FMO DATABASE

FMODB ID: 1N3JZ

Calculation Name: 1K8F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K8F

Chain ID: A

ChEMBL ID:

UniProt ID: Q01518

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	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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1456733.606233
FMO2-HF: Nuclear repulsion	1395599.677527
FMO2-HF: Total energy	-61133.928705
FMO2-MP2: Total energy	-61311.154055

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:319:PRO)

Summations of interaction energy for fragment #1(A:319: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.
-1.643	1.365	0.101	-1.325	-1.785	-0.004

Interaction energy analysis for fragmet #1(A:319:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.011

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	321	VAL	0	-0.027	-0.007	3.443	-1.118	0.543	0.018	-0.715	-0.965	0.001
4	A	322	LEU	0	0.004	-0.015	5.628	0.513	0.513	0.000	0.000	0.000	0.000
5	A	323	GLU	-1	-0.843	-0.903	8.572	-1.406	-1.406	0.000	0.000	0.000	0.000
6	A	324	LEU	0	0.025	0.023	11.143	0.006	0.006	0.000	0.000	0.000	0.000
7	A	325	GLU	-1	-0.761	-0.855	11.956	-0.745	-0.745	0.000	0.000	0.000	0.000
8	A	326	GLY	0	0.016	0.012	14.562	0.059	0.059	0.000	0.000	0.000	0.000
9	A	327	LYS	1	0.799	0.870	18.245	0.336	0.336	0.000	0.000	0.000	0.000
10	A	328	LYS	1	0.845	0.920	13.715	0.619	0.619	0.000	0.000	0.000	0.000
11	A	329	TRP	0	0.047	0.017	13.177	-0.106	-0.106	0.000	0.000	0.000	0.000
12	A	330	ARG	1	0.684	0.820	7.009	1.825	1.825	0.000	0.000	0.000	0.000
13	A	331	VAL	0	-0.007	-0.006	9.761	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	332	GLU	-1	-0.821	-0.910	5.483	-1.916	-1.916	0.000	0.000	0.000	0.000
15	A	333	ASN	0	-0.026	-0.027	2.802	-0.323	1.024	0.083	-0.610	-0.820	-0.005
16	A	334	GLN	0	0.007	-0.010	5.500	0.489	0.489	0.000	0.000	0.000	0.000
17	A	335	GLU	-1	-0.895	-0.957	6.961	1.102	1.102	0.000	0.000	0.000	0.000
18	A	336	ASN	0	-0.054	-0.022	9.424	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	337	VAL	0	0.012	0.034	9.810	0.015	0.015	0.000	0.000	0.000	0.000
20	A	338	SER	0	0.017	-0.010	12.818	-0.046	-0.046	0.000	0.000	0.000	0.000
21	A	339	ASN	0	-0.002	-0.008	15.402	0.020	0.020	0.000	0.000	0.000	0.000
22	A	340	LEU	0	0.001	0.013	11.478	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	341	VAL	0	0.005	-0.008	15.335	0.036	0.036	0.000	0.000	0.000	0.000
24	A	342	ILE	0	-0.027	0.005	14.869	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	343	GLU	-1	-0.798	-0.897	17.979	-0.205	-0.205	0.000	0.000	0.000	0.000
26	A	344	ASP	-1	-0.909	-0.942	19.123	-0.359	-0.359	0.000	0.000	0.000	0.000
27	A	345	THR	0	0.021	-0.005	20.781	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	346	GLU	-1	-0.831	-0.890	22.748	-0.259	-0.259	0.000	0.000	0.000	0.000
29	A	347	LEU	0	0.033	0.015	24.591	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	348	LYS	1	0.815	0.897	23.768	0.276	0.276	0.000	0.000	0.000	0.000
31	A	349	GLN	0	-0.012	-0.013	20.376	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	350	VAL	0	-0.019	-0.005	18.646	0.032	0.032	0.000	0.000	0.000	0.000
33	A	351	ALA	0	0.015	0.015	16.710	-0.046	-0.046	0.000	0.000	0.000	0.000
