FMO DATABASE

FMODB ID: 3J7GL

Calculation Name: 3TRB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TRB

Chain ID: A

ChEMBL ID:

UniProt ID: Q83BL4

Base Structure: X-ray

Registration Date: 2023-09-22

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	OptAll
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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-597318.114863
FMO2-HF: Nuclear repulsion	561518.978906
FMO2-HF: Total energy	-35799.135957
FMO2-MP2: Total energy	-35903.871656

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:6:MET)

Summations of interaction energy for fragment #1(A:6:MET)

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.
-15.725	-15.888	11.434	-4.647	-6.623	0.016

Interaction energy analysis for fragmet #1(A:6:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.007

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	8	PRO	0	0.012	-0.016	2.689	-3.990	-1.144	0.533	-1.608	-1.771	-0.010
4	A	9	ILE	0	0.010	0.024	3.339	-0.805	-0.280	0.020	-0.070	-0.475	0.000
5	A	10	HIS	0	0.035	0.045	6.061	0.356	0.356	0.000	0.000	0.000	0.000
6	A	11	PRO	0	0.040	0.005	9.658	-0.090	-0.090	0.000	0.000	0.000	0.000
7	A	12	GLY	0	0.023	0.008	11.751	-0.093	-0.093	0.000	0.000	0.000	0.000
8	A	13	GLU	-1	-0.793	-0.862	8.804	0.123	0.123	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.024	0.006	8.247	-0.049	-0.049	0.000	0.000	0.000	0.000
10	A	15	LEU	0	-0.029	-0.012	12.217	-0.060	-0.060	0.000	0.000	0.000	0.000
11	A	16	ALA	0	-0.003	-0.005	15.346	-0.031	-0.031	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.916	-0.946	12.519	-0.100	-0.100	0.000	0.000	0.000	0.000
13	A	18	GLU	-1	-0.947	-0.973	15.298	-0.041	-0.041	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.075	-0.044	17.645	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	20	GLY	0	-0.025	-0.011	19.219	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	21	PHE	0	-0.031	-0.018	18.876	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	22	LEU	0	-0.013	0.000	20.861	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	23	ASP	-1	-0.928	-0.970	23.525	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.888	0.945	23.491	0.017	0.017	0.000	0.000	0.000	0.000
20	A	25	MET	0	-0.044	0.011	24.149	0.014	0.014	0.000	0.000	0.000	0.000
21	A	26	SER	0	0.023	-0.019	24.008	0.012	0.012	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.075	0.013	23.512	0.001	0.001	0.000	0.000	0.000	0.000
23	A	28	ASN	0	0.014	0.001	24.848	0.006	0.006	0.000	0.000	0.000	0.000
24	A	29	GLN	0	0.016	0.044	27.738	0.002	0.002	0.000	0.000	0.000	0.000
25	A	30	LEU	0	0.100	0.056	21.525	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.041	-0.014	25.856	0.004	0.004	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.941	0.967	27.344	-0.052	-0.052	0.000	0.000	0.000	0.000
28	A	33	HIS	0	0.020	0.019	27.454	0.000	0.000	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.018	0.002	22.832	0.001	0.001	0.000	0.000	0.000	0.000
30	A	35	ALA	0	0.007	0.010	27.356	0.006	0.006	0.000	0.000	0.000	0.000
31	A	36	ILE	0	-0.056	-0.025	24.373	0.006	0.006	0.000	0.000	0.000	0.000
32	A	37	PRO	0	0.031	0.003	28.582	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	38	THR	0	0.064	0.001	26.782	0.011	0.011	0.000	0.000	0.000	0.000
34	A	39	ASN	0	-0.004	0.015	25.505	0.005	0.005	0.000	0.000	0.000	0.000
35	A	40	ARG	1	0.827	0.904	22.699	-0.152	-0.152	0.000	0.000	0.000	0.000
36	A	41	VAL	0	0.051	0.030	21.670	0.020	0.020	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.005	-0.012	20.648	0.010	0.010	0.000	0.000	0.000	0.000
38	A	43	ALA	0	-0.041	-0.021	20.633	0.009	0.009	0.000	0.000	0.000	0.000
39	A	44	ILE	0	-0.036	-0.016	16.408	0.019	0.019	0.000	0.000	0.000	0.000
40	A	45	LEU	0	0.016	0.008	16.110	0.032	0.032	0.000	0.000	0.000	0.000
41	A	46	ASN	0	-0.033	-0.014	16.096	0.003	0.003	0.000	0.000	0.000	0.000
42	A	47	GLY	0	0.035	0.018	14.531	0.004	0.004	0.000	0.000	0.000	0.000
