FMO DATABASE

FMODB ID: 39K6L

Calculation Name: 1KAG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KAG

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6D7

Base Structure: X-ray

Registration Date: 2023-06-22

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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1807385.092688
FMO2-HF: Nuclear repulsion	1740680.703322
FMO2-HF: Total energy	-66704.389367
FMO2-MP2: Total energy	-66901.209068

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
69.598	73.104	0.72	-1.733	-2.493	0.007

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.922 / q_NPA : -0.974

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	5	ARG	1	0.947	0.980	2.482	-52.539	-49.142	0.720	-1.698	-2.419	0.007
4	A	6	ASN	0	0.013	0.016	4.272	-2.866	-2.846	0.001	-0.027	0.006	0.000
5	A	7	ILE	0	0.030	0.032	5.360	1.451	1.451	0.000	0.000	0.000	0.000
6	A	8	PHE	0	-0.034	-0.013	8.910	-2.034	-2.034	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.006	0.013	12.122	-0.089	-0.089	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.037	0.032	14.845	-0.984	-0.984	0.000	0.000	0.000	0.000
9	A	11	GLY	0	0.076	0.026	18.233	0.141	0.141	0.000	0.000	0.000	0.000
10	A	12	PRO	0	0.016	0.030	21.327	-0.143	-0.143	0.000	0.000	0.000	0.000
11	A	13	MET	0	-0.026	-0.016	23.724	0.432	0.432	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.059	0.002	24.881	-0.228	-0.228	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.015	0.019	21.073	-0.052	-0.052	0.000	0.000	0.000	0.000
14	A	16	GLY	0	-0.004	-0.002	20.381	0.287	0.287	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.864	0.946	17.433	-12.852	-12.852	0.000	0.000	0.000	0.000
16	A	18	SER	0	0.075	0.034	16.738	0.687	0.687	0.000	0.000	0.000	0.000
17	A	19	THR	0	-0.100	-0.053	17.685	0.099	0.099	0.000	0.000	0.000	0.000
18	A	20	ILE	0	0.030	0.001	13.782	0.025	0.025	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.070	0.029	12.984	0.827	0.827	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.889	0.955	12.829	-12.431	-12.431	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.032	-0.027	13.943	0.412	0.412	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.045	0.035	8.688	0.217	0.217	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.003	0.012	9.199	1.112	1.112	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.020	-0.006	10.432	0.633	0.633	0.000	0.000	0.000	0.000
25	A	27	GLN	0	-0.100	-0.071	10.011	-0.799	-0.799	0.000	0.000	0.000	0.000
26	A	28	LEU	0	0.014	0.009	4.201	0.550	0.639	-0.001	-0.008	-0.080	0.000
27	A	29	ASN	0	-0.081	-0.019	7.085	-0.068	-0.068	0.000	0.000	0.000	0.000
28	A	30	MET	0	-0.060	-0.040	5.671	1.321	1.321	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.886	-0.936	9.557	16.772	16.772	0.000	0.000	0.000	0.000
30	A	32	PHE	0	0.002	-0.010	11.967	0.546	0.546	0.000	0.000	0.000	0.000
31	A	33	TYR	0	-0.031	-0.022	14.271	-1.163	-1.163	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.800	-0.898	16.636	13.307	13.307	0.000	0.000	0.000	0.000
33	A	35	SER	0	0.067	0.005	19.450	-0.230	-0.230	0.000	0.000	0.000	0.000
34	A	36	ASP	-1	-0.880	-0.937	21.446	11.227	11.227	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.042	-0.040	21.280	-0.491	-0.491	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.879	-0.901	21.869	12.241	12.241	0.000	0.000	0.000	0.000