34	A	352	TYR	0	-0.070	-0.061	12.224	0.072	0.072	0.000	0.000	0.000	0.000
35	A	353	ILE	0	0.031	0.018	12.434	-0.141	-0.141	0.000	0.000	0.000	0.000
36	A	354	TYR	0	0.050	0.010	8.146	0.221	0.221	0.000	0.000	0.000	0.000
37	A	355	LYS	1	0.892	0.931	7.937	-0.158	-0.158	0.000	0.000	0.000	0.000
38	A	356	CYS	0	-0.042	0.007	8.592	-0.032	-0.032	0.000	0.000	0.000	0.000
39	A	357	VAL	0	0.016	-0.014	10.482	0.091	0.091	0.000	0.000	0.000	0.000
40	A	358	ASN	0	-0.065	-0.032	12.347	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	359	THR	0	0.015	0.004	12.054	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	360	THR	0	-0.099	-0.052	14.440	0.040	0.040	0.000	0.000	0.000	0.000
43	A	361	LEU	0	-0.025	0.000	14.529	-0.039	-0.039	0.000	0.000	0.000	0.000
44	A	362	GLN	0	0.011	0.000	16.956	0.039	0.039	0.000	0.000	0.000	0.000
45	A	363	ILE	0	-0.017	-0.017	18.289	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	364	LYS	1	0.840	0.916	20.911	0.252	0.252	0.000	0.000	0.000	0.000
47	A	365	GLY	0	0.005	-0.004	23.721	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	366	LYS	1	0.819	0.902	26.032	0.161	0.161	0.000	0.000	0.000	0.000
49	A	367	ILE	0	0.019	0.024	20.857	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	368	ASN	0	0.000	-0.014	24.473	0.012	0.012	0.000	0.000	0.000	0.000
51	A	369	SER	0	-0.005	-0.023	23.216	0.014	0.014	0.000	0.000	0.000	0.000
52	A	370	ILE	0	0.007	0.008	18.535	-0.033	-0.033	0.000	0.000	0.000	0.000
53	A	371	THR	0	-0.001	0.008	17.155	0.036	0.036	0.000	0.000	0.000	0.000
54	A	372	VAL	0	0.013	0.015	15.858	-0.064	-0.064	0.000	0.000	0.000	0.000
55	A	373	ASP	-1	-0.764	-0.873	14.251	-0.226	-0.226	0.000	0.000	0.000	0.000
56	A	374	ASN	0	-0.048	-0.017	12.867	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	375	CYS	0	-0.002	0.049	12.813	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	376	LYS	1	0.889	0.914	14.072	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	377	LYS	1	0.840	0.908	15.685	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	378	LEU	0	0.023	0.014	13.919	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	379	GLY	0	0.028	0.016	17.478	0.018	0.018	0.000	0.000	0.000	0.000
62	A	380	LEU	0	-0.005	0.003	18.752	-0.032	-0.032	0.000	0.000	0.000	0.000
63	A	381	VAL	0	-0.057	-0.037	20.147	0.035	0.035	0.000	0.000	0.000	0.000
64	A	382	PHE	0	0.038	0.009	22.093	-0.030	-0.030	0.000	0.000	0.000	0.000
65	A	383	ASP	-1	-0.795	-0.879	24.303	-0.165	-0.165	0.000	0.000	0.000	0.000
66	A	384	ASP	-1	-0.810	-0.909	26.990	-0.131	-0.131	0.000	0.000	0.000	0.000
67	A	385	VAL	0	0.007	0.002	24.745	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	386	VAL	0	-0.138	-0.062	27.554	0.017	0.017	0.000	0.000	0.000	0.000
69	A	387	GLY	0	-0.004	0.001	27.863	0.013	0.013	0.000	0.000	0.000	0.000
70	A	388	ILE	0	0.016	0.007	24.554	0.009	0.009	0.000	0.000	0.000	0.000
71	A	389	VAL	0	0.005	0.003	21.937	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	390	GLU	-1	-0.882	-0.924	21.088	-0.154	-0.154	0.000	0.000	0.000	0.000
73	A	391	ILE	0	0.008	0.009	19.940	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	392	ILE	0	0.000	0.022	18.009	0.037	0.037	0.000	0.000	0.000	0.000
75	A	393	ASN	0	-0.039	-0.014	16.969	0.008	0.008	0.000	0.000	0.000	0.000
