FMO DATABASE

FMODB ID: 7GLVK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-637062.857943
FMO2-HF: Nuclear repulsion	597822.757589
FMO2-HF: Total energy	-39240.100354
FMO2-MP2: Total energy	-39353.675452

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.
-2.432	0.234	1.257	-1.621	-2.302	0.003

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 : -0.008 / q_NPA : -0.019

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	B	26	ALA	0	0.016	0.017	3.834	-1.129	0.412	-0.017	-0.749	-0.775	0.000
4	B	27	CYS	0	-0.027	-0.013	3.986	0.921	1.080	-0.001	-0.010	-0.148	0.000
5	B	28	VAL	0	-0.044	-0.003	5.979	-0.126	-0.126	0.000	0.000	0.000	0.000
6	B	29	THR	0	-0.021	-0.029	9.192	0.037	0.037	0.000	0.000	0.000	0.000
7	B	30	SER	0	-0.022	-0.007	11.542	0.005	0.005	0.000	0.000	0.000	0.000
8	B	31	TRP	0	-0.039	-0.020	14.834	-0.008	-0.008	0.000	0.000	0.000	0.000
9	B	32	LEU	0	-0.008	0.002	17.661	0.002	0.002	0.000	0.000	0.000	0.000
10	B	33	TRP	0	-0.018	-0.010	20.443	0.003	0.003	0.000	0.000	0.000	0.000
11	B	34	SER	0	0.060	0.047	23.621	-0.002	-0.002	0.000	0.000	0.000	0.000
12	B	35	GLU	-1	-0.830	-0.891	27.139	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	36	GLY	0	-0.016	-0.016	30.512	0.003	0.003	0.000	0.000	0.000	0.000
14	B	37	GLU	-1	-0.926	-0.973	32.031	0.020	0.020	0.000	0.000	0.000	0.000
15	B	38	GLY	0	-0.012	-0.004	30.537	0.002	0.002	0.000	0.000	0.000	0.000
16	B	39	ALA	0	-0.035	0.005	28.207	0.003	0.003	0.000	0.000	0.000	0.000
17	B	40	VAL	0	-0.039	-0.018	23.393	0.004	0.004	0.000	0.000	0.000	0.000
18	B	41	PHE	0	0.008	-0.019	21.892	-0.006	-0.006	0.000	0.000	0.000	0.000
19	B	42	TYR	0	0.029	0.017	17.142	0.007	0.007	0.000	0.000	0.000	0.000
20	B	43	ARG	1	0.850	0.911	10.720	0.164	0.164	0.000	0.000	0.000	0.000
21	B	44	VAL	0	0.002	-0.002	12.334	0.021	0.021	0.000	0.000	0.000	0.000
22	B	45	ASP	-1	-0.784	-0.867	7.393	-0.253	-0.253	0.000	0.000	0.000	0.000
23	B	46	LEU	0	-0.024	-0.011	8.754	0.110	0.110	0.000	0.000	0.000	0.000
24	B	47	HIS	0	-0.026	-0.029	2.362	-3.117	-2.186	1.276	-0.859	-1.348	0.003
25	B	48	PHE	0	-0.024	-0.017	5.685	-0.180	-0.180	0.000	0.000	0.000	0.000
26	B	49	THR	0	0.010	0.001	4.732	0.375	0.410	-0.001	-0.003	-0.031	0.000
27	B	50	ASN	0	-0.060	-0.036	7.103	0.070	0.070	0.000	0.000	0.000	0.000
28	B	51	LEU	0	0.023	0.005	9.799	-0.050	-0.050	0.000	0.000	0.000	0.000
29	B	52	GLY	0	-0.008	0.012	11.945	0.003	0.003	0.000	0.000	0.000	0.000
30	B	53	THR	0	-0.018	-0.011	14.759	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	54	PRO	0	-0.015	-0.014	17.836	0.016	0.016	0.000	0.000	0.000	0.000
