FMO DATABASE

FMODB ID: 6YNQZ

Calculation Name: 3JV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JV0

Chain ID: A

ChEMBL ID:

UniProt ID: Q04863

Base Structure: X-ray

Registration Date: 2023-09-21

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-610464.197006
FMO2-HF: Nuclear repulsion	569777.993504
FMO2-HF: Total energy	-40686.203501
FMO2-MP2: Total energy	-40803.241111

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:278:THR)

Summations of interaction energy for fragment #1(A:278: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.
-5.238	-1.194	0.092	-1.584	-2.551	0.003

Interaction energy analysis for fragmet #1(A:278:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.015

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	280	GLU	-1	-0.935	-0.964	2.908	-5.545	-1.802	0.093	-1.540	-2.296	0.003
4	A	281	LEU	0	0.018	0.043	4.070	1.038	1.339	-0.001	-0.044	-0.255	0.000
5	A	282	ARG	1	0.845	0.872	6.118	0.707	0.707	0.000	0.000	0.000	0.000
6	A	283	ILE	0	0.032	0.020	8.837	0.145	0.145	0.000	0.000	0.000	0.000
7	A	284	CYS	0	-0.083	-0.049	12.257	0.095	0.095	0.000	0.000	0.000	0.000
8	A	285	ARG	1	0.921	0.948	14.944	0.280	0.280	0.000	0.000	0.000	0.000
9	A	286	ILE	0	0.039	0.016	16.587	-0.049	-0.049	0.000	0.000	0.000	0.000
10	A	287	ASP	-1	-0.830	-0.915	19.807	-0.217	-0.217	0.000	0.000	0.000	0.000
11	A	288	LYS	1	0.857	0.940	23.310	0.219	0.219	0.000	0.000	0.000	0.000
12	A	289	GLU	-1	-0.959	-0.986	22.545	-0.198	-0.198	0.000	0.000	0.000	0.000
13	A	290	SER	0	-0.091	-0.056	23.848	0.008	0.008	0.000	0.000	0.000	0.000
14	A	291	GLY	0	0.099	0.060	26.254	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	292	PRO	0	-0.055	-0.011	28.306	0.005	0.005	0.000	0.000	0.000	0.000
16	A	293	CYS	0	0.015	-0.004	28.183	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	294	THR	0	-0.034	-0.020	28.940	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	295	GLY	0	-0.027	-0.002	26.906	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	296	GLY	0	-0.014	-0.022	26.631	0.012	0.012	0.000	0.000	0.000	0.000
20	A	297	GLU	-1	-0.867	-0.930	26.861	-0.178	-0.178	0.000	0.000	0.000	0.000
21	A	298	GLU	-1	-0.950	-0.962	25.507	-0.216	-0.216	0.000	0.000	0.000	0.000
22	A	299	LEU	0	-0.042	-0.025	22.237	0.010	0.010	0.000	0.000	0.000	0.000
23	A	300	TYR	0	-0.016	-0.009	20.857	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	301	LEU	0	0.004	-0.003	14.454	0.003	0.003	0.000	0.000	0.000	0.000
25	A	302	LEU	0	-0.038	-0.004	17.091	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	303	CYS	0	-0.003	-0.014	11.873	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	304	ASP	-1	-0.814	-0.854	9.889	-0.449	-0.449	0.000	0.000	0.000	0.000
28	A	305	LYS	1	0.911	0.948	10.877	0.303	0.303	0.000	0.000	0.000	0.000
29	A	306	VAL	0	0.068	0.030	9.411	-0.238	-0.238	0.000	0.000	0.000	0.000
30	A	307	GLN	0	-0.048	-0.026	9.277	0.268	0.268	0.000	0.000	0.000	0.000
31	A	308	LYS	1	0.934	0.964	11.606	0.267	0.267	0.000	0.000	0.000	0.000
32	A	309	GLU	-1	-0.912	-0.951	13.824	-0.386	-0.386	0.000	0.000	0.000	0.000
33	A	310	ASP	-1	-1.009	-1.017	8.897	-0.984	-0.984	0.000	0.000	0.000	0.000
34	A	311	ILE	0	0.029	0.021	9.459	-0.228	-0.228	0.000	0.000	0.000	0.000
35	A	312	SER	0	-0.053	-0.025	11.600	0.187	0.187	0.000	0.000	0.000	0.000
36	A	313	VAL	0	0.059	0.033	12.149	-0.130	-0.130	0.000	0.000	0.000	0.000
37	A	314	ARG	1	0.868	0.915	11.905	0.596	0.596	0.000	0.000	0.000	0.000
38	A	315	PHE	0	0.017	0.008	14.590	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	316	SER	0	-0.050	-0.035	15.789	0.007	0.007	0.000	0.000	0.000	0.000
40	A	317	THR	0	0.026	0.007	18.061	0.012	0.012	0.000	0.000	0.000	0.000
41	A	318	ALA	0	0.010	0.000	18.921	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	319	SER	0	-0.016	-0.008	19.956	0.007	0.007	0.000	0.000	0.000	0.000
43	A	320	TRP	0	-0.008	0.008	20.847	0.000	0.000	0.000	0.000	0.000	0.000
44	A	321	GLU	-1	-0.840	-0.919	15.531	-0.439	-0.439	0.000	0.000	0.000	0.000
45	A	322	GLY	0	0.000	0.011	18.505	0.028	0.028	0.000	0.000	0.000	0.000
46	A	323	ARG	1	0.940	0.966	16.204	0.434	0.434	0.000	0.000	0.000	0.000
47	A	324	GLY	0	-0.007	0.012	17.770	0.039	0.039	0.000	0.000	0.000	0.000