37	A	39	ILE	0	0.034	0.014	23.911	-0.331	-0.331	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.739	-0.816	27.065	9.691	9.691	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.898	0.956	24.662	-11.418	-11.418	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.725	0.806	23.004	-12.432	-12.432	0.000	0.000	0.000	0.000
41	A	43	THR	0	-0.037	-0.019	29.378	-0.313	-0.313	0.000	0.000	0.000	0.000
42	A	44	GLY	0	-0.037	-0.005	31.379	-0.297	-0.297	0.000	0.000	0.000	0.000
43	A	45	ALA	0	-0.023	-0.010	32.366	-0.278	-0.278	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.844	-0.905	31.624	9.324	9.324	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.023	-0.017	27.779	-0.111	-0.111	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.049	0.018	30.647	0.007	0.007	0.000	0.000	0.000	0.000
47	A	49	TRP	0	-0.016	0.006	33.213	-0.151	-0.151	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.003	-0.011	32.211	-0.150	-0.150	0.000	0.000	0.000	0.000
49	A	51	PHE	0	-0.071	-0.026	32.147	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.905	-0.962	34.293	8.042	8.042	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.110	-0.053	37.800	-0.224	-0.224	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.841	-0.884	34.022	8.901	8.901	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.006	0.023	37.336	-0.071	-0.071	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.853	-0.955	32.356	9.855	9.855	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.977	-0.987	33.164	8.559	8.559	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.090	0.051	33.348	0.226	0.226	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.001	0.002	28.229	0.342	0.342	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.800	0.871	27.568	-10.051	-10.051	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.870	-0.917	28.135	10.163	10.163	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.762	0.844	28.266	-9.143	-9.143	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.817	-0.925	24.484	12.228	12.228	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.868	-0.871	23.928	12.388	12.388	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.905	0.951	23.342	-10.164	-10.164	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.022	0.018	22.029	0.465	0.465	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.013	-0.002	18.481	0.692	0.692	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.013	0.000	18.594	1.514	1.514	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.827	-0.895	18.832	13.211	13.211	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.064	-0.032	16.988	0.681	0.681	0.000	0.000	0.000	0.000
69	A	71	THR	0	-0.057	-0.042	14.264	1.053	1.053	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.938	-0.961	13.695	17.053	17.053	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.890	0.965	13.744	-15.797	-15.797	0.000	0.000	0.000	0.000
72	A	74	GLN	0	0.006	-0.002	8.974	2.896	2.896	0.000	0.000	0.000	0.000
73	A	75	GLY	0	-0.002	-0.001	7.429	-0.943	-0.943	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.041	-0.017	8.373	-1.786	-1.786	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.009	-0.002	8.683	1.347	1.347	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.028	-0.023	10.918	-1.444	-1.444	0.000	0.000	0.000	0.000
77	A	79	ALA	0	-0.021	-0.006	14.269	0.302	0.302	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.021	-0.028	16.747	-0.724	-0.724	0.000	0.000	0.000	0.000
79	A	81	GLY	0	0.120	0.061	19.202	-0.295	-0.295	0.000	0.000	0.000	0.000
