FMO DATABASE

FMODB ID: R9M78

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	OptHSide
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	-1055447.259989
FMO2-HF: Nuclear repulsion	1006354.613127
FMO2-HF: Total energy	-49092.646862
FMO2-MP2: Total energy	-49234.712295

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.
16.206	18.355	-0.018	-0.971	-1.161	0.003

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 : 0.957 / 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	0.003	-0.002	3.838	-3.816	-1.823	-0.017	-0.946	-1.031	0.003
4	A	208	ILE	0	-0.031	0.010	6.261	1.451	1.451	0.000	0.000	0.000	0.000
5	A	209	SER	0	-0.033	-0.052	6.942	-1.243	-1.243	0.000	0.000	0.000	0.000
6	A	210	ALA	0	0.032	-0.011	7.751	2.394	2.394	0.000	0.000	0.000	0.000
7	A	211	LYS	1	0.808	0.897	10.637	22.572	22.572	0.000	0.000	0.000	0.000
8	A	212	ASP	-1	-0.755	-0.847	10.069	-23.973	-23.973	0.000	0.000	0.000	0.000
9	A	213	LEU	0	0.028	0.029	11.729	1.369	1.369	0.000	0.000	0.000	0.000
10	A	214	LYS	1	0.926	0.939	13.420	16.920	16.920	0.000	0.000	0.000	0.000
11	A	215	GLU	-1	-0.939	-0.952	15.635	-16.736	-16.736	0.000	0.000	0.000	0.000
12	A	216	ILE	0	0.104	0.054	14.453	0.891	0.891	0.000	0.000	0.000	0.000
13	A	217	MET	0	-0.034	-0.009	16.349	0.906	0.906	0.000	0.000	0.000	0.000
14	A	218	TYR	0	-0.087	-0.074	19.475	0.850	0.850	0.000	0.000	0.000	0.000
15	A	219	ASP	-1	-0.882	-0.920	20.751	-13.234	-13.234	0.000	0.000	0.000	0.000
16	A	220	HIS	0	-0.085	-0.044	20.646	0.779	0.779	0.000	0.000	0.000	0.000
17	A	221	LEU	0	-0.094	-0.044	23.436	0.557	0.557	0.000	0.000	0.000	0.000
18	A	222	PRO	0	0.020	0.023	26.158	0.113	0.113	0.000	0.000	0.000	0.000
19	A	223	GLY	0	0.002	-0.012	29.247	-0.052	-0.052	0.000	0.000	0.000	0.000
20	A	224	PHE	0	0.017	-0.002	27.901	-0.319	-0.319	0.000	0.000	0.000	0.000
21	A	225	GLY	0	0.031	0.014	27.222	0.308	0.308	0.000	0.000	0.000	0.000
22	A	226	THR	0	0.020	-0.020	27.601	0.337	0.337	0.000	0.000	0.000	0.000
23	A	227	ALA	0	0.034	-0.007	27.125	-0.323	-0.323	0.000	0.000	0.000	0.000
24	A	228	PHE	0	0.055	0.021	25.269	-0.237	-0.237	0.000	0.000	0.000	0.000
25	A	229	HIS	0	0.080	0.084	23.316	-0.257	-0.257	0.000	0.000	0.000	0.000
26	A	230	GLN	0	0.010	0.000	22.144	-1.062	-1.062	0.000	0.000	0.000	0.000
27	A	231	LEU	0	0.019	-0.004	21.736	-0.375	-0.375	0.000	0.000	0.000	0.000
28	A	232	VAL	0	0.048	0.040	17.904	-0.525	-0.525	0.000	0.000	0.000	0.000
