FMO DATABASE

FMODB ID: QYM2Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1058571.047448
FMO2-HF: Nuclear repulsion	1009478.14798
FMO2-HF: Total energy	-49092.899468
FMO2-MP2: Total energy	-49234.934044

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.
10.479	12.862	0.002	-1.171	-1.214	0.002

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 : 0.955 / q_NPA : 0.966

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	-0.010	-0.017	3.617	-5.014	-2.900	0.000	-1.102	-1.012	0.002
4	A	208	ILE	0	-0.038	0.004	6.343	1.555	1.555	0.000	0.000	0.000	0.000
5	A	209	SER	0	-0.020	-0.048	6.916	-1.099	-1.099	0.000	0.000	0.000	0.000
6	A	210	ALA	0	0.024	-0.016	7.670	2.398	2.398	0.000	0.000	0.000	0.000
7	A	211	LYS	1	0.782	0.890	10.700	22.586	22.586	0.000	0.000	0.000	0.000
8	A	212	ASP	-1	-0.773	-0.855	9.967	-24.142	-24.142	0.000	0.000	0.000	0.000
9	A	213	LEU	0	0.037	0.025	11.579	1.331	1.331	0.000	0.000	0.000	0.000
10	A	214	LYS	1	0.928	0.938	13.305	16.840	16.840	0.000	0.000	0.000	0.000
11	A	215	GLU	-1	-0.917	-0.945	15.499	-17.223	-17.223	0.000	0.000	0.000	0.000
12	A	216	ILE	0	0.095	0.048	14.443	0.915	0.915	0.000	0.000	0.000	0.000
13	A	217	MET	0	-0.025	-0.008	16.504	0.884	0.884	0.000	0.000	0.000	0.000
14	A	218	TYR	0	-0.115	-0.090	19.376	0.865	0.865	0.000	0.000	0.000	0.000
15	A	219	ASP	-1	-0.883	-0.924	20.455	-13.349	-13.349	0.000	0.000	0.000	0.000
16	A	220	HIS	0	-0.064	-0.028	20.853	0.766	0.766	0.000	0.000	0.000	0.000
17	A	221	LEU	0	-0.059	-0.037	23.179	0.501	0.501	0.000	0.000	0.000	0.000
18	A	222	PRO	0	0.018	0.021	26.028	0.045	0.045	0.000	0.000	0.000	0.000
19	A	223	GLY	0	-0.009	-0.012	29.557	0.054	0.054	0.000	0.000	0.000	0.000
20	A	224	PHE	0	0.019	-0.002	27.755	-0.302	-0.302	0.000	0.000	0.000	0.000
21	A	225	GLY	0	0.029	0.007	27.048	0.306	0.306	0.000	0.000	0.000	0.000
22	A	226	THR	0	0.027	-0.011	27.582	0.293	0.293	0.000	0.000	0.000	0.000
23	A	227	ALA	0	0.020	-0.014	27.106	-0.336	-0.336	0.000	0.000	0.000	0.000
24	A	228	PHE	0	0.043	0.028	25.289	-0.195	-0.195	0.000	0.000	0.000	0.000
25	A	229	HIS	0	0.079	0.072	23.325	-0.265	-0.265	0.000	0.000	0.000	0.000
26	A	230	GLN	0	-0.004	0.011	22.397	-1.037	-1.037	0.000	0.000	0.000	0.000
27	A	231	LEU	0	0.013	-0.006	21.725	-0.407	-0.407	0.000	0.000	0.000	0.000
28	A	232	VAL	0	0.066	0.048	17.983	-0.478	-0.478	0.000	0.000	0.000	0.000
29	A	233	GLN	0	-0.019	0.001	17.487	-1.333	-1.333	0.000	0.000	0.000	0.000