80	A	82	GLY	0	-0.016	0.000	22.760	0.221	0.221	0.000	0.000	0.000	0.000
81	A	83	GLY	0	0.005	0.003	24.432	0.049	0.049	0.000	0.000	0.000	0.000
82	A	84	SER	0	0.019	0.011	21.723	0.010	0.010	0.000	0.000	0.000	0.000
83	A	85	VAL	0	0.007	-0.001	20.749	0.093	0.093	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.883	0.956	23.223	-10.310	-10.310	0.000	0.000	0.000	0.000
85	A	87	SER	0	-0.095	-0.089	24.867	-0.076	-0.076	0.000	0.000	0.000	0.000
86	A	88	ARG	1	1.014	0.991	23.945	-10.349	-10.349	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.870	-0.942	23.006	12.800	12.800	0.000	0.000	0.000	0.000
88	A	90	THR	0	-0.043	0.000	20.124	0.736	0.736	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.927	0.979	19.201	-12.140	-12.140	0.000	0.000	0.000	0.000
90	A	92	ASN	0	0.026	0.007	18.288	1.129	1.129	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.854	0.919	17.361	-13.053	-13.053	0.000	0.000	0.000	0.000
92	A	94	LEU	0	-0.032	-0.018	14.922	1.279	1.279	0.000	0.000	0.000	0.000
93	A	95	SER	0	0.024	0.014	13.307	1.518	1.518	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.001	0.003	12.707	1.855	1.855	0.000	0.000	0.000	0.000
95	A	97	ARG	1	0.822	0.901	11.687	-16.074	-16.074	0.000	0.000	0.000	0.000
96	A	98	GLY	0	-0.032	-0.036	8.356	1.603	1.603	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.011	0.023	6.124	-0.075	-0.075	0.000	0.000	0.000	0.000
98	A	100	VAL	0	0.011	-0.009	8.967	-1.463	-1.463	0.000	0.000	0.000	0.000
99	A	101	VAL	0	0.007	0.001	10.625	-0.170	-0.170	0.000	0.000	0.000	0.000
100	A	102	TYR	0	0.027	0.000	13.568	-1.138	-1.138	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.051	-0.024	15.522	-0.113	-0.113	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.855	-0.924	18.755	12.179	12.179	0.000	0.000	0.000	0.000
103	A	105	THR	0	-0.085	-0.067	22.019	-0.151	-0.151	0.000	0.000	0.000	0.000
104	A	106	THR	0	0.038	0.016	24.748	-0.174	-0.174	0.000	0.000	0.000	0.000
105	A	107	ILE	0	0.053	0.008	28.423	0.040	0.040	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.925	-0.957	31.233	8.905	8.905	0.000	0.000	0.000	0.000
107	A	109	LYS	1	0.815	0.897	25.510	-10.607	-10.607	0.000	0.000	0.000	0.000
108	A	110	GLN	0	0.002	-0.001	27.391	-0.140	-0.140	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.049	-0.024	29.121	-0.097	-0.097	0.000	0.000	0.000	0.000
110	A	112	ALA	0	0.057	0.005	29.699	-0.207	-0.207	0.000	0.000	0.000	0.000
111	A	113	ARG	1	1.504	1.434	29.161	-9.132	-9.132	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.453	-0.260	28.736	-0.171	-0.171	0.000	0.000	0.000	0.000
113	A	115	GLN	0	-0.133	-0.188	26.815	0.315	0.315	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.746	0.852	22.817	-11.679	-11.679	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.689	-0.820	24.331	10.405	10.405	0.000	0.000	0.000	0.000
116	A	118	LYS	1	0.788	0.874	24.364	-10.183	-10.183	0.000	0.000	0.000	0.000
117	A	119	LYS	1	0.819	0.920	22.372	-10.889	-10.889	0.000	0.000	0.000	0.000
118	A	120	ARG	1	0.751	0.817	23.834	-9.910	-9.910	0.000	0.000	0.000	0.000
119	A	121	PRO	0	0.017	0.023	24.448	-0.286	-0.286	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.041	-0.020	26.860	0.306	0.306	0.000	0.000	0.000	0.000
121	A	123	LEU	0	0.015	0.017	28.696	-0.132	-0.132	0.000	0.000	0.000	0.000
122	A	124	HIS	0	0.038	0.013	30.438	-0.069	-0.069	0.000	0.000	0.000	0.000
123	A	125	VAL	0	-0.015	-0.001	32.980	0.143	0.143	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.924	-0.967	35.281	7.842	7.842	0.000	0.000	0.000	0.000
