FMO DATABASE

FMODB ID: M3G1Z

Calculation Name: 4HBE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HBE

Chain ID: B

ChEMBL ID:

UniProt ID: P08563

Base Structure: X-ray

Registration Date: 2023-06-20

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-636741.238547
FMO2-HF: Nuclear repulsion	597501.408272
FMO2-HF: Total energy	-39239.830275
FMO2-MP2: Total energy	-39353.416876

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(B:24:THR)

Summations of interaction energy for fragment #1(B:24:THR)

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.
-1.502	1.064	0.191	-1.106	-1.653	0

Interaction energy analysis for fragmet #1(B:24:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.021

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].
3	B	26	ALA	0	0.030	0.023	3.834	-1.206	0.348	-0.018	-0.765	-0.771
4	B	27	CYS	0	-0.030	-0.014	4.012	0.888	1.041	-0.001	-0.010	-0.143
5	B	28	VAL	0	-0.048	-0.007	5.995	-0.136	-0.136	0.000	0.000	0.000
6	B	29	THR	0	-0.011	-0.005	9.195	0.029	0.029	0.000	0.000	0.000
7	B	30	SER	0	-0.034	-0.012	11.540	0.009	0.009	0.000	0.000	0.000
8	B	31	TRP	0	-0.024	-0.016	14.832	-0.008	-0.008	0.000	0.000	0.000
9	B	32	LEU	0	-0.005	-0.002	17.652	0.003	0.003	0.000	0.000	0.000
10	B	33	TRP	0	-0.023	-0.013	20.435	0.003	0.003	0.000	0.000	0.000
11	B	34	SER	0	0.056	0.053	23.609	-0.002	-0.002	0.000	0.000	0.000
12	B	35	GLU	-1	-0.883	-0.935	27.128	-0.004	-0.004	0.000	0.000	0.000
13	B	36	GLY	0	-0.021	-0.016	30.499	0.003	0.003	0.000	0.000	0.000
14	B	37	GLU	-1	-0.912	-0.973	32.042	0.020	0.020	0.000	0.000	0.000
15	B	38	GLY	0	-0.026	-0.005	30.545	0.001	0.001	0.000	0.000	0.000
16	B	39	ALA	0	-0.035	-0.001	28.227	0.002	0.002	0.000	0.000	0.000
17	B	40	VAL	0	-0.033	-0.016	23.111	0.004	0.004	0.000	0.000	0.000
18	B	41	PHE	0	0.005	-0.023	21.903	-0.006	-0.006	0.000	0.000	0.000
19	B	42	TYR	0	0.019	0.014	17.068	0.010	0.010	0.000	0.000	0.000
20	B	43	ARG	1	0.870	0.934	10.963	0.143	0.143	0.000	0.000	0.000
21	B	44	VAL	0	0.002	0.000	12.280	0.018	0.018	0.000	0.000	0.000
22	B	45	ASP	-1	-0.806	-0.910	7.447	-0.214	-0.214	0.000	0.000	0.000
23	B	46	LEU	0	-0.023	-0.011	8.757	0.101	0.101	0.000	0.000	0.000
24	B	47	HIS	0	-0.037	-0.034	2.772	-1.802	-0.971	0.211	-0.328	-0.714
25	B	48	PHE	0	-0.021	-0.015	5.713	-0.206	-0.206	0.000	0.000	0.000
26	B	49	THR	0	0.024	0.006	4.799	0.243	0.271	-0.001	-0.003	-0.025
