FMO DATABASE

FMODB ID: G61J1

Calculation Name: 5IP4-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IP4

Chain ID: D

ChEMBL ID:

UniProt ID: O43602

Base Structure: X-ray

Registration Date: 2023-09-20

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-517795.079941
FMO2-HF: Nuclear repulsion	486728.279319
FMO2-HF: Total energy	-31066.800622
FMO2-MP2: Total energy	-31158.410065

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(D:255:LYS)

Summations of interaction energy for fragment #1(D:255: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.
80.96	86.227	1.199	-2.243	-4.223	0.013

Interaction energy analysis for fragmet #1(D:255:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.030 / q_NPA : 1.011

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

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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	D	257	PHE	0	-0.003	-0.016	2.692	0.924	4.176	0.656	-1.709	-2.200	0.013
4	D	258	VAL	0	-0.053	-0.021	2.563	1.368	2.492	0.536	-0.373	-1.286	0.000
5	D	259	ARG	1	0.915	0.962	3.403	53.891	54.570	0.008	-0.139	-0.547	0.000
6	D	260	PRO	0	-0.007	0.002	5.294	-4.922	-4.922	0.000	0.000	0.000	0.000
7	D	261	LYS	1	0.903	0.949	3.917	43.447	43.659	-0.001	-0.022	-0.190	0.000
8	D	262	LEU	0	-0.064	-0.029	5.648	7.035	7.035	0.000	0.000	0.000	0.000
9	D	263	VAL	0	0.040	0.032	7.227	-2.712	-2.712	0.000	0.000	0.000	0.000
10	D	264	THR	0	-0.034	-0.028	9.575	2.994	2.994	0.000	0.000	0.000	0.000
11	D	265	ILE	0	0.006	0.005	12.753	0.031	0.031	0.000	0.000	0.000	0.000
12	D	266	ILE	0	-0.002	-0.008	15.855	0.908	0.908	0.000	0.000	0.000	0.000
13	D	267	ARG	1	0.950	0.991	19.066	12.506	12.506	0.000	0.000	0.000	0.000
14	D	268	SER	0	-0.003	-0.034	22.328	0.244	0.244	0.000	0.000	0.000	0.000
15	D	269	GLY	0	0.000	0.008	24.787	0.183	0.183	0.000	0.000	0.000	0.000
16	D	270	VAL	0	-0.034	-0.016	26.549	0.327	0.327	0.000	0.000	0.000	0.000
17	D	271	LYS	1	1.009	0.986	28.143	9.422	9.422	0.000	0.000	0.000	0.000
18	D	272	PRO	0	0.001	0.020	29.032	-0.097	-0.097	0.000	0.000	0.000	0.000
19	D	273	ARG	1	0.961	0.978	23.073	12.807	12.807	0.000	0.000	0.000	0.000
20	D	274	LYS	1	0.911	0.968	22.055	13.422	13.422	0.000	0.000	0.000	0.000
21	D	275	ALA	0	0.046	0.031	17.611	-0.228	-0.228	0.000	0.000	0.000	0.000
22	D	276	VAL	0	-0.039	-0.014	16.606	0.497	0.497	0.000	0.000	0.000	0.000
23	D	277	ARG	1	0.950	0.975	12.382	20.683	20.683	0.000	0.000	0.000	0.000
24	D	278	VAL	0	0.031	0.019	12.471	1.263	1.263	0.000	0.000	0.000	0.000
25	D	279	LEU	0	0.003	-0.002	9.101	-2.468	-2.468	0.000	0.000	0.000	0.000
26	D	280	LEU	0	0.028	0.028	9.078	2.450	2.450	0.000	0.000	0.000	0.000
27	D	281	ASN	0	0.025	-0.006	8.574	-5.175	-5.175	0.000	0.000	0.000	0.000
28	D	282	LYS	1	0.999	1.002	6.102	35.256	35.256	0.000	0.000	0.000	0.000
29	D	283	LYS	1	0.893	0.947	7.901	26.613	26.613	0.000	0.000	0.000	0.000
30	D	284	THR	0	0.005	-0.001	10.929	1.665	1.665	0.000	0.000	0.000	0.000
31	D	285	ALA	0	-0.014	0.024	12.917	1.230	1.230	0.000	0.000	0.000	0.000
32	D	286	HIS	0	0.023	0.003	14.431	-0.013	-0.013	0.000	0.000	0.000	0.000
33	D	287	SER	0	0.046	0.025	16.815	0.295	0.295	0.000	0.000	0.000	0.000
34	D	288	PHE	0	0.013	0.000	16.334	-0.495	-0.495	0.000	0.000	0.000	0.000
35	D	289	GLU	-1	-0.873	-0.935	18.428	-12.650	-12.650	0.000	0.000	0.000	0.000
