FMO DATABASE

FMODB ID: 858JY

Calculation Name: 3H9W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H9W

Chain ID: A

ChEMBL ID:

UniProt ID: A1U4R9

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-927929.073893
FMO2-HF: Nuclear repulsion	882601.52558
FMO2-HF: Total energy	-45327.548313
FMO2-MP2: Total energy	-45459.081722

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:23:LYS)

Summations of interaction energy for fragment #1(A:23: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.
-149.279	-145.035	1.533	-1.456	-4.318	-0.01

Interaction energy analysis for fragmet #1(A:23:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.973 / q_NPA : 0.972

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

Sort

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	25	ILE	0	0.016	0.007	3.235	5.453	6.889	0.050	-0.370	-1.115	0.000
4	A	26	PRO	0	-0.009	0.017	5.960	1.186	1.186	0.000	0.000	0.000	0.000
5	A	27	TRP	0	0.017	-0.003	8.828	2.354	2.354	0.000	0.000	0.000	0.000
6	A	28	LYS	1	0.893	0.944	12.382	14.848	14.848	0.000	0.000	0.000	0.000
7	A	29	ILE	0	-0.031	-0.008	16.008	0.344	0.344	0.000	0.000	0.000	0.000
8	A	30	ASN	0	-0.021	-0.009	19.091	0.539	0.539	0.000	0.000	0.000	0.000
9	A	31	TRP	0	0.060	0.016	22.678	-0.135	-0.135	0.000	0.000	0.000	0.000
10	A	32	GLN	0	-0.009	0.005	24.206	0.420	0.420	0.000	0.000	0.000	0.000
11	A	33	THR	0	-0.024	-0.024	25.540	0.158	0.158	0.000	0.000	0.000	0.000
12	A	34	MET	0	0.017	0.017	23.114	-0.235	-0.235	0.000	0.000	0.000	0.000
13	A	35	ALA	0	0.006	0.004	22.274	-0.405	-0.405	0.000	0.000	0.000	0.000
14	A	36	PHE	0	-0.019	-0.020	14.545	-0.370	-0.370	0.000	0.000	0.000	0.000
15	A	37	GLU	-1	-0.854	-0.914	18.148	-13.739	-13.739	0.000	0.000	0.000	0.000
16	A	38	TYR	0	-0.051	-0.033	12.266	0.701	0.701	0.000	0.000	0.000	0.000
17	A	39	ILE	0	0.041	0.015	10.946	-0.692	-0.692	0.000	0.000	0.000	0.000
18	A	40	GLY	0	-0.013	0.008	7.867	0.992	0.992	0.000	0.000	0.000	0.000
19	A	41	PRO	0	0.041	0.009	8.102	-0.135	-0.135	0.000	0.000	0.000	0.000
20	A	42	GLN	0	-0.019	-0.021	3.372	4.504	4.951	0.015	-0.107	-0.355	0.000
21	A	43	ILE	0	0.040	0.026	6.047	-1.276	-1.276	0.000	0.000	0.000	0.000
22	A	44	GLU	-1	-0.887	-0.918	8.492	-16.808	-16.808	0.000	0.000	0.000	0.000
23	A	45	ALA	0	-0.059	-0.026	6.713	0.830	0.830	0.000	0.000	0.000	0.000
24	A	46	LEU	0	-0.025	-0.003	5.724	0.418	0.418	0.000	0.000	0.000	0.000
25	A	47	LEU	0	0.023	-0.009	8.105	1.301	1.301	0.000	0.000	0.000	0.000
26	A	48	GLY	0	0.000	0.000	11.407	1.770	1.770	0.000	0.000	0.000	0.000
27	A	49	TRP	0	-0.070	-0.053	13.473	1.576	1.576	0.000	0.000	0.000	0.000
28	A	50	PRO	0	0.030	0.017	13.909	-0.756	-0.756	0.000	0.000	0.000	0.000
29	A	51	GLN	0	0.034	0.027	12.035	0.706	0.706	0.000	0.000	0.000	0.000
30	A	52	GLY	0	-0.025	-0.015	14.008	0.083	0.083	0.000	0.000	0.000	0.000
31	A	53	SER	0	-0.064	-0.064	16.657	0.664	0.664	0.000	0.000	0.000	0.000