32	B	55	PRO	0	0.023	0.002	18.501	-0.004	-0.004	0.000	0.000	0.000	0.000
33	B	56	LEU	0	-0.033	0.002	20.129	0.006	0.006	0.000	0.000	0.000	0.000
34	B	57	ASP	-1	-0.747	-0.867	23.381	-0.015	-0.015	0.000	0.000	0.000	0.000
35	B	58	GLU	-1	-0.952	-0.993	24.959	-0.025	-0.025	0.000	0.000	0.000	0.000
36	B	59	ASP	-1	-0.899	-0.914	27.977	-0.017	-0.017	0.000	0.000	0.000	0.000
37	B	60	GLY	0	-0.090	-0.035	28.099	0.001	0.001	0.000	0.000	0.000	0.000
38	B	61	ARG	1	0.716	0.829	25.125	0.009	0.009	0.000	0.000	0.000	0.000
39	B	62	TRP	0	0.023	-0.003	22.132	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	63	ASP	-1	-0.833	-0.917	16.247	0.046	0.046	0.000	0.000	0.000	0.000
41	B	64	PRO	0	-0.056	-0.032	17.713	0.013	0.013	0.000	0.000	0.000	0.000
42	B	65	ALA	0	0.002	0.000	13.253	0.026	0.026	0.000	0.000	0.000	0.000
43	B	66	LEU	0	-0.025	-0.010	14.466	0.038	0.038	0.000	0.000	0.000	0.000
44	B	67	MET	0	-0.061	-0.044	15.920	-0.008	-0.008	0.000	0.000	0.000	0.000
45	B	68	TYR	0	0.012	0.022	12.683	0.007	0.007	0.000	0.000	0.000	0.000
46	B	69	ASN	0	-0.087	-0.035	11.147	0.005	0.005	0.000	0.000	0.000	0.000
47	B	70	PRO	0	0.033	0.026	12.213	0.056	0.056	0.000	0.000	0.000	0.000
48	B	71	CYS	0	-0.016	-0.010	10.132	0.002	0.002	0.000	0.000	0.000	0.000
49	B	72	GLY	0	0.031	0.024	12.212	-0.049	-0.049	0.000	0.000	0.000	0.000
50	B	73	PRO	0	-0.049	-0.035	13.982	0.024	0.024	0.000	0.000	0.000	0.000
51	B	74	GLU	-1	-0.915	-0.961	16.101	0.179	0.179	0.000	0.000	0.000	0.000
52	B	75	PRO	0	-0.027	-0.015	16.323	-0.015	-0.015	0.000	0.000	0.000	0.000
53	B	76	PRO	0	0.033	0.016	19.016	-0.003	-0.003	0.000	0.000	0.000	0.000
54	B	77	ALA	0	0.079	0.024	22.503	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	78	HIS	0	0.006	-0.001	24.647	0.001	0.001	0.000	0.000	0.000	0.000
56	B	79	VAL	0	0.026	0.019	19.798	-0.007	-0.007	0.000	0.000	0.000	0.000
57	B	80	VAL	0	0.039	0.027	19.130	-0.006	-0.006	0.000	0.000	0.000	0.000
58	B	81	ARG	1	0.971	0.986	21.157	-0.044	-0.044	0.000	0.000	0.000	0.000
59	B	82	ALA	0	-0.012	-0.003	23.591	-0.006	-0.006	0.000	0.000	0.000	0.000
60	B	83	TYR	0	-0.003	-0.022	15.524	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	84	ASN	0	-0.034	-0.029	19.315	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	85	GLN	0	-0.040	0.009	22.115	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	86	PRO	0	0.030	0.011	25.065	-0.005	-0.005	0.000	0.000	0.000	0.000
64	B	87	ALA	0	-0.021	-0.016	26.534	0.000	0.000	0.000	0.000	0.000	0.000