76	A	394	SER	0	0.026	0.015	17.029	0.008	0.008	0.000	0.000	0.000	0.000
77	A	395	LYS	1	0.786	0.874	18.125	0.046	0.046	0.000	0.000	0.000	0.000
78	A	396	ASP	-1	-0.789	-0.857	19.145	0.006	0.006	0.000	0.000	0.000	0.000
79	A	397	VAL	0	-0.007	0.001	18.743	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	398	LYS	1	0.897	0.954	21.094	0.144	0.144	0.000	0.000	0.000	0.000
81	A	399	VAL	0	0.008	0.000	21.670	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	400	GLN	0	0.010	0.012	23.812	0.019	0.019	0.000	0.000	0.000	0.000
83	A	401	VAL	0	0.023	0.030	25.569	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	402	MET	0	-0.016	0.008	27.879	0.014	0.014	0.000	0.000	0.000	0.000
85	A	403	GLY	0	-0.005	0.007	30.338	0.013	0.013	0.000	0.000	0.000	0.000
86	A	404	LYS	1	0.792	0.863	31.880	0.109	0.109	0.000	0.000	0.000	0.000
87	A	405	VAL	0	0.053	0.007	27.300	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	406	PRO	0	-0.039	-0.001	30.176	0.009	0.009	0.000	0.000	0.000	0.000
89	A	407	THR	0	-0.028	-0.036	29.024	0.006	0.006	0.000	0.000	0.000	0.000
90	A	408	ILE	0	0.014	0.000	25.681	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	409	SER	0	-0.062	-0.033	25.233	0.019	0.019	0.000	0.000	0.000	0.000
92	A	410	ILE	0	0.032	0.009	24.368	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	411	ASN	0	0.032	-0.002	23.272	0.026	0.026	0.000	0.000	0.000	0.000
94	A	412	LYS	1	0.817	0.896	20.945	0.087	0.087	0.000	0.000	0.000	0.000
95	A	413	THR	0	-0.021	-0.039	21.426	0.005	0.005	0.000	0.000	0.000	0.000
96	A	414	ASP	-1	-0.814	-0.867	22.502	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	415	GLY	0	0.096	0.051	23.237	0.007	0.007	0.000	0.000	0.000	0.000
98	A	416	CYS	0	-0.113	-0.057	23.349	-0.019	-0.019	0.000	0.000	0.000	0.000
99	A	417	HIS	0	-0.017	0.002	25.140	0.010	0.010	0.000	0.000	0.000	0.000
100	A	418	ALA	0	0.019	0.000	26.136	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	419	TYR	0	-0.007	-0.008	27.537	0.008	0.008	0.000	0.000	0.000	0.000
102	A	420	LEU	0	0.031	0.019	29.441	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	421	SER	0	0.010	-0.015	31.938	0.008	0.008	0.000	0.000	0.000	0.000
104	A	422	LYS	1	0.812	0.865	33.950	0.066	0.066	0.000	0.000	0.000	0.000
105	A	423	ASN	0	-0.056	-0.018	34.806	0.007	0.007	0.000	0.000	0.000	0.000
106	A	424	SER	0	-0.007	-0.023	32.558	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	425	LEU	0	0.006	0.006	34.553	0.000	0.000	0.000	0.000	0.000	0.000
108	A	426	ASP	-1	-0.865	-0.908	36.805	-0.090	-0.090	0.000	0.000	0.000	0.000
109	A	427	CYS	0	-0.086	-0.013	31.369	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	428	GLU	-1	-0.858	-0.905	32.872	-0.090	-0.090	0.000	0.000	0.000	0.000
111	A	429	ILE	0	0.007	-0.013	30.039	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	430	VAL	0	0.015	0.019	29.339	0.009	0.009	0.000	0.000	0.000	0.000
113	A	431	SER	0	0.029	0.010	28.819	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	432	ALA	0	-0.013	-0.007	27.872	0.006	0.006	0.000	0.000	0.000	0.000
115	A	433	LYS	1	0.875	0.929	25.484	0.017	0.017	0.000	0.000	0.000	0.000
116	A	434	SER	0	0.010	0.007	26.088	0.001	0.001	0.000	0.000	0.000	0.000
