FMO DATABASE

FMODB ID: 3QY6L

Calculation Name: 4JO7-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JO7

Chain ID: E

ChEMBL ID:

UniProt ID: Q7Z3B4

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-519828.553729
FMO2-HF: Nuclear repulsion	484017.763448
FMO2-HF: Total energy	-35810.790281
FMO2-MP2: Total energy	-35915.213043

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(E:330:PRO)

Summations of interaction energy for fragment #1(E:330:PRO)

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.
-1.52	1.18	0.001	-1.214	-1.486	0.006

Interaction energy analysis for fragmet #1(E:330:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.012

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	E	332	ASP	-1	-0.806	-0.915	3.565	-3.928	-1.465	0.002	-1.200	-1.264	0.006
4	E	333	TYR	0	0.040	-0.009	4.404	0.291	0.528	-0.001	-0.014	-0.222	0.000
5	E	334	PHE	0	0.011	0.020	8.003	0.219	0.219	0.000	0.000	0.000	0.000
6	E	335	ARG	1	0.937	0.967	9.429	1.129	1.129	0.000	0.000	0.000	0.000
7	E	336	ILE	0	-0.015	0.004	8.376	0.131	0.131	0.000	0.000	0.000	0.000
8	E	337	LEU	0	-0.022	-0.018	11.885	0.114	0.114	0.000	0.000	0.000	0.000
9	E	338	VAL	0	0.009	0.013	13.859	0.068	0.068	0.000	0.000	0.000	0.000
10	E	339	GLN	0	0.011	0.002	13.402	-0.010	-0.010	0.000	0.000	0.000	0.000
11	E	340	GLN	0	-0.018	-0.008	15.201	0.068	0.068	0.000	0.000	0.000	0.000
12	E	341	PHE	0	-0.007	0.011	18.137	0.042	0.042	0.000	0.000	0.000	0.000
13	E	342	GLU	-1	-0.930	-0.979	19.055	-0.360	-0.360	0.000	0.000	0.000	0.000
14	E	343	VAL	0	-0.015	-0.009	20.174	0.025	0.025	0.000	0.000	0.000	0.000
15	E	344	GLN	0	-0.016	-0.007	22.299	0.018	0.018	0.000	0.000	0.000	0.000
16	E	345	LEU	0	-0.029	-0.007	24.059	0.020	0.020	0.000	0.000	0.000	0.000
17	E	346	GLN	0	-0.008	-0.005	23.734	0.020	0.020	0.000	0.000	0.000	0.000
18	E	347	GLN	0	0.015	0.003	24.602	0.016	0.016	0.000	0.000	0.000	0.000
19	E	348	TYR	0	0.003	-0.011	28.280	0.013	0.013	0.000	0.000	0.000	0.000
20	E	349	ARG	1	0.815	0.923	29.866	0.117	0.117	0.000	0.000	0.000	0.000
21	E	350	GLN	0	-0.027	-0.033	31.331	0.014	0.014	0.000	0.000	0.000	0.000
22	E	351	GLN	0	0.002	0.012	31.034	0.004	0.004	0.000	0.000	0.000	0.000
23	E	352	ILE	0	-0.046	-0.033	33.498	0.006	0.006	0.000	0.000	0.000	0.000
24	E	353	GLU	-1	-0.869	-0.927	35.338	-0.101	-0.101	0.000	0.000	0.000	0.000
25	E	354	GLU	-1	-0.949	-0.974	36.594	-0.068	-0.068	0.000	0.000	0.000	0.000
26	E	355	LEU	0	-0.065	-0.032	37.874	0.005	0.005	0.000	0.000	0.000	0.000
27	E	356	GLU	-1	-0.784	-0.903	38.593	-0.085	-0.085	0.000	0.000	0.000	0.000
28	E	357	ASN	0	0.026	0.012	42.014	0.002	0.002	0.000	0.000	0.000	0.000
29	E	358	HIS	0	-0.007	0.007	43.199	0.004	0.004	0.000	0.000	0.000	0.000
30	E	359	LEU	0	-0.073	-0.026	43.325	0.002	0.002	0.000	0.000	0.000	0.000
31	E	360	ALA	0	0.001	0.018	46.240	0.002	0.002	0.000	0.000	0.000	0.000
32	E	361	THR	0	-0.047	-0.039	47.905	0.004	0.004	0.000	0.000	0.000	0.000
33	E	362	GLN	0	-0.060	-0.039	48.817	0.000	0.000	0.000	0.000	0.000	0.000
34	E	363	ALA	0	-0.032	-0.021	49.821	-0.002	-0.002	0.000	0.000	0.000	0.000
35	E	364	ASN	0	0.014	0.001	51.081	0.003	0.003	0.000	0.000	0.000	0.000
36	E	365	ASN	0	-0.023	-0.021	52.704	0.000	0.000	0.000	0.000	0.000	0.000
37	E	366	SER	0	0.010	-0.002	53.319	-0.001	-0.001	0.000	0.000	0.000	0.000
38	E	367	HIS	0	-0.011	0.001	52.013	0.000	0.000	0.000	0.000	0.000	0.000
39	E	368	ILE	0	0.005	0.025	47.684	-0.002	-0.002	0.000	0.000	0.000	0.000
40	E	369	THR	0	-0.025	-0.012	48.299	0.001	0.001	0.000	0.000	0.000	0.000
