FMO DATABASE

FMODB ID: Z6L4N

Calculation Name: 3KS4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KS4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8JPY0

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1055430.505963
FMO2-HF: Nuclear repulsion	1006338.724008
FMO2-HF: Total energy	-49091.781956
FMO2-MP2: Total energy	-49233.87324

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:205:LYS)

Summations of interaction energy for fragment #1(A:205: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.
20.188	22.329	-0.016	-0.995	-1.131	0.004

Interaction energy analysis for fragmet #1(A:205:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.958 / q_NPA : 0.967

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	207	TYR	0	-0.008	-0.005	3.804	-4.576	-2.534	-0.015	-0.979	-1.048	0.004
4	A	208	ILE	0	-0.011	0.022	6.076	1.252	1.252	0.000	0.000	0.000	0.000
5	A	209	SER	0	-0.005	-0.004	7.021	-1.138	-1.138	0.000	0.000	0.000	0.000
6	A	210	ALA	0	0.032	-0.010	7.818	2.335	2.335	0.000	0.000	0.000	0.000
7	A	211	LYS	1	0.898	0.952	10.669	23.900	23.900	0.000	0.000	0.000	0.000
8	A	212	ASP	-1	-0.793	-0.906	10.618	-23.055	-23.055	0.000	0.000	0.000	0.000
9	A	213	LEU	0	0.007	0.020	11.779	1.359	1.359	0.000	0.000	0.000	0.000
10	A	214	LYS	1	0.953	0.958	13.436	17.298	17.298	0.000	0.000	0.000	0.000
11	A	215	GLU	-1	-0.991	-0.982	15.682	-16.188	-16.188	0.000	0.000	0.000	0.000
12	A	216	ILE	0	0.097	0.054	14.378	0.923	0.923	0.000	0.000	0.000	0.000
13	A	217	MET	0	-0.032	-0.010	16.206	0.952	0.952	0.000	0.000	0.000	0.000
14	A	218	TYR	0	-0.095	-0.077	19.480	0.810	0.810	0.000	0.000	0.000	0.000
15	A	219	ASP	-1	-0.874	-0.916	20.676	-13.456	-13.456	0.000	0.000	0.000	0.000
16	A	220	HIS	0	-0.083	-0.046	20.437	0.842	0.842	0.000	0.000	0.000	0.000
17	A	221	LEU	0	-0.109	-0.056	23.510	0.569	0.569	0.000	0.000	0.000	0.000
18	A	222	PRO	0	0.029	0.029	26.171	0.118	0.118	0.000	0.000	0.000	0.000
19	A	223	GLY	0	0.004	-0.011	29.289	-0.052	-0.052	0.000	0.000	0.000	0.000
20	A	224	PHE	0	0.012	-0.005	27.978	-0.320	-0.320	0.000	0.000	0.000	0.000
21	A	225	GLY	0	0.031	0.014	27.255	0.312	0.312	0.000	0.000	0.000	0.000
22	A	226	THR	0	0.027	-0.031	27.585	0.344	0.344	0.000	0.000	0.000	0.000
23	A	227	ALA	0	0.022	-0.013	27.153	-0.319	-0.319	0.000	0.000	0.000	0.000
24	A	228	PHE	0	0.046	0.020	25.292	-0.215	-0.215	0.000	0.000	0.000	0.000
25	A	229	HIS	0	0.078	0.094	23.353	-0.259	-0.259	0.000	0.000	0.000	0.000