65	B	88	GLY	0	0.017	0.017	26.889	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	89	ASP	-1	-0.855	-0.925	24.967	-0.035	-0.035	0.000	0.000	0.000	0.000
67	B	90	VAL	0	-0.051	-0.031	27.607	0.000	0.000	0.000	0.000	0.000	0.000
68	B	91	ARG	1	0.815	0.867	27.207	0.040	0.040	0.000	0.000	0.000	0.000
69	B	92	GLY	0	0.023	0.024	25.002	0.000	0.000	0.000	0.000	0.000	0.000
70	B	93	VAL	0	-0.042	-0.022	22.298	0.002	0.002	0.000	0.000	0.000	0.000
71	B	94	TRP	0	0.037	0.028	21.722	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	95	GLY	0	0.019	0.012	19.266	0.012	0.012	0.000	0.000	0.000	0.000
73	B	96	LYS	1	0.940	0.939	17.540	0.125	0.125	0.000	0.000	0.000	0.000
74	B	97	GLY	0	-0.005	-0.009	17.785	-0.022	-0.022	0.000	0.000	0.000	0.000
75	B	98	GLU	-1	-0.894	-0.935	19.429	-0.142	-0.142	0.000	0.000	0.000	0.000
76	B	99	ARG	1	0.895	0.962	11.737	0.381	0.381	0.000	0.000	0.000	0.000
77	B	100	THR	0	0.061	0.009	18.851	0.005	0.005	0.000	0.000	0.000	0.000
78	B	101	TYR	0	-0.062	-0.026	14.326	-0.029	-0.029	0.000	0.000	0.000	0.000
79	B	102	ALA	0	0.040	0.041	20.288	0.003	0.003	0.000	0.000	0.000	0.000
80	B	103	GLU	-1	-0.795	-0.879	21.876	-0.037	-0.037	0.000	0.000	0.000	0.000
81	B	104	GLN	0	0.007	0.005	22.197	0.009	0.009	0.000	0.000	0.000	0.000
82	B	105	ASP	-1	-0.766	-0.842	25.948	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	106	PHE	0	-0.009	-0.001	24.518	0.001	0.001	0.000	0.000	0.000	0.000
84	B	107	ARG	1	0.951	0.975	29.973	-0.007	-0.007	0.000	0.000	0.000	0.000
85	B	108	VAL	0	0.008	0.003	27.811	0.000	0.000	0.000	0.000	0.000	0.000
86	B	109	GLY	0	0.016	0.011	31.239	0.001	0.001	0.000	0.000	0.000	0.000
87	B	110	GLY	0	-0.004	-0.001	32.898	0.001	0.001	0.000	0.000	0.000	0.000
88	B	111	THR	0	-0.028	-0.006	29.399	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	112	ARG	1	0.720	0.803	30.533	0.006	0.006	0.000	0.000	0.000	0.000
90	B	113	TRP	0	-0.005	-0.023	23.401	0.003	0.003	0.000	0.000	0.000	0.000
91	B	114	HIS	0	-0.019	-0.005	25.153	-0.005	-0.005	0.000	0.000	0.000	0.000
92	B	115	ARG	1	0.811	0.885	20.190	-0.007	-0.007	0.000	0.000	0.000	0.000
93	B	116	LEU	0	-0.022	0.001	19.237	-0.008	-0.008	0.000	0.000	0.000	0.000
94	B	117	LEU	0	0.037	0.013	17.091	0.002	0.002	0.000	0.000	0.000	0.000
95	B	118	ARG	1	0.859	0.923	13.471	0.188	0.188	0.000	0.000	0.000	0.000
96	B	119	MET	0	0.031	0.013	16.307	0.007	0.007	0.000	0.000	0.000	0.000
97	B	120	PRO	0	-0.038	0.000	15.905	-0.003	-0.003	0.000	0.000	0.000	0.000
98	B	121	VAL	0	0.044	0.029	18.863	0.008	0.008	0.000	0.000	0.000	0.000

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