29	A	233	GLN	0	-0.037	-0.015	17.483	-1.259	-1.259	0.000	0.000	0.000	0.000
30	A	234	VAL	0	-0.048	-0.017	17.190	-0.744	-0.744	0.000	0.000	0.000	0.000
31	A	235	ILE	0	0.036	0.017	15.492	-0.591	-0.591	0.000	0.000	0.000	0.000
32	A	236	CYS	0	-0.009	0.000	13.218	-1.017	-1.017	0.000	0.000	0.000	0.000
33	A	237	LYS	1	0.825	0.900	12.192	15.688	15.688	0.000	0.000	0.000	0.000
34	A	238	ILE	0	0.030	0.018	13.011	-0.800	-0.800	0.000	0.000	0.000	0.000
35	A	239	GLY	0	0.084	0.032	11.412	-0.482	-0.482	0.000	0.000	0.000	0.000
36	A	240	LYS	1	0.923	0.954	8.250	26.924	26.924	0.000	0.000	0.000	0.000
37	A	241	ASP	-1	-0.905	-0.942	8.293	-21.725	-21.725	0.000	0.000	0.000	0.000
38	A	242	ASN	0	-0.052	-0.032	10.548	0.359	0.359	0.000	0.000	0.000	0.000
39	A	243	ASN	0	-0.049	-0.009	3.907	-2.400	-2.244	-0.001	-0.025	-0.130	0.000
40	A	244	LEU	0	0.043	0.011	7.255	0.235	0.235	0.000	0.000	0.000	0.000
41	A	245	LEU	0	-0.036	-0.015	6.520	1.344	1.344	0.000	0.000	0.000	0.000
42	A	246	ASP	-1	-0.742	-0.881	6.494	-30.385	-30.385	0.000	0.000	0.000	0.000
43	A	247	THR	0	-0.008	-0.003	9.577	1.069	1.069	0.000	0.000	0.000	0.000
44	A	248	ILE	0	-0.015	-0.006	11.964	1.242	1.242	0.000	0.000	0.000	0.000
45	A	249	HIS	0	0.008	0.007	12.195	1.084	1.084	0.000	0.000	0.000	0.000
46	A	250	ALA	0	0.034	0.014	13.661	0.964	0.964	0.000	0.000	0.000	0.000
47	A	251	GLU	-1	-0.848	-0.907	15.557	-12.046	-12.046	0.000	0.000	0.000	0.000
48	A	252	PHE	0	-0.015	-0.021	17.148	0.833	0.833	0.000	0.000	0.000	0.000
49	A	253	GLN	0	-0.029	-0.026	16.242	-0.048	-0.048	0.000	0.000	0.000	0.000
50	A	254	ALA	0	0.013	0.012	19.600	0.567	0.567	0.000	0.000	0.000	0.000
51	A	255	SER	0	0.014	0.000	21.479	0.515	0.515	0.000	0.000	0.000	0.000
52	A	256	LEU	0	-0.051	-0.032	21.539	0.449	0.449	0.000	0.000	0.000	0.000
53	A	257	ALA	0	-0.047	-0.016	23.808	0.408	0.408	0.000	0.000	0.000	0.000
54	A	258	ASP	-1	-0.898	-0.946	25.513	-10.508	-10.508	0.000	0.000	0.000	0.000
55	A	259	GLY	0	-0.037	-0.013	27.645	0.419	0.419	0.000	0.000	0.000	0.000
56	A	260	ASP	-1	-0.804	-0.855	26.469	-9.997	-9.997	0.000	0.000	0.000	0.000
57	A	261	SER	0	-0.042	-0.042	27.435	-0.209	-0.209	0.000	0.000	0.000	0.000
58	A	262	PRO	0	0.111	0.039	24.250	-0.179	-0.179	0.000	0.000	0.000	0.000
59	A	263	GLN	0	-0.021	-0.012	24.372	-0.327	-0.327	0.000	0.000	0.000	0.000
60	A	264	CYS	0	-0.073	-0.043	25.946	-0.129	-0.129	0.000	0.000	0.000	0.000
61	A	265	ALA	0	0.110	0.064	22.382	-0.095	-0.095	0.000	0.000	0.000	0.000
