355	0.355	0.000	0.000	0.000	0.000
142	A	143	ARG	1	0.868	0.933	23.798	10.714	10.714	0.000	0.000	0.000	0.000
143	A	144	LYS	1	0.885	0.955	26.810	12.049	12.049	0.000	0.000	0.000	0.000
144	A	145	ASN	0	0.013	0.005	24.214	-0.171	-0.171	0.000	0.000	0.000	0.000
145	A	146	ASN	0	0.010	0.003	25.944	0.628	0.628	0.000	0.000	0.000	0.000
146	A	147	THR	0	0.020	0.009	26.312	-0.343	-0.343	0.000	0.000	0.000	0.000
147	A	148	GLN	0	0.008	0.022	27.800	-0.245	-0.245	0.000	0.000	0.000	0.000
148	A	149	SER	0	-0.050	-0.021	22.316	-0.221	-0.221	0.000	0.000	0.000	0.000
149	A	150	GLY	0	0.019	0.020	22.912	-0.606	-0.606	0.000	0.000	0.000	0.000
150	A	151	PHE	0	0.009	-0.013	23.781	0.189	0.189	0.000	0.000	0.000	0.000
151	A	152	SER	0	0.002	0.006	20.769	-0.815	-0.815	0.000	0.000	0.000	0.000
152	A	153	HIS	1	0.757	0.858	19.033	16.771	16.771	0.000	0.000	0.000	0.000
153	A	154	GLU	-1	-0.781	-0.879	19.120	-15.459	-15.459	0.000	0.000	0.000	0.000
154	A	155	ASP	-1	-0.813	-0.874	17.710	-15.593	-15.593	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.025	0.001	17.559	-1.216	-1.216	0.000	0.000	0.000	0.000
156	A	157	TYR	0	-0.064	-0.042	16.360	0.368	0.368	0.000	0.000	0.000	0.000
157	A	158	HIS	0	0.008	-0.005	18.164	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	159	TYR	0	0.047	0.016	13.922	-1.220	-1.220	0.000	0.000	0.000	0.000
159	A	160	PRO	0	-0.025	0.014	17.930	0.838	0.838	0.000	0.000	0.000	0.000

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