41	E	370	PRO	0	0.054	0.012	45.830	-0.003	-0.003	0.000	0.000	0.000	0.000
42	E	371	GLN	0	0.030	0.026	43.964	-0.003	-0.003	0.000	0.000	0.000	0.000
43	E	372	ASP	-1	-0.821	-0.912	43.164	-0.071	-0.071	0.000	0.000	0.000	0.000
44	E	373	LEU	0	-0.037	-0.026	42.600	-0.004	-0.004	0.000	0.000	0.000	0.000
45	E	374	SER	0	-0.004	0.001	39.452	-0.006	-0.006	0.000	0.000	0.000	0.000
46	E	375	MET	0	-0.019	-0.010	38.266	-0.006	-0.006	0.000	0.000	0.000	0.000
47	E	376	ALA	0	-0.032	-0.018	37.900	-0.007	-0.007	0.000	0.000	0.000	0.000
48	E	377	MET	0	0.036	0.031	35.345	-0.007	-0.007	0.000	0.000	0.000	0.000
49	E	378	GLN	0	0.025	0.014	31.296	-0.002	-0.002	0.000	0.000	0.000	0.000
50	E	379	LYS	1	0.898	0.936	33.006	0.094	0.094	0.000	0.000	0.000	0.000
51	E	380	ILE	0	0.031	0.020	32.055	-0.008	-0.008	0.000	0.000	0.000	0.000
52	E	381	TYR	0	0.023	0.006	28.633	-0.010	-0.010	0.000	0.000	0.000	0.000
53	E	382	GLN	0	-0.013	-0.004	28.372	-0.014	-0.014	0.000	0.000	0.000	0.000
54	E	383	THR	0	-0.002	0.006	28.248	-0.011	-0.011	0.000	0.000	0.000	0.000
55	E	384	PHE	0	0.003	0.000	25.902	-0.010	-0.010	0.000	0.000	0.000	0.000
56	E	385	VAL	0	-0.003	0.005	23.965	-0.019	-0.019	0.000	0.000	0.000	0.000
57	E	386	ALA	0	-0.019	-0.007	23.199	-0.026	-0.026	0.000	0.000	0.000	0.000
58	E	387	LEU	0	0.014	-0.003	23.329	-0.018	-0.018	0.000	0.000	0.000	0.000
59	E	388	ALA	0	0.021	0.022	19.815	-0.016	-0.016	0.000	0.000	0.000	0.000
60	E	389	ALA	0	0.042	0.020	18.740	-0.043	-0.043	0.000	0.000	0.000	0.000
61	E	390	GLN	0	-0.021	-0.018	18.883	-0.027	-0.027	0.000	0.000	0.000	0.000
62	E	391	LEU	0	0.021	0.022	17.911	-0.014	-0.014	0.000	0.000	0.000	0.000
63	E	392	GLN	0	0.002	0.006	11.295	0.000	0.000	0.000	0.000	0.000	0.000
64	E	393	SER	0	-0.077	-0.053	14.524	-0.051	-0.051	0.000	0.000	0.000	0.000
65	E	394	ILE	0	0.029	0.014	16.633	-0.001	-0.001	0.000	0.000	0.000	0.000
66	E	395	HIS	0	-0.018	-0.011	8.559	0.137	0.137	0.000	0.000	0.000	0.000
67	E	396	GLU	-1	-0.855	-0.945	10.992	-1.121	-1.121	0.000	0.000	0.000	0.000
68	E	397	ASN	0	0.046	0.019	12.625	-0.026	-0.026	0.000	0.000	0.000	0.000
69	E	398	VAL	0	-0.038	-0.008	12.399	0.041	0.041	0.000	0.000	0.000	0.000
70	E	399	LYS	1	0.848	0.924	6.449	1.877	1.877	0.000	0.000	0.000	0.000
71	E	400	VAL	0	0.075	0.046	10.476	0.031	0.031	0.000	0.000	0.000	0.000
72	E	401	LEU	0	0.004	0.012	12.617	0.055	0.055	0.000	0.000	0.000	0.000
73	E	402	LYS	1	0.908	0.950	8.784	0.469	0.469	0.000	0.000	0.000	0.000
74	E	403	GLU	-1	-0.930	-0.963	7.886	-0.750	-0.750	0.000	0.000	0.000	0.000
75	E	404	GLN	0	0.006	-0.003	11.227	0.072	0.072	0.000	0.000	0.000	0.000
76	E	405	TYR	0	-0.024	-0.012	14.648	0.045	0.045	0.000	0.000	0.000	0.000
77	E	406	LEU	0	-0.058	-0.026	9.826	0.052	0.052	0.000	0.000	0.000	0.000
78	E	407	GLY	0	0.050	0.024	13.936	0.036	0.036	0.000	0.000	0.000	0.000
79	E	408	TYR	0	0.020	0.005	15.531	0.021	0.021	0.000	0.000	0.000	0.000
80	E	409	ARG	1	0.935	0.963	14.767	-0.026	-0.026	0.000	0.000	0.000	0.000
81	E	410	LYS	1	0.920	0.959	12.852	-0.100	-0.100	0.000	0.000	0.000	0.000
82	E	411	MET	0	-0.010	0.007	18.116	0.009	0.009	0.000	0.000	0.000	0.000
83	E	412	PHE	0	-0.043	-0.013	21.108	0.006	0.006	0.000	0.000	0.000	0.000
84	E	413	LEU	0	-0.067	-0.045	19.434	0.006	0.006	0.000	0.000	0.000	0.000
85	E	414	GLY	0	-0.007	0.017	22.610	0.011	0.011	0.000	0.000	0.000	0.000
86	E	415	ASP	-1	-0.931	-0.971	16.674	0.133	0.133	0.000	0.000	0.000	0.000
87	E	416	ALA	0	-0.036	-0.011	18.245	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:330:PRO)