26	A	230	GLN	0	0.005	-0.009	22.173	-0.993	-0.993	0.000	0.000	0.000	0.000
27	A	231	LEU	0	0.017	-0.006	21.635	-0.383	-0.383	0.000	0.000	0.000	0.000
28	A	232	VAL	0	0.045	0.039	17.972	-0.542	-0.542	0.000	0.000	0.000	0.000
29	A	233	GLN	0	-0.060	-0.033	17.509	-0.521	-0.521	0.000	0.000	0.000	0.000
30	A	234	VAL	0	-0.038	-0.010	17.215	-0.767	-0.767	0.000	0.000	0.000	0.000
31	A	235	ILE	0	0.041	0.021	15.395	-0.591	-0.591	0.000	0.000	0.000	0.000
32	A	236	CYS	0	-0.011	0.001	13.245	-1.074	-1.074	0.000	0.000	0.000	0.000
33	A	237	LYS	1	0.887	0.954	12.216	15.414	15.414	0.000	0.000	0.000	0.000
34	A	238	ILE	0	0.034	0.020	13.029	-0.810	-0.810	0.000	0.000	0.000	0.000
35	A	239	GLY	0	0.077	0.024	11.428	-0.471	-0.471	0.000	0.000	0.000	0.000
36	A	240	LYS	1	0.911	0.945	7.608	28.504	28.504	0.000	0.000	0.000	0.000
37	A	241	ASP	-1	-0.942	-0.977	8.305	-21.940	-21.940	0.000	0.000	0.000	0.000
38	A	242	ASN	0	-0.060	-0.029	10.554	0.269	0.269	0.000	0.000	0.000	0.000
39	A	243	ASN	0	-0.051	-0.010	3.832	-1.873	-1.774	-0.001	-0.016	-0.083	0.000
40	A	244	LEU	0	0.038	0.012	7.257	0.284	0.284	0.000	0.000	0.000	0.000
41	A	245	LEU	0	-0.038	-0.021	6.483	1.328	1.328	0.000	0.000	0.000	0.000
42	A	246	ASP	-1	-0.744	-0.880	6.661	-29.985	-29.985	0.000	0.000	0.000	0.000
43	A	247	THR	0	-0.012	-0.002	9.592	1.182	1.182	0.000	0.000	0.000	0.000
44	A	248	ILE	0	-0.016	-0.011	11.977	1.235	1.235	0.000	0.000	0.000	0.000
45	A	249	HIS	0	-0.005	0.000	11.868	1.478	1.478	0.000	0.000	0.000	0.000
46	A	250	ALA	0	0.049	0.023	13.656	0.950	0.950	0.000	0.000	0.000	0.000
47	A	251	GLU	-1	-0.906	-0.955	15.557	-12.337	-12.337	0.000	0.000	0.000	0.000
48	A	252	PHE	0	-0.037	-0.028	17.164	0.846	0.846	0.000	0.000	0.000	0.000
49	A	253	GLN	0	-0.030	-0.026	15.907	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	254	ALA	0	0.020	0.015	19.598	0.565	0.565	0.000	0.000	0.000	0.000
51	A	255	SER	0	0.021	0.004	21.482	0.534	0.534	0.000	0.000	0.000	0.000
52	A	256	LEU	0	-0.049	-0.034	21.652	0.453	0.453	0.000	0.000	0.000	0.000
53	A	257	ALA	0	-0.052	-0.019	23.816	0.406	0.406	0.000	0.000	0.000	0.000
54	A	258	ASP	-1	-0.948	-0.963	25.513	-10.456	-10.456	0.000	0.000	0.000	0.000
55	A	259	GLY	0	-0.052	-0.019	27.637	0.426	0.426	0.000	0.000	0.000	0.000
56	A	260	ASP	-1	-0.868	-0.917	26.499	-10.055	-10.055	0.000	0.000	0.000	0.000
57	A	261	SER	0	-0.025	-0.026	27.456	-0.273	-0.273	0.000	0.000	0.000	0.000
58	A	262	PRO	0	0.119	0.044	24.352	-0.170	-0.170	0.000	0.000	0.000	0.000
59	A	263	GLN	0	-0.016	-0.017	24.396	-0.418	-0.418	0.000	0.000	0.000	0.000