43	A	48	ALA	0	-0.033	-0.004	15.181	0.023	0.023	0.000	0.000	0.000	0.000
44	A	49	ARG	1	0.850	0.910	17.654	-0.236	-0.236	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.057	0.033	15.556	0.005	0.005	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.014	-0.006	14.885	-0.061	-0.061	0.000	0.000	0.000	0.000
47	A	52	THR	0	0.026	0.027	17.692	0.015	0.015	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.090	0.035	20.606	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.777	-0.862	21.768	0.128	0.128	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.004	-0.017	20.429	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	56	ALA	0	0.023	0.019	18.557	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.007	0.005	19.946	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.769	0.880	23.280	-0.133	-0.133	0.000	0.000	0.000	0.000
54	A	59	LEU	0	0.011	0.000	17.948	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	60	ALA	0	-0.019	0.006	20.622	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	61	LYS	1	0.911	0.953	21.566	-0.072	-0.072	0.000	0.000	0.000	0.000
57	A	62	PHE	0	-0.043	-0.024	23.316	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	63	PHE	0	0.039	-0.002	19.761	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	64	GLY	0	0.001	0.020	21.361	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	65	THR	0	-0.015	-0.003	16.936	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	66	THR	0	-0.003	-0.026	17.850	0.005	0.005	0.000	0.000	0.000	0.000
62	A	67	PRO	0	0.000	-0.003	18.269	0.019	0.019	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.794	-0.905	16.115	0.200	0.200	0.000	0.000	0.000	0.000
64	A	69	PHE	0	-0.008	0.012	11.786	0.101	0.101	0.000	0.000	0.000	0.000
65	A	70	TRP	0	0.054	0.006	12.751	0.138	0.138	0.000	0.000	0.000	0.000
66	A	71	LEU	0	-0.021	-0.011	13.612	0.084	0.084	0.000	0.000	0.000	0.000
67	A	72	ASN	0	0.044	0.015	10.548	0.111	0.111	0.000	0.000	0.000	0.000
68	A	73	LEU	0	-0.012	0.003	8.243	0.394	0.394	0.000	0.000	0.000	0.000
69	A	74	GLN	0	-0.027	-0.029	9.108	0.219	0.219	0.000	0.000	0.000	0.000
70	A	75	ASP	-1	-0.864	-0.924	10.822	0.813	0.813	0.000	0.000	0.000	0.000
71	A	76	ALA	0	-0.044	-0.024	5.390	0.179	0.236	-0.001	-0.007	-0.048	0.000
72	A	77	TYR	0	-0.030	-0.008	5.875	1.101	1.221	-0.001	-0.006	-0.113	0.000
73	A	78	ASP	-1	-0.780	-0.906	7.845	0.486	0.486	0.000	0.000	0.000	0.000
74	A	79	ILE	0	0.008	0.009	8.852	-0.165	-0.165	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.855	0.934	2.021	-12.311	-16.022	10.883	-2.956	-4.216	0.026
76	A	81	MET	0	-0.021	-0.010	7.833	-0.339	-0.339	0.000	0.000	0.000	0.000
77	A	82	ALA	0	-0.003	0.001	10.655	-0.113	-0.113	0.000	0.000	0.000	0.000
78	A	83	LEU	0	0.022	0.002	8.159	-0.103	-0.103	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.899	0.943	8.281	-0.538	-0.538	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.942	0.989	11.313	-0.320	-0.320	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.035	-0.034	14.616	-0.037	-0.037	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.070	0.057	13.048	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.933	0.952	12.670	-0.234	-0.234	0.000	0.000	0.000	0.000
84	A	89	LYS	1	0.759	0.863	15.849	-0.173	-0.173	0.000	0.000	0.000	0.000
85	A	90	ILE	0	0.075	0.024	15.622	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.918	-0.959	15.295	0.102	0.102	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.856	0.936	18.444	-0.130	-0.130	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.832	-0.884	21.723	0.136	0.136	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.031	-0.013	20.269	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	95	THR	0	0.013	0.004	22.487	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.004	0.011	22.098	0.006	0.006	0.000	0.000	0.000	0.000
92	A	97	TYR	0	-0.017	-0.004	23.717	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:MET)