125	A	127	THR	0	-0.045	-0.009	33.794	0.233	0.233	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.002	0.014	34.344	-0.228	-0.228	0.000	0.000	0.000	0.000
127	A	129	PRO	0	0.053	0.004	37.332	0.045	0.045	0.000	0.000	0.000	0.000
128	A	130	ARG	1	0.956	0.954	34.760	-8.269	-8.269	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.891	-0.937	36.549	7.464	7.464	0.000	0.000	0.000	0.000
130	A	132	VAL	0	0.011	0.015	35.222	0.117	0.117	0.000	0.000	0.000	0.000
131	A	133	LEU	0	-0.007	-0.009	31.420	0.220	0.220	0.000	0.000	0.000	0.000
132	A	134	GLU	-1	-0.919	-0.967	32.535	8.595	8.595	0.000	0.000	0.000	0.000
133	A	135	ALA	0	-0.009	0.000	34.068	0.179	0.179	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.023	-0.018	30.823	0.195	0.195	0.000	0.000	0.000	0.000
135	A	137	ALA	0	-0.007	0.000	29.383	0.325	0.325	0.000	0.000	0.000	0.000
136	A	138	ASN	0	-0.003	-0.002	29.767	0.420	0.420	0.000	0.000	0.000	0.000
137	A	139	GLU	-1	-0.876	-0.936	30.120	9.988	9.988	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.892	0.925	26.324	-10.279	-10.279	0.000	0.000	0.000	0.000
139	A	141	ASN	0	0.019	0.019	25.510	0.657	0.657	0.000	0.000	0.000	0.000
140	A	142	PRO	0	0.047	0.028	24.761	0.514	0.514	0.000	0.000	0.000	0.000
141	A	143	LEU	0	-0.038	-0.018	24.207	0.380	0.380	0.000	0.000	0.000	0.000
142	A	144	TYR	0	-0.084	-0.076	20.902	0.412	0.412	0.000	0.000	0.000	0.000
143	A	145	GLU	-1	-0.933	-0.976	19.814	13.481	13.481	0.000	0.000	0.000	0.000
144	A	146	GLU	-1	-0.987	-0.983	20.472	13.992	13.992	0.000	0.000	0.000	0.000
145	A	147	ILE	0	-0.041	-0.029	17.142	0.507	0.507	0.000	0.000	0.000	0.000
146	A	148	ALA	0	-0.055	-0.017	15.771	1.176	1.176	0.000	0.000	0.000	0.000
147	A	149	ASP	-1	-0.831	-0.883	11.398	25.631	25.631	0.000	0.000	0.000	0.000
148	A	150	VAL	0	-0.033	-0.025	10.653	0.206	0.206	0.000	0.000	0.000	0.000
149	A	151	THR	0	0.040	0.018	13.925	-0.388	-0.388	0.000	0.000	0.000	0.000
150	A	152	ILE	0	-0.020	0.005	14.140	-0.101	-0.101	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.888	0.922	17.912	-12.345	-12.345	0.000	0.000	0.000	0.000
152	A	154	THR	0	0.013	-0.001	18.554	-0.068	-0.068	0.000	0.000	0.000	0.000
153	A	155	ASP	-1	-0.806	-0.891	20.577	12.254	12.254	0.000	0.000	0.000	0.000
154	A	156	ASP	-1	-0.825	-0.886	22.691	10.704	10.704	0.000	0.000	0.000	0.000
155	A	157	GLN	0	0.013	-0.002	19.054	-0.206	-0.206	0.000	0.000	0.000	0.000
156	A	158	SER	0	-0.050	-0.019	20.284	0.022	0.022	0.000	0.000	0.000	0.000
157	A	159	ALA	0	0.052	0.010	17.540	0.336	0.336	0.000	0.000	0.000	0.000
158	A	160	LYS	1	0.986	0.996	15.754	-12.159	-12.159	0.000	0.000	0.000	0.000
159	A	161	VAL	0	-0.013	0.005	15.118	0.659	0.659	0.000	0.000	0.000	0.000
160	A	162	VAL	0	0.047	0.026	14.992	0.618	0.618	0.000	0.000	0.000	0.000
161	A	163	ALA	0	-0.001	-0.002	11.869	0.901	0.901	0.000	0.000	0.000	0.000
162	A	164	ASN	0	0.073	0.039	10.753	2.180	2.180	0.000	0.000	0.000	0.000
163	A	165	GLN	0	0.016	0.027	11.396	0.876	0.876	0.000	0.000	0.000	0.000
164	A	166	ILE	0	0.023	-0.005	9.068	0.672	0.672	0.000	0.000	0.000	0.000
165	A	167	ILE	0	-0.002	-0.002	6.416	1.586	1.586	0.000	0.000	0.000	0.000
166	A	168	HIS	0	-0.066	-0.037	7.596	0.641	0.641	0.000	0.000	0.000	0.000
167	A	169	MET	0	-0.084	-0.026	10.098	0.045	0.045	0.000	0.000	0.000	0.000
168	A	170	LEU	0	-0.052	-0.019	5.332	0.566	0.566	0.000	0.000	0.000	0.000
169	A	171	GLU	-1	-0.956	-0.960	5.941	36.107	36.107	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)