60	A	264	CYS	0	-0.041	-0.017	25.969	-0.140	-0.140	0.000	0.000	0.000	0.000
61	A	265	ALA	0	0.120	0.070	22.325	-0.072	-0.072	0.000	0.000	0.000	0.000
62	A	266	LEU	0	-0.034	-0.021	20.303	-0.356	-0.356	0.000	0.000	0.000	0.000
63	A	267	ILE	0	-0.055	-0.028	22.233	-0.092	-0.092	0.000	0.000	0.000	0.000
64	A	268	GLN	0	-0.002	0.009	23.428	-0.044	-0.044	0.000	0.000	0.000	0.000
65	A	269	ILE	0	0.018	0.025	17.519	-0.145	-0.145	0.000	0.000	0.000	0.000
66	A	270	THR	0	-0.139	-0.090	20.154	0.015	0.015	0.000	0.000	0.000	0.000
67	A	271	LYS	1	0.886	0.933	21.893	10.189	10.189	0.000	0.000	0.000	0.000
68	A	272	ARG	1	0.943	0.988	21.319	11.303	11.303	0.000	0.000	0.000	0.000
69	A	273	VAL	0	-0.004	0.009	15.286	-0.352	-0.352	0.000	0.000	0.000	0.000
70	A	274	PRO	0	0.048	0.011	16.864	0.027	0.027	0.000	0.000	0.000	0.000
71	A	275	ILE	0	0.054	0.041	14.687	0.244	0.244	0.000	0.000	0.000	0.000
72	A	276	PHE	0	-0.075	-0.043	15.850	0.150	0.150	0.000	0.000	0.000	0.000
73	A	277	GLN	0	-0.056	-0.031	20.162	0.301	0.301	0.000	0.000	0.000	0.000
74	A	278	ASP	-1	-0.907	-0.945	19.958	-12.145	-12.145	0.000	0.000	0.000	0.000
75	A	279	VAL	0	-0.056	-0.022	18.201	-0.093	-0.093	0.000	0.000	0.000	0.000
76	A	280	PRO	0	-0.030	-0.009	21.566	0.333	0.333	0.000	0.000	0.000	0.000
77	A	281	PRO	0	-0.009	-0.019	22.535	-0.439	-0.439	0.000	0.000	0.000	0.000
78	A	282	PRO	0	0.017	0.023	20.420	0.128	0.128	0.000	0.000	0.000	0.000
79	A	283	ILE	0	-0.001	-0.007	22.830	0.460	0.460	0.000	0.000	0.000	0.000
80	A	284	ILE	0	-0.027	-0.023	22.921	-0.402	-0.402	0.000	0.000	0.000	0.000
81	A	285	HIS	0	0.000	-0.001	25.584	0.680	0.680	0.000	0.000	0.000	0.000
82	A	286	ILE	0	-0.017	-0.004	27.260	-0.275	-0.275	0.000	0.000	0.000	0.000
83	A	287	ARG	1	0.976	1.005	29.812	9.173	9.173	0.000	0.000	0.000	0.000
84	A	288	SER	0	-0.022	-0.024	33.018	0.386	0.386	0.000	0.000	0.000	0.000
85	A	289	ARG	1	0.991	0.976	33.932	7.889	7.889	0.000	0.000	0.000	0.000
86	A	290	GLY	0	0.000	-0.002	35.025	-0.061	-0.061	0.000	0.000	0.000	0.000
87	A	291	ASP	-1	-0.805	-0.911	30.535	-9.801	-9.801	0.000	0.000	0.000	0.000
88	A	292	ILE	0	-0.062	-0.014	30.416	-0.362	-0.362	0.000	0.000	0.000	0.000
89	A	293	PRO	0	0.069	0.035	28.139	0.334	0.334	0.000	0.000	0.000	0.000
90	A	294	ARG	1	1.047	1.008	31.267	8.224	8.224	0.000	0.000	0.000	0.000
91	A	295	ALA	0	-0.021	-0.004	31.559	0.238	0.238	0.000	0.000	0.000	0.000
92	A	296	CYS	0	-0.042	-0.020	29.309	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	297	GLN	0	-0.001	-0.006	32.037	0.345	0.345	0.000	0.000	0.000	0.000
