FMO DATABASE

FMODB ID: Q1QRY

Calculation Name: 4JE3-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JE3

Chain ID: B

ChEMBL ID:

UniProt ID: P38265

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-448420.662125
FMO2-HF: Nuclear repulsion	418497.263059
FMO2-HF: Total energy	-29923.399066
FMO2-MP2: Total energy	-30011.070263

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:374:SER)

Summations of interaction energy for fragment #1(B:374:SER)

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.
-3.678	0.832	0.027	-2.202	-2.336	0.006

Interaction energy analysis for fragmet #1(B:374:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / 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	B	376	TYR	0	-0.088	-0.155	3.456	-2.231	1.333	-0.036	-1.851	-1.677	0.004
4	B	377	SER	0	-0.055	0.015	3.267	-0.947	-0.012	0.064	-0.349	-0.651	0.002
5	B	378	SER	0	0.037	0.010	5.114	-1.172	-1.161	-0.001	-0.002	-0.008	0.000
6	B	379	LEU	0	-0.036	-0.022	8.454	0.223	0.223	0.000	0.000	0.000	0.000
7	B	380	VAL	0	-0.012	-0.016	10.495	0.010	0.010	0.000	0.000	0.000	0.000
8	B	381	PRO	0	-0.003	0.013	8.692	-0.153	-0.153	0.000	0.000	0.000	0.000
9	B	382	ILE	0	0.002	0.017	11.320	-0.162	-0.162	0.000	0.000	0.000	0.000
10	B	383	GLU	-1	-0.893	-0.939	13.654	0.751	0.751	0.000	0.000	0.000	0.000
11	B	384	LYS	1	0.932	0.940	15.423	-0.369	-0.369	0.000	0.000	0.000	0.000
12	B	385	VAL	0	0.002	0.022	18.433	-0.002	-0.002	0.000	0.000	0.000	0.000
13	B	386	GLY	0	-0.037	-0.032	20.631	-0.017	-0.017	0.000	0.000	0.000	0.000
14	B	387	PHE	0	0.069	0.033	20.719	-0.005	-0.005	0.000	0.000	0.000	0.000
15	B	388	THR	0	-0.063	-0.027	25.964	-0.011	-0.011	0.000	0.000	0.000	0.000
16	B	389	LEU	0	0.015	0.019	29.011	0.000	0.000	0.000	0.000	0.000	0.000
17	B	390	LYS	1	0.920	0.947	30.771	-0.080	-0.080	0.000	0.000	0.000	0.000
18	B	391	ASN	0	0.054	0.026	32.691	0.001	0.001	0.000	0.000	0.000	0.000
19	B	392	GLU	-1	-0.893	-0.945	36.361	0.035	0.035	0.000	0.000	0.000	0.000
20	B	393	ILE	0	-0.027	-0.024	37.122	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	394	ASN	0	-0.023	-0.014	41.373	0.000	0.000	0.000	0.000	0.000	0.000
22	B	395	SER	0	0.025	0.019	44.509	-0.001	-0.001	0.000	0.000	0.000	0.000
23	B	396	ARG	1	0.950	0.987	42.241	-0.029	-0.029	0.000	0.000	0.000	0.000
24	B	397	ILE	0	0.012	0.009	38.565	0.000	0.000	0.000	0.000	0.000	0.000
25	B	398	ILE	0	-0.031	-0.009	35.562	0.001	0.001	0.000	0.000	0.000	0.000
26	B	399	THR	0	-0.010	-0.022	33.746	0.005	0.005	0.000	0.000	0.000	0.000
27	B	400	ILE	0	0.014	0.017	28.951	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	401	LYS	1	0.917	0.946	28.940	-0.106	-0.106	0.000	0.000	0.000	0.000
29	B	402	LEU	0	0.021	0.022	23.673	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	403	LYS	1	0.926	0.951	23.149	-0.149	-0.149	0.000	0.000	0.000	0.000
31	B	404	PHE	0	0.025	0.024	17.620	-0.019	-0.019	0.000	0.000	0.000	0.000
32	B	405	ASN	0	-0.016	-0.029	17.905	0.021	0.021	0.000	0.000	0.000	0.000
33	B	406	GLY	0	0.001	0.001	13.816	-0.040	-0.040	0.000	0.000	0.000	0.000
34	B	407	ASN	0	0.040	0.022	9.866	-0.097	-0.097	0.000	0.000	0.000	0.000
35	B	408	ASP	-1	-0.790	-0.903	7.875	2.125	2.125	0.000	0.000	0.000	0.000