30	A	234	VAL	0	-0.057	-0.021	17.072	-0.770	-0.770	0.000	0.000	0.000	0.000
31	A	235	ILE	0	0.034	0.017	15.782	-0.565	-0.565	0.000	0.000	0.000	0.000
32	A	236	CYS	0	0.011	0.012	13.291	-0.970	-0.970	0.000	0.000	0.000	0.000
33	A	237	LYS	1	0.840	0.911	12.245	15.585	15.585	0.000	0.000	0.000	0.000
34	A	238	ILE	0	-0.001	0.000	12.773	-0.930	-0.930	0.000	0.000	0.000	0.000
35	A	239	GLY	0	0.100	0.040	11.431	-0.402	-0.402	0.000	0.000	0.000	0.000
36	A	240	LYS	1	0.860	0.917	8.165	23.310	23.310	0.000	0.000	0.000	0.000
37	A	241	ASP	-1	-0.884	-0.934	8.179	-22.219	-22.219	0.000	0.000	0.000	0.000
38	A	242	ASN	0	-0.035	-0.019	10.354	0.813	0.813	0.000	0.000	0.000	0.000
39	A	243	ASN	0	-0.034	-0.009	3.970	-2.984	-2.715	0.002	-0.069	-0.202	0.000
40	A	244	LEU	0	0.031	0.010	7.067	0.048	0.048	0.000	0.000	0.000	0.000
41	A	245	LEU	0	-0.048	-0.017	6.636	1.310	1.310	0.000	0.000	0.000	0.000
42	A	246	ASP	-1	-0.715	-0.861	6.670	-30.632	-30.632	0.000	0.000	0.000	0.000
43	A	247	THR	0	-0.005	-0.005	9.724	1.015	1.015	0.000	0.000	0.000	0.000
44	A	248	ILE	0	-0.007	0.004	12.220	1.308	1.308	0.000	0.000	0.000	0.000
45	A	249	HIS	0	-0.006	0.000	12.433	0.716	0.716	0.000	0.000	0.000	0.000
46	A	250	ALA	0	0.006	0.003	13.796	0.905	0.905	0.000	0.000	0.000	0.000
47	A	251	GLU	-1	-0.824	-0.900	15.595	-12.051	-12.051	0.000	0.000	0.000	0.000
48	A	252	PHE	0	-0.017	-0.019	17.311	0.807	0.807	0.000	0.000	0.000	0.000
49	A	253	GLN	0	0.000	-0.012	16.534	-0.171	-0.171	0.000	0.000	0.000	0.000
50	A	254	ALA	0	0.010	0.016	19.688	0.548	0.548	0.000	0.000	0.000	0.000
51	A	255	SER	0	0.002	-0.025	21.605	0.504	0.504	0.000	0.000	0.000	0.000
52	A	256	LEU	0	-0.054	-0.040	21.452	0.462	0.462	0.000	0.000	0.000	0.000
53	A	257	ALA	0	-0.053	-0.016	23.954	0.346	0.346	0.000	0.000	0.000	0.000
54	A	258	ASP	-1	-0.838	-0.908	25.626	-10.554	-10.554	0.000	0.000	0.000	0.000
55	A	259	GLY	0	-0.021	-0.002	27.660	0.414	0.414	0.000	0.000	0.000	0.000
56	A	260	ASP	-1	-0.802	-0.842	26.507	-10.098	-10.098	0.000	0.000	0.000	0.000
57	A	261	SER	0	-0.019	-0.024	27.892	-0.126	-0.126	0.000	0.000	0.000	0.000
58	A	262	PRO	0	0.069	0.020	24.173	-0.154	-0.154	0.000	0.000	0.000	0.000
59	A	263	GLN	0	-0.023	-0.009	24.620	-0.278	-0.278	0.000	0.000	0.000	0.000
60	A	264	CYS	0	-0.068	-0.037	26.469	-0.080	-0.080	0.000	0.000	0.000	0.000
61	A	265	ALA	0	0.107	0.057	22.573	-0.129	-0.129	0.000	0.000	0.000	0.000
