FMO DATABASE

FMODB ID: JQ2K9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-596937.559097
FMO2-HF: Nuclear repulsion	561138.558243
FMO2-HF: Total energy	-35799.000853
FMO2-MP2: Total energy	-35903.774208

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.
-19.087	-21.545	14.827	-5.484	-6.884	0.027

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 : 0.024 / q_NPA : 0.011

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	0.003	-0.015	2.685	-4.114	-1.358	0.537	-1.539	-1.754	-0.010
4	A	9	ILE	0	0.000	0.010	3.597	-0.641	-0.246	0.006	-0.043	-0.358	0.000
5	A	10	HIS	0	0.047	0.049	6.218	0.310	0.310	0.000	0.000	0.000	0.000
6	A	11	PRO	0	0.063	0.020	9.858	-0.094	-0.094	0.000	0.000	0.000	0.000
7	A	12	GLY	0	0.030	0.009	11.836	-0.088	-0.088	0.000	0.000	0.000	0.000
8	A	13	GLU	-1	-0.812	-0.868	8.954	-0.120	-0.120	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.031	0.009	8.313	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	15	LEU	0	-0.036	-0.014	12.362	-0.052	-0.052	0.000	0.000	0.000	0.000
11	A	16	ALA	0	-0.002	-0.012	15.412	-0.031	-0.031	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.938	-0.963	12.425	-0.205	-0.205	0.000	0.000	0.000	0.000
13	A	18	GLU	-1	-0.945	-0.970	15.287	-0.095	-0.095	0.000	0.000	0.000	0.000
14	A	19	LEU	0	-0.072	-0.043	17.598	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	20	GLY	0	-0.017	-0.007	19.418	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	21	PHE	0	-0.015	-0.007	18.925	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	22	LEU	0	-0.029	-0.001	20.914	0.000	0.000	0.000	0.000	0.000	0.000
18	A	23	ASP	-1	-0.930	-0.967	23.687	-0.034	-0.034	0.000	0.000	0.000	0.000
19	A	24	LYS	1	0.877	0.940	23.753	0.056	0.056	0.000	0.000	0.000	0.000
20	A	25	MET	0	-0.011	0.026	23.981	0.016	0.016	0.000	0.000	0.000	0.000
21	A	26	SER	0	0.009	-0.035	23.920	0.010	0.010	0.000	0.000	0.000	0.000
22	A	27	ALA	0	0.074	0.013	23.767	0.004	0.004	0.000	0.000	0.000	0.000
23	A	28	ASN	0	0.006	-0.008	24.978	0.009	0.009	0.000	0.000	0.000	0.000
24	A	29	GLN	0	0.040	0.055	27.747	0.004	0.004	0.000	0.000	0.000	0.000
25	A	30	LEU	0	0.092	0.058	21.679	0.001	0.001	0.000	0.000	0.000	0.000
26	A	31	ALA	0	-0.023	-0.007	26.021	0.005	0.005	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.942	0.963	27.481	-0.036	-0.036	0.000	0.000	0.000	0.000
28	A	33	HIS	0	0.000	0.014	27.566	0.002	0.002	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.028	-0.009	23.135	0.003	0.003	0.000	0.000	0.000	0.000
30	A	35	ALA	0	-0.010	0.004	27.786	0.006	0.006	0.000	0.000	0.000	0.000
31	A	36	ILE	0	-0.068	-0.029	24.270	0.008	0.008	0.000	0.000	0.000	0.000
32	A	37	PRO	0	0.017	-0.001	28.227	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	38	THR	0	0.085	0.011	27.028	0.009	0.009	0.000	0.000	0.000	0.000
34	A	39	ASN	0	-0.013	0.001	25.712	0.003	0.003	0.000	0.000	0.000	0.000
35	A	40	ARG	1	0.880	0.941	22.982	-0.140	-0.140	0.000	0.000	0.000	0.000
36	A	41	VAL	0	0.059	0.038	21.824	0.018	0.018	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.009	-0.010	20.819	0.006	0.006	0.000	0.000	0.000	0.000
38	A	43	ALA	0	-0.034	-0.015	20.623	0.006	0.006	0.000	0.000	0.000	0.000
39	A	44	ILE	0	-0.037	-0.012	16.567	0.017	0.017	0.000	0.000	0.000	0.000
40	A	45	LEU	0	0.013	0.010	16.196	0.026	0.026	0.000	0.000	0.000	0.000
41	A	46	ASN	0	-0.037	-0.014	16.268	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	47	GLY	0	0.027	0.023	14.496	0.006	0.006	0.000	0.000	0.000	0.000
43	A	48	ALA	0	-0.038	-0.014	15.269	0.017	0.017	0.000	0.000	0.000	0.000
44	A	49	ARG	1	0.850	0.905	17.804	-0.213	-0.213	0.000	0.000	0.000	0.000
45	A	50	SER	0	0.041	0.026	16.104	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	51	ILE	0	-0.010	0.001	15.241	-0.057	-0.057	0.000	0.000	0.000	0.000