32	A	54	TRP	0	0.037	0.026	13.417	0.287	0.287	0.000	0.000	0.000	0.000
33	A	55	LYS	1	0.892	0.952	17.192	13.449	13.449	0.000	0.000	0.000	0.000
34	A	56	SER	0	0.007	0.008	20.479	0.210	0.210	0.000	0.000	0.000	0.000
35	A	57	VAL	0	0.093	0.038	19.330	-0.557	-0.557	0.000	0.000	0.000	0.000
36	A	58	GLU	-1	-0.913	-0.945	20.311	-12.061	-12.061	0.000	0.000	0.000	0.000
37	A	59	ASP	-1	-0.824	-0.898	18.874	-14.258	-14.258	0.000	0.000	0.000	0.000
38	A	60	TRP	0	-0.081	-0.059	14.123	0.474	0.474	0.000	0.000	0.000	0.000
39	A	61	ALA	0	0.010	0.011	17.446	-0.390	-0.390	0.000	0.000	0.000	0.000
40	A	62	THR	0	-0.018	-0.016	20.076	0.381	0.381	0.000	0.000	0.000	0.000
41	A	63	ARG	1	0.736	0.863	16.328	16.376	16.376	0.000	0.000	0.000	0.000
42	A	64	MET	0	-0.004	0.005	16.071	-1.132	-1.132	0.000	0.000	0.000	0.000
43	A	65	HIS	0	0.007	0.001	17.783	0.771	0.771	0.000	0.000	0.000	0.000
44	A	66	PRO	0	0.024	0.005	19.621	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.815	-0.894	21.788	-13.300	-13.300	0.000	0.000	0.000	0.000
46	A	68	ASP	-1	-0.773	-0.874	17.151	-17.337	-17.337	0.000	0.000	0.000	0.000
47	A	69	GLN	0	-0.051	-0.032	19.984	0.409	0.409	0.000	0.000	0.000	0.000
48	A	70	GLU	-1	-0.971	-0.985	21.795	-11.432	-11.432	0.000	0.000	0.000	0.000
49	A	71	TRP	0	-0.099	-0.042	16.352	0.371	0.371	0.000	0.000	0.000	0.000
50	A	72	VAL	0	0.008	0.008	16.518	0.041	0.041	0.000	0.000	0.000	0.000
51	A	73	VAL	0	0.041	0.019	19.513	-0.171	-0.171	0.000	0.000	0.000	0.000
52	A	74	ASN	0	-0.002	-0.008	21.645	0.258	0.258	0.000	0.000	0.000	0.000
53	A	75	PHE	0	-0.023	-0.003	17.236	0.459	0.459	0.000	0.000	0.000	0.000
54	A	76	CYS	0	0.026	0.005	17.004	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	77	VAL	0	0.019	0.042	20.161	0.079	0.079	0.000	0.000	0.000	0.000
56	A	78	LYS	1	0.963	0.986	23.549	11.601	11.601	0.000	0.000	0.000	0.000
57	A	79	GLN	0	-0.027	-0.019	20.506	0.509	0.509	0.000	0.000	0.000	0.000
58	A	80	SER	0	0.018	-0.005	20.627	-0.166	-0.166	0.000	0.000	0.000	0.000
59	A	81	GLU	-1	-0.922	-0.958	22.205	-11.095	-11.095	0.000	0.000	0.000	0.000
60	A	82	CYS	0	-0.162	-0.072	25.192	0.665	0.665	0.000	0.000	0.000	0.000
61	A	83	GLY	0	0.023	-0.003	23.271	0.200	0.200	0.000	0.000	0.000	0.000
62	A	84	VAL	0	-0.078	-0.033	20.902	-0.061	-0.061	0.000	0.000	0.000	0.000
63	A	85	ASP	-1	-0.769	-0.851	16.271	-17.893	-17.893	0.000	0.000	0.000	0.000
64	A	86	HIS	0	-0.093	-0.062	16.169	0.294	0.294	0.000	0.000	0.000	0.000
65	A	87	GLU	-1	-0.907	-0.965	11.532	-27.864	-27.864	0.000	0.000	0.000	0.000
66	A	88	ALA	0	-0.014	-0.004	12.632	1.691	1.691	0.000	0.000	0.000	0.000
67	A	89	ASP	-1	-0.798	-0.863	10.818	-28.818	-28.818	0.000	0.000	0.000	0.000
68	A	90	TYR	0	-0.055	-0.054	12.042	1.702	1.702	0.000	0.000	0.000	0.000
69	A	91	ARG	1	0.700	0.818	12.442	14.047	14.047	0.000	0.000	0.000	0.000
70	A	92	ALA	0	0.046	0.020	12.030	1.238	1.238	0.000	0.000	0.000	0.000