94	A	298	LYS	1	0.970	0.987	34.385	8.769	8.769	0.000	0.000	0.000	0.000
95	A	299	SER	0	-0.027	-0.013	32.361	0.213	0.213	0.000	0.000	0.000	0.000
96	A	300	LEU	0	-0.019	0.013	32.197	-0.126	-0.126	0.000	0.000	0.000	0.000
97	A	301	ARG	1	0.822	0.908	34.498	8.427	8.427	0.000	0.000	0.000	0.000
98	A	302	PRO	0	0.048	0.022	35.397	-0.215	-0.215	0.000	0.000	0.000	0.000
99	A	303	ALA	0	0.023	0.010	33.300	-0.081	-0.081	0.000	0.000	0.000	0.000
100	A	304	PRO	0	-0.014	0.008	33.122	0.186	0.186	0.000	0.000	0.000	0.000
101	A	305	PRO	0	0.058	0.014	34.037	-0.209	-0.209	0.000	0.000	0.000	0.000
102	A	306	SER	0	-0.011	-0.006	31.691	-0.176	-0.176	0.000	0.000	0.000	0.000
103	A	307	PRO	0	-0.054	-0.001	29.163	0.046	0.046	0.000	0.000	0.000	0.000
104	A	308	LYS	1	0.985	0.982	27.260	9.071	9.071	0.000	0.000	0.000	0.000
105	A	309	ILE	0	0.091	0.048	21.175	0.269	0.269	0.000	0.000	0.000	0.000
106	A	310	ASP	-1	-0.785	-0.877	24.677	-10.267	-10.267	0.000	0.000	0.000	0.000
107	A	311	ARG	1	0.876	0.923	25.944	9.364	9.364	0.000	0.000	0.000	0.000
108	A	312	GLY	0	-0.010	-0.011	27.686	0.364	0.364	0.000	0.000	0.000	0.000
109	A	313	TRP	0	-0.045	-0.024	28.264	0.133	0.133	0.000	0.000	0.000	0.000
110	A	314	VAL	0	0.042	0.027	23.670	-0.288	-0.288	0.000	0.000	0.000	0.000
111	A	315	CYS	0	0.023	0.005	23.961	-0.464	-0.464	0.000	0.000	0.000	0.000
112	A	316	LEU	0	-0.045	-0.018	25.834	0.544	0.544	0.000	0.000	0.000	0.000
113	A	317	PHE	0	0.018	0.010	27.108	-0.338	-0.338	0.000	0.000	0.000	0.000
114	A	318	LYS	1	0.923	0.973	29.623	9.615	9.615	0.000	0.000	0.000	0.000
115	A	319	MET	0	0.009	-0.002	31.091	-0.276	-0.276	0.000	0.000	0.000	0.000
116	A	320	GLN	0	0.055	0.029	33.764	-0.063	-0.063	0.000	0.000	0.000	0.000
117	A	321	ASP	-1	-0.932	-0.969	34.900	-8.121	-8.121	0.000	0.000	0.000	0.000
118	A	322	GLY	0	0.018	0.006	36.101	0.188	0.188	0.000	0.000	0.000	0.000
119	A	323	LYS	1	0.913	0.962	36.728	7.483	7.483	0.000	0.000	0.000	0.000
120	A	324	THR	0	0.013	-0.006	32.172	-0.345	-0.345	0.000	0.000	0.000	0.000
121	A	325	LEU	0	-0.060	-0.013	33.253	0.284	0.284	0.000	0.000	0.000	0.000
122	A	326	GLY	0	0.036	0.020	30.917	-0.334	-0.334	0.000	0.000	0.000	0.000
123	A	327	LEU	0	-0.016	0.004	26.999	0.289	0.289	0.000	0.000	0.000	0.000
124	A	328	LYS	1	0.893	0.960	29.277	8.713	8.713	0.000	0.000	0.000	0.000
125	A	329	ILE	0	-0.020	-0.016	27.002	0.280	0.280	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:205:LYS)