FMO DATABASE

FMODB ID: LJ5N9

Calculation Name: 1IIB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IIB

Chain ID: A

ChEMBL ID:

UniProt ID: P69795

Base Structure: X-ray

Registration Date: 2023-06-21

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-736089.744661
FMO2-HF: Nuclear repulsion	697780.727919
FMO2-HF: Total energy	-38309.016743
FMO2-MP2: Total energy	-38421.539743

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:3:LYS)

Summations of interaction energy for fragment #1(A:3: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.
-104.557	-100.331	21.446	-10.041	-15.629	-0.11

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.889 / q_NPA : 0.938

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	5	HIS	0	0.055	0.038	3.781	-7.567	-5.929	-0.016	-0.672	-0.949	0.003
4	A	6	ILE	0	0.010	0.006	5.884	4.433	4.433	0.000	0.000	0.000	0.000
5	A	7	TYR	0	-0.038	-0.032	8.145	0.005	0.005	0.000	0.000	0.000	0.000
6	A	8	LEU	0	-0.012	-0.003	11.566	1.448	1.448	0.000	0.000	0.000	0.000
7	A	9	PHE	0	0.009	0.012	14.524	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.009	-0.027	18.094	0.663	0.663	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.084	0.060	21.125	-0.274	-0.274	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.026	-0.008	22.945	0.366	0.366	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.043	0.024	20.549	-0.707	-0.707	0.000	0.000	0.000	0.000
12	A	14	MET	0	0.040	0.020	19.559	-1.027	-1.027	0.000	0.000	0.000	0.000
13	A	15	SER	0	0.031	0.001	19.627	-0.506	-0.506	0.000	0.000	0.000	0.000
14	A	16	THR	0	0.022	0.010	16.118	-0.664	-0.664	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.025	0.002	15.230	-1.555	-1.555	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.031	-0.002	14.851	-1.291	-1.291	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.030	0.014	14.497	-0.837	-0.837	0.000	0.000	0.000	0.000
18	A	20	VAL	0	0.043	0.012	9.902	-1.345	-1.345	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.075	-0.035	10.411	-2.417	-2.417	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.963	0.977	11.310	16.603	16.603	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.029	-0.010	9.614	-0.176	-0.176	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.864	0.927	6.345	32.481	32.481	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.010	0.020	7.048	-2.960	-2.960	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.029	-0.029	9.363	0.008	0.008	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.006	-0.014	5.032	1.342	1.342	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.908	-0.938	4.094	-61.684	-61.473	-0.001	-0.070	-0.139	0.000
27	A	29	LYS	1	0.887	0.956	6.398	23.776	23.776	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.097	-0.065	9.110	3.311	3.311	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.905	-0.931	6.189	-28.618	-28.618	0.000	0.000	0.000	0.000
30	A	32	VAL	0	-0.015	-0.002	5.908	0.765	0.765	0.000	0.000	0.000	0.000
31	A	33	PRO	0	0.012	-0.003	2.015	-15.688	-15.023	4.325	-2.072	-2.919	-0.012
32	A	34	VAL	0	-0.023	-0.021	2.114	6.527	5.166	9.757	-2.902	-5.494	-0.041
33	A	35	ILE	0	0.003	0.006	2.014	-37.968	-35.047	7.378	-4.279	-6.019	-0.060
34	A	36	ILE	0	-0.010	-0.006	4.044	7.821	7.973	0.003	-0.046	-0.109	0.000
35	A	37	GLU	-1	-0.846	-0.915	7.364	-34.340	-34.340	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.009	-0.001	10.615	1.091	1.091	0.000	0.000	0.000	0.000
37	A	39	PHE	0	-0.006	-0.007	12.080	0.152	0.152	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.046	0.023	17.158	0.194	0.194	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.815	-0.942	20.099	-13.342	-13.342	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.026	-0.013	21.922	-0.104	-0.104	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.005	0.007	18.454	0.174	0.174	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.003	0.005	18.082	-0.663	-0.663	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.048	0.010	18.134	-0.420	-0.420	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.827	-0.890	18.354	-16.372	-16.372	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.834	0.886	13.942	17.190	17.190	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.036	0.020	13.562	-1.345	-1.345	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.010	-0.019	14.029	-0.659	-0.659	0.000	0.000	0.000	0.000