71	A	93	LEU	0	-0.015	0.000	14.048	0.050	0.050	0.000	0.000	0.000	0.000
72	A	94	HIS	0	0.050	0.040	12.191	0.501	0.501	0.000	0.000	0.000	0.000
73	A	95	ARG	1	0.964	0.989	15.270	15.564	15.564	0.000	0.000	0.000	0.000
74	A	96	ASP	-1	-0.970	-0.965	16.602	-15.934	-15.934	0.000	0.000	0.000	0.000
75	A	97	GLY	0	0.020	0.010	18.717	0.651	0.651	0.000	0.000	0.000	0.000
76	A	98	HIS	1	0.790	0.884	12.782	19.161	19.161	0.000	0.000	0.000	0.000
77	A	99	TYR	0	0.046	0.007	15.446	-0.162	-0.162	0.000	0.000	0.000	0.000
78	A	100	VAL	0	-0.035	-0.023	8.962	0.018	0.018	0.000	0.000	0.000	0.000
79	A	101	TRP	0	0.018	0.015	10.460	0.427	0.427	0.000	0.000	0.000	0.000
80	A	102	ILE	0	0.012	-0.006	7.751	-3.676	-3.676	0.000	0.000	0.000	0.000
81	A	103	ARG	1	0.760	0.836	6.736	34.534	34.534	0.000	0.000	0.000	0.000
82	A	104	ASP	-1	-0.782	-0.895	7.785	-29.341	-29.341	0.000	0.000	0.000	0.000
83	A	105	VAL	0	0.002	-0.008	8.476	1.282	1.282	0.000	0.000	0.000	0.000
84	A	106	VAL	0	-0.017	-0.014	10.773	-0.625	-0.625	0.000	0.000	0.000	0.000
85	A	107	HIS	0	-0.062	-0.043	13.828	0.985	0.985	0.000	0.000	0.000	0.000
86	A	108	VAL	0	-0.017	-0.025	15.787	0.127	0.127	0.000	0.000	0.000	0.000
87	A	109	VAL	0	-0.008	0.004	18.735	0.186	0.186	0.000	0.000	0.000	0.000
88	A	110	ARG	1	0.874	0.943	21.324	12.539	12.539	0.000	0.000	0.000	0.000
89	A	111	ASP	-1	-0.749	-0.850	25.126	-10.751	-10.751	0.000	0.000	0.000	0.000
90	A	112	ASP	-1	-0.924	-0.973	27.737	-10.327	-10.327	0.000	0.000	0.000	0.000
91	A	113	SER	0	-0.140	-0.082	30.704	0.375	0.375	0.000	0.000	0.000	0.000
92	A	114	GLY	0	-0.076	-0.037	29.388	0.211	0.211	0.000	0.000	0.000	0.000
93	A	115	GLU	-1	-0.973	-0.986	29.304	-9.934	-9.934	0.000	0.000	0.000	0.000
94	A	116	VAL	0	-0.056	-0.025	23.389	-0.345	-0.345	0.000	0.000	0.000	0.000
95	A	117	GLU	-1	-0.933	-0.961	24.227	-12.332	-12.332	0.000	0.000	0.000	0.000
96	A	118	ALA	0	-0.045	-0.049	20.356	-0.085	-0.085	0.000	0.000	0.000	0.000
97	A	119	LEU	0	0.002	0.024	17.321	-0.116	-0.116	0.000	0.000	0.000	0.000
98	A	120	ILE	0	0.002	-0.004	14.533	-0.183	-0.183	0.000	0.000	0.000	0.000
99	A	121	GLY	0	0.054	0.026	11.246	0.174	0.174	0.000	0.000	0.000	0.000
100	A	122	PHE	0	-0.058	-0.035	5.956	-1.545	-1.545	0.000	0.000	0.000	0.000
101	A	123	MET	0	0.004	0.028	7.214	1.126	1.126	0.000	0.000	0.000	0.000
102	A	124	PHE	0	-0.049	-0.045	2.137	-18.054	-16.747	1.446	-0.745	-2.007	-0.010
103	A	125	ASP	-1	-0.797	-0.867	3.381	-32.439	-31.780	0.022	-0.133	-0.547	0.000
104	A	126	ILE	0	-0.033	-0.019	4.067	-7.838	-7.443	0.000	-0.101	-0.294	0.000
105	A	127	SER	0	-0.004	-0.048	6.355	5.765	5.765	0.000	0.000	0.000	0.000
106	A	128	LEU	0	-0.058	-0.032	6.049	2.830	2.830	0.000	0.000	0.000	0.000
107	A	129	GLU	-1	-0.862	-0.892	7.158	-32.836	-32.836	0.000	0.000	0.000	0.000
108	A	130	HIS	1	0.831	0.923	10.351	25.434	25.434	0.000	0.000	0.000	0.000
109	A	131	HIS	0	0.009	0.029	10.876	2.087	2.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:LYS)