47	A	52	THR	0	0.015	0.013	17.894	0.021	0.021	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.106	0.035	20.668	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	54	ASP	-1	-0.821	-0.892	22.091	0.125	0.125	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.006	-0.023	20.881	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	56	ALA	0	0.024	0.025	19.048	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.013	0.007	20.435	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.803	0.903	23.718	-0.128	-0.128	0.000	0.000	0.000	0.000
54	A	59	LEU	0	0.003	-0.003	18.306	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	60	ALA	0	-0.019	0.008	21.109	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	61	LYS	1	0.936	0.968	22.004	-0.068	-0.068	0.000	0.000	0.000	0.000
57	A	62	PHE	0	-0.050	-0.033	23.426	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	63	PHE	0	0.028	-0.002	20.231	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	64	GLY	0	0.002	0.025	21.945	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	65	THR	0	-0.005	-0.001	17.651	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	66	THR	0	-0.021	-0.032	18.156	0.005	0.005	0.000	0.000	0.000	0.000
62	A	67	PRO	0	0.006	-0.005	18.480	0.019	0.019	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.796	-0.907	16.659	0.215	0.215	0.000	0.000	0.000	0.000
64	A	69	PHE	0	-0.009	0.006	11.745	0.105	0.105	0.000	0.000	0.000	0.000
65	A	70	TRP	0	0.043	0.003	13.164	0.128	0.128	0.000	0.000	0.000	0.000
66	A	71	LEU	0	-0.012	-0.012	14.034	0.075	0.075	0.000	0.000	0.000	0.000
67	A	72	ASN	0	0.057	0.029	11.176	0.089	0.089	0.000	0.000	0.000	0.000
68	A	73	LEU	0	-0.025	0.003	8.839	0.368	0.368	0.000	0.000	0.000	0.000
69	A	74	GLN	0	-0.022	-0.035	9.563	0.201	0.201	0.000	0.000	0.000	0.000
70	A	75	ASP	-1	-0.868	-0.924	11.505	0.797	0.797	0.000	0.000	0.000	0.000
71	A	76	ALA	0	-0.048	-0.021	5.868	0.225	0.259	-0.001	-0.002	-0.030	0.000
72	A	77	TYR	0	-0.047	-0.024	7.250	0.315	0.315	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.792	-0.906	8.237	0.485	0.485	0.000	0.000	0.000	0.000
74	A	79	ILE	0	-0.001	0.004	8.788	-0.134	-0.134	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.906	0.953	2.007	-14.464	-20.107	14.285	-3.900	-4.742	0.037
76	A	81	MET	0	-0.025	-0.016	7.731	-0.379	-0.379	0.000	0.000	0.000	0.000
77	A	82	ALA	0	-0.012	-0.003	10.429	-0.121	-0.121	0.000	0.000	0.000	0.000
78	A	83	LEU	0	0.015	0.002	8.055	-0.108	-0.108	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.896	0.949	7.817	-0.572	-0.572	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.934	0.983	10.990	-0.346	-0.346	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.029	-0.033	14.431	-0.039	-0.039	0.000	0.000	0.000	0.000
82	A	87	GLY	0	0.050	0.044	12.753	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	88	LYS	1	0.950	0.960	12.920	-0.262	-0.262	0.000	0.000	0.000	0.000
84	A	89	LYS	1	0.827	0.906	15.792	-0.195	-0.195	0.000	0.000	0.000	0.000
85	A	90	ILE	0	0.060	0.020	15.895	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.935	-0.959	15.282	0.194	0.194	0.000	0.000	0.000	0.000
87	A	92	LYS	1	0.870	0.940	18.340	-0.163	-0.163	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.877	-0.923	21.401	0.170	0.170	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.031	-0.012	20.699	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	95	THR	0	-0.002	-0.003	22.681	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.004	0.017	22.016	0.008	0.008	0.000	0.000	0.000	0.000
92	A	97	TYR	0	0.006	0.002	23.720	-0.017	-0.017	0.000	0.000	0.000	0.000

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