27	B	50	ASN	0	-0.044	-0.015	7.089	0.041	0.041	0.000	0.000	0.000
28	B	51	LEU	0	0.025	0.001	9.821	-0.049	-0.049	0.000	0.000	0.000
29	B	52	GLY	0	-0.003	0.012	11.962	0.001	0.001	0.000	0.000	0.000
30	B	53	THR	0	-0.021	-0.013	14.781	-0.001	-0.001	0.000	0.000	0.000
31	B	54	PRO	0	-0.012	-0.013	17.852	0.015	0.015	0.000	0.000	0.000
32	B	55	PRO	0	0.029	0.008	18.581	-0.004	-0.004	0.000	0.000	0.000
33	B	56	LEU	0	-0.037	-0.008	20.120	0.005	0.005	0.000	0.000	0.000
34	B	57	ASP	-1	-0.749	-0.861	23.474	-0.015	-0.015	0.000	0.000	0.000
35	B	58	GLU	-1	-0.969	-1.004	24.976	-0.024	-0.024	0.000	0.000	0.000
36	B	59	ASP	-1	-0.933	-0.948	27.995	-0.018	-0.018	0.000	0.000	0.000
37	B	60	GLY	0	-0.107	-0.041	28.127	0.001	0.001	0.000	0.000	0.000
38	B	61	ARG	1	0.785	0.873	25.060	0.007	0.007	0.000	0.000	0.000
39	B	62	TRP	0	0.023	0.002	22.233	-0.003	-0.003	0.000	0.000	0.000
40	B	63	ASP	-1	-0.850	-0.931	16.372	0.032	0.032	0.000	0.000	0.000
41	B	64	PRO	0	-0.051	-0.028	17.784	0.013	0.013	0.000	0.000	0.000
42	B	65	ALA	0	0.007	0.008	13.328	0.024	0.024	0.000	0.000	0.000
43	B	66	LEU	0	-0.019	-0.011	14.445	0.036	0.036	0.000	0.000	0.000
44	B	67	MET	0	-0.060	-0.041	15.884	-0.008	-0.008	0.000	0.000	0.000
45	B	68	TYR	0	-0.001	0.018	12.690	0.007	0.007	0.000	0.000	0.000
46	B	69	ASN	0	-0.084	-0.039	10.935	0.010	0.010	0.000	0.000	0.000
47	B	70	PRO	0	0.036	0.035	12.187	0.050	0.050	0.000	0.000	0.000
48	B	71	CYS	0	-0.022	-0.017	10.107	-0.016	-0.016	0.000	0.000	0.000
49	B	72	GLY	0	0.046	0.029	12.180	-0.043	-0.043	0.000	0.000	0.000
50	B	73	PRO	0	-0.054	-0.037	13.954	0.021	0.021	0.000	0.000	0.000
51	B	74	GLU	-1	-0.910	-0.962	16.079	0.167	0.167	0.000	0.000	0.000
52	B	75	PRO	0	-0.033	-0.015	16.176	-0.015	-0.015	0.000	0.000	0.000
53	B	76	PRO	0	0.044	0.020	19.002	-0.003	-0.003	0.000	0.000	0.000
54	B	77	ALA	0	0.084	0.026	22.491	-0.002	-0.002	0.000	0.000	0.000
55	B	78	HIS	0	0.000	-0.005	24.632	-0.001	-0.001	0.000	0.000	0.000
56	B	79	VAL	0	0.014	0.013	19.749	-0.007	-0.007	0.000	0.000	0.000
57	B	80	VAL	0	0.032	0.025	19.374	-0.005	-0.005	0.000	0.000	0.000
58	B	81	ARG	1	0.964	0.974	21.146	-0.043	-0.043	0.000	0.000	0.000
59	B	82	ALA	0	-0.015	-0.006	23.567	-0.005	-0.005	0.000	0.000	0.000
60	B	83	TYR	0	-0.008	-0.022	15.434	-0.003	-0.003	0.000	0.000	0.000
61	B	84	ASN	0	-0.017	-0.016	19.342	-0.004	-0.004	0.000	0.000	0.000
62	B	85	GLN	0	-0.023	0.015	22.124	0.000	0.000	0.000	0.000	0.000
63	B	86	PRO	0	0.012	0.009	25.074	-0.005	-0.005	0.000	0.000	0.000