62	A	266	LEU	0	-0.039	-0.024	20.257	-0.403	-0.403	0.000	0.000	0.000	0.000
63	A	267	ILE	0	-0.042	-0.026	22.303	-0.140	-0.140	0.000	0.000	0.000	0.000
64	A	268	GLN	0	-0.002	0.004	23.582	-0.046	-0.046	0.000	0.000	0.000	0.000
65	A	269	ILE	0	0.035	0.016	17.664	-0.191	-0.191	0.000	0.000	0.000	0.000
66	A	270	THR	0	-0.143	-0.100	20.179	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	271	LYS	1	0.811	0.895	22.098	10.228	10.228	0.000	0.000	0.000	0.000
68	A	272	ARG	1	0.767	0.879	21.589	11.817	11.817	0.000	0.000	0.000	0.000
69	A	273	VAL	0	0.006	0.012	15.310	-0.427	-0.427	0.000	0.000	0.000	0.000
70	A	274	PRO	0	0.015	-0.004	17.523	0.078	0.078	0.000	0.000	0.000	0.000
71	A	275	ILE	0	0.067	0.039	14.616	0.389	0.389	0.000	0.000	0.000	0.000
72	A	276	PHE	0	-0.052	-0.025	15.953	0.199	0.199	0.000	0.000	0.000	0.000
73	A	277	GLN	0	-0.055	-0.038	20.550	0.831	0.831	0.000	0.000	0.000	0.000
74	A	278	ASP	-1	-0.900	-0.938	19.948	-12.280	-12.280	0.000	0.000	0.000	0.000
75	A	279	VAL	0	-0.038	-0.009	18.411	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	280	PRO	0	-0.019	-0.007	21.742	0.303	0.303	0.000	0.000	0.000	0.000
77	A	281	PRO	0	-0.005	-0.019	22.542	-0.431	-0.431	0.000	0.000	0.000	0.000
78	A	282	PRO	0	-0.002	0.009	20.078	0.219	0.219	0.000	0.000	0.000	0.000
79	A	283	ILE	0	0.008	0.006	22.697	0.407	0.407	0.000	0.000	0.000	0.000
80	A	284	ILE	0	-0.043	-0.022	23.337	-0.458	-0.458	0.000	0.000	0.000	0.000
81	A	285	HIS	0	0.032	0.010	25.526	0.698	0.698	0.000	0.000	0.000	0.000
82	A	286	ILE	0	-0.027	-0.007	27.549	-0.280	-0.280	0.000	0.000	0.000	0.000
83	A	287	ARG	1	0.955	0.967	30.268	9.209	9.209	0.000	0.000	0.000	0.000
84	A	288	SER	0	-0.039	-0.050	33.667	0.363	0.363	0.000	0.000	0.000	0.000
85	A	289	ARG	1	0.953	0.947	34.138	7.932	7.932	0.000	0.000	0.000	0.000
86	A	290	GLY	0	0.012	0.008	35.219	-0.060	-0.060	0.000	0.000	0.000	0.000
87	A	291	ASP	-1	-0.793	-0.863	31.498	-9.369	-9.369	0.000	0.000	0.000	0.000
88	A	292	ILE	0	-0.031	0.006	30.258	-0.389	-0.389	0.000	0.000	0.000	0.000
89	A	293	PRO	0	0.048	0.021	27.974	0.344	0.344	0.000	0.000	0.000	0.000
90	A	294	ARG	1	1.026	0.999	31.297	8.120	8.120	0.000	0.000	0.000	0.000
91	A	295	ALA	0	-0.002	0.008	31.367	0.249	0.249	0.000	0.000	0.000	0.000
92	A	296	CYS	0	-0.031	-0.014	28.974	-0.087	-0.087	0.000	0.000	0.000	0.000
93	A	297	GLN	0	0.010	0.004	31.684	0.373	0.373	0.000	0.000	0.000	0.000