36	B	409	ILE	0	-0.044	-0.011	10.494	-0.060	-0.060	0.000	0.000	0.000	0.000
37	B	410	PHE	0	0.003	0.000	13.049	-0.089	-0.089	0.000	0.000	0.000	0.000
38	B	411	GLY	0	0.103	0.071	8.800	-0.133	-0.133	0.000	0.000	0.000	0.000
39	B	412	GLY	0	-0.009	-0.007	9.533	-0.238	-0.238	0.000	0.000	0.000	0.000
40	B	413	LEU	0	-0.037	-0.036	10.874	-0.168	-0.168	0.000	0.000	0.000	0.000
41	B	414	HIS	0	0.003	0.021	9.998	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	415	GLU	-1	-0.856	-0.935	8.374	-0.560	-0.560	0.000	0.000	0.000	0.000
43	B	416	LEU	0	-0.080	-0.045	10.859	-0.075	-0.075	0.000	0.000	0.000	0.000
44	B	417	CYS	0	-0.056	-0.026	14.395	-0.007	-0.007	0.000	0.000	0.000	0.000
45	B	418	ASP	-1	-0.736	-0.754	11.495	-0.649	-0.649	0.000	0.000	0.000	0.000
46	B	419	LYS	1	0.825	0.910	11.478	0.426	0.426	0.000	0.000	0.000	0.000
47	B	420	ASN	0	-0.028	-0.013	15.462	0.005	0.005	0.000	0.000	0.000	0.000
48	B	421	LEU	0	-0.041	-0.010	16.279	0.034	0.034	0.000	0.000	0.000	0.000
49	B	422	ILE	0	-0.028	-0.014	17.674	0.042	0.042	0.000	0.000	0.000	0.000
50	B	423	ASN	0	0.018	-0.003	19.678	-0.033	-0.033	0.000	0.000	0.000	0.000
51	B	424	ILE	0	0.067	0.021	17.990	0.032	0.032	0.000	0.000	0.000	0.000
52	B	425	ASP	-1	-0.865	-0.921	20.905	-0.103	-0.103	0.000	0.000	0.000	0.000
53	B	426	LYS	1	0.827	0.901	24.158	0.053	0.053	0.000	0.000	0.000	0.000
54	B	427	VAL	0	-0.042	-0.005	19.798	0.018	0.018	0.000	0.000	0.000	0.000
55	B	428	PRO	0	-0.026	0.004	23.025	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	429	GLY	0	0.113	0.039	22.596	0.010	0.010	0.000	0.000	0.000	0.000
57	B	430	TRP	0	0.037	-0.005	21.741	0.018	0.018	0.000	0.000	0.000	0.000
58	B	431	LEU	0	-0.056	-0.016	20.076	0.026	0.026	0.000	0.000	0.000	0.000
59	B	432	ALA	0	0.011	0.001	18.154	0.027	0.027	0.000	0.000	0.000	0.000
60	B	433	GLY	0	0.030	0.006	17.155	0.027	0.027	0.000	0.000	0.000	0.000
61	B	434	GLU	-1	-0.950	-0.961	18.508	0.121	0.121	0.000	0.000	0.000	0.000
62	B	435	ASN	0	-0.076	-0.032	20.247	0.003	0.003	0.000	0.000	0.000	0.000
63	B	436	GLY	0	0.088	0.029	18.075	0.017	0.017	0.000	0.000	0.000	0.000
64	B	437	SER	0	-0.085	-0.046	18.196	0.008	0.008	0.000	0.000	0.000	0.000
65	B	438	PHE	0	-0.022	-0.011	19.014	-0.009	-0.009	0.000	0.000	0.000	0.000
66	B	439	SER	0	0.032	0.014	22.594	-0.005	-0.005	0.000	0.000	0.000	0.000
67	B	440	GLY	0	0.026	0.010	24.302	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	441	THR	0	-0.070	-0.022	27.502	-0.003	-0.003	0.000	0.000	0.000	0.000
69	B	442	ILE	0	0.018	0.015	26.518	0.000	0.000	0.000	0.000	0.000	0.000
70	B	443	MET	0	-0.010	-0.015	30.812	-0.006	-0.006	0.000	0.000	0.000	0.000
71	B	444	ASN	0	0.018	0.006	34.560	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	445	GLY	0	-0.022	-0.017	31.511	-0.004	-0.004	0.000	0.000	0.000	0.000
73	B	446	ASP	-1	-0.916	-0.939	31.267	0.078	0.078	0.000	0.000	0.000	0.000
74	B	447	PHE	0	0.001	-0.009	25.237	0.005	0.005	0.000	0.000	0.000	0.000
75	B	448	GLN	0	0.010	0.005	29.683	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	449	ARG	1	0.910	0.955	24.484	-0.197	-0.197	0.000	0.000	0.000	0.000
77	B	450	GLU	-1	-0.976	-0.979	27.777	0.158	0.158	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:374:SER)