64	B	87	ALA	0	-0.021	-0.017	26.615	0.000	0.000	0.000	0.000	0.000
65	B	88	GLY	0	0.017	0.019	26.901	-0.002	-0.002	0.000	0.000	0.000
66	B	89	ASP	-1	-0.854	-0.923	24.942	-0.032	-0.032	0.000	0.000	0.000
67	B	90	VAL	0	-0.047	-0.027	27.618	0.000	0.000	0.000	0.000	0.000
68	B	91	ARG	1	0.853	0.921	27.348	0.036	0.036	0.000	0.000	0.000
69	B	92	GLY	0	0.027	0.025	25.009	0.000	0.000	0.000	0.000	0.000
70	B	93	VAL	0	-0.037	-0.016	22.257	0.002	0.002	0.000	0.000	0.000
71	B	94	TRP	0	0.046	0.027	21.729	-0.007	-0.007	0.000	0.000	0.000
72	B	95	GLY	0	0.017	0.008	19.270	0.011	0.011	0.000	0.000	0.000
73	B	96	LYS	1	0.939	0.941	17.346	0.122	0.122	0.000	0.000	0.000
74	B	97	GLY	0	-0.012	-0.009	17.781	-0.021	-0.021	0.000	0.000	0.000
75	B	98	GLU	-1	-0.897	-0.937	19.426	-0.134	-0.134	0.000	0.000	0.000
76	B	99	ARG	1	0.889	0.956	11.836	0.353	0.353	0.000	0.000	0.000
77	B	100	THR	0	0.048	-0.002	18.855	0.005	0.005	0.000	0.000	0.000
78	B	101	TYR	0	-0.051	-0.020	15.177	-0.021	-0.021	0.000	0.000	0.000
79	B	102	ALA	0	0.044	0.042	20.294	0.002	0.002	0.000	0.000	0.000
80	B	103	GLU	-1	-0.840	-0.934	21.882	-0.032	-0.032	0.000	0.000	0.000
81	B	104	GLN	0	-0.021	-0.015	22.385	0.008	0.008	0.000	0.000	0.000
82	B	105	ASP	-1	-0.763	-0.858	25.948	-0.006	-0.006	0.000	0.000	0.000
83	B	106	PHE	0	-0.012	-0.003	24.577	0.001	0.001	0.000	0.000	0.000
84	B	107	ARG	1	0.956	0.972	29.972	-0.006	-0.006	0.000	0.000	0.000
85	B	108	VAL	0	0.012	0.005	27.836	0.000	0.000	0.000	0.000	0.000
86	B	109	GLY	0	0.003	0.004	31.238	0.001	0.001	0.000	0.000	0.000
87	B	110	GLY	0	-0.010	-0.005	32.893	0.001	0.001	0.000	0.000	0.000
88	B	111	THR	0	-0.008	0.006	29.331	-0.002	-0.002	0.000	0.000	0.000
89	B	112	ARG	1	0.785	0.870	30.554	0.004	0.004	0.000	0.000	0.000
90	B	113	TRP	0	-0.006	-0.018	23.454	0.003	0.003	0.000	0.000	0.000
91	B	114	HIS	0	-0.023	-0.006	25.104	-0.005	-0.005	0.000	0.000	0.000
92	B	115	ARG	1	0.823	0.893	20.277	-0.007	-0.007	0.000	0.000	0.000
93	B	116	LEU	0	-0.012	0.005	19.228	-0.008	-0.008	0.000	0.000	0.000
94	B	117	LEU	0	0.043	0.015	17.098	0.002	0.002	0.000	0.000	0.000
95	B	118	ARG	1	0.869	0.937	13.519	0.171	0.171	0.000	0.000	0.000
96	B	119	MET	0	0.027	0.010	16.317	0.008	0.008	0.000	0.000	0.000
97	B	120	PRO	0	-0.047	-0.001	15.961	-0.004	-0.004	0.000	0.000	0.000
98	B	121	VAL	0	0.049	0.029	18.882	0.006	0.006	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:24:THR)