117	A	435	SER	0	0.004	-0.018	26.990	0.004	0.004	0.000	0.000	0.000	0.000
118	A	436	GLU	-1	-0.930	-0.970	27.409	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	437	MET	0	-0.056	-0.009	27.659	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	438	ASN	0	0.012	0.008	29.215	0.008	0.008	0.000	0.000	0.000	0.000
121	A	439	VAL	0	0.014	0.006	29.910	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	440	LEU	0	-0.021	-0.005	30.158	0.007	0.007	0.000	0.000	0.000	0.000
123	A	441	ILE	0	0.023	-0.002	33.196	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	442	PRO	0	-0.011	0.015	34.796	0.005	0.005	0.000	0.000	0.000	0.000
125	A	443	THR	0	-0.055	-0.063	36.883	0.002	0.002	0.000	0.000	0.000	0.000
126	A	444	GLU	-1	-0.851	-0.926	39.695	-0.059	-0.059	0.000	0.000	0.000	0.000
127	A	445	GLY	0	0.007	0.021	40.889	0.001	0.001	0.000	0.000	0.000	0.000
128	A	446	GLY	0	-0.073	-0.027	36.797	0.000	0.000	0.000	0.000	0.000	0.000
129	A	447	ASP	-1	-0.848	-0.896	35.384	-0.051	-0.051	0.000	0.000	0.000	0.000
130	A	448	PHE	0	-0.014	-0.028	32.265	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	449	ASN	0	-0.043	-0.008	36.234	0.008	0.008	0.000	0.000	0.000	0.000
132	A	450	GLU	-1	-0.854	-0.936	31.712	-0.049	-0.049	0.000	0.000	0.000	0.000
133	A	451	PHE	0	-0.029	-0.014	35.116	0.005	0.005	0.000	0.000	0.000	0.000
134	A	452	PRO	0	0.028	0.028	33.819	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	453	VAL	0	-0.019	-0.020	31.825	0.001	0.001	0.000	0.000	0.000	0.000
136	A	454	PRO	0	-0.049	-0.038	33.607	0.002	0.002	0.000	0.000	0.000	0.000
137	A	455	GLU	-1	-0.806	-0.900	31.953	-0.022	-0.022	0.000	0.000	0.000	0.000
138	A	456	GLN	0	-0.058	-0.022	34.005	0.004	0.004	0.000	0.000	0.000	0.000
139	A	457	PHE	0	0.024	0.005	34.586	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	458	LYS	1	0.881	0.956	39.930	0.021	0.021	0.000	0.000	0.000	0.000
141	A	459	THR	0	-0.024	-0.031	42.440	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	460	LEU	0	0.030	0.009	44.627	0.002	0.002	0.000	0.000	0.000	0.000
143	A	461	TRP	0	0.034	0.023	47.999	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	462	ASN	0	-0.044	-0.035	50.376	0.000	0.000	0.000	0.000	0.000	0.000
145	A	463	GLY	0	0.046	0.033	52.848	0.000	0.000	0.000	0.000	0.000	0.000
146	A	464	GLN	0	-0.053	-0.030	53.356	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	465	LYS	1	0.939	0.963	47.401	0.026	0.026	0.000	0.000	0.000	0.000
148	A	466	LEU	0	0.062	0.033	43.716	0.002	0.002	0.000	0.000	0.000	0.000
149	A	467	VAL	0	-0.027	-0.013	46.763	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	468	THR	0	0.030	0.013	40.402	0.003	0.003	0.000	0.000	0.000	0.000
151	A	469	THR	0	-0.010	0.003	43.483	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	470	VAL	0	0.027	0.018	38.772	0.002	0.002	0.000	0.000	0.000	0.000
153	A	471	THR	0	-0.015	-0.002	39.908	0.002	0.002	0.000	0.000	0.000	0.000
154	A	472	GLU	-1	-0.888	-0.953	39.919	-0.021	-0.021	0.000	0.000	0.000	0.000
155	A	473	ILE	0	-0.006	0.006	35.871	0.003	0.003	0.000	0.000	0.000	0.000
156	A	474	ALA	0	0.029	0.016	39.171	-0.003	-0.003	0.000	0.000	0.000	0.000
157	A	475	GLY	0	-0.036	-0.015	37.902	0.005	0.005	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:319:PRO)