48	A	325	ASP	-1	-0.951	-0.979	19.173	-0.303	-0.303	0.000	0.000	0.000	0.000
49	A	326	PHE	0	-0.038	-0.008	15.258	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	327	SER	0	-0.038	-0.042	20.566	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	328	GLN	0	0.041	-0.001	18.103	0.001	0.001	0.000	0.000	0.000	0.000
52	A	329	ALA	0	-0.004	-0.002	19.915	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	330	ASP	-1	-0.845	-0.879	21.407	-0.258	-0.258	0.000	0.000	0.000	0.000
54	A	331	VAL	0	-0.043	-0.013	15.896	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	332	HIS	0	0.012	0.010	19.234	0.039	0.039	0.000	0.000	0.000	0.000
56	A	333	ARG	1	0.911	0.950	18.421	0.148	0.148	0.000	0.000	0.000	0.000
57	A	334	GLN	0	0.021	0.010	20.210	0.031	0.031	0.000	0.000	0.000	0.000
58	A	335	PHE	0	-0.003	0.006	21.107	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	336	ALA	0	0.012	-0.005	21.659	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	337	ILE	0	0.001	0.000	23.669	0.011	0.011	0.000	0.000	0.000	0.000
61	A	338	VAL	0	0.001	0.007	22.723	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	339	PHE	0	-0.016	-0.013	25.985	0.013	0.013	0.000	0.000	0.000	0.000
63	A	340	LYS	1	0.951	0.974	29.497	0.032	0.032	0.000	0.000	0.000	0.000
64	A	341	THR	0	0.029	0.017	32.099	0.001	0.001	0.000	0.000	0.000	0.000
65	A	342	PRO	0	0.013	0.017	35.026	0.003	0.003	0.000	0.000	0.000	0.000
66	A	343	PRO	0	0.002	0.005	38.359	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	344	TYR	0	0.005	-0.004	41.047	0.000	0.000	0.000	0.000	0.000	0.000
68	A	345	GLU	-1	-0.948	-0.971	43.641	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	346	ASP	-1	-0.855	-0.925	47.157	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	347	LEU	0	-0.052	-0.038	44.064	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	348	GLU	-1	-0.884	-0.929	47.155	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	349	ILE	0	-0.039	0.010	44.859	0.000	0.000	0.000	0.000	0.000	0.000
73	A	350	SER	0	-0.014	-0.039	48.613	0.000	0.000	0.000	0.000	0.000	0.000
74	A	351	GLU	-1	-0.908	-0.944	48.774	-0.038	-0.038	0.000	0.000	0.000	0.000
75	A	352	PRO	0	-0.020	-0.019	43.619	0.000	0.000	0.000	0.000	0.000	0.000
76	A	353	VAL	0	0.013	0.012	44.249	0.001	0.001	0.000	0.000	0.000	0.000
77	A	354	THR	0	0.003	-0.023	41.592	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	355	VAL	0	-0.014	0.010	40.436	0.002	0.002	0.000	0.000	0.000	0.000
79	A	356	ASN	0	0.004	-0.008	40.330	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	357	VAL	0	-0.025	-0.008	34.343	0.003	0.003	0.000	0.000	0.000	0.000
81	A	358	GLN	0	-0.005	-0.017	35.956	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	359	LEU	0	-0.032	-0.009	30.999	0.003	0.003	0.000	0.000	0.000	0.000
83	A	360	GLN	0	0.040	0.003	35.152	0.003	0.003	0.000	0.000	0.000	0.000
84	A	361	ARG	1	0.692	0.827	36.101	0.042	0.042	0.000	0.000	0.000	0.000
85	A	362	LEU	0	0.004	-0.006	35.632	0.002	0.002	0.000	0.000	0.000	0.000
86	A	363	THR	0	-0.022	-0.015	38.271	0.001	0.001	0.000	0.000	0.000	0.000
87	A	364	ASP	-1	-0.806	-0.901	40.408	-0.031	-0.031	0.000	0.000	0.000	0.000
88	A	365	GLY	0	0.014	0.019	41.353	0.000	0.000	0.000	0.000	0.000	0.000
89	A	366	GLU	-1	-0.869	-0.906	39.714	-0.046	-0.046	0.000	0.000	0.000	0.000
90	A	367	CYS	0	-0.043	-0.024	39.052	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	368	SER	0	-0.010	0.008	35.672	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	369	GLU	-1	-0.898	-0.956	37.600	-0.061	-0.061	0.000	0.000	0.000	0.000
93	A	370	PRO	0	-0.049	-0.013	37.418	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	371	LEU	0	0.013	0.000	32.927	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	372	PRO	0	0.000	0.003	36.839	0.004	0.004	0.000	0.000	0.000	0.000
96	A	373	PHE	0	-0.005	-0.005	34.196	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	374	THR	0	-0.039	-0.001	37.681	0.006	0.006	0.000	0.000	0.000	0.000
98	A	375	TYR	0	-0.043	-0.026	39.131	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	376	LEU	0	-0.006	-0.012	38.721	0.000	0.000	0.000	0.000	0.000	0.000
100	A	377	PRO	0	0.026	0.032	42.424	0.001	0.001	0.000	0.000	0.000	0.000
101	A	378	ARG	1	0.787	0.877	43.415	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:278:THR)