62	A	266	LEU	0	-0.042	-0.024	20.137	-0.373	-0.373	0.000	0.000	0.000	0.000
63	A	267	ILE	0	-0.050	-0.030	22.214	-0.125	-0.125	0.000	0.000	0.000	0.000
64	A	268	GLN	0	0.001	-0.003	23.518	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	269	ILE	0	0.019	0.021	17.508	-0.184	-0.184	0.000	0.000	0.000	0.000
66	A	270	THR	0	-0.142	-0.085	20.142	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	271	LYS	1	0.812	0.898	21.880	10.127	10.127	0.000	0.000	0.000	0.000
68	A	272	ARG	1	0.834	0.919	21.337	11.683	11.683	0.000	0.000	0.000	0.000
69	A	273	VAL	0	-0.007	0.005	15.199	-0.371	-0.371	0.000	0.000	0.000	0.000
70	A	274	PRO	0	0.052	0.013	16.867	0.049	0.049	0.000	0.000	0.000	0.000
71	A	275	ILE	0	0.048	0.036	14.436	0.296	0.296	0.000	0.000	0.000	0.000
72	A	276	PHE	0	-0.053	-0.031	15.844	0.183	0.183	0.000	0.000	0.000	0.000
73	A	277	GLN	0	-0.071	-0.040	20.154	0.576	0.576	0.000	0.000	0.000	0.000
74	A	278	ASP	-1	-0.912	-0.944	19.884	-12.145	-12.145	0.000	0.000	0.000	0.000
75	A	279	VAL	0	-0.047	-0.019	18.229	-0.077	-0.077	0.000	0.000	0.000	0.000
76	A	280	PRO	0	-0.028	-0.010	21.561	0.323	0.323	0.000	0.000	0.000	0.000
77	A	281	PRO	0	-0.008	-0.019	22.525	-0.424	-0.424	0.000	0.000	0.000	0.000
78	A	282	PRO	0	0.015	0.019	20.257	0.164	0.164	0.000	0.000	0.000	0.000
79	A	283	ILE	0	-0.006	-0.006	22.815	0.456	0.456	0.000	0.000	0.000	0.000
80	A	284	ILE	0	-0.024	-0.019	23.182	-0.399	-0.399	0.000	0.000	0.000	0.000
81	A	285	HIS	0	0.005	0.001	25.587	0.714	0.714	0.000	0.000	0.000	0.000
82	A	286	ILE	0	-0.013	0.000	27.635	-0.265	-0.265	0.000	0.000	0.000	0.000
83	A	287	ARG	1	0.981	0.994	30.203	9.121	9.121	0.000	0.000	0.000	0.000
84	A	288	SER	0	-0.043	-0.039	33.495	0.379	0.379	0.000	0.000	0.000	0.000
85	A	289	ARG	1	0.968	0.957	34.243	7.907	7.907	0.000	0.000	0.000	0.000
86	A	290	GLY	0	0.001	0.002	35.187	-0.059	-0.059	0.000	0.000	0.000	0.000
87	A	291	ASP	-1	-0.810	-0.897	31.073	-9.602	-9.602	0.000	0.000	0.000	0.000
88	A	292	ILE	0	-0.057	-0.010	30.452	-0.362	-0.362	0.000	0.000	0.000	0.000
89	A	293	PRO	0	0.065	0.029	28.093	0.332	0.332	0.000	0.000	0.000	0.000
90	A	294	ARG	1	1.043	1.008	31.397	8.135	8.135	0.000	0.000	0.000	0.000
91	A	295	ALA	0	-0.017	-0.003	31.557	0.233	0.233	0.000	0.000	0.000	0.000
92	A	296	CYS	0	-0.037	-0.019	29.264	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	297	GLN	0	0.023	0.023	32.010	0.321	0.321	0.000	0.000	0.000	0.000