48	A	50	ASN	0	-0.054	-0.022	10.701	0.172	0.172	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.017	0.017	9.351	-2.253	-2.253	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.813	-0.895	6.351	-28.283	-28.283	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.025	-0.025	9.403	1.523	1.523	0.000	0.000	0.000	0.000
52	A	54	VAL	0	-0.014	0.007	11.692	-1.333	-1.333	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.007	0.001	13.212	0.762	0.762	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.012	-0.003	16.167	-0.170	-0.170	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.025	0.010	19.579	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	58	PRO	0	0.024	-0.001	21.000	0.514	0.514	0.000	0.000	0.000	0.000
57	A	59	GLN	0	0.001	-0.005	22.833	0.219	0.219	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.000	-0.003	21.308	0.409	0.409	0.000	0.000	0.000	0.000
59	A	61	ALA	0	0.028	0.024	24.909	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.005	-0.010	25.904	0.038	0.038	0.000	0.000	0.000	0.000
61	A	63	MET	0	0.032	0.024	24.954	0.089	0.089	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.029	-0.006	22.181	-0.170	-0.170	0.000	0.000	0.000	0.000
63	A	65	PRO	0	-0.002	-0.010	24.401	-0.188	-0.188	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.952	-0.981	26.489	-10.528	-10.528	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.024	0.003	19.933	-0.188	-0.188	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.034	-0.016	21.771	0.126	0.126	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.933	0.964	22.931	10.253	10.253	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.032	0.009	21.793	0.092	0.092	0.000	0.000	0.000	0.000
69	A	71	LEU	0	-0.052	-0.018	16.728	-0.340	-0.340	0.000	0.000	0.000	0.000
70	A	72	PRO	0	0.033	0.019	19.675	-0.293	-0.293	0.000	0.000	0.000	0.000
71	A	73	ASN	0	-0.041	-0.020	16.767	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.827	0.916	11.897	18.740	18.740	0.000	0.000	0.000	0.000
73	A	75	PRO	0	0.001	0.024	13.603	0.827	0.827	0.000	0.000	0.000	0.000
74	A	76	VAL	0	0.007	-0.014	15.560	-0.927	-0.927	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.951	-0.985	17.202	-15.231	-15.231	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.007	0.005	18.865	-0.549	-0.549	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.037	-0.011	16.585	-0.188	-0.188	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.794	-0.905	19.868	-12.570	-12.570	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.028	-0.004	21.888	-0.410	-0.410	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.028	0.027	24.260	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.040	-0.025	18.714	-0.261	-0.261	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.013	-0.012	18.991	-0.324	-0.324	0.000	0.000	0.000	0.000
83	A	85	GLY	0	-0.018	-0.008	20.631	-0.178	-0.178	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.850	0.921	21.583	14.346	14.346	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.043	-0.019	17.284	-0.373	-0.373	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.828	-0.899	17.737	-17.559	-17.559	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.043	0.009	13.692	-0.522	-0.522	0.000	0.000	0.000	0.000
88	A	90	LEU	0	-0.001	-0.004	12.870	-1.352	-1.352	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.005	-0.001	14.152	-0.528	-0.528	0.000	0.000	0.000	0.000
90	A	92	VAL	0	0.044	0.007	13.870	0.220	0.220	0.000	0.000	0.000	0.000
91	A	93	LEU	0	-0.008	0.013	7.907	-0.279	-0.279	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.929	0.952	11.703	17.864	17.864	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.019	0.016	14.199	0.338	0.338	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.043	0.030	11.386	0.530	0.530	0.000	0.000	0.000	0.000
95	A	97	VAL	0	0.007	-0.001	8.593	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.035	-0.018	10.807	0.889	0.889	0.000	0.000	0.000	0.000
97	A	99	ALA	0	0.032	0.021	13.862	0.751	0.751	0.000	0.000	0.000	0.000
98	A	100	ILE	0	0.006	0.001	7.551	0.388	0.388	0.000	0.000	0.000	0.000
99	A	101	LYS	1	0.907	0.948	11.445	19.264	19.264	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.940	0.968	13.168	14.513	14.513	0.000	0.000	0.000	0.000
101	A	103	ALA	0	-0.002	0.005	13.766	0.808	0.808	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.043	-0.007	12.318	0.443	0.443	0.000	0.000	0.000	0.000
103	A	105	ALA	0	-0.026	-0.001	14.479	0.664	0.664	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)