94	A	298	LYS	1	0.983	0.994	34.162	8.818	8.818	0.000	0.000	0.000	0.000
95	A	299	SER	0	-0.013	-0.013	32.195	0.216	0.216	0.000	0.000	0.000	0.000
96	A	300	LEU	0	-0.050	0.006	31.910	-0.131	-0.131	0.000	0.000	0.000	0.000
97	A	301	ARG	1	0.837	0.909	34.476	8.445	8.445	0.000	0.000	0.000	0.000
98	A	302	PRO	0	0.066	0.019	35.363	-0.210	-0.210	0.000	0.000	0.000	0.000
99	A	303	ALA	0	0.015	0.013	33.004	-0.086	-0.086	0.000	0.000	0.000	0.000
100	A	304	PRO	0	-0.016	0.006	32.934	0.185	0.185	0.000	0.000	0.000	0.000
101	A	305	PRO	0	0.057	0.006	33.826	-0.231	-0.231	0.000	0.000	0.000	0.000
102	A	306	SER	0	0.012	0.009	31.557	-0.152	-0.152	0.000	0.000	0.000	0.000
103	A	307	PRO	0	-0.020	0.021	28.827	0.080	0.080	0.000	0.000	0.000	0.000
104	A	308	LYS	1	0.928	0.945	26.782	9.047	9.047	0.000	0.000	0.000	0.000
105	A	309	ILE	0	0.044	0.027	21.035	0.283	0.283	0.000	0.000	0.000	0.000
106	A	310	ASP	-1	-0.686	-0.819	24.835	-9.762	-9.762	0.000	0.000	0.000	0.000
107	A	311	ARG	1	0.821	0.902	25.972	9.603	9.603	0.000	0.000	0.000	0.000
108	A	312	GLY	0	0.048	0.030	27.456	0.356	0.356	0.000	0.000	0.000	0.000
109	A	313	TRP	0	-0.060	-0.031	28.075	0.189	0.189	0.000	0.000	0.000	0.000
110	A	314	VAL	0	0.038	0.021	23.765	-0.306	-0.306	0.000	0.000	0.000	0.000
111	A	315	CYS	0	0.016	0.004	23.878	-0.454	-0.454	0.000	0.000	0.000	0.000
112	A	316	LEU	0	-0.017	-0.007	25.767	0.536	0.536	0.000	0.000	0.000	0.000
113	A	317	PHE	0	0.034	0.017	27.123	-0.246	-0.246	0.000	0.000	0.000	0.000
114	A	318	LYS	1	0.854	0.917	29.484	9.444	9.444	0.000	0.000	0.000	0.000
115	A	319	MET	0	0.004	0.012	31.195	-0.262	-0.262	0.000	0.000	0.000	0.000
116	A	320	GLN	0	0.037	0.016	33.938	-0.030	-0.030	0.000	0.000	0.000	0.000
117	A	321	ASP	-1	-0.845	-0.908	35.091	-7.951	-7.951	0.000	0.000	0.000	0.000
118	A	322	GLY	0	0.049	0.028	36.779	0.220	0.220	0.000	0.000	0.000	0.000
119	A	323	LYS	1	0.845	0.917	36.812	7.520	7.520	0.000	0.000	0.000	0.000
120	A	324	THR	0	0.028	0.000	31.976	-0.305	-0.305	0.000	0.000	0.000	0.000
121	A	325	LEU	0	-0.045	-0.011	32.904	0.291	0.291	0.000	0.000	0.000	0.000
122	A	326	GLY	0	0.025	0.014	30.673	-0.339	-0.339	0.000	0.000	0.000	0.000
123	A	327	LEU	0	-0.044	-0.018	27.078	0.293	0.293	0.000	0.000	0.000	0.000
124	A	328	LYS	1	0.838	0.911	29.274	8.781	8.781	0.000	0.000	0.000	0.000
125	A	329	ILE	0	0.026	0.031	26.748	0.332	0.332	0.000	0.000	0.000	0.000

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