94	A	298	LYS	1	0.975	0.986	34.509	8.712	8.712	0.000	0.000	0.000	0.000
95	A	299	SER	0	-0.018	-0.005	32.158	0.199	0.199	0.000	0.000	0.000	0.000
96	A	300	LEU	0	-0.040	0.005	32.071	-0.127	-0.127	0.000	0.000	0.000	0.000
97	A	301	ARG	1	0.819	0.898	34.480	8.404	8.404	0.000	0.000	0.000	0.000
98	A	302	PRO	0	0.061	0.027	35.377	-0.212	-0.212	0.000	0.000	0.000	0.000
99	A	303	ALA	0	0.018	0.008	33.310	-0.084	-0.084	0.000	0.000	0.000	0.000
100	A	304	PRO	0	-0.018	0.006	33.306	0.172	0.172	0.000	0.000	0.000	0.000
101	A	305	PRO	0	0.071	0.019	34.025	-0.216	-0.216	0.000	0.000	0.000	0.000
102	A	306	SER	0	-0.001	-0.002	31.677	-0.201	-0.201	0.000	0.000	0.000	0.000
103	A	307	PRO	0	-0.021	0.013	29.055	0.059	0.059	0.000	0.000	0.000	0.000
104	A	308	LYS	1	0.955	0.966	27.253	8.953	8.953	0.000	0.000	0.000	0.000
105	A	309	ILE	0	0.072	0.040	21.205	0.281	0.281	0.000	0.000	0.000	0.000
106	A	310	ASP	-1	-0.706	-0.846	25.028	-9.922	-9.922	0.000	0.000	0.000	0.000
107	A	311	ARG	1	0.849	0.931	25.932	9.448	9.448	0.000	0.000	0.000	0.000
108	A	312	GLY	0	0.022	0.015	27.670	0.383	0.383	0.000	0.000	0.000	0.000
109	A	313	TRP	0	-0.043	-0.025	28.254	0.137	0.137	0.000	0.000	0.000	0.000
110	A	314	VAL	0	0.050	0.029	23.715	-0.296	-0.296	0.000	0.000	0.000	0.000
111	A	315	CYS	0	0.016	0.000	23.942	-0.472	-0.472	0.000	0.000	0.000	0.000
112	A	316	LEU	0	-0.035	-0.014	25.815	0.530	0.530	0.000	0.000	0.000	0.000
113	A	317	PHE	0	0.018	0.009	27.045	-0.347	-0.347	0.000	0.000	0.000	0.000
114	A	318	LYS	1	0.896	0.950	29.601	9.471	9.471	0.000	0.000	0.000	0.000
115	A	319	MET	0	0.002	-0.004	31.257	-0.272	-0.272	0.000	0.000	0.000	0.000
116	A	320	GLN	0	0.058	0.026	33.951	-0.027	-0.027	0.000	0.000	0.000	0.000
117	A	321	ASP	-1	-0.865	-0.922	35.239	-7.984	-7.984	0.000	0.000	0.000	0.000
118	A	322	GLY	0	0.036	0.013	36.226	0.184	0.184	0.000	0.000	0.000	0.000
119	A	323	LYS	1	0.853	0.933	36.712	7.546	7.546	0.000	0.000	0.000	0.000
120	A	324	THR	0	0.016	-0.009	32.126	-0.340	-0.340	0.000	0.000	0.000	0.000
121	A	325	LEU	0	-0.050	-0.007	33.240	0.276	0.276	0.000	0.000	0.000	0.000
122	A	326	GLY	0	0.036	0.019	30.899	-0.334	-0.334	0.000	0.000	0.000	0.000
123	A	327	LEU	0	-0.027	-0.003	26.977	0.282	0.282	0.000	0.000	0.000	0.000
124	A	328	LYS	1	0.825	0.910	29.257	8.768	8.768	0.000	0.000	0.000	0.000
125	A	329	ILE	0	0.012	0.006	26.829	0.254	0.254	0.000	0.000	0.000	0.000

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