36	D	290	GLN	0	-0.012	-0.022	20.145	0.676	0.676	0.000	0.000	0.000	0.000
37	D	291	VAL	0	0.035	0.029	14.337	-0.156	-0.156	0.000	0.000	0.000	0.000
38	D	292	LEU	0	-0.019	0.003	17.590	-0.132	-0.132	0.000	0.000	0.000	0.000
39	D	293	THR	0	0.014	0.005	19.583	0.488	0.488	0.000	0.000	0.000	0.000
40	D	294	ASP	-1	-0.853	-0.912	18.230	-15.800	-15.800	0.000	0.000	0.000	0.000
41	D	295	ILE	0	-0.088	-0.055	14.905	-0.042	-0.042	0.000	0.000	0.000	0.000
42	D	296	THR	0	-0.019	-0.019	18.700	0.383	0.383	0.000	0.000	0.000	0.000
43	D	297	GLU	-1	-0.861	-0.923	22.317	-12.537	-12.537	0.000	0.000	0.000	0.000
44	D	298	ALA	0	-0.053	-0.019	19.384	0.369	0.369	0.000	0.000	0.000	0.000
45	D	299	ILE	0	-0.116	-0.070	19.706	0.219	0.219	0.000	0.000	0.000	0.000
46	D	300	LYS	1	0.863	0.927	22.369	12.989	12.989	0.000	0.000	0.000	0.000
47	D	301	LEU	0	-0.023	-0.008	24.216	0.422	0.422	0.000	0.000	0.000	0.000
48	D	302	GLU	-1	-0.884	-0.934	26.870	-10.124	-10.124	0.000	0.000	0.000	0.000
49	D	303	THR	0	0.050	-0.003	26.244	-0.268	-0.268	0.000	0.000	0.000	0.000
50	D	304	GLY	0	-0.001	0.008	26.435	0.377	0.377	0.000	0.000	0.000	0.000
51	D	305	VAL	0	-0.020	-0.005	27.663	0.133	0.133	0.000	0.000	0.000	0.000
52	D	306	VAL	0	-0.035	-0.001	22.233	0.002	0.002	0.000	0.000	0.000	0.000
53	D	307	LYS	1	0.907	0.942	23.667	11.453	11.453	0.000	0.000	0.000	0.000
54	D	308	LYS	1	0.912	0.946	20.605	12.436	12.436	0.000	0.000	0.000	0.000
55	D	309	LEU	0	-0.031	0.003	15.880	0.333	0.333	0.000	0.000	0.000	0.000
56	D	310	TYR	0	0.001	0.017	18.734	0.610	0.610	0.000	0.000	0.000	0.000
57	D	311	THR	0	0.080	0.047	14.381	0.036	0.036	0.000	0.000	0.000	0.000
58	D	312	LEU	0	0.006	-0.011	15.000	1.227	1.227	0.000	0.000	0.000	0.000
59	D	313	ASP	-1	-0.896	-0.934	16.247	-17.603	-17.603	0.000	0.000	0.000	0.000
60	D	314	GLY	0	-0.042	-0.019	18.777	0.844	0.844	0.000	0.000	0.000	0.000
61	D	315	LYS	1	0.949	0.981	17.395	17.275	17.275	0.000	0.000	0.000	0.000
62	D	316	GLN	0	-0.004	-0.023	18.615	-0.099	-0.099	0.000	0.000	0.000	0.000
63	D	317	VAL	0	-0.010	0.003	14.742	-0.332	-0.332	0.000	0.000	0.000	0.000
64	D	318	THR	0	-0.056	-0.045	17.579	0.895	0.895	0.000	0.000	0.000	0.000
65	D	319	CYS	0	0.000	0.014	16.596	0.316	0.316	0.000	0.000	0.000	0.000
66	D	320	LEU	0	0.057	0.007	13.304	-1.027	-1.027	0.000	0.000	0.000	0.000
67	D	321	HIS	0	-0.012	-0.004	11.656	-2.367	-2.367	0.000	0.000	0.000	0.000
68	D	322	ASP	-1	-0.783	-0.908	10.909	-21.525	-21.525	0.000	0.000	0.000	0.000
69	D	323	PHE	0	-0.048	-0.013	9.946	-0.528	-0.528	0.000	0.000	0.000	0.000
70	D	324	PHE	0	-0.109	-0.050	6.371	-3.348	-3.348	0.000	0.000	0.000	0.000
71	D	325	GLY	0	0.040	0.016	6.704	-1.293	-1.293	0.000	0.000	0.000	0.000
72	D	326	ASP	-1	-0.891	-0.952	6.475	-39.172	-39.172	0.000	0.000	0.000	0.000
73	D	327	ASP	-1	-0.944	-0.949	7.974	-25.189	-25.189	0.000	0.000	0.000	0.000
74	D	328	ASP	-1	-0.892	-0.959	5.698	-53.598	-53.598	0.000	0.000	0.000	0.000
75	D	329	VAL	0	-0.056	-0.038	8.664	1.715	1.715	0.000	0.000	0.000	0.000
76	D	330	PHE	0	0.029	0.010	10.208	0.932	0.932	0.000	0.000	0.000	0.000
77	D	331	ILE	0	-0.046	-0.015	15.187	0.643	0.643	0.000	0.000	0.000	0.000
78	D	332	ALA	0	0.049	0.015	18.918	0.026	0.026	0.000	0.000	0.000	0.000
79	D	333	CYS	0	-0.064	-0.047	21.041	0.337	0.337	0.000	0.000	0.000	0.000
80	D	334	GLY	0	0.062	0.047	24.619	0.263	0.263	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:255:LYS)